Starting phenix.real_space_refine on Mon Mar 18 11:32:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o8z_0659/03_2024/6o8z_0659.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o8z_0659/03_2024/6o8z_0659.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o8z_0659/03_2024/6o8z_0659.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o8z_0659/03_2024/6o8z_0659.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o8z_0659/03_2024/6o8z_0659.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o8z_0659/03_2024/6o8z_0659.pdb" } resolution = 3.49 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.096 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 4542 5.49 5 S 130 5.16 5 C 69182 2.51 5 N 25651 2.21 5 O 38989 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "c TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ASP 34": "OD1" <-> "OD2" Residue "j TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ARG 89": "NH1" <-> "NH2" Residue "p TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 22": "OE1" <-> "OE2" Residue "F GLU 140": "OE1" <-> "OE2" Residue "K GLU 92": "OE1" <-> "OE2" Residue "M ARG 21": "NH1" <-> "NH2" Residue "M ARG 33": "NH1" <-> "NH2" Residue "M ARG 41": "NH1" <-> "NH2" Residue "M ARG 47": "NH1" <-> "NH2" Residue "M PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 60": "NH1" <-> "NH2" Residue "M PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 114": "NH1" <-> "NH2" Residue "Q GLU 11": "OE1" <-> "OE2" Residue "T ARG 16": "NH1" <-> "NH2" Residue "T PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 15": "NH1" <-> "NH2" Residue "W TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 53": "NH1" <-> "NH2" Residue "X ASP 65": "OD1" <-> "OD2" Residue "X ARG 80": "NH1" <-> "NH2" Residue "Y ARG 52": "NH1" <-> "NH2" Residue "1 PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 138498 Number of models: 1 Model: "" Number of chains: 53 Chain: "a" Number of atoms: 32646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1523, 32646 Classifications: {'RNA': 1523} Modifications used: {'rna2p_pur': 119, 'rna2p_pyr': 88, 'rna3p_pur': 738, 'rna3p_pyr': 578} Link IDs: {'rna2p': 207, 'rna3p': 1315} Chain breaks: 1 Chain: "c" Number of atoms: 1610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1610 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 4, 'TRANS': 199} Chain: "d" Number of atoms: 1620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1620 Classifications: {'peptide': 201} Link IDs: {'CIS': 2, 'PTRANS': 8, 'TRANS': 190} Chain: "e" Number of atoms: 1204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1204 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 7, 'TRANS': 155} Chain: "f" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 795 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "g" Number of atoms: 1229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1229 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 7, 'TRANS': 146} Chain: "h" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1041 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 125} Chain: "i" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 990 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 5, 'TRANS': 120} Chain: "j" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 800 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 92} Chain: "k" Number of atoms: 863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 863 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 109} Chain: "l" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1065 Classifications: {'peptide': 136} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 7, 'TRANS': 126} Chain: "m" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 884 Classifications: {'peptide': 112} Link IDs: {'CIS': 3, 'PTRANS': 3, 'TRANS': 105} Chain: "n" Number of atoms: 492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 492 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 56} Chain: "o" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 741 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "p" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 708 Classifications: {'peptide': 89} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 83} Chain: "q" Number of atoms: 681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 681 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 2, 'TRANS': 80} Chain: "r" Number of atoms: 537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 537 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "s" Number of atoms: 634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 634 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 4, 'TRANS': 73} Chain: "t" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 610 Classifications: {'peptide': 81} Link IDs: {'TRANS': 80} Chain: "A" Number of atoms: 62311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2903, 62311 Classifications: {'RNA': 2903} Modifications used: {'rna2p_pur': 300, 'rna2p_pyr': 155, 'rna3p_pur': 1386, 'rna3p_pyr': 1062} Link IDs: {'rna2p': 455, 'rna3p': 2447} Chain breaks: 3 Chain: "B" Number of atoms: 2480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 2480 Classifications: {'RNA': 116} Modifications used: {'p5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 56, 'rna3p_pyr': 49} Link IDs: {'rna2p': 11, 'rna3p': 104} Chain: "C" Number of atoms: 2115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2115 Classifications: {'peptide': 275} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 257} Chain: "D" Number of atoms: 1579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1579 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 9, 'TRANS': 197} Chain: "E" Number of atoms: 1574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1574 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 8, 'TRANS': 197} Chain: "F" Number of atoms: 1392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1392 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 7, 'TRANS': 169} Chain: "G" Number of atoms: 1345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1345 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 9, 'TRANS': 166} Chain: "K" Number of atoms: 1130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1130 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 7, 'TRANS': 137} Chain: "L" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 922 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "M" Number of atoms: 1095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1095 Classifications: {'peptide': 146} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 140} Chain: "N" Number of atoms: 1118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1118 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 6, 'TRANS': 134} Chain: "O" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 979 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 3, 'TRANS': 119} Chain: "P" Number of atoms: 899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 899 Classifications: {'peptide': 117} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 113} Chain: "Q" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 924 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "R" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 950 Classifications: {'peptide': 118} Link IDs: {'TRANS': 117} Chain: "S" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 784 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "T" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 849 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 5, 'TRANS': 106} Chain: "U" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 720 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 2, 'TRANS': 86} Chain: "V" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 763 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 5, 'TRANS': 95} Chain: "W" Number of atoms: 758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 758 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 3, 'TRANS': 90} Chain: "X" Number of atoms: 572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 572 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain: "Y" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 425 Classifications: {'peptide': 54} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "Z" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 504 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "0" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 435 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "1" Number of atoms: 673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 673 Classifications: {'peptide': 83} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 77} Chain: "2" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 429 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 2, 'TRANS': 53} Chain: "3" Number of atoms: 419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 419 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "4" Number of atoms: 374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 374 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "5" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 522 Classifications: {'peptide': 64} Link IDs: {'TRANS': 63} Chain: "6" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 304 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 4, 'TRANS': 33} Chain: "n" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "2" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "6" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 44928 SG CYS n 24 55.491 143.160 115.969 1.00140.65 S ATOM 44954 SG CYS n 27 58.935 143.689 115.753 1.00143.47 S ATOM 45066 SG CYS n 40 58.818 142.124 118.861 1.00141.45 S ATOM 45091 SG CYS n 43 57.905 145.354 118.711 1.00140.54 S ATOM A0SAQ SG CYS 2 30 252.459 138.552 87.447 1.00104.34 S ATOM A0SDG SG CYS 2 43 249.674 139.729 89.284 1.00101.19 S ATOM A0SDY SG CYS 2 46 254.088 137.790 90.373 1.00102.08 S ATOM A0SIB SG CYS 3 9 139.668 42.588 138.011 1.00126.91 S ATOM A0SIU SG CYS 3 12 142.983 41.851 138.181 1.00126.00 S ATOM A0SOR SG CYS 3 36 142.966 40.631 134.581 1.00117.67 S ATOM A0TJ7 SG CYS 6 11 142.713 123.572 50.423 1.00113.89 S ATOM A0TJW SG CYS 6 14 146.421 121.261 49.905 1.00114.00 S ATOM A0TMU SG CYS 6 27 145.960 124.241 48.262 1.00115.84 S Time building chain proxies: 53.78, per 1000 atoms: 0.39 Number of scatterers: 138498 At special positions: 0 Unit cell: (287.414, 275.347, 227.079, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 130 16.00 P 4542 15.00 O 38989 8.00 N 25651 7.00 C 69182 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 59.14 Conformation dependent library (CDL) restraints added in 6.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 2 101 " pdb="ZN ZN 2 101 " - pdb=" SG CYS 2 46 " pdb="ZN ZN 2 101 " - pdb=" SG CYS 2 30 " pdb="ZN ZN 2 101 " - pdb=" SG CYS 2 43 " pdb=" ZN 3 101 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 12 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 36 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 9 " pdb=" ZN 6 101 " pdb="ZN ZN 6 101 " - pdb=" SG CYS 6 27 " pdb="ZN ZN 6 101 " - pdb=" SG CYS 6 14 " pdb="ZN ZN 6 101 " - pdb=" SG CYS 6 11 " pdb="ZN ZN 6 101 " - pdb=" NE2 HIS 6 33 " pdb=" ZN n 101 " pdb="ZN ZN n 101 " - pdb=" SG CYS n 24 " pdb="ZN ZN n 101 " - pdb=" SG CYS n 43 " pdb="ZN ZN n 101 " - pdb=" SG CYS n 27 " pdb="ZN ZN n 101 " - pdb=" SG CYS n 40 " Number of angles added : 9 10286 Ramachandran restraints generated. 5143 Oldfield, 0 Emsley, 5143 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9608 Finding SS restraints... Secondary structure from input PDB file: 146 helices and 67 sheets defined 29.0% alpha, 13.4% beta 1464 base pairs and 2086 stacking pairs defined. Time for finding SS restraints: 47.93 Creating SS restraints... Processing helix chain 'c' and resid 6 through 10 Processing helix chain 'c' and resid 29 through 42 removed outlier: 3.959A pdb=" N ARG c 37 " --> pdb=" O HIS c 33 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE c 42 " --> pdb=" O ILE c 38 " (cutoff:3.500A) Processing helix chain 'c' and resid 42 through 47 removed outlier: 3.598A pdb=" N LEU c 46 " --> pdb=" O ILE c 42 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA c 47 " --> pdb=" O ALA c 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 42 through 47' Processing helix chain 'c' and resid 71 through 77 removed outlier: 3.620A pdb=" N VAL c 75 " --> pdb=" O LYS c 71 " (cutoff:3.500A) Processing helix chain 'c' and resid 80 through 95 removed outlier: 3.578A pdb=" N GLU c 84 " --> pdb=" O GLY c 80 " (cutoff:3.500A) Processing helix chain 'c' and resid 112 through 125 Processing helix chain 'c' and resid 128 through 142 Processing helix chain 'c' and resid 155 through 159 Processing helix chain 'd' and resid 9 through 16 removed outlier: 3.557A pdb=" N LEU d 15 " --> pdb=" O VAL d 11 " (cutoff:3.500A) Processing helix chain 'd' and resid 45 through 60 removed outlier: 3.817A pdb=" N MET d 60 " --> pdb=" O LYS d 56 " (cutoff:3.500A) Processing helix chain 'd' and resid 64 through 76 removed outlier: 3.820A pdb=" N PHE d 68 " --> pdb=" O ASN d 64 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N THR d 70 " --> pdb=" O ARG d 66 " (cutoff:3.500A) Processing helix chain 'd' and resid 82 through 93 removed outlier: 3.609A pdb=" N GLN d 93 " --> pdb=" O VAL d 89 " (cutoff:3.500A) Processing helix chain 'd' and resid 94 through 102 Processing helix chain 'd' and resid 107 through 117 Processing helix chain 'd' and resid 143 through 147 removed outlier: 3.781A pdb=" N SER d 146 " --> pdb=" O ARG d 143 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLN d 147 " --> pdb=" O GLU d 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 143 through 147' Processing helix chain 'd' and resid 149 through 157 Processing helix chain 'd' and resid 182 through 186 Processing helix chain 'd' and resid 192 through 199 Processing helix chain 'e' and resid 55 through 68 removed outlier: 3.647A pdb=" N LYS e 68 " --> pdb=" O ILE e 64 " (cutoff:3.500A) Processing helix chain 'e' and resid 108 through 118 removed outlier: 3.646A pdb=" N VAL e 114 " --> pdb=" O PRO e 110 " (cutoff:3.500A) Processing helix chain 'e' and resid 134 through 145 Processing helix chain 'e' and resid 149 through 157 Processing helix chain 'f' and resid 19 through 35 removed outlier: 3.817A pdb=" N THR f 23 " --> pdb=" O GLU f 19 " (cutoff:3.500A) Processing helix chain 'f' and resid 77 through 85 removed outlier: 3.558A pdb=" N LEU f 83 " --> pdb=" O GLU f 79 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS f 85 " --> pdb=" O ASP f 81 " (cutoff:3.500A) Processing helix chain 'g' and resid 20 through 28 Processing helix chain 'g' and resid 36 through 53 removed outlier: 3.619A pdb=" N SER g 53 " --> pdb=" O ILE g 49 " (cutoff:3.500A) Processing helix chain 'g' and resid 59 through 68 Processing helix chain 'g' and resid 92 through 110 removed outlier: 3.561A pdb=" N ARG g 96 " --> pdb=" O ARG g 92 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR g 97 " --> pdb=" O PRO g 93 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU g 110 " --> pdb=" O ASN g 106 " (cutoff:3.500A) Processing helix chain 'g' and resid 117 through 128 Processing helix chain 'g' and resid 132 through 145 Processing helix chain 'h' and resid 5 through 20 Processing helix chain 'h' and resid 30 through 43 removed outlier: 3.549A pdb=" N ARG h 34 " --> pdb=" O SER h 30 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASP h 35 " --> pdb=" O LYS h 31 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU h 43 " --> pdb=" O ILE h 39 " (cutoff:3.500A) Processing helix chain 'h' and resid 90 through 94 removed outlier: 3.628A pdb=" N VAL h 94 " --> pdb=" O ALA h 91 " (cutoff:3.500A) Processing helix chain 'h' and resid 96 through 101 removed outlier: 4.163A pdb=" N ASN h 99 " --> pdb=" O LYS h 96 " (cutoff:3.500A) Processing helix chain 'h' and resid 115 through 120 Processing helix chain 'i' and resid 35 through 39 removed outlier: 3.569A pdb=" N ILE i 39 " --> pdb=" O VAL i 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 35 through 39' Processing helix chain 'i' and resid 45 through 50 Processing helix chain 'i' and resid 51 through 55 Processing helix chain 'i' and resid 71 through 91 removed outlier: 3.804A pdb=" N ARG i 80 " --> pdb=" O SER i 76 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N HIS i 81 " --> pdb=" O GLY i 77 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLY i 82 " --> pdb=" O ALA i 78 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASP i 91 " --> pdb=" O LEU i 87 " (cutoff:3.500A) Processing helix chain 'i' and resid 94 through 101 Processing helix chain 'j' and resid 14 through 31 removed outlier: 3.685A pdb=" N LEU j 18 " --> pdb=" O GLU j 14 " (cutoff:3.500A) Processing helix chain 'j' and resid 80 through 90 Processing helix chain 'k' and resid 53 through 57 Processing helix chain 'k' and resid 61 through 75 removed outlier: 4.479A pdb=" N VAL k 73 " --> pdb=" O ALA k 69 " (cutoff:3.500A) Processing helix chain 'k' and resid 92 through 103 removed outlier: 4.362A pdb=" N ILE k 97 " --> pdb=" O ARG k 93 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG k 98 " --> pdb=" O GLU k 94 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR k 103 " --> pdb=" O SER k 99 " (cutoff:3.500A) Processing helix chain 'l' and resid 3 through 9 removed outlier: 3.542A pdb=" N LEU l 7 " --> pdb=" O THR l 3 " (cutoff:3.500A) Processing helix chain 'l' and resid 21 through 25 Processing helix chain 'm' and resid 14 through 22 removed outlier: 3.541A pdb=" N THR m 20 " --> pdb=" O VAL m 16 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N TYR m 21 " --> pdb=" O VAL m 17 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ILE m 22 " --> pdb=" O SER m 18 " (cutoff:3.500A) Processing helix chain 'm' and resid 27 through 38 Processing helix chain 'm' and resid 49 through 61 removed outlier: 3.576A pdb=" N ASP m 61 " --> pdb=" O ARG m 57 " (cutoff:3.500A) Processing helix chain 'm' and resid 68 through 82 removed outlier: 3.912A pdb=" N GLU m 72 " --> pdb=" O ASP m 68 " (cutoff:3.500A) Processing helix chain 'm' and resid 85 through 90 Processing helix chain 'n' and resid 3 through 11 removed outlier: 3.803A pdb=" N LYS n 11 " --> pdb=" O ILE n 7 " (cutoff:3.500A) Processing helix chain 'n' and resid 40 through 50 removed outlier: 3.542A pdb=" N PHE n 44 " --> pdb=" O CYS n 40 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TYR n 49 " --> pdb=" O ARG n 45 " (cutoff:3.500A) Processing helix chain 'o' and resid 4 through 12 removed outlier: 3.948A pdb=" N ILE o 12 " --> pdb=" O LYS o 8 " (cutoff:3.500A) Processing helix chain 'o' and resid 24 through 46 removed outlier: 3.681A pdb=" N GLN o 28 " --> pdb=" O SER o 24 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE o 29 " --> pdb=" O PRO o 25 " (cutoff:3.500A) Processing helix chain 'o' and resid 49 through 72 removed outlier: 3.620A pdb=" N ARG o 54 " --> pdb=" O HIS o 50 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N GLY o 55 " --> pdb=" O HIS o 51 " (cutoff:3.500A) Processing helix chain 'o' and resid 75 through 86 Processing helix chain 'p' and resid 55 through 60 Processing helix chain 'p' and resid 67 through 76 Processing helix chain 'p' and resid 78 through 88 removed outlier: 3.503A pdb=" N LYS p 82 " --> pdb=" O GLY p 78 " (cutoff:3.500A) Processing helix chain 'r' and resid 16 through 20 removed outlier: 3.764A pdb=" N ALA r 19 " --> pdb=" O TYR r 16 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ASN r 20 " --> pdb=" O ILE r 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 16 through 20' Processing helix chain 'r' and resid 29 through 34 Processing helix chain 'r' and resid 35 through 37 No H-bonds generated for 'chain 'r' and resid 35 through 37' Processing helix chain 'r' and resid 45 through 50 Processing helix chain 'r' and resid 54 through 67 removed outlier: 3.758A pdb=" N LYS r 58 " --> pdb=" O LYS r 54 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR r 60 " --> pdb=" O GLN r 56 " (cutoff:3.500A) Processing helix chain 's' and resid 12 through 21 removed outlier: 5.252A pdb=" N LYS s 18 " --> pdb=" O HIS s 14 " (cutoff:3.500A) Processing helix chain 's' and resid 41 through 45 removed outlier: 3.650A pdb=" N VAL s 45 " --> pdb=" O PRO s 42 " (cutoff:3.500A) Processing helix chain 's' and resid 70 through 74 removed outlier: 3.728A pdb=" N GLU s 73 " --> pdb=" O LYS s 70 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N PHE s 74 " --> pdb=" O LEU s 71 " (cutoff:3.500A) No H-bonds generated for 'chain 's' and resid 70 through 74' Processing helix chain 't' and resid 7 through 42 removed outlier: 3.627A pdb=" N ARG t 12 " --> pdb=" O ILE t 8 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ALA t 38 " --> pdb=" O LYS t 34 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL t 39 " --> pdb=" O PHE t 35 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA t 40 " --> pdb=" O GLU t 36 " (cutoff:3.500A) Processing helix chain 't' and resid 47 through 63 Processing helix chain 't' and resid 68 through 83 removed outlier: 3.617A pdb=" N LEU t 81 " --> pdb=" O ARG t 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 14 Processing helix chain 'C' and resid 30 through 32 No H-bonds generated for 'chain 'C' and resid 30 through 32' Processing helix chain 'C' and resid 133 through 135 No H-bonds generated for 'chain 'C' and resid 133 through 135' Processing helix chain 'C' and resid 177 through 179 No H-bonds generated for 'chain 'C' and resid 177 through 179' Processing helix chain 'C' and resid 226 through 230 removed outlier: 3.644A pdb=" N HIS C 230 " --> pdb=" O PRO C 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 45 Processing helix chain 'D' and resid 62 through 70 removed outlier: 3.710A pdb=" N ALA D 70 " --> pdb=" O LYS D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 103 removed outlier: 3.896A pdb=" N VAL D 101 " --> pdb=" O LYS D 98 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE D 102 " --> pdb=" O VAL D 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 25 removed outlier: 3.639A pdb=" N GLY E 25 " --> pdb=" O GLU E 21 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 42 Processing helix chain 'E' and resid 102 through 119 removed outlier: 3.886A pdb=" N ARG E 106 " --> pdb=" O PRO E 102 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ARG E 107 " --> pdb=" O LYS E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 147 removed outlier: 4.080A pdb=" N PHE E 139 " --> pdb=" O LYS E 135 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS E 140 " --> pdb=" O THR E 136 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 164 Processing helix chain 'E' and resid 183 through 188 Processing helix chain 'E' and resid 196 through 206 removed outlier: 3.636A pdb=" N THR E 200 " --> pdb=" O GLN E 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 21 removed outlier: 5.143A pdb=" N THR F 13 " --> pdb=" O ILE F 9 " (cutoff:3.500A) Proline residue: F 14 - end of helix Processing helix chain 'F' and resid 24 through 28 Processing helix chain 'F' and resid 49 through 61 removed outlier: 4.542A pdb=" N GLU F 55 " --> pdb=" O ASP F 51 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 106 removed outlier: 4.026A pdb=" N TYR F 97 " --> pdb=" O GLY F 93 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 111 Processing helix chain 'F' and resid 162 through 173 removed outlier: 4.202A pdb=" N SER F 166 " --> pdb=" O THR F 162 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 81 removed outlier: 3.929A pdb=" N THR G 67 " --> pdb=" O THR G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 150 removed outlier: 3.592A pdb=" N VAL G 141 " --> pdb=" O ASN G 137 " (cutoff:3.500A) Processing helix chain 'K' and resid 25 through 38 removed outlier: 3.553A pdb=" N LEU K 29 " --> pdb=" O PRO K 25 " (cutoff:3.500A) Processing helix chain 'K' and resid 97 through 106 removed outlier: 3.971A pdb=" N LEU K 101 " --> pdb=" O ASN K 97 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ILE K 102 " --> pdb=" O SER K 98 " (cutoff:3.500A) Processing helix chain 'K' and resid 114 through 119 Processing helix chain 'K' and resid 133 through 137 removed outlier: 3.561A pdb=" N GLN K 137 " --> pdb=" O ALA K 134 " (cutoff:3.500A) Processing helix chain 'L' and resid 105 through 110 removed outlier: 4.136A pdb=" N GLU L 108 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ASN L 110 " --> pdb=" O ARG L 107 " (cutoff:3.500A) Processing helix chain 'L' and resid 111 through 116 Processing helix chain 'M' and resid 2 through 6 removed outlier: 3.906A pdb=" N LEU M 6 " --> pdb=" O LEU M 3 " (cutoff:3.500A) Processing helix chain 'M' and resid 56 through 61 removed outlier: 3.723A pdb=" N LEU M 61 " --> pdb=" O LEU M 57 " (cutoff:3.500A) Processing helix chain 'M' and resid 129 through 140 removed outlier: 3.526A pdb=" N GLN M 133 " --> pdb=" O SER M 129 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU M 134 " --> pdb=" O LYS M 130 " (cutoff:3.500A) Processing helix chain 'N' and resid 43 through 56 removed outlier: 4.142A pdb=" N ILE N 47 " --> pdb=" O THR N 43 " (cutoff:3.500A) Processing helix chain 'N' and resid 110 through 121 Processing helix chain 'N' and resid 122 through 124 No H-bonds generated for 'chain 'N' and resid 122 through 124' Processing helix chain 'O' and resid 9 through 21 Processing helix chain 'O' and resid 34 through 47 Processing helix chain 'O' and resid 49 through 54 removed outlier: 3.604A pdb=" N ARG O 53 " --> pdb=" O THR O 49 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLY O 54 " --> pdb=" O LEU O 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 49 through 54' Processing helix chain 'O' and resid 55 through 63 Processing helix chain 'O' and resid 86 through 92 Processing helix chain 'O' and resid 93 through 97 Processing helix chain 'P' and resid 6 through 20 removed outlier: 3.927A pdb=" N THR P 10 " --> pdb=" O ASP P 6 " (cutoff:3.500A) Processing helix chain 'P' and resid 68 through 87 removed outlier: 4.067A pdb=" N LYS P 86 " --> pdb=" O ARG P 82 " (cutoff:3.500A) Processing helix chain 'P' and resid 104 through 114 Processing helix chain 'Q' and resid 3 through 7 Processing helix chain 'Q' and resid 97 through 101 removed outlier: 3.533A pdb=" N LEU Q 100 " --> pdb=" O LEU Q 97 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG Q 101 " --> pdb=" O TYR Q 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 97 through 101' Processing helix chain 'Q' and resid 104 through 108 Processing helix chain 'R' and resid 9 through 20 removed outlier: 4.277A pdb=" N ARG R 13 " --> pdb=" O VAL R 9 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS R 19 " --> pdb=" O LYS R 15 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU R 20 " --> pdb=" O LYS R 16 " (cutoff:3.500A) Processing helix chain 'R' and resid 33 through 51 removed outlier: 3.833A pdb=" N GLU R 37 " --> pdb=" O LYS R 33 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG R 51 " --> pdb=" O PHE R 47 " (cutoff:3.500A) Processing helix chain 'R' and resid 52 through 71 removed outlier: 4.069A pdb=" N PHE R 57 " --> pdb=" O LYS R 53 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ARG R 58 " --> pdb=" O LYS R 54 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS R 59 " --> pdb=" O ARG R 55 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N MET R 71 " --> pdb=" O ALA R 67 " (cutoff:3.500A) Processing helix chain 'R' and resid 75 through 84 removed outlier: 4.090A pdb=" N MET R 80 " --> pdb=" O TYR R 76 " (cutoff:3.500A) Processing helix chain 'R' and resid 91 through 102 Processing helix chain 'R' and resid 102 through 117 Processing helix chain 'T' and resid 20 through 29 removed outlier: 4.462A pdb=" N VAL T 25 " --> pdb=" O ALA T 22 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ILE T 26 " --> pdb=" O ARG T 23 " (cutoff:3.500A) Processing helix chain 'T' and resid 33 through 43 removed outlier: 3.854A pdb=" N SER T 39 " --> pdb=" O ALA T 35 " (cutoff:3.500A) Processing helix chain 'T' and resid 48 through 66 removed outlier: 3.789A pdb=" N ILE T 52 " --> pdb=" O SER T 48 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU T 53 " --> pdb=" O ALA T 49 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N LYS T 54 " --> pdb=" O GLY T 50 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL T 55 " --> pdb=" O ILE T 51 " (cutoff:3.500A) Processing helix chain 'T' and resid 70 through 74 removed outlier: 3.833A pdb=" N LEU T 74 " --> pdb=" O VAL T 71 " (cutoff:3.500A) Processing helix chain 'U' and resid 13 through 20 removed outlier: 3.573A pdb=" N LEU U 18 " --> pdb=" O GLU U 14 " (cutoff:3.500A) Processing helix chain 'U' and resid 34 through 47 removed outlier: 3.556A pdb=" N VAL U 38 " --> pdb=" O ASN U 34 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASP U 47 " --> pdb=" O GLU U 43 " (cutoff:3.500A) Processing helix chain 'V' and resid 66 through 68 No H-bonds generated for 'chain 'V' and resid 66 through 68' Processing helix chain 'W' and resid 16 through 22 removed outlier: 4.030A pdb=" N GLN W 20 " --> pdb=" O SER W 16 " (cutoff:3.500A) Processing helix chain 'W' and resid 45 through 55 removed outlier: 4.260A pdb=" N SER W 49 " --> pdb=" O GLU W 45 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LYS W 50 " --> pdb=" O LYS W 46 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ILE W 51 " --> pdb=" O ASP W 47 " (cutoff:3.500A) Processing helix chain 'Z' and resid 3 through 8 removed outlier: 4.016A pdb=" N ARG Z 7 " --> pdb=" O VAL Z 3 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLU Z 8 " --> pdb=" O LYS Z 4 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 3 through 8' Processing helix chain 'Z' and resid 10 through 34 removed outlier: 3.601A pdb=" N ALA Z 33 " --> pdb=" O ARG Z 29 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR Z 34 " --> pdb=" O PHE Z 30 " (cutoff:3.500A) Processing helix chain 'Z' and resid 41 through 61 removed outlier: 4.089A pdb=" N GLU Z 45 " --> pdb=" O ALA Z 41 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ARG Z 47 " --> pdb=" O ILE Z 43 " (cutoff:3.500A) Processing helix chain '0' and resid 16 through 24 Processing helix chain '0' and resid 42 through 50 Processing helix chain '1' and resid 70 through 77 removed outlier: 4.363A pdb=" N PHE 1 74 " --> pdb=" O ARG 1 70 " (cutoff:3.500A) Processing helix chain '2' and resid 9 through 18 removed outlier: 3.682A pdb=" N LYS 2 13 " --> pdb=" O SER 2 9 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA 2 14 " --> pdb=" O LYS 2 10 " (cutoff:3.500A) Processing helix chain '4' and resid 10 through 14 Processing helix chain '4' and resid 18 through 22 Processing helix chain '4' and resid 26 through 37 Processing helix chain '5' and resid 38 through 43 Processing helix chain '5' and resid 53 through 58 removed outlier: 3.742A pdb=" N ARG 5 57 " --> pdb=" O GLY 5 53 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'c' and resid 51 through 58 removed outlier: 6.960A pdb=" N HIS c 68 " --> pdb=" O SER c 52 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ILE c 54 " --> pdb=" O SER c 66 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N SER c 66 " --> pdb=" O ILE c 54 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N ILE c 56 " --> pdb=" O ASN c 64 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ASN c 64 " --> pdb=" O ILE c 56 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N VAL c 63 " --> pdb=" O HIS c 99 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'c' and resid 51 through 58 removed outlier: 6.960A pdb=" N HIS c 68 " --> pdb=" O SER c 52 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ILE c 54 " --> pdb=" O SER c 66 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N SER c 66 " --> pdb=" O ILE c 54 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N ILE c 56 " --> pdb=" O ASN c 64 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ASN c 64 " --> pdb=" O ILE c 56 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N VAL c 103 " --> pdb=" O ILE c 65 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N ILE c 67 " --> pdb=" O VAL c 103 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'c' and resid 163 through 164 Processing sheet with id=AA4, first strand: chain 'c' and resid 163 through 164 removed outlier: 3.833A pdb=" N GLY c 147 " --> pdb=" O TYR c 202 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL c 197 " --> pdb=" O GLU c 186 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'd' and resid 125 through 126 removed outlier: 3.884A pdb=" N THR d 121 " --> pdb=" O GLY d 141 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'e' and resid 12 through 17 removed outlier: 3.835A pdb=" N ARG e 14 " --> pdb=" O VAL e 38 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N VAL e 38 " --> pdb=" O ARG e 14 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N LEU e 36 " --> pdb=" O VAL e 16 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'e' and resid 12 through 17 removed outlier: 3.835A pdb=" N ARG e 14 " --> pdb=" O VAL e 38 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N VAL e 38 " --> pdb=" O ARG e 14 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N LEU e 36 " --> pdb=" O VAL e 16 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY e 51 " --> pdb=" O ALA e 35 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL e 37 " --> pdb=" O GLY e 49 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'e' and resid 85 through 87 removed outlier: 3.706A pdb=" N ARG e 93 " --> pdb=" O LEU e 128 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU e 95 " --> pdb=" O LYS e 126 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'f' and resid 39 through 50 removed outlier: 5.297A pdb=" N VAL f 40 " --> pdb=" O THR f 69 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N THR f 69 " --> pdb=" O VAL f 40 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLU f 42 " --> pdb=" O ASN f 67 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN f 67 " --> pdb=" O GLU f 42 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N TYR f 63 " --> pdb=" O TRP f 46 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LYS f 48 " --> pdb=" O GLY f 61 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N GLY f 61 " --> pdb=" O LYS f 48 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N MET f 10 " --> pdb=" O MET f 94 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ARG f 92 " --> pdb=" O ILE f 12 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'g' and resid 73 through 77 Processing sheet with id=AB2, first strand: chain 'h' and resid 26 through 27 removed outlier: 3.508A pdb=" N ASP h 48 " --> pdb=" O PHE h 63 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'h' and resid 76 through 79 removed outlier: 3.793A pdb=" N ASN h 76 " --> pdb=" O TRP h 132 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N TRP h 132 " --> pdb=" O ASN h 76 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LYS h 78 " --> pdb=" O TYR h 130 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU h 126 " --> pdb=" O SER h 107 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ILE h 105 " --> pdb=" O ILE h 128 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N TYR h 130 " --> pdb=" O ILE h 103 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N ILE h 103 " --> pdb=" O TYR h 130 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'i' and resid 6 through 12 removed outlier: 3.668A pdb=" N GLY i 8 " --> pdb=" O VAL i 19 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL i 16 " --> pdb=" O ASN i 68 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL i 65 " --> pdb=" O THR i 29 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'j' and resid 45 through 46 removed outlier: 3.757A pdb=" N GLU j 45 " --> pdb=" O THR j 69 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG j 9 " --> pdb=" O GLU j 99 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU j 99 " --> pdb=" O ARG j 9 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ASN j 97 " --> pdb=" O LYS j 11 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'j' and resid 51 through 52 Processing sheet with id=AB7, first strand: chain 'j' and resid 65 through 66 removed outlier: 3.542A pdb=" N GLU j 66 " --> pdb=" O LYS n 57 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS n 57 " --> pdb=" O GLU j 66 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'k' and resid 41 through 46 removed outlier: 7.221A pdb=" N ALA k 41 " --> pdb=" O ASP k 36 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ASP k 36 " --> pdb=" O ALA k 41 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLY k 19 " --> pdb=" O THR k 81 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL k 82 " --> pdb=" O VAL k 107 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ALA k 109 " --> pdb=" O VAL k 82 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL k 84 " --> pdb=" O ALA k 109 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ARG k 111 " --> pdb=" O VAL k 84 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL k 86 " --> pdb=" O ARG k 111 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'l' and resid 42 through 53 removed outlier: 6.246A pdb=" N CYS l 47 " --> pdb=" O ARG l 69 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ARG l 69 " --> pdb=" O CYS l 47 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ILE l 74 " --> pdb=" O LEU l 70 " (cutoff:3.500A) removed outlier: 9.481A pdb=" N TYR l 108 " --> pdb=" O GLU l 75 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N THR l 77 " --> pdb=" O TYR l 108 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N ILE l 110 " --> pdb=" O THR l 77 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N TYR l 79 " --> pdb=" O ILE l 110 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LYS l 43 " --> pdb=" O LEU l 95 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'p' and resid 4 through 6 removed outlier: 3.900A pdb=" N ALA p 23 " --> pdb=" O LYS p 4 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU p 35 " --> pdb=" O VAL p 22 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'p' and resid 39 through 41 removed outlier: 3.550A pdb=" N GLU p 48 " --> pdb=" O ASN p 41 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'q' and resid 40 through 46 removed outlier: 3.521A pdb=" N LYS q 45 " --> pdb=" O VAL q 28 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N GLU q 29 " --> pdb=" O GLN q 12 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N GLN q 12 " --> pdb=" O GLU q 29 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N ILE q 61 " --> pdb=" O VAL q 81 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N VAL q 81 " --> pdb=" O ILE q 61 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N LYS q 63 " --> pdb=" O LEU q 79 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 's' and resid 48 through 52 Processing sheet with id=AC5, first strand: chain 'C' and resid 3 through 4 removed outlier: 4.038A pdb=" N SER C 18 " --> pdb=" O LYS C 4 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 34 through 35 Processing sheet with id=AC7, first strand: chain 'C' and resid 101 through 105 removed outlier: 3.685A pdb=" N ALA C 102 " --> pdb=" O VAL C 94 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ILE C 91 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ILE C 81 " --> pdb=" O ILE C 91 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU C 93 " --> pdb=" O LYS C 79 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 129 through 131 Processing sheet with id=AC9, first strand: chain 'C' and resid 172 through 175 Processing sheet with id=AD1, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AD2, first strand: chain 'D' and resid 12 through 16 removed outlier: 3.749A pdb=" N ILE D 188 " --> pdb=" O THR D 26 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL D 185 " --> pdb=" O VAL D 179 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N VAL D 179 " --> pdb=" O VAL D 185 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LEU D 187 " --> pdb=" O VAL D 177 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 37 through 39 removed outlier: 4.116A pdb=" N GLN D 37 " --> pdb=" O GLN D 50 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 3 through 4 Processing sheet with id=AD5, first strand: chain 'E' and resid 123 through 126 removed outlier: 6.172A pdb=" N LEU E 153 " --> pdb=" O LEU E 193 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N THR E 195 " --> pdb=" O LEU E 153 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N VAL E 155 " --> pdb=" O THR E 195 " (cutoff:3.500A) removed outlier: 8.847A pdb=" N VAL E 176 " --> pdb=" O VAL E 152 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N VAL E 154 " --> pdb=" O VAL E 176 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 86 through 91 removed outlier: 4.152A pdb=" N LYS F 33 " --> pdb=" O VAL F 157 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL F 35 " --> pdb=" O VAL F 155 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASN F 37 " --> pdb=" O ASP F 153 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ILE F 154 " --> pdb=" O LEU F 130 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 16 through 17 removed outlier: 4.261A pdb=" N ILE G 24 " --> pdb=" O ARG G 35 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ARG G 35 " --> pdb=" O ILE G 24 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 83 through 87 removed outlier: 3.777A pdb=" N GLY G 135 " --> pdb=" O PHE G 83 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS G 134 " --> pdb=" O THR G 122 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 95 through 98 removed outlier: 3.515A pdb=" N ARG G 95 " --> pdb=" O ASN G 106 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLN G 97 " --> pdb=" O THR G 104 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'K' and resid 123 through 125 removed outlier: 6.983A pdb=" N TRP K 16 " --> pdb=" O GLU K 139 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'L' and resid 7 through 9 removed outlier: 4.181A pdb=" N ILE L 19 " --> pdb=" O LEU L 8 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU L 20 " --> pdb=" O THR L 42 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR L 42 " --> pdb=" O LEU L 20 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL L 40 " --> pdb=" O ILE L 22 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N LYS L 59 " --> pdb=" O ILE L 87 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL L 61 " --> pdb=" O VAL L 85 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'L' and resid 76 through 77 removed outlier: 3.509A pdb=" N TYR L 76 " --> pdb=" O THR Q 73 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N THR Q 73 " --> pdb=" O TYR L 76 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TYR Q 59 " --> pdb=" O PHE Q 74 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N THR Q 58 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ARG Q 50 " --> pdb=" O THR Q 58 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N THR Q 60 " --> pdb=" O ILE Q 48 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL Q 46 " --> pdb=" O ARG Q 62 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N VAL Q 64 " --> pdb=" O GLU Q 44 " (cutoff:3.500A) removed outlier: 9.277A pdb=" N GLU Q 44 " --> pdb=" O VAL Q 64 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLN Q 83 " --> pdb=" O HIS Q 29 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'L' and resid 102 through 103 removed outlier: 5.976A pdb=" N VAL L 102 " --> pdb=" O LEU L 122 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'N' and resid 63 through 66 removed outlier: 3.680A pdb=" N GLU N 105 " --> pdb=" O TRP N 65 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'N' and resid 72 through 73 Processing sheet with id=AE7, first strand: chain 'O' and resid 30 through 32 removed outlier: 3.560A pdb=" N ILE O 30 " --> pdb=" O ILE O 123 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'S' and resid 10 through 14 removed outlier: 3.511A pdb=" N ALA S 3 " --> pdb=" O VAL S 14 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ILE S 4 " --> pdb=" O ILE S 39 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'S' and resid 19 through 22 removed outlier: 3.593A pdb=" N VAL S 22 " --> pdb=" O THR S 93 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'S' and resid 19 through 22 removed outlier: 3.593A pdb=" N VAL S 22 " --> pdb=" O THR S 93 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY S 66 " --> pdb=" O TYR S 92 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'S' and resid 75 through 76 Processing sheet with id=AF3, first strand: chain 'T' and resid 9 through 15 removed outlier: 6.412A pdb=" N LYS T 9 " --> pdb=" O VAL T 112 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N VAL T 112 " --> pdb=" O LYS T 9 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N THR T 11 " --> pdb=" O VAL T 110 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N VAL T 110 " --> pdb=" O THR T 11 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N LYS T 13 " --> pdb=" O ILE T 108 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N ILE T 108 " --> pdb=" O LYS T 13 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR T 109 " --> pdb=" O PHE T 80 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE T 80 " --> pdb=" O THR T 109 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLU T 78 " --> pdb=" O VAL T 111 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N THR T 113 " --> pdb=" O VAL T 76 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N VAL T 76 " --> pdb=" O THR T 113 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'T' and resid 87 through 89 removed outlier: 3.553A pdb=" N LYS T 103 " --> pdb=" O MET T 87 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'U' and resid 7 through 10 removed outlier: 3.596A pdb=" N ARG U 9 " --> pdb=" O GLU U 28 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'V' and resid 8 through 10 Processing sheet with id=AF7, first strand: chain 'V' and resid 25 through 27 removed outlier: 3.727A pdb=" N ALA V 25 " --> pdb=" O ILE V 34 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'V' and resid 40 through 44 Processing sheet with id=AF9, first strand: chain 'V' and resid 82 through 83 Processing sheet with id=AG1, first strand: chain 'W' and resid 29 through 30 Processing sheet with id=AG2, first strand: chain 'W' and resid 61 through 63 Processing sheet with id=AG3, first strand: chain 'X' and resid 31 through 32 removed outlier: 3.630A pdb=" N GLY X 31 " --> pdb=" O ARG X 48 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ARG X 48 " --> pdb=" O GLY X 31 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG3 Processing sheet with id=AG4, first strand: chain 'X' and resid 39 through 40 removed outlier: 3.756A pdb=" N VAL X 75 " --> pdb=" O TYR X 91 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER X 89 " --> pdb=" O ARG X 77 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'X' and resid 60 through 62 Processing sheet with id=AG6, first strand: chain 'Y' and resid 34 through 36 Processing sheet with id=AG7, first strand: chain 'Y' and resid 39 through 40 Processing sheet with id=AG8, first strand: chain '0' and resid 34 through 38 Processing sheet with id=AG9, first strand: chain '2' and resid 27 through 29 Processing sheet with id=AH1, first strand: chain '2' and resid 48 through 49 Processing sheet with id=AH2, first strand: chain '3' and resid 18 through 22 removed outlier: 3.873A pdb=" N LYS 3 41 " --> pdb=" O CYS 3 36 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N CYS 3 36 " --> pdb=" O LYS 3 41 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS 3 34 " --> pdb=" O THR 3 43 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain '5' and resid 15 through 16 Processing sheet with id=AH4, first strand: chain '6' and resid 15 through 17 1197 hydrogen bonds defined for protein. 3267 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3674 hydrogen bonds 5898 hydrogen bond angles 0 basepair planarities 1464 basepair parallelities 2086 stacking parallelities Total time for adding SS restraints: 204.17 Time building geometry restraints manager: 63.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.58: 141424 1.58 - 1.96: 9319 1.96 - 2.34: 3 2.34 - 2.72: 0 2.72 - 3.11: 1 Bond restraints: 150747 Sorted by residual: bond pdb=" CD LYS K 107 " pdb=" CE LYS K 107 " ideal model delta sigma weight residual 1.520 3.106 -1.586 3.00e-02 1.11e+03 2.79e+03 bond pdb=" CE1 PHE K 120 " pdb=" CZ PHE K 120 " ideal model delta sigma weight residual 1.382 1.978 -0.596 3.00e-02 1.11e+03 3.94e+02 bond pdb=" CD1 PHE K 120 " pdb=" CE1 PHE K 120 " ideal model delta sigma weight residual 1.382 1.977 -0.595 3.00e-02 1.11e+03 3.93e+02 bond pdb=" CD2 PHE K 120 " pdb=" CE2 PHE K 120 " ideal model delta sigma weight residual 1.382 1.977 -0.595 3.00e-02 1.11e+03 3.93e+02 bond pdb=" CE2 PHE K 120 " pdb=" CZ PHE K 120 " ideal model delta sigma weight residual 1.382 1.949 -0.567 3.00e-02 1.11e+03 3.58e+02 ... (remaining 150742 not shown) Histogram of bond angle deviations from ideal: 97.93 - 106.39: 27653 106.39 - 114.84: 98674 114.84 - 123.30: 76413 123.30 - 131.75: 22536 131.75 - 140.21: 768 Bond angle restraints: 226044 Sorted by residual: angle pdb=" CG LYS K 107 " pdb=" CD LYS K 107 " pdb=" CE LYS K 107 " ideal model delta sigma weight residual 111.30 131.92 -20.62 2.30e+00 1.89e-01 8.04e+01 angle pdb=" N3 C A 956 " pdb=" C4 C A 956 " pdb=" N4 C A 956 " ideal model delta sigma weight residual 118.00 97.93 20.07 3.00e+00 1.11e-01 4.47e+01 angle pdb=" CD LYS K 107 " pdb=" CE LYS K 107 " pdb=" NZ LYS K 107 " ideal model delta sigma weight residual 111.90 131.81 -19.91 3.20e+00 9.77e-02 3.87e+01 angle pdb=" C LYS U 49 " pdb=" N VAL U 50 " pdb=" CA VAL U 50 " ideal model delta sigma weight residual 121.97 132.44 -10.47 1.80e+00 3.09e-01 3.38e+01 angle pdb=" C ILE V 71 " pdb=" N ASP V 72 " pdb=" CA ASP V 72 " ideal model delta sigma weight residual 121.80 134.81 -13.01 2.44e+00 1.68e-01 2.84e+01 ... (remaining 226039 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.80: 84961 35.80 - 71.60: 10305 71.60 - 107.41: 1115 107.41 - 143.21: 32 143.21 - 179.01: 26 Dihedral angle restraints: 96439 sinusoidal: 81507 harmonic: 14932 Sorted by residual: dihedral pdb=" CA GLY G 47 " pdb=" C GLY G 47 " pdb=" N ASN G 48 " pdb=" CA ASN G 48 " ideal model delta harmonic sigma weight residual -180.00 -108.72 -71.28 0 5.00e+00 4.00e-02 2.03e+02 dihedral pdb=" CA ASP V 72 " pdb=" C ASP V 72 " pdb=" N PRO V 73 " pdb=" CA PRO V 73 " ideal model delta harmonic sigma weight residual -180.00 -118.48 -61.52 0 5.00e+00 4.00e-02 1.51e+02 dihedral pdb=" CA GLY D 89 " pdb=" C GLY D 89 " pdb=" N GLU D 90 " pdb=" CA GLU D 90 " ideal model delta harmonic sigma weight residual 180.00 125.23 54.77 0 5.00e+00 4.00e-02 1.20e+02 ... (remaining 96436 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 26478 0.082 - 0.164: 2298 0.164 - 0.246: 181 0.246 - 0.328: 21 0.328 - 0.410: 2 Chirality restraints: 28980 Sorted by residual: chirality pdb=" C1' C a 996 " pdb=" O4' C a 996 " pdb=" C2' C a 996 " pdb=" N1 C a 996 " both_signs ideal model delta sigma weight residual False 2.47 2.06 0.41 2.00e-01 2.50e+01 4.19e+00 chirality pdb=" C3' G a1080 " pdb=" C4' G a1080 " pdb=" O3' G a1080 " pdb=" C2' G a1080 " both_signs ideal model delta sigma weight residual False -2.74 -2.40 -0.34 2.00e-01 2.50e+01 2.97e+00 chirality pdb=" C1' U a 267 " pdb=" O4' U a 267 " pdb=" C2' U a 267 " pdb=" N1 U a 267 " both_signs ideal model delta sigma weight residual False 2.47 2.15 0.32 2.00e-01 2.50e+01 2.48e+00 ... (remaining 28977 not shown) Planarity restraints: 11734 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C A2454 " -0.064 2.00e-02 2.50e+03 3.59e-02 2.91e+01 pdb=" N1 C A2454 " 0.085 2.00e-02 2.50e+03 pdb=" C2 C A2454 " 0.002 2.00e-02 2.50e+03 pdb=" O2 C A2454 " 0.003 2.00e-02 2.50e+03 pdb=" N3 C A2454 " -0.002 2.00e-02 2.50e+03 pdb=" C4 C A2454 " -0.007 2.00e-02 2.50e+03 pdb=" N4 C A2454 " -0.016 2.00e-02 2.50e+03 pdb=" C5 C A2454 " -0.005 2.00e-02 2.50e+03 pdb=" C6 C A2454 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP V 72 " 0.069 5.00e-02 4.00e+02 1.05e-01 1.76e+01 pdb=" N PRO V 73 " -0.181 5.00e-02 4.00e+02 pdb=" CA PRO V 73 " 0.057 5.00e-02 4.00e+02 pdb=" CD PRO V 73 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' G a1237 " -0.057 2.00e-02 2.50e+03 2.37e-02 1.69e+01 pdb=" N9 G a1237 " 0.054 2.00e-02 2.50e+03 pdb=" C8 G a1237 " 0.011 2.00e-02 2.50e+03 pdb=" N7 G a1237 " -0.000 2.00e-02 2.50e+03 pdb=" C5 G a1237 " -0.003 2.00e-02 2.50e+03 pdb=" C6 G a1237 " -0.009 2.00e-02 2.50e+03 pdb=" O6 G a1237 " -0.014 2.00e-02 2.50e+03 pdb=" N1 G a1237 " -0.005 2.00e-02 2.50e+03 pdb=" C2 G a1237 " 0.002 2.00e-02 2.50e+03 pdb=" N2 G a1237 " 0.005 2.00e-02 2.50e+03 pdb=" N3 G a1237 " 0.008 2.00e-02 2.50e+03 pdb=" C4 G a1237 " 0.008 2.00e-02 2.50e+03 ... (remaining 11731 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 1428 2.53 - 3.12: 104641 3.12 - 3.72: 258454 3.72 - 4.31: 346848 4.31 - 4.90: 486609 Nonbonded interactions: 1197980 Sorted by model distance: nonbonded pdb=" O2' C A2454 " pdb=" O5' C A2455 " model vdw 1.940 2.440 nonbonded pdb=" NZ LYS 2 37 " pdb="ZN ZN 2 101 " model vdw 1.943 2.310 nonbonded pdb=" O6 G A2154 " pdb=" O2 U A2165 " model vdw 1.974 2.432 nonbonded pdb=" O2' C A2361 " pdb=" OH TYR 3 17 " model vdw 1.990 2.440 nonbonded pdb=" C2 G a1019 " pdb=" N6 A a1052 " model vdw 1.995 3.340 ... (remaining 1197975 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.110 Extract box with map and model: 22.490 Check model and map are aligned: 1.660 Set scattering table: 0.910 Process input model: 484.270 Find NCS groups from input model: 2.590 Set up NCS constraints: 0.310 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 520.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 1.586 150747 Z= 0.666 Angle : 0.877 20.619 226044 Z= 0.449 Chirality : 0.048 0.410 28980 Planarity : 0.005 0.105 11734 Dihedral : 23.410 179.012 86831 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 17.12 Ramachandran Plot: Outliers : 0.33 % Allowed : 18.53 % Favored : 81.14 % Rotamer: Outliers : 15.40 % Allowed : 14.28 % Favored : 70.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.28 % Twisted Proline : 0.52 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.38 (0.09), residues: 5143 helix: -2.73 (0.11), residues: 1336 sheet: -3.50 (0.14), residues: 917 loop : -4.19 (0.09), residues: 2890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP N 93 HIS 0.018 0.002 HIS C 142 PHE 0.025 0.002 PHE l 31 TYR 0.027 0.002 TYR r 27 ARG 0.016 0.001 ARG R 58 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10286 Ramachandran restraints generated. 5143 Oldfield, 0 Emsley, 5143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10286 Ramachandran restraints generated. 5143 Oldfield, 0 Emsley, 5143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1878 residues out of total 4391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 676 poor density : 1202 time to evaluate : 6.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 16 ARG cc_start: 0.8609 (OUTLIER) cc_final: 0.8099 (tmm160) REVERT: c 22 TRP cc_start: 0.7757 (OUTLIER) cc_final: 0.7476 (p-90) REVERT: c 36 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8895 (mp) REVERT: c 40 LYS cc_start: 0.9337 (OUTLIER) cc_final: 0.9030 (tmmm) REVERT: c 55 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7350 (mp0) REVERT: c 91 ASN cc_start: 0.9282 (t0) cc_final: 0.9039 (t0) REVERT: c 135 GLN cc_start: 0.8863 (pt0) cc_final: 0.8351 (pp30) REVERT: c 156 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.7979 (mm) REVERT: c 164 SER cc_start: 0.8969 (p) cc_final: 0.8736 (m) REVERT: d 71 LEU cc_start: 0.9379 (OUTLIER) cc_final: 0.9003 (tt) REVERT: d 162 ARG cc_start: 0.7568 (OUTLIER) cc_final: 0.7330 (mmt-90) REVERT: e 76 MET cc_start: 0.8234 (mtm) cc_final: 0.7822 (mtm) REVERT: f 25 LEU cc_start: 0.9519 (tp) cc_final: 0.9264 (tp) REVERT: f 39 GLU cc_start: 0.8411 (mt-10) cc_final: 0.8145 (tm-30) REVERT: f 55 MET cc_start: 0.8649 (mmm) cc_final: 0.8251 (mmm) REVERT: f 59 ARG cc_start: 0.8389 (mmt180) cc_final: 0.7572 (mmm-85) REVERT: f 60 GLU cc_start: 0.8498 (mt-10) cc_final: 0.8160 (pt0) REVERT: f 82 ARG cc_start: 0.9120 (ttp80) cc_final: 0.8603 (ttt90) REVERT: g 31 MET cc_start: 0.8616 (ttp) cc_final: 0.8246 (ttt) REVERT: g 86 GLN cc_start: 0.8153 (pt0) cc_final: 0.7815 (mp10) REVERT: g 110 LEU cc_start: 0.9111 (mt) cc_final: 0.8908 (tp) REVERT: g 125 MET cc_start: 0.8824 (mtm) cc_final: 0.8609 (mtt) REVERT: g 126 ASP cc_start: 0.8669 (m-30) cc_final: 0.8361 (m-30) REVERT: g 136 LYS cc_start: 0.9452 (OUTLIER) cc_final: 0.9021 (ttmm) REVERT: h 5 ASP cc_start: 0.8417 (t0) cc_final: 0.7964 (p0) REVERT: h 25 LEU cc_start: 0.9017 (tp) cc_final: 0.8813 (tt) REVERT: i 14 ASN cc_start: 0.8746 (OUTLIER) cc_final: 0.8429 (t0) REVERT: i 38 TYR cc_start: 0.8025 (OUTLIER) cc_final: 0.7350 (t80) REVERT: i 46 GLU cc_start: 0.9045 (mt-10) cc_final: 0.8639 (pm20) REVERT: i 49 ASN cc_start: 0.9178 (m110) cc_final: 0.8749 (p0) REVERT: i 110 MET cc_start: 0.8150 (ptp) cc_final: 0.7848 (mtp) REVERT: i 112 GLU cc_start: 0.8750 (tp30) cc_final: 0.8287 (tp30) REVERT: i 127 PHE cc_start: 0.8675 (OUTLIER) cc_final: 0.7969 (p90) REVERT: j 4 GLN cc_start: 0.2668 (OUTLIER) cc_final: 0.2381 (tm130) REVERT: j 14 GLU cc_start: 0.8827 (mm-30) cc_final: 0.8514 (pm20) REVERT: j 15 HIS cc_start: 0.8449 (OUTLIER) cc_final: 0.8122 (m-70) REVERT: j 27 GLU cc_start: 0.8873 (tt0) cc_final: 0.8515 (tm-30) REVERT: j 47 SER cc_start: 0.9570 (m) cc_final: 0.9202 (p) REVERT: j 66 GLU cc_start: 0.8615 (pt0) cc_final: 0.8191 (pt0) REVERT: k 13 LYS cc_start: 0.7922 (mttt) cc_final: 0.7506 (ttmt) REVERT: k 68 GLU cc_start: 0.8728 (mt-10) cc_final: 0.8390 (mm-30) REVERT: k 98 ARG cc_start: 0.8511 (ttp-110) cc_final: 0.8148 (ttp80) REVERT: k 105 LEU cc_start: 0.8765 (mt) cc_final: 0.8184 (mp) REVERT: l 7 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8514 (mp) REVERT: l 122 ASP cc_start: 0.8605 (t0) cc_final: 0.8274 (t0) REVERT: m 14 ARG cc_start: 0.6725 (OUTLIER) cc_final: 0.6375 (ttp-110) REVERT: m 54 ASP cc_start: 0.8913 (m-30) cc_final: 0.8657 (m-30) REVERT: m 98 ARG cc_start: 0.6316 (OUTLIER) cc_final: 0.5765 (ptm160) REVERT: n 25 GLU cc_start: 0.8673 (mm-30) cc_final: 0.8377 (mm-30) REVERT: n 35 ARG cc_start: 0.8155 (ptt180) cc_final: 0.7894 (ptm160) REVERT: o 45 THR cc_start: 0.8799 (m) cc_final: 0.8579 (p) REVERT: p 10 MET cc_start: 0.8699 (OUTLIER) cc_final: 0.8329 (mtp) REVERT: p 13 LYS cc_start: 0.8284 (OUTLIER) cc_final: 0.8046 (tptp) REVERT: p 30 ASP cc_start: 0.8594 (p0) cc_final: 0.8201 (t0) REVERT: p 55 LEU cc_start: 0.9287 (mp) cc_final: 0.8908 (mt) REVERT: q 19 LYS cc_start: 0.8795 (mmtt) cc_final: 0.8504 (mtpt) REVERT: q 60 ASP cc_start: 0.7523 (t0) cc_final: 0.6520 (t0) REVERT: q 70 LEU cc_start: 0.9311 (OUTLIER) cc_final: 0.9092 (tt) REVERT: r 25 ILE cc_start: 0.9106 (OUTLIER) cc_final: 0.8888 (pt) REVERT: r 26 ASP cc_start: 0.8762 (t0) cc_final: 0.8510 (t70) REVERT: r 46 ARG cc_start: 0.8651 (ttp-170) cc_final: 0.8202 (ttm170) REVERT: r 54 LYS cc_start: 0.8902 (ptmt) cc_final: 0.8525 (ptpp) REVERT: r 65 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.8221 (mtt180) REVERT: r 69 MET cc_start: 0.8474 (mmm) cc_final: 0.7986 (mmt) REVERT: s 12 ASP cc_start: 0.7591 (m-30) cc_final: 0.7258 (m-30) REVERT: s 20 GLU cc_start: 0.8853 (mt-10) cc_final: 0.8504 (pp20) REVERT: s 40 ILE cc_start: 0.8326 (mm) cc_final: 0.7860 (mt) REVERT: t 44 ASP cc_start: 0.8272 (t0) cc_final: 0.7822 (p0) REVERT: t 49 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.8125 (pp) REVERT: t 59 MET cc_start: 0.8689 (mmm) cc_final: 0.8008 (mmt) REVERT: t 78 LEU cc_start: 0.9316 (OUTLIER) cc_final: 0.8985 (mp) REVERT: C 66 ASP cc_start: 0.8775 (t0) cc_final: 0.8436 (t0) REVERT: C 67 PHE cc_start: 0.9383 (OUTLIER) cc_final: 0.8528 (m-10) REVERT: C 156 ARG cc_start: 0.9102 (OUTLIER) cc_final: 0.8749 (mtp180) REVERT: D 140 HIS cc_start: 0.8551 (OUTLIER) cc_final: 0.8077 (m-70) REVERT: D 146 MET cc_start: 0.9149 (OUTLIER) cc_final: 0.8583 (mtm) REVERT: D 168 ARG cc_start: 0.9154 (OUTLIER) cc_final: 0.8676 (ptm160) REVERT: E 9 GLN cc_start: 0.7498 (OUTLIER) cc_final: 0.7251 (mp10) REVERT: E 12 THR cc_start: 0.8322 (OUTLIER) cc_final: 0.7070 (m) REVERT: E 13 GLN cc_start: 0.8708 (mp10) cc_final: 0.8435 (mp10) REVERT: E 35 ASP cc_start: 0.8686 (t70) cc_final: 0.8439 (t0) REVERT: E 65 TRP cc_start: 0.8221 (OUTLIER) cc_final: 0.7889 (p-90) REVERT: E 74 ARG cc_start: 0.8422 (OUTLIER) cc_final: 0.7922 (mtm180) REVERT: E 75 GLN cc_start: 0.8807 (mm110) cc_final: 0.8580 (mp10) REVERT: F 38 MET cc_start: 0.7122 (OUTLIER) cc_final: 0.6196 (tmm) REVERT: F 52 LYS cc_start: 0.9203 (mttt) cc_final: 0.8853 (mtmm) REVERT: F 83 MET cc_start: 0.8765 (mmm) cc_final: 0.8187 (mtt) REVERT: F 110 ARG cc_start: 0.8127 (mmt-90) cc_final: 0.7864 (tpt90) REVERT: F 120 LYS cc_start: 0.9147 (mttt) cc_final: 0.8945 (tptp) REVERT: F 152 MET cc_start: 0.8860 (pmm) cc_final: 0.8631 (pmm) REVERT: G 19 GLN cc_start: 0.7436 (mt0) cc_final: 0.6799 (tm-30) REVERT: G 99 GLN cc_start: 0.8827 (mt0) cc_final: 0.8530 (pp30) REVERT: G 130 GLN cc_start: 0.8151 (mp10) cc_final: 0.7458 (mp10) REVERT: K 37 LEU cc_start: 0.9339 (OUTLIER) cc_final: 0.9023 (tt) REVERT: K 76 TYR cc_start: 0.9200 (m-80) cc_final: 0.8999 (m-80) REVERT: K 79 SER cc_start: 0.9215 (p) cc_final: 0.9014 (p) REVERT: K 120 PHE cc_start: 0.9162 (t80) cc_final: 0.8754 (t80) REVERT: K 137 GLN cc_start: 0.9138 (mt0) cc_final: 0.8266 (mp10) REVERT: L 13 ASN cc_start: 0.9105 (t0) cc_final: 0.8639 (t0) REVERT: M 84 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.7968 (mpp80) REVERT: M 90 GLU cc_start: 0.7905 (tt0) cc_final: 0.7512 (tp30) REVERT: M 122 THR cc_start: 0.8499 (OUTLIER) cc_final: 0.7958 (p) REVERT: N 1 MET cc_start: -0.1893 (mmm) cc_final: -0.3720 (mmm) REVERT: N 77 LYS cc_start: 0.8033 (mttt) cc_final: 0.7802 (mttp) REVERT: N 116 GLU cc_start: 0.7060 (OUTLIER) cc_final: 0.6829 (tt0) REVERT: O 19 ASP cc_start: 0.8166 (m-30) cc_final: 0.7629 (m-30) REVERT: O 23 ASP cc_start: 0.8022 (m-30) cc_final: 0.7773 (m-30) REVERT: O 24 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.8692 (tt) REVERT: O 41 ARG cc_start: 0.8364 (OUTLIER) cc_final: 0.7302 (ppt90) REVERT: O 46 LYS cc_start: 0.9208 (tttt) cc_final: 0.8554 (tptp) REVERT: O 125 PHE cc_start: 0.8629 (OUTLIER) cc_final: 0.7538 (m-10) REVERT: P 62 GLU cc_start: 0.7506 (OUTLIER) cc_final: 0.7010 (mp0) REVERT: Q 44 GLU cc_start: 0.8149 (tm-30) cc_final: 0.7873 (tm-30) REVERT: Q 62 ARG cc_start: 0.8855 (OUTLIER) cc_final: 0.7639 (tmm160) REVERT: Q 106 LYS cc_start: 0.8923 (mtpt) cc_final: 0.8101 (mtpt) REVERT: Q 111 LYS cc_start: 0.9203 (mttt) cc_final: 0.8873 (mtpt) REVERT: R 38 GLN cc_start: 0.9499 (OUTLIER) cc_final: 0.9174 (tp40) REVERT: S 1 MET cc_start: 0.8850 (tmm) cc_final: 0.7980 (ttt) REVERT: S 81 HIS cc_start: 0.8463 (OUTLIER) cc_final: 0.7822 (m-70) REVERT: S 96 MET cc_start: 0.9062 (tmm) cc_final: 0.8503 (tmm) REVERT: T 67 PHE cc_start: 0.7730 (OUTLIER) cc_final: 0.6239 (p90) REVERT: U 5 ASP cc_start: 0.8156 (m-30) cc_final: 0.7463 (t0) REVERT: U 40 GLN cc_start: 0.8772 (mt0) cc_final: 0.8484 (mt0) REVERT: U 65 MET cc_start: 0.7534 (mmm) cc_final: 0.7239 (mmm) REVERT: V 20 GLU cc_start: 0.8751 (mt-10) cc_final: 0.8371 (mp0) REVERT: V 53 GLN cc_start: 0.8799 (mt0) cc_final: 0.8288 (mm-40) REVERT: W 63 MET cc_start: -0.0140 (mmm) cc_final: -0.0392 (tmm) REVERT: W 80 ASP cc_start: 0.5566 (OUTLIER) cc_final: 0.5213 (m-30) REVERT: W 86 MET cc_start: 0.5610 (mtm) cc_final: 0.5065 (ptp) REVERT: X 26 GLU cc_start: 0.7205 (mt-10) cc_final: 0.6935 (mp0) REVERT: X 50 ARG cc_start: 0.8796 (OUTLIER) cc_final: 0.8440 (tpm170) REVERT: X 77 ARG cc_start: 0.8619 (OUTLIER) cc_final: 0.8379 (mtt-85) REVERT: Y 17 ASN cc_start: 0.8394 (t0) cc_final: 0.8120 (t0) REVERT: Y 30 LYS cc_start: 0.9199 (mtmt) cc_final: 0.8966 (mttm) REVERT: Z 15 LEU cc_start: 0.8813 (mt) cc_final: 0.8304 (mp) REVERT: Z 27 ASN cc_start: 0.8630 (m-40) cc_final: 0.7800 (m-40) REVERT: 0 44 LYS cc_start: 0.8846 (mttt) cc_final: 0.8640 (mttp) REVERT: 1 12 VAL cc_start: 0.8975 (t) cc_final: 0.8511 (p) REVERT: 1 22 LYS cc_start: 0.7666 (mttt) cc_final: 0.7222 (mptt) REVERT: 1 43 TYR cc_start: 0.7832 (m-80) cc_final: 0.7468 (m-80) REVERT: 1 73 ARG cc_start: 0.8489 (tmt170) cc_final: 0.8138 (ttt-90) REVERT: 2 36 MET cc_start: 0.8826 (mmm) cc_final: 0.8152 (mmm) REVERT: 3 5 ILE cc_start: 0.7748 (OUTLIER) cc_final: 0.7415 (tt) REVERT: 3 23 LYS cc_start: 0.8932 (pttt) cc_final: 0.8690 (ptpp) REVERT: 3 32 LYS cc_start: 0.8032 (mmtt) cc_final: 0.7808 (mmtt) REVERT: 3 41 LYS cc_start: 0.8789 (tppt) cc_final: 0.8477 (ptpp) REVERT: 3 44 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8663 (tm) REVERT: 4 3 ARG cc_start: 0.6932 (OUTLIER) cc_final: 0.5365 (mtt90) REVERT: 5 22 LEU cc_start: 0.9362 (mt) cc_final: 0.8191 (mp) REVERT: 5 57 ARG cc_start: 0.9192 (OUTLIER) cc_final: 0.7977 (ptp90) outliers start: 676 outliers final: 372 residues processed: 1707 average time/residue: 1.2582 time to fit residues: 3714.6234 Evaluate side-chains 1348 residues out of total 4391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 425 poor density : 923 time to evaluate : 5.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 15 ILE Chi-restraints excluded: chain c residue 16 ARG Chi-restraints excluded: chain c residue 22 TRP Chi-restraints excluded: chain c residue 36 LEU Chi-restraints excluded: chain c residue 40 LYS Chi-restraints excluded: chain c residue 42 ILE Chi-restraints excluded: chain c residue 55 GLU Chi-restraints excluded: chain c residue 83 VAL Chi-restraints excluded: chain c residue 98 VAL Chi-restraints excluded: chain c residue 102 ILE Chi-restraints excluded: chain c residue 137 ILE Chi-restraints excluded: chain c residue 156 LEU Chi-restraints excluded: chain c residue 200 TRP Chi-restraints excluded: chain d residue 57 LEU Chi-restraints excluded: chain d residue 71 LEU Chi-restraints excluded: chain d residue 85 VAL Chi-restraints excluded: chain d residue 96 ASP Chi-restraints excluded: chain d residue 107 THR Chi-restraints excluded: chain d residue 114 LEU Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 162 ARG Chi-restraints excluded: chain d residue 184 ASP Chi-restraints excluded: chain d residue 189 GLU Chi-restraints excluded: chain d residue 195 VAL Chi-restraints excluded: chain e residue 9 LEU Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 72 VAL Chi-restraints excluded: chain e residue 105 VAL Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain e residue 127 SER Chi-restraints excluded: chain e residue 131 ASN Chi-restraints excluded: chain e residue 132 THR Chi-restraints excluded: chain e residue 144 LEU Chi-restraints excluded: chain e residue 147 LEU Chi-restraints excluded: chain e residue 159 LYS Chi-restraints excluded: chain f residue 11 TYR Chi-restraints excluded: chain f residue 17 ILE Chi-restraints excluded: chain f residue 18 ASP Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 56 ASN Chi-restraints excluded: chain f residue 65 ILE Chi-restraints excluded: chain f residue 66 VAL Chi-restraints excluded: chain f residue 67 ASN Chi-restraints excluded: chain g residue 19 ASN Chi-restraints excluded: chain g residue 20 SER Chi-restraints excluded: chain g residue 42 ILE Chi-restraints excluded: chain g residue 87 VAL Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain g residue 136 LYS Chi-restraints excluded: chain h residue 7 ILE Chi-restraints excluded: chain h residue 20 VAL Chi-restraints excluded: chain h residue 22 HIS Chi-restraints excluded: chain h residue 32 ILE Chi-restraints excluded: chain h residue 59 VAL Chi-restraints excluded: chain h residue 60 ILE Chi-restraints excluded: chain h residue 69 ASN Chi-restraints excluded: chain h residue 73 VAL Chi-restraints excluded: chain h residue 74 ILE Chi-restraints excluded: chain h residue 89 VAL Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 98 LEU Chi-restraints excluded: chain h residue 99 ASN Chi-restraints excluded: chain h residue 103 ILE Chi-restraints excluded: chain h residue 112 VAL Chi-restraints excluded: chain h residue 114 THR Chi-restraints excluded: chain h residue 127 VAL Chi-restraints excluded: chain i residue 9 THR Chi-restraints excluded: chain i residue 12 ARG Chi-restraints excluded: chain i residue 14 ASN Chi-restraints excluded: chain i residue 16 VAL Chi-restraints excluded: chain i residue 30 VAL Chi-restraints excluded: chain i residue 34 ASP Chi-restraints excluded: chain i residue 38 TYR Chi-restraints excluded: chain i residue 57 THR Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain i residue 66 ASN Chi-restraints excluded: chain i residue 79 ILE Chi-restraints excluded: chain i residue 93 ASP Chi-restraints excluded: chain i residue 127 PHE Chi-restraints excluded: chain j residue 4 GLN Chi-restraints excluded: chain j residue 8 ILE Chi-restraints excluded: chain j residue 15 HIS Chi-restraints excluded: chain j residue 52 ILE Chi-restraints excluded: chain j residue 55 THR Chi-restraints excluded: chain j residue 96 VAL Chi-restraints excluded: chain k residue 26 THR Chi-restraints excluded: chain k residue 32 VAL Chi-restraints excluded: chain k residue 35 THR Chi-restraints excluded: chain k residue 55 SER Chi-restraints excluded: chain k residue 73 VAL Chi-restraints excluded: chain l residue 4 ILE Chi-restraints excluded: chain l residue 7 LEU Chi-restraints excluded: chain l residue 20 ASP Chi-restraints excluded: chain l residue 26 LYS Chi-restraints excluded: chain l residue 30 SER Chi-restraints excluded: chain l residue 32 LYS Chi-restraints excluded: chain l residue 50 VAL Chi-restraints excluded: chain l residue 72 ASN Chi-restraints excluded: chain l residue 74 ILE Chi-restraints excluded: chain l residue 115 LEU Chi-restraints excluded: chain l residue 132 THR Chi-restraints excluded: chain m residue 4 ILE Chi-restraints excluded: chain m residue 9 ILE Chi-restraints excluded: chain m residue 14 ARG Chi-restraints excluded: chain m residue 29 THR Chi-restraints excluded: chain m residue 60 ILE Chi-restraints excluded: chain m residue 77 ILE Chi-restraints excluded: chain m residue 98 ARG Chi-restraints excluded: chain m residue 101 ASN Chi-restraints excluded: chain m residue 102 THR Chi-restraints excluded: chain n residue 5 SER Chi-restraints excluded: chain n residue 7 ILE Chi-restraints excluded: chain n residue 18 THR Chi-restraints excluded: chain n residue 57 LYS Chi-restraints excluded: chain o residue 24 SER Chi-restraints excluded: chain o residue 37 ASN Chi-restraints excluded: chain o residue 52 SER Chi-restraints excluded: chain o residue 80 GLU Chi-restraints excluded: chain o residue 87 LEU Chi-restraints excluded: chain o residue 89 ARG Chi-restraints excluded: chain p residue 3 VAL Chi-restraints excluded: chain p residue 5 ILE Chi-restraints excluded: chain p residue 10 MET Chi-restraints excluded: chain p residue 13 LYS Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain p residue 39 THR Chi-restraints excluded: chain p residue 40 TYR Chi-restraints excluded: chain p residue 84 HIS Chi-restraints excluded: chain q residue 5 ARG Chi-restraints excluded: chain q residue 7 GLN Chi-restraints excluded: chain q residue 44 SER Chi-restraints excluded: chain q residue 58 VAL Chi-restraints excluded: chain q residue 70 LEU Chi-restraints excluded: chain q residue 78 LEU Chi-restraints excluded: chain r residue 16 TYR Chi-restraints excluded: chain r residue 25 ILE Chi-restraints excluded: chain r residue 49 THR Chi-restraints excluded: chain r residue 51 THR Chi-restraints excluded: chain r residue 63 ILE Chi-restraints excluded: chain r residue 65 ARG Chi-restraints excluded: chain s residue 7 LYS Chi-restraints excluded: chain s residue 14 HIS Chi-restraints excluded: chain s residue 33 THR Chi-restraints excluded: chain s residue 65 ASP Chi-restraints excluded: chain s residue 78 ARG Chi-restraints excluded: chain t residue 4 ILE Chi-restraints excluded: chain t residue 46 VAL Chi-restraints excluded: chain t residue 49 LEU Chi-restraints excluded: chain t residue 65 LEU Chi-restraints excluded: chain t residue 78 LEU Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 15 ASN Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 20 ASP Chi-restraints excluded: chain C residue 23 GLU Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 45 ASN Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 67 PHE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 134 ASN Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 156 ARG Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 194 SER Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 211 SER Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 228 ASN Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 119 PHE Chi-restraints excluded: chain D residue 140 HIS Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 146 MET Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 167 ASP Chi-restraints excluded: chain D residue 168 ARG Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 188 ILE Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain E residue 7 PHE Chi-restraints excluded: chain E residue 8 LYS Chi-restraints excluded: chain E residue 9 GLN Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 65 TRP Chi-restraints excluded: chain E residue 74 ARG Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 80 SER Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain E residue 121 ASN Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain E residue 169 ASN Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 177 THR Chi-restraints excluded: chain E residue 179 ASP Chi-restraints excluded: chain E residue 195 THR Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 38 MET Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 123 ASP Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 165 GLU Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 43 MET Chi-restraints excluded: chain G residue 52 PHE Chi-restraints excluded: chain G residue 65 HIS Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 90 ILE Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 37 LEU Chi-restraints excluded: chain K residue 41 ASN Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 50 ASP Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 85 LEU Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 113 ASN Chi-restraints excluded: chain K residue 115 LEU Chi-restraints excluded: chain K residue 123 LEU Chi-restraints excluded: chain L residue 6 SER Chi-restraints excluded: chain L residue 19 ILE Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 35 ILE Chi-restraints excluded: chain L residue 37 ASP Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 66 LYS Chi-restraints excluded: chain L residue 73 ASP Chi-restraints excluded: chain L residue 90 ASP Chi-restraints excluded: chain L residue 92 SER Chi-restraints excluded: chain L residue 110 ASN Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain M residue 18 ARG Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain M residue 46 VAL Chi-restraints excluded: chain M residue 73 ASP Chi-restraints excluded: chain M residue 76 VAL Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 79 LEU Chi-restraints excluded: chain M residue 84 ARG Chi-restraints excluded: chain M residue 92 THR Chi-restraints excluded: chain M residue 95 VAL Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain M residue 97 LYS Chi-restraints excluded: chain M residue 103 LYS Chi-restraints excluded: chain M residue 117 LEU Chi-restraints excluded: chain M residue 122 THR Chi-restraints excluded: chain M residue 143 ILE Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 65 TRP Chi-restraints excluded: chain N residue 68 ILE Chi-restraints excluded: chain N residue 76 SER Chi-restraints excluded: chain N residue 82 ARG Chi-restraints excluded: chain N residue 113 VAL Chi-restraints excluded: chain N residue 116 GLU Chi-restraints excluded: chain N residue 120 LEU Chi-restraints excluded: chain N residue 122 SER Chi-restraints excluded: chain N residue 127 VAL Chi-restraints excluded: chain O residue 24 LEU Chi-restraints excluded: chain O residue 27 ASN Chi-restraints excluded: chain O residue 41 ARG Chi-restraints excluded: chain O residue 42 SER Chi-restraints excluded: chain O residue 56 LEU Chi-restraints excluded: chain O residue 70 VAL Chi-restraints excluded: chain O residue 75 GLU Chi-restraints excluded: chain O residue 81 VAL Chi-restraints excluded: chain O residue 89 LEU Chi-restraints excluded: chain O residue 104 TYR Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain O residue 114 ARG Chi-restraints excluded: chain O residue 121 VAL Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain O residue 123 ILE Chi-restraints excluded: chain O residue 125 PHE Chi-restraints excluded: chain O residue 126 VAL Chi-restraints excluded: chain P residue 3 THR Chi-restraints excluded: chain P residue 23 SER Chi-restraints excluded: chain P residue 31 LEU Chi-restraints excluded: chain P residue 33 ILE Chi-restraints excluded: chain P residue 62 GLU Chi-restraints excluded: chain P residue 71 THR Chi-restraints excluded: chain P residue 101 HIS Chi-restraints excluded: chain P residue 104 VAL Chi-restraints excluded: chain Q residue 15 THR Chi-restraints excluded: chain Q residue 16 ASP Chi-restraints excluded: chain Q residue 39 ARG Chi-restraints excluded: chain Q residue 48 ILE Chi-restraints excluded: chain Q residue 61 VAL Chi-restraints excluded: chain Q residue 62 ARG Chi-restraints excluded: chain Q residue 73 THR Chi-restraints excluded: chain Q residue 76 LEU Chi-restraints excluded: chain Q residue 92 VAL Chi-restraints excluded: chain Q residue 110 ILE Chi-restraints excluded: chain Q residue 113 ILE Chi-restraints excluded: chain R residue 9 VAL Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 34 SER Chi-restraints excluded: chain R residue 38 GLN Chi-restraints excluded: chain R residue 56 ASP Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 79 LEU Chi-restraints excluded: chain R residue 85 LEU Chi-restraints excluded: chain R residue 102 ASP Chi-restraints excluded: chain R residue 115 ASP Chi-restraints excluded: chain S residue 11 GLN Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 23 GLU Chi-restraints excluded: chain S residue 27 VAL Chi-restraints excluded: chain S residue 61 THR Chi-restraints excluded: chain S residue 81 HIS Chi-restraints excluded: chain S residue 82 SER Chi-restraints excluded: chain S residue 83 HIS Chi-restraints excluded: chain T residue 26 ILE Chi-restraints excluded: chain T residue 44 THR Chi-restraints excluded: chain T residue 67 PHE Chi-restraints excluded: chain T residue 86 THR Chi-restraints excluded: chain T residue 102 ASN Chi-restraints excluded: chain T residue 114 GLU Chi-restraints excluded: chain U residue 6 VAL Chi-restraints excluded: chain U residue 7 ILE Chi-restraints excluded: chain U residue 11 VAL Chi-restraints excluded: chain U residue 31 THR Chi-restraints excluded: chain U residue 37 LEU Chi-restraints excluded: chain U residue 47 ASP Chi-restraints excluded: chain U residue 80 VAL Chi-restraints excluded: chain V residue 12 ILE Chi-restraints excluded: chain V residue 18 ASN Chi-restraints excluded: chain V residue 31 ASP Chi-restraints excluded: chain V residue 33 VAL Chi-restraints excluded: chain V residue 35 VAL Chi-restraints excluded: chain V residue 70 VAL Chi-restraints excluded: chain V residue 94 SER Chi-restraints excluded: chain W residue 31 VAL Chi-restraints excluded: chain W residue 43 PHE Chi-restraints excluded: chain W residue 71 ASN Chi-restraints excluded: chain W residue 80 ASP Chi-restraints excluded: chain W residue 94 VAL Chi-restraints excluded: chain X residue 34 SER Chi-restraints excluded: chain X residue 50 ARG Chi-restraints excluded: chain X residue 67 THR Chi-restraints excluded: chain X residue 73 ASP Chi-restraints excluded: chain X residue 77 ARG Chi-restraints excluded: chain X residue 88 VAL Chi-restraints excluded: chain Y residue 8 THR Chi-restraints excluded: chain Y residue 12 THR Chi-restraints excluded: chain Y residue 14 SER Chi-restraints excluded: chain Y residue 16 ASN Chi-restraints excluded: chain Y residue 25 THR Chi-restraints excluded: chain Y residue 36 VAL Chi-restraints excluded: chain Y residue 41 ASP Chi-restraints excluded: chain Y residue 55 LYS Chi-restraints excluded: chain Z residue 6 ILE Chi-restraints excluded: chain Z residue 32 LEU Chi-restraints excluded: chain Z residue 62 ASN Chi-restraints excluded: chain 0 residue 13 ILE Chi-restraints excluded: chain 0 residue 22 THR Chi-restraints excluded: chain 0 residue 34 THR Chi-restraints excluded: chain 0 residue 40 ASN Chi-restraints excluded: chain 0 residue 43 ILE Chi-restraints excluded: chain 0 residue 47 VAL Chi-restraints excluded: chain 0 residue 53 LEU Chi-restraints excluded: chain 1 residue 13 VAL Chi-restraints excluded: chain 1 residue 18 THR Chi-restraints excluded: chain 1 residue 23 PHE Chi-restraints excluded: chain 1 residue 25 SER Chi-restraints excluded: chain 1 residue 27 SER Chi-restraints excluded: chain 1 residue 70 ARG Chi-restraints excluded: chain 1 residue 71 VAL Chi-restraints excluded: chain 2 residue 9 SER Chi-restraints excluded: chain 2 residue 18 THR Chi-restraints excluded: chain 3 residue 5 ILE Chi-restraints excluded: chain 3 residue 8 GLU Chi-restraints excluded: chain 3 residue 11 SER Chi-restraints excluded: chain 3 residue 26 ASN Chi-restraints excluded: chain 3 residue 39 GLU Chi-restraints excluded: chain 3 residue 44 LEU Chi-restraints excluded: chain 4 residue 3 ARG Chi-restraints excluded: chain 4 residue 5 TYR Chi-restraints excluded: chain 4 residue 24 THR Chi-restraints excluded: chain 4 residue 42 ILE Chi-restraints excluded: chain 5 residue 32 ARG Chi-restraints excluded: chain 5 residue 54 ASP Chi-restraints excluded: chain 5 residue 57 ARG Chi-restraints excluded: chain 5 residue 58 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 954 random chunks: chunk 805 optimal weight: 3.9990 chunk 723 optimal weight: 6.9990 chunk 401 optimal weight: 7.9990 chunk 247 optimal weight: 0.0170 chunk 487 optimal weight: 8.9990 chunk 386 optimal weight: 10.0000 chunk 747 optimal weight: 7.9990 chunk 289 optimal weight: 9.9990 chunk 454 optimal weight: 7.9990 chunk 556 optimal weight: 7.9990 chunk 866 optimal weight: 4.9990 overall best weight: 4.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 125 ASN d 39 ASN ** d 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 28 ASN ** g 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 122 ASN i 126 GLN j 4 GLN j 20 GLN m 50 ASN n 10 ASN n 19 GLN n 52 GLN ** p 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 72 ASN ** q 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 12 GLN ** q 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 GLN D 54 GLN D 68 HIS E 75 GLN E 160 ASN E 169 ASN F 37 ASN G 23 ASN ** G 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 84 GLN G 130 GLN K 131 HIS M 4 HIS M 38 GLN M 54 GLN N 35 GLN O 61 GLN O 68 ASN ** P 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 83 GLN ** R 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 11 GLN S 83 HIS S 88 HIS T 66 ASN V 44 HIS ** W 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 87 GLN Z 36 GLN ** 0 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 40 HIS 5 61 GLN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 150747 Z= 0.253 Angle : 0.678 14.698 226044 Z= 0.349 Chirality : 0.039 0.320 28980 Planarity : 0.005 0.098 11734 Dihedral : 23.461 179.340 77093 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.25 % Allowed : 12.21 % Favored : 87.54 % Rotamer: Outliers : 12.21 % Allowed : 20.56 % Favored : 67.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.28 % Twisted Proline : 0.52 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.04 (0.10), residues: 5143 helix: -1.24 (0.13), residues: 1414 sheet: -2.82 (0.15), residues: 925 loop : -3.54 (0.10), residues: 2804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP f 46 HIS 0.018 0.001 HIS C 142 PHE 0.022 0.002 PHE g 62 TYR 0.022 0.002 TYR r 27 ARG 0.013 0.001 ARG Q 51 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10286 Ramachandran restraints generated. 5143 Oldfield, 0 Emsley, 5143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10286 Ramachandran restraints generated. 5143 Oldfield, 0 Emsley, 5143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1581 residues out of total 4391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 536 poor density : 1045 time to evaluate : 6.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 10 MET cc_start: 0.8914 (mmm) cc_final: 0.8683 (mmm) REVERT: c 16 ARG cc_start: 0.8553 (OUTLIER) cc_final: 0.8032 (tmm-80) REVERT: c 22 TRP cc_start: 0.7819 (OUTLIER) cc_final: 0.7486 (p-90) REVERT: c 40 LYS cc_start: 0.9292 (OUTLIER) cc_final: 0.8916 (tmmm) REVERT: c 48 ASP cc_start: 0.8669 (p0) cc_final: 0.8219 (p0) REVERT: c 55 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7301 (mp0) REVERT: c 64 ASN cc_start: 0.8077 (OUTLIER) cc_final: 0.7867 (p0) REVERT: c 74 MET cc_start: 0.8476 (mmm) cc_final: 0.8160 (tmm) REVERT: c 141 MET cc_start: 0.7949 (mmm) cc_final: 0.7472 (mmm) REVERT: d 71 LEU cc_start: 0.9471 (OUTLIER) cc_final: 0.9199 (tt) REVERT: d 88 MET cc_start: 0.8905 (mmm) cc_final: 0.8666 (mmm) REVERT: d 94 ARG cc_start: 0.8395 (OUTLIER) cc_final: 0.7619 (ptm-80) REVERT: e 76 MET cc_start: 0.8113 (mtm) cc_final: 0.7791 (mtm) REVERT: e 117 LEU cc_start: 0.9394 (OUTLIER) cc_final: 0.9165 (mp) REVERT: f 12 ILE cc_start: 0.7847 (OUTLIER) cc_final: 0.7422 (mt) REVERT: f 25 LEU cc_start: 0.9454 (tp) cc_final: 0.9146 (tp) REVERT: f 28 ARG cc_start: 0.8570 (tmm-80) cc_final: 0.8359 (tmm-80) REVERT: f 39 GLU cc_start: 0.8427 (mt-10) cc_final: 0.8156 (tm-30) REVERT: f 55 MET cc_start: 0.8551 (mmm) cc_final: 0.8304 (mmm) REVERT: f 60 GLU cc_start: 0.8361 (mt-10) cc_final: 0.8145 (pt0) REVERT: f 72 SER cc_start: 0.9338 (p) cc_final: 0.9063 (m) REVERT: f 82 ARG cc_start: 0.8940 (ttp80) cc_final: 0.8620 (ttt90) REVERT: g 31 MET cc_start: 0.8639 (ttp) cc_final: 0.8219 (ttt) REVERT: g 66 MET cc_start: 0.8308 (tpp) cc_final: 0.8020 (tmm) REVERT: g 86 GLN cc_start: 0.8142 (pt0) cc_final: 0.7788 (mp10) REVERT: g 116 MET cc_start: 0.8090 (mmp) cc_final: 0.7750 (mmp) REVERT: g 126 ASP cc_start: 0.8540 (m-30) cc_final: 0.8155 (m-30) REVERT: g 140 ASP cc_start: 0.8768 (t0) cc_final: 0.8377 (t0) REVERT: g 144 MET cc_start: 0.8066 (tpp) cc_final: 0.7748 (mmp) REVERT: h 5 ASP cc_start: 0.8103 (t0) cc_final: 0.7684 (p0) REVERT: i 14 ASN cc_start: 0.8628 (OUTLIER) cc_final: 0.8290 (t0) REVERT: i 46 GLU cc_start: 0.9053 (mt-10) cc_final: 0.8588 (pm20) REVERT: i 110 MET cc_start: 0.7835 (ptp) cc_final: 0.7199 (mtp) REVERT: i 112 GLU cc_start: 0.8702 (tp30) cc_final: 0.8219 (tp30) REVERT: j 37 SER cc_start: 0.7671 (t) cc_final: 0.7177 (m) REVERT: j 47 SER cc_start: 0.9510 (m) cc_final: 0.9261 (p) REVERT: j 66 GLU cc_start: 0.8592 (pt0) cc_final: 0.8139 (pt0) REVERT: j 88 MET cc_start: 0.8912 (OUTLIER) cc_final: 0.8661 (mpp) REVERT: k 13 LYS cc_start: 0.8007 (mttt) cc_final: 0.7730 (ttmm) REVERT: k 64 GLN cc_start: 0.8572 (mm-40) cc_final: 0.8362 (mm-40) REVERT: k 105 LEU cc_start: 0.8830 (mt) cc_final: 0.8226 (mp) REVERT: l 75 GLU cc_start: 0.7693 (mm-30) cc_final: 0.7294 (tm-30) REVERT: m 13 LYS cc_start: 0.8714 (OUTLIER) cc_final: 0.8509 (mmmm) REVERT: m 32 LYS cc_start: 0.8426 (mmmt) cc_final: 0.7906 (tptp) REVERT: m 54 ASP cc_start: 0.8834 (m-30) cc_final: 0.8569 (m-30) REVERT: m 82 GLU cc_start: 0.8685 (mt-10) cc_final: 0.8232 (mt-10) REVERT: m 98 ARG cc_start: 0.6139 (OUTLIER) cc_final: 0.5689 (ptm160) REVERT: n 25 GLU cc_start: 0.8679 (mm-30) cc_final: 0.8385 (mm-30) REVERT: n 36 LYS cc_start: 0.9114 (tppt) cc_final: 0.8764 (tmtt) REVERT: o 45 THR cc_start: 0.8649 (m) cc_final: 0.8414 (p) REVERT: o 70 LEU cc_start: 0.9396 (tp) cc_final: 0.9164 (tt) REVERT: o 80 GLU cc_start: 0.8998 (OUTLIER) cc_final: 0.8659 (pp20) REVERT: p 10 MET cc_start: 0.8650 (OUTLIER) cc_final: 0.8260 (mtp) REVERT: p 30 ASP cc_start: 0.8592 (p0) cc_final: 0.8243 (t0) REVERT: p 65 GLN cc_start: 0.8158 (mt0) cc_final: 0.7848 (mp10) REVERT: q 11 TYR cc_start: 0.8393 (m-10) cc_final: 0.8164 (m-10) REVERT: q 20 MET cc_start: 0.7668 (mmm) cc_final: 0.7454 (mmt) REVERT: q 70 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8982 (tt) REVERT: r 26 ASP cc_start: 0.8592 (t0) cc_final: 0.8151 (t70) REVERT: r 69 MET cc_start: 0.8289 (mmm) cc_final: 0.7994 (mmt) REVERT: s 12 ASP cc_start: 0.7960 (m-30) cc_final: 0.7667 (m-30) REVERT: s 14 HIS cc_start: 0.7942 (OUTLIER) cc_final: 0.7213 (p-80) REVERT: s 20 GLU cc_start: 0.8412 (mt-10) cc_final: 0.8163 (pp20) REVERT: s 40 ILE cc_start: 0.8244 (mm) cc_final: 0.7778 (mt) REVERT: s 73 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.6743 (tm-30) REVERT: t 44 ASP cc_start: 0.8250 (t0) cc_final: 0.7806 (p0) REVERT: t 49 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.8082 (pp) REVERT: t 59 MET cc_start: 0.8355 (mmm) cc_final: 0.7964 (mmt) REVERT: C 108 LYS cc_start: 0.8464 (ttmt) cc_final: 0.7987 (mttt) REVERT: C 123 ASP cc_start: 0.8318 (t0) cc_final: 0.7865 (t0) REVERT: C 156 ARG cc_start: 0.8912 (OUTLIER) cc_final: 0.8709 (mtp180) REVERT: D 168 ARG cc_start: 0.9120 (OUTLIER) cc_final: 0.8598 (ptm160) REVERT: E 9 GLN cc_start: 0.7411 (OUTLIER) cc_final: 0.7171 (mp10) REVERT: E 12 THR cc_start: 0.8374 (OUTLIER) cc_final: 0.7164 (m) REVERT: E 13 GLN cc_start: 0.8769 (mp10) cc_final: 0.8513 (mp10) REVERT: E 65 TRP cc_start: 0.8170 (OUTLIER) cc_final: 0.7788 (p-90) REVERT: E 74 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.8153 (mtm180) REVERT: F 83 MET cc_start: 0.8753 (mmm) cc_final: 0.8175 (mtt) REVERT: F 120 LYS cc_start: 0.9173 (mttt) cc_final: 0.8911 (tptp) REVERT: F 165 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7915 (pt0) REVERT: G 19 GLN cc_start: 0.7969 (mt0) cc_final: 0.6887 (tm-30) REVERT: G 94 TYR cc_start: 0.8389 (m-10) cc_final: 0.7993 (m-80) REVERT: G 99 GLN cc_start: 0.8857 (mt0) cc_final: 0.8635 (pp30) REVERT: G 130 GLN cc_start: 0.8041 (mp-120) cc_final: 0.7473 (mp10) REVERT: K 37 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.9004 (tt) REVERT: K 137 GLN cc_start: 0.8979 (mt0) cc_final: 0.8311 (mp10) REVERT: L 25 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8700 (mp) REVERT: M 84 ARG cc_start: 0.8365 (OUTLIER) cc_final: 0.7961 (mpp80) REVERT: M 90 GLU cc_start: 0.7770 (tt0) cc_final: 0.7453 (tp30) REVERT: M 101 ILE cc_start: 0.7974 (mp) cc_final: 0.7732 (mm) REVERT: M 122 THR cc_start: 0.8442 (OUTLIER) cc_final: 0.7993 (p) REVERT: N 1 MET cc_start: -0.1093 (mmm) cc_final: -0.2644 (mmm) REVERT: N 58 MET cc_start: 0.8899 (mmm) cc_final: 0.8649 (ttm) REVERT: N 65 TRP cc_start: 0.8414 (OUTLIER) cc_final: 0.7062 (m100) REVERT: O 24 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8494 (tt) REVERT: O 41 ARG cc_start: 0.8063 (OUTLIER) cc_final: 0.6863 (ppt90) REVERT: O 46 LYS cc_start: 0.9044 (tttt) cc_final: 0.8440 (tptp) REVERT: O 76 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7367 (pm20) REVERT: O 125 PHE cc_start: 0.8519 (OUTLIER) cc_final: 0.7264 (m-10) REVERT: P 33 ILE cc_start: 0.9272 (OUTLIER) cc_final: 0.8968 (pt) REVERT: P 62 GLU cc_start: 0.7252 (OUTLIER) cc_final: 0.6941 (mm-30) REVERT: Q 7 GLU cc_start: 0.8680 (mt-10) cc_final: 0.8421 (mt-10) REVERT: Q 62 ARG cc_start: 0.8692 (OUTLIER) cc_final: 0.8293 (ttt90) REVERT: Q 106 LYS cc_start: 0.8915 (mtpt) cc_final: 0.8078 (mtpt) REVERT: Q 111 LYS cc_start: 0.9192 (mttt) cc_final: 0.8873 (mtpt) REVERT: Q 115 ARG cc_start: 0.7863 (mmt90) cc_final: 0.7418 (mpt180) REVERT: R 59 LYS cc_start: 0.7937 (mttt) cc_final: 0.7631 (mmtt) REVERT: S 1 MET cc_start: 0.8864 (OUTLIER) cc_final: 0.7931 (ttt) REVERT: S 6 LYS cc_start: 0.8471 (mttt) cc_final: 0.8245 (mtpt) REVERT: S 37 GLU cc_start: 0.7911 (mt-10) cc_final: 0.7511 (mt-10) REVERT: S 81 HIS cc_start: 0.8200 (OUTLIER) cc_final: 0.7385 (m-70) REVERT: S 83 HIS cc_start: 0.8927 (OUTLIER) cc_final: 0.8663 (p-80) REVERT: T 67 PHE cc_start: 0.7923 (OUTLIER) cc_final: 0.6337 (p90) REVERT: T 93 ARG cc_start: 0.8651 (OUTLIER) cc_final: 0.8375 (mmp-170) REVERT: U 5 ASP cc_start: 0.7996 (m-30) cc_final: 0.7353 (t0) REVERT: U 7 ILE cc_start: 0.8986 (OUTLIER) cc_final: 0.8515 (mt) REVERT: U 59 ARG cc_start: 0.7477 (mtt180) cc_final: 0.7105 (mtt180) REVERT: V 20 GLU cc_start: 0.8722 (mt-10) cc_final: 0.8449 (mp0) REVERT: V 53 GLN cc_start: 0.8809 (mt0) cc_final: 0.8294 (mm-40) REVERT: W 74 MET cc_start: 0.7149 (ptp) cc_final: 0.6820 (ppp) REVERT: W 80 ASP cc_start: 0.5442 (OUTLIER) cc_final: 0.5097 (m-30) REVERT: W 86 MET cc_start: 0.5615 (mtm) cc_final: 0.5046 (ptp) REVERT: X 72 VAL cc_start: 0.8707 (t) cc_final: 0.8428 (p) REVERT: X 87 GLN cc_start: 0.8768 (mt0) cc_final: 0.8430 (mt0) REVERT: Y 17 ASN cc_start: 0.8263 (t0) cc_final: 0.7996 (t0) REVERT: Y 30 LYS cc_start: 0.9171 (mtmt) cc_final: 0.8962 (mttm) REVERT: Y 35 LYS cc_start: 0.8742 (mtpm) cc_final: 0.8333 (tttp) REVERT: Z 23 GLU cc_start: 0.8402 (tm-30) cc_final: 0.8104 (tm-30) REVERT: Z 24 GLU cc_start: 0.8534 (tm-30) cc_final: 0.8282 (tm-30) REVERT: Z 29 ARG cc_start: 0.8851 (mtm-85) cc_final: 0.8470 (mtm110) REVERT: Z 37 LEU cc_start: 0.8672 (mt) cc_final: 0.8331 (mp) REVERT: Z 38 GLU cc_start: 0.7413 (mp0) cc_final: 0.7030 (pp20) REVERT: Z 39 ASN cc_start: 0.8330 (OUTLIER) cc_final: 0.7198 (t0) REVERT: 0 9 LYS cc_start: 0.8503 (pttp) cc_final: 0.8271 (pttp) REVERT: 0 41 GLU cc_start: 0.8563 (mm-30) cc_final: 0.8282 (mm-30) REVERT: 1 12 VAL cc_start: 0.9149 (t) cc_final: 0.8759 (p) REVERT: 1 15 MET cc_start: 0.7984 (ptm) cc_final: 0.6974 (ptm) REVERT: 1 73 ARG cc_start: 0.8113 (tmt170) cc_final: 0.7752 (ttt-90) REVERT: 2 36 MET cc_start: 0.8625 (mmm) cc_final: 0.8296 (mmm) REVERT: 3 8 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.6792 (tp30) REVERT: 3 13 LYS cc_start: 0.8884 (mmtm) cc_final: 0.8470 (mmtm) REVERT: 3 20 ASN cc_start: 0.9030 (p0) cc_final: 0.8652 (p0) REVERT: 3 41 LYS cc_start: 0.8747 (tppt) cc_final: 0.8474 (ptpp) REVERT: 3 44 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8397 (tm) REVERT: 5 32 ARG cc_start: 0.8560 (OUTLIER) cc_final: 0.8328 (ptp-170) REVERT: 5 57 ARG cc_start: 0.8916 (OUTLIER) cc_final: 0.8047 (ptp90) REVERT: 6 24 MET cc_start: 0.8529 (mmm) cc_final: 0.8307 (mmt) outliers start: 536 outliers final: 336 residues processed: 1443 average time/residue: 1.2067 time to fit residues: 3049.0164 Evaluate side-chains 1317 residues out of total 4391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 386 poor density : 931 time to evaluate : 5.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 15 ILE Chi-restraints excluded: chain c residue 16 ARG Chi-restraints excluded: chain c residue 22 TRP Chi-restraints excluded: chain c residue 40 LYS Chi-restraints excluded: chain c residue 42 ILE Chi-restraints excluded: chain c residue 55 GLU Chi-restraints excluded: chain c residue 64 ASN Chi-restraints excluded: chain c residue 83 VAL Chi-restraints excluded: chain c residue 85 ASN Chi-restraints excluded: chain c residue 102 ILE Chi-restraints excluded: chain c residue 200 TRP Chi-restraints excluded: chain d residue 4 TYR Chi-restraints excluded: chain d residue 57 LEU Chi-restraints excluded: chain d residue 64 ASN Chi-restraints excluded: chain d residue 71 LEU Chi-restraints excluded: chain d residue 94 ARG Chi-restraints excluded: chain d residue 96 ASP Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 184 ASP Chi-restraints excluded: chain d residue 195 VAL Chi-restraints excluded: chain e residue 9 LEU Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 31 LEU Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 105 VAL Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain e residue 131 ASN Chi-restraints excluded: chain e residue 132 THR Chi-restraints excluded: chain e residue 144 LEU Chi-restraints excluded: chain e residue 159 LYS Chi-restraints excluded: chain f residue 11 TYR Chi-restraints excluded: chain f residue 12 ILE Chi-restraints excluded: chain f residue 13 ILE Chi-restraints excluded: chain f residue 17 ILE Chi-restraints excluded: chain f residue 18 ASP Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 56 ASN Chi-restraints excluded: chain f residue 65 ILE Chi-restraints excluded: chain f residue 66 VAL Chi-restraints excluded: chain f residue 67 ASN Chi-restraints excluded: chain f residue 98 VAL Chi-restraints excluded: chain g residue 19 ASN Chi-restraints excluded: chain g residue 42 ILE Chi-restraints excluded: chain g residue 43 ILE Chi-restraints excluded: chain g residue 87 VAL Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain h residue 7 ILE Chi-restraints excluded: chain h residue 20 VAL Chi-restraints excluded: chain h residue 22 HIS Chi-restraints excluded: chain h residue 32 ILE Chi-restraints excluded: chain h residue 59 VAL Chi-restraints excluded: chain h residue 60 ILE Chi-restraints excluded: chain h residue 69 ASN Chi-restraints excluded: chain h residue 74 ILE Chi-restraints excluded: chain h residue 89 VAL Chi-restraints excluded: chain h residue 98 LEU Chi-restraints excluded: chain h residue 103 ILE Chi-restraints excluded: chain h residue 112 VAL Chi-restraints excluded: chain h residue 114 THR Chi-restraints excluded: chain h residue 127 VAL Chi-restraints excluded: chain i residue 9 THR Chi-restraints excluded: chain i residue 12 ARG Chi-restraints excluded: chain i residue 14 ASN Chi-restraints excluded: chain i residue 30 VAL Chi-restraints excluded: chain i residue 34 ASP Chi-restraints excluded: chain i residue 57 THR Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain i residue 66 ASN Chi-restraints excluded: chain i residue 88 LEU Chi-restraints excluded: chain i residue 93 ASP Chi-restraints excluded: chain j residue 72 ARG Chi-restraints excluded: chain j residue 74 ILE Chi-restraints excluded: chain j residue 82 LYS Chi-restraints excluded: chain j residue 88 MET Chi-restraints excluded: chain j residue 90 LEU Chi-restraints excluded: chain j residue 96 VAL Chi-restraints excluded: chain k residue 46 SER Chi-restraints excluded: chain k residue 76 GLU Chi-restraints excluded: chain k residue 99 SER Chi-restraints excluded: chain l residue 4 ILE Chi-restraints excluded: chain l residue 7 LEU Chi-restraints excluded: chain l residue 20 ASP Chi-restraints excluded: chain l residue 26 LYS Chi-restraints excluded: chain l residue 32 LYS Chi-restraints excluded: chain l residue 47 CYS Chi-restraints excluded: chain l residue 72 ASN Chi-restraints excluded: chain l residue 83 ILE Chi-restraints excluded: chain l residue 124 LYS Chi-restraints excluded: chain l residue 126 SER Chi-restraints excluded: chain m residue 9 ILE Chi-restraints excluded: chain m residue 13 LYS Chi-restraints excluded: chain m residue 29 THR Chi-restraints excluded: chain m residue 60 ILE Chi-restraints excluded: chain m residue 98 ARG Chi-restraints excluded: chain m residue 101 ASN Chi-restraints excluded: chain m residue 102 THR Chi-restraints excluded: chain n residue 5 SER Chi-restraints excluded: chain n residue 7 ILE Chi-restraints excluded: chain n residue 18 THR Chi-restraints excluded: chain n residue 57 LYS Chi-restraints excluded: chain o residue 24 SER Chi-restraints excluded: chain o residue 80 GLU Chi-restraints excluded: chain o residue 89 ARG Chi-restraints excluded: chain p residue 3 VAL Chi-restraints excluded: chain p residue 5 ILE Chi-restraints excluded: chain p residue 10 MET Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain p residue 39 THR Chi-restraints excluded: chain p residue 40 TYR Chi-restraints excluded: chain p residue 84 HIS Chi-restraints excluded: chain q residue 5 ARG Chi-restraints excluded: chain q residue 7 GLN Chi-restraints excluded: chain q residue 17 SER Chi-restraints excluded: chain q residue 23 THR Chi-restraints excluded: chain q residue 44 SER Chi-restraints excluded: chain q residue 58 VAL Chi-restraints excluded: chain q residue 70 LEU Chi-restraints excluded: chain q residue 78 LEU Chi-restraints excluded: chain r residue 16 TYR Chi-restraints excluded: chain r residue 30 THR Chi-restraints excluded: chain r residue 37 ILE Chi-restraints excluded: chain r residue 51 THR Chi-restraints excluded: chain r residue 63 ILE Chi-restraints excluded: chain r residue 72 LEU Chi-restraints excluded: chain s residue 7 LYS Chi-restraints excluded: chain s residue 14 HIS Chi-restraints excluded: chain s residue 33 THR Chi-restraints excluded: chain s residue 65 ASP Chi-restraints excluded: chain s residue 73 GLU Chi-restraints excluded: chain s residue 78 ARG Chi-restraints excluded: chain t residue 4 ILE Chi-restraints excluded: chain t residue 23 SER Chi-restraints excluded: chain t residue 46 VAL Chi-restraints excluded: chain t residue 49 LEU Chi-restraints excluded: chain t residue 65 LEU Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 15 ASN Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 20 ASP Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 45 ASN Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 53 HIS Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 156 ARG Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 194 SER Chi-restraints excluded: chain C residue 211 SER Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 225 MET Chi-restraints excluded: chain C residue 228 ASN Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 130 ARG Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 167 ASP Chi-restraints excluded: chain D residue 168 ARG Chi-restraints excluded: chain D residue 188 ILE Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain E residue 7 PHE Chi-restraints excluded: chain E residue 8 LYS Chi-restraints excluded: chain E residue 9 GLN Chi-restraints excluded: chain E residue 10 ASP Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 65 TRP Chi-restraints excluded: chain E residue 74 ARG Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 84 ARG Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain E residue 177 THR Chi-restraints excluded: chain E residue 179 ASP Chi-restraints excluded: chain E residue 195 THR Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 123 ASP Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 165 GLU Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 43 MET Chi-restraints excluded: chain G residue 52 PHE Chi-restraints excluded: chain G residue 65 HIS Chi-restraints excluded: chain G residue 90 ILE Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 128 ASN Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain K residue 37 LEU Chi-restraints excluded: chain K residue 41 ASN Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 50 ASP Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 85 LEU Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 113 ASN Chi-restraints excluded: chain K residue 115 LEU Chi-restraints excluded: chain K residue 142 ASP Chi-restraints excluded: chain L residue 6 SER Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 35 ILE Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 73 ASP Chi-restraints excluded: chain L residue 92 SER Chi-restraints excluded: chain L residue 110 ASN Chi-restraints excluded: chain L residue 114 ILE Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain M residue 73 ASP Chi-restraints excluded: chain M residue 76 VAL Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 79 LEU Chi-restraints excluded: chain M residue 84 ARG Chi-restraints excluded: chain M residue 89 THR Chi-restraints excluded: chain M residue 95 VAL Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain M residue 97 LYS Chi-restraints excluded: chain M residue 103 LYS Chi-restraints excluded: chain M residue 117 LEU Chi-restraints excluded: chain M residue 122 THR Chi-restraints excluded: chain M residue 143 ILE Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 43 THR Chi-restraints excluded: chain N residue 52 ILE Chi-restraints excluded: chain N residue 65 TRP Chi-restraints excluded: chain N residue 68 ILE Chi-restraints excluded: chain N residue 76 SER Chi-restraints excluded: chain N residue 82 ARG Chi-restraints excluded: chain N residue 113 VAL Chi-restraints excluded: chain N residue 116 GLU Chi-restraints excluded: chain N residue 120 LEU Chi-restraints excluded: chain N residue 127 VAL Chi-restraints excluded: chain O residue 24 LEU Chi-restraints excluded: chain O residue 26 ILE Chi-restraints excluded: chain O residue 27 ASN Chi-restraints excluded: chain O residue 41 ARG Chi-restraints excluded: chain O residue 42 SER Chi-restraints excluded: chain O residue 56 LEU Chi-restraints excluded: chain O residue 76 GLU Chi-restraints excluded: chain O residue 81 VAL Chi-restraints excluded: chain O residue 89 LEU Chi-restraints excluded: chain O residue 104 TYR Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain O residue 114 ARG Chi-restraints excluded: chain O residue 121 VAL Chi-restraints excluded: chain O residue 125 PHE Chi-restraints excluded: chain P residue 3 THR Chi-restraints excluded: chain P residue 23 SER Chi-restraints excluded: chain P residue 31 LEU Chi-restraints excluded: chain P residue 33 ILE Chi-restraints excluded: chain P residue 62 GLU Chi-restraints excluded: chain P residue 71 THR Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain P residue 101 HIS Chi-restraints excluded: chain P residue 104 VAL Chi-restraints excluded: chain Q residue 8 LEU Chi-restraints excluded: chain Q residue 15 THR Chi-restraints excluded: chain Q residue 16 ASP Chi-restraints excluded: chain Q residue 24 ASP Chi-restraints excluded: chain Q residue 32 VAL Chi-restraints excluded: chain Q residue 39 ARG Chi-restraints excluded: chain Q residue 48 ILE Chi-restraints excluded: chain Q residue 62 ARG Chi-restraints excluded: chain Q residue 73 THR Chi-restraints excluded: chain Q residue 76 LEU Chi-restraints excluded: chain Q residue 110 ILE Chi-restraints excluded: chain R residue 9 VAL Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 34 SER Chi-restraints excluded: chain R residue 85 LEU Chi-restraints excluded: chain R residue 90 ILE Chi-restraints excluded: chain R residue 102 ASP Chi-restraints excluded: chain R residue 115 ASP Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 23 GLU Chi-restraints excluded: chain S residue 27 VAL Chi-restraints excluded: chain S residue 33 VAL Chi-restraints excluded: chain S residue 81 HIS Chi-restraints excluded: chain S residue 83 HIS Chi-restraints excluded: chain T residue 67 PHE Chi-restraints excluded: chain T residue 86 THR Chi-restraints excluded: chain T residue 93 ARG Chi-restraints excluded: chain T residue 102 ASN Chi-restraints excluded: chain T residue 114 GLU Chi-restraints excluded: chain U residue 6 VAL Chi-restraints excluded: chain U residue 7 ILE Chi-restraints excluded: chain U residue 11 VAL Chi-restraints excluded: chain U residue 31 THR Chi-restraints excluded: chain U residue 47 ASP Chi-restraints excluded: chain U residue 80 VAL Chi-restraints excluded: chain U residue 89 ILE Chi-restraints excluded: chain V residue 13 THR Chi-restraints excluded: chain V residue 31 ASP Chi-restraints excluded: chain V residue 35 VAL Chi-restraints excluded: chain V residue 70 VAL Chi-restraints excluded: chain V residue 94 SER Chi-restraints excluded: chain W residue 31 VAL Chi-restraints excluded: chain W residue 43 PHE Chi-restraints excluded: chain W residue 71 ASN Chi-restraints excluded: chain W residue 80 ASP Chi-restraints excluded: chain W residue 94 VAL Chi-restraints excluded: chain X residue 34 SER Chi-restraints excluded: chain X residue 40 VAL Chi-restraints excluded: chain X residue 67 THR Chi-restraints excluded: chain X residue 73 ASP Chi-restraints excluded: chain X residue 88 VAL Chi-restraints excluded: chain Y residue 8 THR Chi-restraints excluded: chain Y residue 12 THR Chi-restraints excluded: chain Y residue 25 THR Chi-restraints excluded: chain Y residue 36 VAL Chi-restraints excluded: chain Y residue 41 ASP Chi-restraints excluded: chain Y residue 55 LYS Chi-restraints excluded: chain Z residue 18 GLU Chi-restraints excluded: chain Z residue 30 PHE Chi-restraints excluded: chain Z residue 32 LEU Chi-restraints excluded: chain Z residue 39 ASN Chi-restraints excluded: chain Z residue 45 GLU Chi-restraints excluded: chain 0 residue 13 ILE Chi-restraints excluded: chain 0 residue 22 THR Chi-restraints excluded: chain 0 residue 34 THR Chi-restraints excluded: chain 0 residue 40 ASN Chi-restraints excluded: chain 0 residue 47 VAL Chi-restraints excluded: chain 0 residue 53 LEU Chi-restraints excluded: chain 1 residue 13 VAL Chi-restraints excluded: chain 1 residue 23 PHE Chi-restraints excluded: chain 1 residue 27 SER Chi-restraints excluded: chain 1 residue 71 VAL Chi-restraints excluded: chain 2 residue 9 SER Chi-restraints excluded: chain 2 residue 18 THR Chi-restraints excluded: chain 3 residue 3 VAL Chi-restraints excluded: chain 3 residue 5 ILE Chi-restraints excluded: chain 3 residue 8 GLU Chi-restraints excluded: chain 3 residue 11 SER Chi-restraints excluded: chain 3 residue 26 ASN Chi-restraints excluded: chain 3 residue 39 GLU Chi-restraints excluded: chain 3 residue 44 LEU Chi-restraints excluded: chain 4 residue 5 TYR Chi-restraints excluded: chain 4 residue 24 THR Chi-restraints excluded: chain 4 residue 42 ILE Chi-restraints excluded: chain 4 residue 43 SER Chi-restraints excluded: chain 5 residue 14 VAL Chi-restraints excluded: chain 5 residue 32 ARG Chi-restraints excluded: chain 5 residue 54 ASP Chi-restraints excluded: chain 5 residue 57 ARG Chi-restraints excluded: chain 5 residue 58 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 954 random chunks: chunk 481 optimal weight: 10.0000 chunk 268 optimal weight: 10.0000 chunk 721 optimal weight: 1.9990 chunk 589 optimal weight: 10.0000 chunk 238 optimal weight: 5.9990 chunk 867 optimal weight: 6.9990 chunk 937 optimal weight: 9.9990 chunk 772 optimal weight: 6.9990 chunk 860 optimal weight: 6.9990 chunk 295 optimal weight: 9.9990 chunk 696 optimal weight: 4.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 113 GLN ** g 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 75 GLN ** j 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 20 GLN k 119 ASN m 50 ASN m 104 ASN ** n 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 28 GLN ** p 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 7 GLN ** q 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 35 GLN ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 135 GLN ** G 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 35 GLN O 68 ASN ** P 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 29 HIS ** R 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 81 HIS ** R 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 66 ASN U 40 GLN 0 32 ASN ** 1 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 150747 Z= 0.277 Angle : 0.670 11.451 226044 Z= 0.343 Chirality : 0.039 0.346 28980 Planarity : 0.005 0.098 11734 Dihedral : 23.343 179.856 76878 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.16 % Allowed : 13.32 % Favored : 86.53 % Rotamer: Outliers : 11.82 % Allowed : 22.71 % Favored : 65.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.28 % Twisted Proline : 0.52 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.49 (0.11), residues: 5143 helix: -0.72 (0.14), residues: 1430 sheet: -2.39 (0.16), residues: 928 loop : -3.29 (0.10), residues: 2785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP c 200 HIS 0.007 0.001 HIS F 115 PHE 0.019 0.002 PHE l 31 TYR 0.023 0.002 TYR r 27 ARG 0.009 0.001 ARG Q 51 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10286 Ramachandran restraints generated. 5143 Oldfield, 0 Emsley, 5143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10286 Ramachandran restraints generated. 5143 Oldfield, 0 Emsley, 5143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1484 residues out of total 4391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 519 poor density : 965 time to evaluate : 6.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 16 ARG cc_start: 0.8542 (OUTLIER) cc_final: 0.8060 (tmm160) REVERT: c 40 LYS cc_start: 0.9281 (OUTLIER) cc_final: 0.8897 (tmmm) REVERT: c 55 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7340 (mp0) REVERT: c 141 MET cc_start: 0.8013 (mmm) cc_final: 0.7522 (mmm) REVERT: d 71 LEU cc_start: 0.9409 (OUTLIER) cc_final: 0.9047 (tt) REVERT: d 88 MET cc_start: 0.8890 (mmm) cc_final: 0.8641 (mmm) REVERT: d 94 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.7402 (ptm-80) REVERT: f 12 ILE cc_start: 0.7808 (OUTLIER) cc_final: 0.7313 (mt) REVERT: f 25 LEU cc_start: 0.9464 (tp) cc_final: 0.9158 (tp) REVERT: f 28 ARG cc_start: 0.8637 (tmm-80) cc_final: 0.8411 (tmm-80) REVERT: f 39 GLU cc_start: 0.8432 (mt-10) cc_final: 0.7951 (tm-30) REVERT: f 55 MET cc_start: 0.8524 (mmm) cc_final: 0.8286 (mmm) REVERT: f 82 ARG cc_start: 0.8976 (ttp80) cc_final: 0.8716 (ttt90) REVERT: g 31 MET cc_start: 0.8685 (ttp) cc_final: 0.8268 (ttt) REVERT: g 75 VAL cc_start: 0.8732 (OUTLIER) cc_final: 0.8250 (p) REVERT: g 86 GLN cc_start: 0.8185 (pt0) cc_final: 0.7911 (mp10) REVERT: g 116 MET cc_start: 0.8237 (mmp) cc_final: 0.7931 (mmp) REVERT: g 126 ASP cc_start: 0.8535 (m-30) cc_final: 0.8244 (m-30) REVERT: h 5 ASP cc_start: 0.8069 (t0) cc_final: 0.7690 (p0) REVERT: h 54 ASP cc_start: 0.8263 (p0) cc_final: 0.7801 (p0) REVERT: h 76 ASN cc_start: 0.9162 (t0) cc_final: 0.8641 (t0) REVERT: i 14 ASN cc_start: 0.8657 (OUTLIER) cc_final: 0.8291 (t0) REVERT: i 38 TYR cc_start: 0.7435 (OUTLIER) cc_final: 0.7085 (t80) REVERT: i 46 GLU cc_start: 0.9048 (mt-10) cc_final: 0.8725 (pm20) REVERT: i 81 HIS cc_start: 0.8080 (m90) cc_final: 0.6466 (t-170) REVERT: i 110 MET cc_start: 0.7940 (ptp) cc_final: 0.7421 (mtp) REVERT: i 112 GLU cc_start: 0.8695 (tp30) cc_final: 0.8265 (tp30) REVERT: j 47 SER cc_start: 0.9510 (m) cc_final: 0.9263 (p) REVERT: j 66 GLU cc_start: 0.8603 (pt0) cc_final: 0.8196 (pt0) REVERT: k 13 LYS cc_start: 0.8003 (mttt) cc_final: 0.7448 (ttmt) REVERT: k 64 GLN cc_start: 0.8601 (mm-40) cc_final: 0.8352 (tp40) REVERT: k 98 ARG cc_start: 0.9165 (mtp-110) cc_final: 0.8414 (ttp80) REVERT: k 105 LEU cc_start: 0.8701 (mt) cc_final: 0.8309 (mp) REVERT: k 111 ARG cc_start: 0.7346 (mtt90) cc_final: 0.7010 (mtt90) REVERT: l 75 GLU cc_start: 0.7694 (mm-30) cc_final: 0.7251 (tm-30) REVERT: m 13 LYS cc_start: 0.8710 (OUTLIER) cc_final: 0.8500 (mmmm) REVERT: m 54 ASP cc_start: 0.8811 (m-30) cc_final: 0.8499 (m-30) REVERT: m 61 ASP cc_start: 0.9070 (t0) cc_final: 0.8693 (t0) REVERT: m 95 LEU cc_start: 0.6468 (OUTLIER) cc_final: 0.6230 (mm) REVERT: n 25 GLU cc_start: 0.8695 (mm-30) cc_final: 0.8398 (mm-30) REVERT: n 35 ARG cc_start: 0.8417 (OUTLIER) cc_final: 0.8168 (ptm160) REVERT: n 36 LYS cc_start: 0.9125 (tppt) cc_final: 0.8740 (tmtt) REVERT: o 45 THR cc_start: 0.8643 (m) cc_final: 0.8422 (p) REVERT: o 80 GLU cc_start: 0.8903 (OUTLIER) cc_final: 0.8594 (pp20) REVERT: p 10 MET cc_start: 0.8647 (OUTLIER) cc_final: 0.8262 (mtp) REVERT: p 30 ASP cc_start: 0.8670 (p0) cc_final: 0.8261 (t0) REVERT: p 65 GLN cc_start: 0.8176 (mt0) cc_final: 0.7854 (mp10) REVERT: p 90 LYS cc_start: 0.8305 (OUTLIER) cc_final: 0.8090 (mmtt) REVERT: q 20 MET cc_start: 0.7577 (mmm) cc_final: 0.7356 (mmt) REVERT: r 26 ASP cc_start: 0.8671 (t0) cc_final: 0.8245 (t70) REVERT: s 12 ASP cc_start: 0.7982 (m-30) cc_final: 0.7673 (m-30) REVERT: s 14 HIS cc_start: 0.8039 (OUTLIER) cc_final: 0.7271 (p-80) REVERT: s 40 ILE cc_start: 0.8372 (mm) cc_final: 0.7884 (mt) REVERT: s 73 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.6875 (tm-30) REVERT: t 44 ASP cc_start: 0.8368 (t0) cc_final: 0.7946 (p0) REVERT: C 66 ASP cc_start: 0.8712 (t0) cc_final: 0.8456 (t0) REVERT: C 108 LYS cc_start: 0.8697 (ttmt) cc_final: 0.8116 (mttt) REVERT: C 123 ASP cc_start: 0.8422 (t0) cc_final: 0.7906 (t0) REVERT: C 199 GLN cc_start: 0.8522 (pm20) cc_final: 0.8295 (pm20) REVERT: D 168 ARG cc_start: 0.9133 (OUTLIER) cc_final: 0.8523 (ptm160) REVERT: E 12 THR cc_start: 0.8261 (OUTLIER) cc_final: 0.6901 (m) REVERT: F 83 MET cc_start: 0.8744 (mmm) cc_final: 0.8130 (mtt) REVERT: F 120 LYS cc_start: 0.9187 (mttt) cc_final: 0.8923 (tptp) REVERT: G 19 GLN cc_start: 0.7959 (mt0) cc_final: 0.6751 (tm-30) REVERT: G 94 TYR cc_start: 0.8457 (m-10) cc_final: 0.8131 (m-80) REVERT: G 130 GLN cc_start: 0.8085 (mp-120) cc_final: 0.7520 (mp-120) REVERT: K 117 ARG cc_start: 0.8841 (mtm180) cc_final: 0.8395 (mtt180) REVERT: L 64 ARG cc_start: 0.7232 (OUTLIER) cc_final: 0.7010 (ptt-90) REVERT: M 84 ARG cc_start: 0.8338 (OUTLIER) cc_final: 0.7941 (mpp80) REVERT: M 101 ILE cc_start: 0.8027 (OUTLIER) cc_final: 0.7735 (mm) REVERT: N 1 MET cc_start: -0.0859 (mmm) cc_final: -0.2528 (mmm) REVERT: N 17 MET cc_start: 0.7514 (mmm) cc_final: 0.7208 (mmm) REVERT: N 58 MET cc_start: 0.8888 (mmm) cc_final: 0.8432 (ttm) REVERT: N 65 TRP cc_start: 0.8380 (OUTLIER) cc_final: 0.7145 (m100) REVERT: N 103 MET cc_start: 0.8131 (mmm) cc_final: 0.7788 (mmm) REVERT: N 106 ILE cc_start: 0.9115 (mm) cc_final: 0.8664 (tp) REVERT: O 24 LEU cc_start: 0.9188 (OUTLIER) cc_final: 0.8546 (tt) REVERT: O 41 ARG cc_start: 0.7995 (OUTLIER) cc_final: 0.6873 (ppt90) REVERT: O 46 LYS cc_start: 0.9026 (tttt) cc_final: 0.8437 (tptp) REVERT: O 125 PHE cc_start: 0.8585 (OUTLIER) cc_final: 0.7400 (m-10) REVERT: P 62 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.7159 (mm-30) REVERT: Q 7 GLU cc_start: 0.8700 (mt-10) cc_final: 0.8433 (mt-10) REVERT: Q 39 ARG cc_start: 0.8160 (OUTLIER) cc_final: 0.6786 (ttm170) REVERT: Q 106 LYS cc_start: 0.8909 (mtpt) cc_final: 0.8048 (mtpt) REVERT: Q 111 LYS cc_start: 0.9216 (mttt) cc_final: 0.8928 (mtpt) REVERT: R 18 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8938 (mp) REVERT: S 1 MET cc_start: 0.8865 (OUTLIER) cc_final: 0.7890 (ttt) REVERT: S 2 TYR cc_start: 0.8177 (t80) cc_final: 0.7919 (t80) REVERT: S 6 LYS cc_start: 0.8526 (mttt) cc_final: 0.8183 (mttt) REVERT: S 37 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7507 (mt-10) REVERT: S 81 HIS cc_start: 0.8212 (OUTLIER) cc_final: 0.7343 (m-70) REVERT: T 93 ARG cc_start: 0.8679 (OUTLIER) cc_final: 0.8397 (mmp-170) REVERT: T 114 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.8366 (tt0) REVERT: U 5 ASP cc_start: 0.7866 (m-30) cc_final: 0.7285 (t0) REVERT: U 7 ILE cc_start: 0.8972 (OUTLIER) cc_final: 0.8578 (mt) REVERT: U 59 ARG cc_start: 0.7465 (mtt180) cc_final: 0.7081 (mtt180) REVERT: V 7 ASP cc_start: 0.8066 (m-30) cc_final: 0.7463 (m-30) REVERT: V 20 GLU cc_start: 0.8784 (mt-10) cc_final: 0.8486 (mp0) REVERT: V 53 GLN cc_start: 0.8806 (mt0) cc_final: 0.8278 (mm-40) REVERT: W 80 ASP cc_start: 0.5472 (OUTLIER) cc_final: 0.5079 (m-30) REVERT: W 86 MET cc_start: 0.5645 (mtm) cc_final: 0.5071 (ptp) REVERT: X 72 VAL cc_start: 0.8700 (t) cc_final: 0.8420 (p) REVERT: X 87 GLN cc_start: 0.8613 (mt0) cc_final: 0.8375 (mt0) REVERT: Y 17 ASN cc_start: 0.8295 (t0) cc_final: 0.8023 (t0) REVERT: Y 30 LYS cc_start: 0.9188 (mtmt) cc_final: 0.8963 (mttm) REVERT: Y 35 LYS cc_start: 0.8742 (mtpm) cc_final: 0.8371 (tttp) REVERT: Z 23 GLU cc_start: 0.8518 (tm-30) cc_final: 0.8308 (tm-30) REVERT: Z 24 GLU cc_start: 0.8582 (tm-30) cc_final: 0.8319 (tm-30) REVERT: Z 39 ASN cc_start: 0.8283 (OUTLIER) cc_final: 0.6927 (m-40) REVERT: 1 12 VAL cc_start: 0.9082 (t) cc_final: 0.8746 (p) REVERT: 1 43 TYR cc_start: 0.7173 (m-80) cc_final: 0.6801 (m-10) REVERT: 1 73 ARG cc_start: 0.8077 (tmt170) cc_final: 0.7536 (ttp-170) REVERT: 2 36 MET cc_start: 0.8836 (mmm) cc_final: 0.8483 (mmt) REVERT: 3 8 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.6728 (tp30) REVERT: 3 13 LYS cc_start: 0.8851 (mmtm) cc_final: 0.8451 (mmtm) REVERT: 3 20 ASN cc_start: 0.9113 (p0) cc_final: 0.8762 (p0) REVERT: 3 41 LYS cc_start: 0.8763 (tppt) cc_final: 0.8402 (ptpp) REVERT: 3 44 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8379 (tm) REVERT: 5 57 ARG cc_start: 0.9110 (OUTLIER) cc_final: 0.8135 (ptp90) REVERT: 6 24 MET cc_start: 0.8460 (mmm) cc_final: 0.8218 (mmt) outliers start: 519 outliers final: 358 residues processed: 1342 average time/residue: 1.1932 time to fit residues: 2816.2446 Evaluate side-chains 1318 residues out of total 4391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 397 poor density : 921 time to evaluate : 5.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 15 ILE Chi-restraints excluded: chain c residue 16 ARG Chi-restraints excluded: chain c residue 40 LYS Chi-restraints excluded: chain c residue 42 ILE Chi-restraints excluded: chain c residue 55 GLU Chi-restraints excluded: chain c residue 83 VAL Chi-restraints excluded: chain c residue 85 ASN Chi-restraints excluded: chain c residue 176 THR Chi-restraints excluded: chain c residue 200 TRP Chi-restraints excluded: chain d residue 4 TYR Chi-restraints excluded: chain d residue 29 ARG Chi-restraints excluded: chain d residue 57 LEU Chi-restraints excluded: chain d residue 64 ASN Chi-restraints excluded: chain d residue 71 LEU Chi-restraints excluded: chain d residue 94 ARG Chi-restraints excluded: chain d residue 107 THR Chi-restraints excluded: chain d residue 113 GLN Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 184 ASP Chi-restraints excluded: chain d residue 190 ILE Chi-restraints excluded: chain d residue 195 VAL Chi-restraints excluded: chain e residue 9 LEU Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 31 LEU Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 105 VAL Chi-restraints excluded: chain e residue 114 VAL Chi-restraints excluded: chain e residue 127 SER Chi-restraints excluded: chain e residue 131 ASN Chi-restraints excluded: chain e residue 132 THR Chi-restraints excluded: chain e residue 144 LEU Chi-restraints excluded: chain e residue 159 LYS Chi-restraints excluded: chain f residue 11 TYR Chi-restraints excluded: chain f residue 12 ILE Chi-restraints excluded: chain f residue 13 ILE Chi-restraints excluded: chain f residue 18 ASP Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 56 ASN Chi-restraints excluded: chain f residue 65 ILE Chi-restraints excluded: chain f residue 66 VAL Chi-restraints excluded: chain f residue 67 ASN Chi-restraints excluded: chain f residue 98 VAL Chi-restraints excluded: chain g residue 19 ASN Chi-restraints excluded: chain g residue 43 ILE Chi-restraints excluded: chain g residue 47 PHE Chi-restraints excluded: chain g residue 75 VAL Chi-restraints excluded: chain g residue 87 VAL Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain h residue 14 ILE Chi-restraints excluded: chain h residue 20 VAL Chi-restraints excluded: chain h residue 22 HIS Chi-restraints excluded: chain h residue 32 ILE Chi-restraints excluded: chain h residue 59 VAL Chi-restraints excluded: chain h residue 60 ILE Chi-restraints excluded: chain h residue 69 ASN Chi-restraints excluded: chain h residue 74 ILE Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 98 LEU Chi-restraints excluded: chain h residue 103 ILE Chi-restraints excluded: chain h residue 112 VAL Chi-restraints excluded: chain h residue 114 THR Chi-restraints excluded: chain i residue 9 THR Chi-restraints excluded: chain i residue 12 ARG Chi-restraints excluded: chain i residue 14 ASN Chi-restraints excluded: chain i residue 30 VAL Chi-restraints excluded: chain i residue 34 ASP Chi-restraints excluded: chain i residue 38 TYR Chi-restraints excluded: chain i residue 57 THR Chi-restraints excluded: chain i residue 88 LEU Chi-restraints excluded: chain i residue 93 ASP Chi-restraints excluded: chain j residue 51 VAL Chi-restraints excluded: chain j residue 72 ARG Chi-restraints excluded: chain j residue 74 ILE Chi-restraints excluded: chain j residue 90 LEU Chi-restraints excluded: chain j residue 96 VAL Chi-restraints excluded: chain j residue 98 ILE Chi-restraints excluded: chain k residue 18 SER Chi-restraints excluded: chain k residue 26 THR Chi-restraints excluded: chain k residue 46 SER Chi-restraints excluded: chain k residue 55 SER Chi-restraints excluded: chain k residue 76 GLU Chi-restraints excluded: chain k residue 97 ILE Chi-restraints excluded: chain k residue 99 SER Chi-restraints excluded: chain k residue 119 ASN Chi-restraints excluded: chain l residue 4 ILE Chi-restraints excluded: chain l residue 7 LEU Chi-restraints excluded: chain l residue 20 ASP Chi-restraints excluded: chain l residue 26 LYS Chi-restraints excluded: chain l residue 32 LYS Chi-restraints excluded: chain l residue 47 CYS Chi-restraints excluded: chain l residue 72 ASN Chi-restraints excluded: chain l residue 76 VAL Chi-restraints excluded: chain l residue 92 VAL Chi-restraints excluded: chain l residue 124 LYS Chi-restraints excluded: chain l residue 126 SER Chi-restraints excluded: chain l residue 132 THR Chi-restraints excluded: chain m residue 4 ILE Chi-restraints excluded: chain m residue 9 ILE Chi-restraints excluded: chain m residue 13 LYS Chi-restraints excluded: chain m residue 81 MET Chi-restraints excluded: chain m residue 95 LEU Chi-restraints excluded: chain m residue 101 ASN Chi-restraints excluded: chain m residue 102 THR Chi-restraints excluded: chain m residue 104 ASN Chi-restraints excluded: chain n residue 7 ILE Chi-restraints excluded: chain n residue 18 THR Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain n residue 35 ARG Chi-restraints excluded: chain n residue 57 LYS Chi-restraints excluded: chain o residue 11 ILE Chi-restraints excluded: chain o residue 24 SER Chi-restraints excluded: chain o residue 52 SER Chi-restraints excluded: chain o residue 80 GLU Chi-restraints excluded: chain o residue 89 ARG Chi-restraints excluded: chain p residue 3 VAL Chi-restraints excluded: chain p residue 5 ILE Chi-restraints excluded: chain p residue 10 MET Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain p residue 39 THR Chi-restraints excluded: chain p residue 40 TYR Chi-restraints excluded: chain p residue 84 HIS Chi-restraints excluded: chain p residue 90 LYS Chi-restraints excluded: chain q residue 5 ARG Chi-restraints excluded: chain q residue 17 SER Chi-restraints excluded: chain q residue 23 THR Chi-restraints excluded: chain q residue 27 VAL Chi-restraints excluded: chain q residue 44 SER Chi-restraints excluded: chain q residue 78 LEU Chi-restraints excluded: chain r residue 16 TYR Chi-restraints excluded: chain r residue 29 ASP Chi-restraints excluded: chain r residue 37 ILE Chi-restraints excluded: chain r residue 51 THR Chi-restraints excluded: chain r residue 63 ILE Chi-restraints excluded: chain r residue 72 LEU Chi-restraints excluded: chain s residue 7 LYS Chi-restraints excluded: chain s residue 14 HIS Chi-restraints excluded: chain s residue 33 THR Chi-restraints excluded: chain s residue 49 ILE Chi-restraints excluded: chain s residue 65 ASP Chi-restraints excluded: chain s residue 73 GLU Chi-restraints excluded: chain t residue 4 ILE Chi-restraints excluded: chain t residue 23 SER Chi-restraints excluded: chain t residue 46 VAL Chi-restraints excluded: chain t residue 65 LEU Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 15 ASN Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 20 ASP Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 45 ASN Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 53 HIS Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 134 ASN Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 171 TYR Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 194 SER Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 225 MET Chi-restraints excluded: chain C residue 228 ASN Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 130 ARG Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 167 ASP Chi-restraints excluded: chain D residue 168 ARG Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 188 ILE Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain E residue 7 PHE Chi-restraints excluded: chain E residue 8 LYS Chi-restraints excluded: chain E residue 10 ASP Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 38 ILE Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 74 ARG Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 84 ARG Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 121 ASN Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain E residue 177 THR Chi-restraints excluded: chain E residue 179 ASP Chi-restraints excluded: chain E residue 195 THR Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 123 ASP Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 41 ILE Chi-restraints excluded: chain G residue 43 MET Chi-restraints excluded: chain G residue 52 PHE Chi-restraints excluded: chain G residue 65 HIS Chi-restraints excluded: chain G residue 90 ILE Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 41 ASN Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 50 ASP Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 80 MET Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 113 ASN Chi-restraints excluded: chain K residue 115 LEU Chi-restraints excluded: chain K residue 142 ASP Chi-restraints excluded: chain L residue 6 SER Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 35 ILE Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 64 ARG Chi-restraints excluded: chain L residue 73 ASP Chi-restraints excluded: chain L residue 90 ASP Chi-restraints excluded: chain L residue 92 SER Chi-restraints excluded: chain L residue 110 ASN Chi-restraints excluded: chain M residue 3 LEU Chi-restraints excluded: chain M residue 18 ARG Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain M residue 73 ASP Chi-restraints excluded: chain M residue 76 VAL Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 84 ARG Chi-restraints excluded: chain M residue 89 THR Chi-restraints excluded: chain M residue 95 VAL Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain M residue 97 LYS Chi-restraints excluded: chain M residue 101 ILE Chi-restraints excluded: chain M residue 103 LYS Chi-restraints excluded: chain M residue 117 LEU Chi-restraints excluded: chain M residue 143 ILE Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 43 THR Chi-restraints excluded: chain N residue 52 ILE Chi-restraints excluded: chain N residue 65 TRP Chi-restraints excluded: chain N residue 68 ILE Chi-restraints excluded: chain N residue 76 SER Chi-restraints excluded: chain N residue 116 GLU Chi-restraints excluded: chain N residue 120 LEU Chi-restraints excluded: chain N residue 127 VAL Chi-restraints excluded: chain O residue 24 LEU Chi-restraints excluded: chain O residue 26 ILE Chi-restraints excluded: chain O residue 27 ASN Chi-restraints excluded: chain O residue 41 ARG Chi-restraints excluded: chain O residue 42 SER Chi-restraints excluded: chain O residue 56 LEU Chi-restraints excluded: chain O residue 70 VAL Chi-restraints excluded: chain O residue 81 VAL Chi-restraints excluded: chain O residue 89 LEU Chi-restraints excluded: chain O residue 104 TYR Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain O residue 114 ARG Chi-restraints excluded: chain O residue 121 VAL Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain O residue 123 ILE Chi-restraints excluded: chain O residue 125 PHE Chi-restraints excluded: chain P residue 3 THR Chi-restraints excluded: chain P residue 6 ASP Chi-restraints excluded: chain P residue 31 LEU Chi-restraints excluded: chain P residue 40 ILE Chi-restraints excluded: chain P residue 62 GLU Chi-restraints excluded: chain P residue 71 THR Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain P residue 101 HIS Chi-restraints excluded: chain P residue 104 VAL Chi-restraints excluded: chain Q residue 8 LEU Chi-restraints excluded: chain Q residue 15 THR Chi-restraints excluded: chain Q residue 16 ASP Chi-restraints excluded: chain Q residue 24 ASP Chi-restraints excluded: chain Q residue 32 VAL Chi-restraints excluded: chain Q residue 39 ARG Chi-restraints excluded: chain Q residue 48 ILE Chi-restraints excluded: chain Q residue 73 THR Chi-restraints excluded: chain Q residue 76 LEU Chi-restraints excluded: chain Q residue 78 THR Chi-restraints excluded: chain Q residue 110 ILE Chi-restraints excluded: chain R residue 9 VAL Chi-restraints excluded: chain R residue 18 LEU Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 34 SER Chi-restraints excluded: chain R residue 76 TYR Chi-restraints excluded: chain R residue 85 LEU Chi-restraints excluded: chain R residue 90 ILE Chi-restraints excluded: chain R residue 102 ASP Chi-restraints excluded: chain R residue 115 ASP Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 22 VAL Chi-restraints excluded: chain S residue 23 GLU Chi-restraints excluded: chain S residue 27 VAL Chi-restraints excluded: chain S residue 81 HIS Chi-restraints excluded: chain T residue 6 THR Chi-restraints excluded: chain T residue 29 ILE Chi-restraints excluded: chain T residue 67 PHE Chi-restraints excluded: chain T residue 68 ASP Chi-restraints excluded: chain T residue 86 THR Chi-restraints excluded: chain T residue 93 ARG Chi-restraints excluded: chain T residue 102 ASN Chi-restraints excluded: chain T residue 114 GLU Chi-restraints excluded: chain U residue 6 VAL Chi-restraints excluded: chain U residue 7 ILE Chi-restraints excluded: chain U residue 11 VAL Chi-restraints excluded: chain U residue 31 THR Chi-restraints excluded: chain U residue 47 ASP Chi-restraints excluded: chain U residue 80 VAL Chi-restraints excluded: chain U residue 89 ILE Chi-restraints excluded: chain V residue 13 THR Chi-restraints excluded: chain V residue 31 ASP Chi-restraints excluded: chain V residue 35 VAL Chi-restraints excluded: chain V residue 40 VAL Chi-restraints excluded: chain V residue 48 ASN Chi-restraints excluded: chain V residue 70 VAL Chi-restraints excluded: chain V residue 94 SER Chi-restraints excluded: chain W residue 31 VAL Chi-restraints excluded: chain W residue 43 PHE Chi-restraints excluded: chain W residue 80 ASP Chi-restraints excluded: chain W residue 94 VAL Chi-restraints excluded: chain X residue 34 SER Chi-restraints excluded: chain X residue 40 VAL Chi-restraints excluded: chain X residue 67 THR Chi-restraints excluded: chain X residue 73 ASP Chi-restraints excluded: chain X residue 88 VAL Chi-restraints excluded: chain Y residue 8 THR Chi-restraints excluded: chain Y residue 12 THR Chi-restraints excluded: chain Y residue 14 SER Chi-restraints excluded: chain Y residue 25 THR Chi-restraints excluded: chain Y residue 33 LEU Chi-restraints excluded: chain Y residue 36 VAL Chi-restraints excluded: chain Y residue 41 ASP Chi-restraints excluded: chain Y residue 55 LYS Chi-restraints excluded: chain Z residue 18 GLU Chi-restraints excluded: chain Z residue 30 PHE Chi-restraints excluded: chain Z residue 32 LEU Chi-restraints excluded: chain Z residue 39 ASN Chi-restraints excluded: chain Z residue 62 ASN Chi-restraints excluded: chain 0 residue 13 ILE Chi-restraints excluded: chain 0 residue 23 VAL Chi-restraints excluded: chain 0 residue 34 THR Chi-restraints excluded: chain 0 residue 40 ASN Chi-restraints excluded: chain 0 residue 43 ILE Chi-restraints excluded: chain 0 residue 47 VAL Chi-restraints excluded: chain 0 residue 53 LEU Chi-restraints excluded: chain 0 residue 56 VAL Chi-restraints excluded: chain 1 residue 13 VAL Chi-restraints excluded: chain 1 residue 23 PHE Chi-restraints excluded: chain 2 residue 9 SER Chi-restraints excluded: chain 2 residue 18 THR Chi-restraints excluded: chain 3 residue 5 ILE Chi-restraints excluded: chain 3 residue 8 GLU Chi-restraints excluded: chain 3 residue 11 SER Chi-restraints excluded: chain 3 residue 39 GLU Chi-restraints excluded: chain 3 residue 44 LEU Chi-restraints excluded: chain 4 residue 5 TYR Chi-restraints excluded: chain 4 residue 24 THR Chi-restraints excluded: chain 4 residue 42 ILE Chi-restraints excluded: chain 4 residue 43 SER Chi-restraints excluded: chain 5 residue 14 VAL Chi-restraints excluded: chain 5 residue 57 ARG Chi-restraints excluded: chain 6 residue 1 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 954 random chunks: chunk 857 optimal weight: 4.9990 chunk 652 optimal weight: 20.0000 chunk 450 optimal weight: 10.0000 chunk 96 optimal weight: 20.0000 chunk 414 optimal weight: 10.0000 chunk 582 optimal weight: 20.0000 chunk 871 optimal weight: 9.9990 chunk 922 optimal weight: 10.0000 chunk 455 optimal weight: 10.0000 chunk 825 optimal weight: 0.0570 chunk 248 optimal weight: 8.9990 overall best weight: 6.8108 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 113 GLN d 148 ASN g 86 GLN i 89 GLN ** j 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 15 ASN m 104 ASN n 10 ASN ** n 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 35 GLN ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 160 ASN ** G 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 35 GLN P 20 ASN ** P 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 66 ASN U 40 GLN V 18 ASN ** 2 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 150747 Z= 0.331 Angle : 0.704 13.695 226044 Z= 0.358 Chirality : 0.040 0.351 28980 Planarity : 0.005 0.099 11734 Dihedral : 23.314 179.721 76782 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.17 % Allowed : 13.57 % Favored : 86.25 % Rotamer: Outliers : 12.39 % Allowed : 23.66 % Favored : 63.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.28 % Twisted Proline : 0.52 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.31 (0.11), residues: 5143 helix: -0.61 (0.14), residues: 1441 sheet: -2.18 (0.16), residues: 930 loop : -3.20 (0.10), residues: 2772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP N 93 HIS 0.006 0.001 HIS 1 55 PHE 0.020 0.002 PHE l 31 TYR 0.030 0.002 TYR D 53 ARG 0.009 0.001 ARG 4 3 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10286 Ramachandran restraints generated. 5143 Oldfield, 0 Emsley, 5143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10286 Ramachandran restraints generated. 5143 Oldfield, 0 Emsley, 5143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1485 residues out of total 4391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 544 poor density : 941 time to evaluate : 6.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 10 MET cc_start: 0.9113 (mmm) cc_final: 0.8788 (mmt) REVERT: c 16 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.8055 (tmm160) REVERT: c 40 LYS cc_start: 0.9337 (OUTLIER) cc_final: 0.8927 (tmmm) REVERT: c 55 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7348 (mp0) REVERT: c 141 MET cc_start: 0.8073 (mmm) cc_final: 0.7593 (mmm) REVERT: d 45 SER cc_start: 0.7514 (OUTLIER) cc_final: 0.7181 (p) REVERT: d 71 LEU cc_start: 0.9349 (OUTLIER) cc_final: 0.8963 (tt) REVERT: d 88 MET cc_start: 0.8975 (mmm) cc_final: 0.8684 (mmm) REVERT: d 162 ARG cc_start: 0.7395 (OUTLIER) cc_final: 0.7148 (mmt-90) REVERT: f 12 ILE cc_start: 0.7719 (OUTLIER) cc_final: 0.7214 (mt) REVERT: f 25 LEU cc_start: 0.9493 (tp) cc_final: 0.9198 (tp) REVERT: f 28 ARG cc_start: 0.8680 (tmm-80) cc_final: 0.8456 (tmm-80) REVERT: f 39 GLU cc_start: 0.8397 (mt-10) cc_final: 0.7844 (tm-30) REVERT: f 82 ARG cc_start: 0.9033 (ttp80) cc_final: 0.8707 (ttt90) REVERT: g 31 MET cc_start: 0.8688 (ttp) cc_final: 0.8250 (ttt) REVERT: g 66 MET cc_start: 0.8275 (tpp) cc_final: 0.7861 (tmm) REVERT: g 70 MET cc_start: 0.7963 (mmt) cc_final: 0.7646 (mmt) REVERT: g 86 GLN cc_start: 0.8023 (pt0) cc_final: 0.7701 (mp10) REVERT: g 116 MET cc_start: 0.8170 (mmp) cc_final: 0.7863 (mmp) REVERT: g 126 ASP cc_start: 0.8542 (m-30) cc_final: 0.8246 (m-30) REVERT: h 5 ASP cc_start: 0.8071 (t0) cc_final: 0.7714 (p0) REVERT: h 54 ASP cc_start: 0.8318 (p0) cc_final: 0.7846 (p0) REVERT: h 76 ASN cc_start: 0.9136 (t0) cc_final: 0.8618 (t0) REVERT: i 14 ASN cc_start: 0.8658 (OUTLIER) cc_final: 0.8306 (t0) REVERT: i 38 TYR cc_start: 0.7504 (OUTLIER) cc_final: 0.7238 (t80) REVERT: i 46 GLU cc_start: 0.9071 (mt-10) cc_final: 0.8857 (pm20) REVERT: i 81 HIS cc_start: 0.8000 (m90) cc_final: 0.6495 (t-170) REVERT: i 110 MET cc_start: 0.8103 (ptp) cc_final: 0.7886 (mtp) REVERT: i 112 GLU cc_start: 0.8762 (tp30) cc_final: 0.8288 (tp30) REVERT: j 47 SER cc_start: 0.9536 (m) cc_final: 0.9284 (p) REVERT: j 66 GLU cc_start: 0.8618 (pt0) cc_final: 0.8213 (pt0) REVERT: j 88 MET cc_start: 0.8673 (mpp) cc_final: 0.8404 (mpp) REVERT: k 13 LYS cc_start: 0.7843 (mttt) cc_final: 0.7528 (ttmt) REVERT: k 76 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.8439 (tm-30) REVERT: k 105 LEU cc_start: 0.8850 (mt) cc_final: 0.8211 (mp) REVERT: l 39 ASN cc_start: 0.8927 (OUTLIER) cc_final: 0.8576 (p0) REVERT: l 75 GLU cc_start: 0.7655 (mm-30) cc_final: 0.7287 (tm-30) REVERT: m 54 ASP cc_start: 0.8844 (m-30) cc_final: 0.8521 (m-30) REVERT: m 61 ASP cc_start: 0.8993 (t0) cc_final: 0.8603 (t0) REVERT: m 95 LEU cc_start: 0.6579 (OUTLIER) cc_final: 0.6364 (mm) REVERT: n 25 GLU cc_start: 0.8729 (mm-30) cc_final: 0.8412 (mm-30) REVERT: n 35 ARG cc_start: 0.8490 (OUTLIER) cc_final: 0.8226 (ptm160) REVERT: n 36 LYS cc_start: 0.9199 (tppt) cc_final: 0.8856 (tmtt) REVERT: o 41 GLU cc_start: 0.8764 (mm-30) cc_final: 0.8259 (mm-30) REVERT: o 44 ARG cc_start: 0.8242 (mtm180) cc_final: 0.7713 (mtm180) REVERT: o 45 THR cc_start: 0.8706 (m) cc_final: 0.8493 (p) REVERT: p 10 MET cc_start: 0.8660 (OUTLIER) cc_final: 0.8249 (mtp) REVERT: p 30 ASP cc_start: 0.8686 (p0) cc_final: 0.8285 (t0) REVERT: q 12 GLN cc_start: 0.8274 (tt0) cc_final: 0.7523 (tp40) REVERT: q 20 MET cc_start: 0.7626 (mmm) cc_final: 0.7416 (mmt) REVERT: q 52 GLU cc_start: 0.8703 (mp0) cc_final: 0.8448 (mp0) REVERT: r 26 ASP cc_start: 0.8652 (t0) cc_final: 0.8283 (t70) REVERT: s 12 ASP cc_start: 0.8039 (m-30) cc_final: 0.7717 (m-30) REVERT: s 14 HIS cc_start: 0.8066 (OUTLIER) cc_final: 0.7297 (p-80) REVERT: s 40 ILE cc_start: 0.8490 (mm) cc_final: 0.8014 (mt) REVERT: s 73 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.6915 (tm-30) REVERT: t 44 ASP cc_start: 0.8272 (t0) cc_final: 0.7841 (p0) REVERT: C 123 ASP cc_start: 0.8485 (t0) cc_final: 0.7923 (t0) REVERT: C 180 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7498 (pm20) REVERT: C 199 GLN cc_start: 0.8610 (pm20) cc_final: 0.8392 (pm20) REVERT: C 274 ARG cc_start: 0.7759 (tpt90) cc_final: 0.7364 (tpt90) REVERT: D 168 ARG cc_start: 0.9135 (OUTLIER) cc_final: 0.8498 (ptm160) REVERT: E 46 GLN cc_start: 0.8305 (OUTLIER) cc_final: 0.7867 (tt0) REVERT: E 65 TRP cc_start: 0.8129 (OUTLIER) cc_final: 0.7917 (p-90) REVERT: E 74 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.7579 (ptt90) REVERT: F 120 LYS cc_start: 0.9173 (mttt) cc_final: 0.8916 (tptp) REVERT: G 94 TYR cc_start: 0.8414 (m-10) cc_final: 0.8185 (m-80) REVERT: G 99 GLN cc_start: 0.8239 (pp30) cc_final: 0.7987 (pp30) REVERT: G 130 GLN cc_start: 0.8084 (mp-120) cc_final: 0.7542 (mp-120) REVERT: K 119 GLN cc_start: 0.9006 (OUTLIER) cc_final: 0.8550 (mt0) REVERT: L 13 ASN cc_start: 0.8944 (t0) cc_final: 0.8389 (p0) REVERT: M 84 ARG cc_start: 0.8371 (OUTLIER) cc_final: 0.7973 (mpp80) REVERT: M 90 GLU cc_start: 0.7916 (tt0) cc_final: 0.7558 (tp30) REVERT: M 101 ILE cc_start: 0.7933 (OUTLIER) cc_final: 0.7687 (mm) REVERT: N 1 MET cc_start: -0.0661 (mmm) cc_final: -0.2309 (mmm) REVERT: N 65 TRP cc_start: 0.8448 (OUTLIER) cc_final: 0.7153 (m100) REVERT: O 24 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.8838 (tp) REVERT: O 41 ARG cc_start: 0.8034 (OUTLIER) cc_final: 0.6887 (ppt90) REVERT: O 46 LYS cc_start: 0.9044 (tttt) cc_final: 0.8444 (tptp) REVERT: O 96 ARG cc_start: 0.8615 (OUTLIER) cc_final: 0.7963 (ttm170) REVERT: O 125 PHE cc_start: 0.8644 (OUTLIER) cc_final: 0.7506 (m-10) REVERT: P 62 GLU cc_start: 0.7415 (OUTLIER) cc_final: 0.7078 (mm-30) REVERT: Q 7 GLU cc_start: 0.8705 (mt-10) cc_final: 0.8434 (mt-10) REVERT: Q 106 LYS cc_start: 0.8924 (mtpt) cc_final: 0.8055 (mtpt) REVERT: Q 111 LYS cc_start: 0.9252 (mttt) cc_final: 0.8963 (mtpt) REVERT: R 89 ASP cc_start: 0.7802 (p0) cc_final: 0.7515 (p0) REVERT: S 1 MET cc_start: 0.8828 (OUTLIER) cc_final: 0.7928 (ttt) REVERT: S 2 TYR cc_start: 0.8301 (t80) cc_final: 0.8074 (t80) REVERT: S 6 LYS cc_start: 0.8566 (mttt) cc_final: 0.8160 (mttt) REVERT: S 37 GLU cc_start: 0.7908 (mt-10) cc_final: 0.7523 (mt-10) REVERT: S 81 HIS cc_start: 0.8273 (OUTLIER) cc_final: 0.7524 (m-70) REVERT: T 93 ARG cc_start: 0.8744 (OUTLIER) cc_final: 0.8449 (mmp-170) REVERT: T 114 GLU cc_start: 0.8693 (OUTLIER) cc_final: 0.8452 (tt0) REVERT: U 5 ASP cc_start: 0.7984 (m-30) cc_final: 0.7763 (t0) REVERT: U 7 ILE cc_start: 0.8975 (OUTLIER) cc_final: 0.8578 (mt) REVERT: V 1 MET cc_start: 0.7709 (OUTLIER) cc_final: 0.7397 (mmt) REVERT: V 7 ASP cc_start: 0.8136 (m-30) cc_final: 0.7497 (m-30) REVERT: V 20 GLU cc_start: 0.8775 (mt-10) cc_final: 0.8485 (mp0) REVERT: V 53 GLN cc_start: 0.8754 (mt0) cc_final: 0.8266 (mm-40) REVERT: W 74 MET cc_start: 0.6858 (ptp) cc_final: 0.6464 (ppp) REVERT: W 80 ASP cc_start: 0.5389 (OUTLIER) cc_final: 0.4997 (m-30) REVERT: W 86 MET cc_start: 0.5618 (mtm) cc_final: 0.5025 (ptp) REVERT: X 72 VAL cc_start: 0.8717 (t) cc_final: 0.8423 (p) REVERT: X 87 GLN cc_start: 0.8638 (mt0) cc_final: 0.8373 (mt0) REVERT: Y 22 MET cc_start: 0.7287 (OUTLIER) cc_final: 0.7051 (mmm) REVERT: Y 30 LYS cc_start: 0.9177 (mtmt) cc_final: 0.8937 (mttm) REVERT: Y 35 LYS cc_start: 0.8736 (mtpm) cc_final: 0.8355 (tttp) REVERT: Z 22 LYS cc_start: 0.9374 (mmmm) cc_final: 0.8925 (tptt) REVERT: Z 23 GLU cc_start: 0.8606 (tm-30) cc_final: 0.8365 (tm-30) REVERT: Z 24 GLU cc_start: 0.8602 (tm-30) cc_final: 0.8188 (tm-30) REVERT: Z 28 LEU cc_start: 0.8573 (mt) cc_final: 0.8139 (mp) REVERT: Z 29 ARG cc_start: 0.8806 (mtm-85) cc_final: 0.8516 (mtm-85) REVERT: Z 39 ASN cc_start: 0.7679 (OUTLIER) cc_final: 0.7206 (m-40) REVERT: 1 12 VAL cc_start: 0.9111 (t) cc_final: 0.8735 (p) REVERT: 1 15 MET cc_start: 0.7604 (ptt) cc_final: 0.7337 (ptt) REVERT: 1 43 TYR cc_start: 0.7373 (m-80) cc_final: 0.6963 (m-10) REVERT: 1 54 SER cc_start: 0.8390 (m) cc_final: 0.7938 (p) REVERT: 1 73 ARG cc_start: 0.7985 (tmt170) cc_final: 0.7397 (ttp-170) REVERT: 1 76 LYS cc_start: 0.9449 (tttt) cc_final: 0.9183 (tptt) REVERT: 2 36 MET cc_start: 0.8900 (mmm) cc_final: 0.8436 (mmt) REVERT: 3 41 LYS cc_start: 0.8754 (tppt) cc_final: 0.8386 (ptpp) REVERT: 3 44 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8257 (tm) REVERT: 6 24 MET cc_start: 0.8462 (mmm) cc_final: 0.8044 (mmt) outliers start: 544 outliers final: 403 residues processed: 1337 average time/residue: 1.1639 time to fit residues: 2733.4981 Evaluate side-chains 1340 residues out of total 4391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 443 poor density : 897 time to evaluate : 6.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 15 ILE Chi-restraints excluded: chain c residue 16 ARG Chi-restraints excluded: chain c residue 40 LYS Chi-restraints excluded: chain c residue 42 ILE Chi-restraints excluded: chain c residue 55 GLU Chi-restraints excluded: chain c residue 83 VAL Chi-restraints excluded: chain c residue 85 ASN Chi-restraints excluded: chain c residue 127 VAL Chi-restraints excluded: chain c residue 176 THR Chi-restraints excluded: chain c residue 200 TRP Chi-restraints excluded: chain d residue 4 TYR Chi-restraints excluded: chain d residue 45 SER Chi-restraints excluded: chain d residue 57 LEU Chi-restraints excluded: chain d residue 60 MET Chi-restraints excluded: chain d residue 64 ASN Chi-restraints excluded: chain d residue 71 LEU Chi-restraints excluded: chain d residue 107 THR Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 162 ARG Chi-restraints excluded: chain d residue 184 ASP Chi-restraints excluded: chain d residue 190 ILE Chi-restraints excluded: chain d residue 195 VAL Chi-restraints excluded: chain e residue 9 LEU Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 72 VAL Chi-restraints excluded: chain e residue 105 VAL Chi-restraints excluded: chain e residue 114 VAL Chi-restraints excluded: chain e residue 127 SER Chi-restraints excluded: chain e residue 131 ASN Chi-restraints excluded: chain e residue 132 THR Chi-restraints excluded: chain e residue 144 LEU Chi-restraints excluded: chain e residue 159 LYS Chi-restraints excluded: chain f residue 11 TYR Chi-restraints excluded: chain f residue 12 ILE Chi-restraints excluded: chain f residue 13 ILE Chi-restraints excluded: chain f residue 18 ASP Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 56 ASN Chi-restraints excluded: chain f residue 65 ILE Chi-restraints excluded: chain f residue 66 VAL Chi-restraints excluded: chain f residue 67 ASN Chi-restraints excluded: chain f residue 98 VAL Chi-restraints excluded: chain g residue 19 ASN Chi-restraints excluded: chain g residue 43 ILE Chi-restraints excluded: chain g residue 47 PHE Chi-restraints excluded: chain g residue 75 VAL Chi-restraints excluded: chain g residue 87 VAL Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain h residue 14 ILE Chi-restraints excluded: chain h residue 20 VAL Chi-restraints excluded: chain h residue 22 HIS Chi-restraints excluded: chain h residue 32 ILE Chi-restraints excluded: chain h residue 59 VAL Chi-restraints excluded: chain h residue 60 ILE Chi-restraints excluded: chain h residue 69 ASN Chi-restraints excluded: chain h residue 74 ILE Chi-restraints excluded: chain h residue 89 VAL Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 98 LEU Chi-restraints excluded: chain h residue 103 ILE Chi-restraints excluded: chain h residue 106 ILE Chi-restraints excluded: chain h residue 112 VAL Chi-restraints excluded: chain h residue 114 THR Chi-restraints excluded: chain h residue 127 VAL Chi-restraints excluded: chain i residue 9 THR Chi-restraints excluded: chain i residue 12 ARG Chi-restraints excluded: chain i residue 14 ASN Chi-restraints excluded: chain i residue 22 VAL Chi-restraints excluded: chain i residue 30 VAL Chi-restraints excluded: chain i residue 34 ASP Chi-restraints excluded: chain i residue 38 TYR Chi-restraints excluded: chain i residue 57 THR Chi-restraints excluded: chain i residue 88 LEU Chi-restraints excluded: chain i residue 91 ASP Chi-restraints excluded: chain i residue 93 ASP Chi-restraints excluded: chain j residue 15 HIS Chi-restraints excluded: chain j residue 51 VAL Chi-restraints excluded: chain j residue 72 ARG Chi-restraints excluded: chain j residue 74 ILE Chi-restraints excluded: chain j residue 90 LEU Chi-restraints excluded: chain j residue 98 ILE Chi-restraints excluded: chain k residue 18 SER Chi-restraints excluded: chain k residue 26 THR Chi-restraints excluded: chain k residue 35 THR Chi-restraints excluded: chain k residue 46 SER Chi-restraints excluded: chain k residue 55 SER Chi-restraints excluded: chain k residue 73 VAL Chi-restraints excluded: chain k residue 76 GLU Chi-restraints excluded: chain k residue 97 ILE Chi-restraints excluded: chain k residue 99 SER Chi-restraints excluded: chain k residue 119 ASN Chi-restraints excluded: chain l residue 4 ILE Chi-restraints excluded: chain l residue 7 LEU Chi-restraints excluded: chain l residue 20 ASP Chi-restraints excluded: chain l residue 26 LYS Chi-restraints excluded: chain l residue 32 LYS Chi-restraints excluded: chain l residue 39 ASN Chi-restraints excluded: chain l residue 47 CYS Chi-restraints excluded: chain l residue 50 VAL Chi-restraints excluded: chain l residue 72 ASN Chi-restraints excluded: chain l residue 76 VAL Chi-restraints excluded: chain l residue 83 ILE Chi-restraints excluded: chain l residue 92 VAL Chi-restraints excluded: chain l residue 95 LEU Chi-restraints excluded: chain l residue 122 ASP Chi-restraints excluded: chain l residue 124 LYS Chi-restraints excluded: chain l residue 126 SER Chi-restraints excluded: chain l residue 132 THR Chi-restraints excluded: chain m residue 4 ILE Chi-restraints excluded: chain m residue 9 ILE Chi-restraints excluded: chain m residue 13 LYS Chi-restraints excluded: chain m residue 28 THR Chi-restraints excluded: chain m residue 37 VAL Chi-restraints excluded: chain m residue 40 SER Chi-restraints excluded: chain m residue 45 VAL Chi-restraints excluded: chain m residue 60 ILE Chi-restraints excluded: chain m residue 95 LEU Chi-restraints excluded: chain m residue 101 ASN Chi-restraints excluded: chain m residue 102 THR Chi-restraints excluded: chain n residue 7 ILE Chi-restraints excluded: chain n residue 18 THR Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain n residue 35 ARG Chi-restraints excluded: chain n residue 57 LYS Chi-restraints excluded: chain o residue 11 ILE Chi-restraints excluded: chain o residue 24 SER Chi-restraints excluded: chain o residue 52 SER Chi-restraints excluded: chain o residue 80 GLU Chi-restraints excluded: chain o residue 89 ARG Chi-restraints excluded: chain p residue 3 VAL Chi-restraints excluded: chain p residue 5 ILE Chi-restraints excluded: chain p residue 10 MET Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain p residue 39 THR Chi-restraints excluded: chain p residue 40 TYR Chi-restraints excluded: chain p residue 84 HIS Chi-restraints excluded: chain q residue 5 ARG Chi-restraints excluded: chain q residue 7 GLN Chi-restraints excluded: chain q residue 17 SER Chi-restraints excluded: chain q residue 23 THR Chi-restraints excluded: chain q residue 27 VAL Chi-restraints excluded: chain q residue 44 SER Chi-restraints excluded: chain q residue 54 ASN Chi-restraints excluded: chain q residue 58 VAL Chi-restraints excluded: chain q residue 78 LEU Chi-restraints excluded: chain r residue 16 TYR Chi-restraints excluded: chain r residue 29 ASP Chi-restraints excluded: chain r residue 30 THR Chi-restraints excluded: chain r residue 37 ILE Chi-restraints excluded: chain r residue 51 THR Chi-restraints excluded: chain r residue 63 ILE Chi-restraints excluded: chain s residue 7 LYS Chi-restraints excluded: chain s residue 14 HIS Chi-restraints excluded: chain s residue 33 THR Chi-restraints excluded: chain s residue 48 THR Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain s residue 65 ASP Chi-restraints excluded: chain s residue 73 GLU Chi-restraints excluded: chain t residue 4 ILE Chi-restraints excluded: chain t residue 8 ILE Chi-restraints excluded: chain t residue 23 SER Chi-restraints excluded: chain t residue 46 VAL Chi-restraints excluded: chain t residue 65 LEU Chi-restraints excluded: chain t residue 81 LEU Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 15 ASN Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 20 ASP Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 45 ASN Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 53 HIS Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 134 ASN Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 171 TYR Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 194 SER Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 225 MET Chi-restraints excluded: chain C residue 228 ASN Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 130 ARG Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 167 ASP Chi-restraints excluded: chain D residue 168 ARG Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 188 ILE Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain E residue 7 PHE Chi-restraints excluded: chain E residue 8 LYS Chi-restraints excluded: chain E residue 10 ASP Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain E residue 46 GLN Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 65 TRP Chi-restraints excluded: chain E residue 74 ARG Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 84 ARG Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 121 ASN Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain E residue 177 THR Chi-restraints excluded: chain E residue 179 ASP Chi-restraints excluded: chain E residue 195 THR Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 123 ASP Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 135 GLN Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 41 ILE Chi-restraints excluded: chain G residue 43 MET Chi-restraints excluded: chain G residue 52 PHE Chi-restraints excluded: chain G residue 65 HIS Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 90 ILE Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 23 ASP Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 41 ASN Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 50 ASP Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 80 MET Chi-restraints excluded: chain K residue 85 LEU Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 113 ASN Chi-restraints excluded: chain K residue 115 LEU Chi-restraints excluded: chain K residue 119 GLN Chi-restraints excluded: chain K residue 142 ASP Chi-restraints excluded: chain L residue 6 SER Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 37 ASP Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 73 ASP Chi-restraints excluded: chain L residue 90 ASP Chi-restraints excluded: chain L residue 92 SER Chi-restraints excluded: chain L residue 110 ASN Chi-restraints excluded: chain M residue 3 LEU Chi-restraints excluded: chain M residue 18 ARG Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain M residue 73 ASP Chi-restraints excluded: chain M residue 76 VAL Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 84 ARG Chi-restraints excluded: chain M residue 89 THR Chi-restraints excluded: chain M residue 95 VAL Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain M residue 97 LYS Chi-restraints excluded: chain M residue 101 ILE Chi-restraints excluded: chain M residue 103 LYS Chi-restraints excluded: chain M residue 117 LEU Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 52 ILE Chi-restraints excluded: chain N residue 65 TRP Chi-restraints excluded: chain N residue 68 ILE Chi-restraints excluded: chain N residue 76 SER Chi-restraints excluded: chain N residue 113 VAL Chi-restraints excluded: chain N residue 116 GLU Chi-restraints excluded: chain N residue 120 LEU Chi-restraints excluded: chain N residue 127 VAL Chi-restraints excluded: chain O residue 24 LEU Chi-restraints excluded: chain O residue 26 ILE Chi-restraints excluded: chain O residue 27 ASN Chi-restraints excluded: chain O residue 41 ARG Chi-restraints excluded: chain O residue 56 LEU Chi-restraints excluded: chain O residue 70 VAL Chi-restraints excluded: chain O residue 81 VAL Chi-restraints excluded: chain O residue 86 LEU Chi-restraints excluded: chain O residue 89 LEU Chi-restraints excluded: chain O residue 96 ARG Chi-restraints excluded: chain O residue 104 TYR Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain O residue 114 ARG Chi-restraints excluded: chain O residue 121 VAL Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain O residue 123 ILE Chi-restraints excluded: chain O residue 125 PHE Chi-restraints excluded: chain P residue 3 THR Chi-restraints excluded: chain P residue 6 ASP Chi-restraints excluded: chain P residue 31 LEU Chi-restraints excluded: chain P residue 39 ASN Chi-restraints excluded: chain P residue 40 ILE Chi-restraints excluded: chain P residue 62 GLU Chi-restraints excluded: chain P residue 71 THR Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain P residue 101 HIS Chi-restraints excluded: chain P residue 104 VAL Chi-restraints excluded: chain Q residue 8 LEU Chi-restraints excluded: chain Q residue 15 THR Chi-restraints excluded: chain Q residue 16 ASP Chi-restraints excluded: chain Q residue 24 ASP Chi-restraints excluded: chain Q residue 32 VAL Chi-restraints excluded: chain Q residue 39 ARG Chi-restraints excluded: chain Q residue 48 ILE Chi-restraints excluded: chain Q residue 73 THR Chi-restraints excluded: chain Q residue 76 LEU Chi-restraints excluded: chain Q residue 110 ILE Chi-restraints excluded: chain R residue 9 VAL Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 34 SER Chi-restraints excluded: chain R residue 85 LEU Chi-restraints excluded: chain R residue 90 ILE Chi-restraints excluded: chain R residue 102 ASP Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 22 VAL Chi-restraints excluded: chain S residue 23 GLU Chi-restraints excluded: chain S residue 27 VAL Chi-restraints excluded: chain S residue 33 VAL Chi-restraints excluded: chain S residue 81 HIS Chi-restraints excluded: chain T residue 6 THR Chi-restraints excluded: chain T residue 29 ILE Chi-restraints excluded: chain T residue 67 PHE Chi-restraints excluded: chain T residue 86 THR Chi-restraints excluded: chain T residue 93 ARG Chi-restraints excluded: chain T residue 102 ASN Chi-restraints excluded: chain T residue 114 GLU Chi-restraints excluded: chain U residue 6 VAL Chi-restraints excluded: chain U residue 7 ILE Chi-restraints excluded: chain U residue 11 VAL Chi-restraints excluded: chain U residue 31 THR Chi-restraints excluded: chain U residue 47 ASP Chi-restraints excluded: chain U residue 80 VAL Chi-restraints excluded: chain U residue 89 ILE Chi-restraints excluded: chain V residue 1 MET Chi-restraints excluded: chain V residue 31 ASP Chi-restraints excluded: chain V residue 35 VAL Chi-restraints excluded: chain V residue 40 VAL Chi-restraints excluded: chain V residue 48 ASN Chi-restraints excluded: chain V residue 70 VAL Chi-restraints excluded: chain V residue 72 ASP Chi-restraints excluded: chain V residue 94 SER Chi-restraints excluded: chain W residue 31 VAL Chi-restraints excluded: chain W residue 43 PHE Chi-restraints excluded: chain W residue 71 ASN Chi-restraints excluded: chain W residue 80 ASP Chi-restraints excluded: chain W residue 94 VAL Chi-restraints excluded: chain X residue 34 SER Chi-restraints excluded: chain X residue 40 VAL Chi-restraints excluded: chain X residue 60 VAL Chi-restraints excluded: chain X residue 66 ASP Chi-restraints excluded: chain X residue 67 THR Chi-restraints excluded: chain X residue 73 ASP Chi-restraints excluded: chain X residue 76 VAL Chi-restraints excluded: chain X residue 88 VAL Chi-restraints excluded: chain Y residue 8 THR Chi-restraints excluded: chain Y residue 12 THR Chi-restraints excluded: chain Y residue 14 SER Chi-restraints excluded: chain Y residue 16 ASN Chi-restraints excluded: chain Y residue 22 MET Chi-restraints excluded: chain Y residue 25 THR Chi-restraints excluded: chain Y residue 33 LEU Chi-restraints excluded: chain Y residue 36 VAL Chi-restraints excluded: chain Y residue 41 ASP Chi-restraints excluded: chain Y residue 55 LYS Chi-restraints excluded: chain Z residue 30 PHE Chi-restraints excluded: chain Z residue 32 LEU Chi-restraints excluded: chain Z residue 39 ASN Chi-restraints excluded: chain Z residue 62 ASN Chi-restraints excluded: chain 0 residue 13 ILE Chi-restraints excluded: chain 0 residue 22 THR Chi-restraints excluded: chain 0 residue 23 VAL Chi-restraints excluded: chain 0 residue 40 ASN Chi-restraints excluded: chain 0 residue 43 ILE Chi-restraints excluded: chain 0 residue 47 VAL Chi-restraints excluded: chain 0 residue 53 LEU Chi-restraints excluded: chain 0 residue 56 VAL Chi-restraints excluded: chain 1 residue 13 VAL Chi-restraints excluded: chain 1 residue 23 PHE Chi-restraints excluded: chain 1 residue 36 GLU Chi-restraints excluded: chain 2 residue 3 VAL Chi-restraints excluded: chain 2 residue 6 ARG Chi-restraints excluded: chain 2 residue 9 SER Chi-restraints excluded: chain 2 residue 18 THR Chi-restraints excluded: chain 3 residue 5 ILE Chi-restraints excluded: chain 3 residue 8 GLU Chi-restraints excluded: chain 3 residue 11 SER Chi-restraints excluded: chain 3 residue 39 GLU Chi-restraints excluded: chain 3 residue 44 LEU Chi-restraints excluded: chain 4 residue 5 TYR Chi-restraints excluded: chain 4 residue 24 THR Chi-restraints excluded: chain 4 residue 42 ILE Chi-restraints excluded: chain 4 residue 43 SER Chi-restraints excluded: chain 5 residue 14 VAL Chi-restraints excluded: chain 5 residue 54 ASP Chi-restraints excluded: chain 5 residue 57 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 954 random chunks: chunk 767 optimal weight: 7.9990 chunk 523 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 686 optimal weight: 0.9990 chunk 380 optimal weight: 30.0000 chunk 786 optimal weight: 6.9990 chunk 637 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 470 optimal weight: 10.0000 chunk 827 optimal weight: 7.9990 chunk 232 optimal weight: 9.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 148 ASN g 114 HIS ** j 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 119 ASN n 10 ASN ** n 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 35 GLN C 197 ASN ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 191 ASN ** G 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 35 GLN P 20 ASN ** P 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 66 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 150747 Z= 0.332 Angle : 0.705 16.646 226044 Z= 0.359 Chirality : 0.041 0.338 28980 Planarity : 0.005 0.098 11734 Dihedral : 23.295 179.556 76771 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.17 % Allowed : 13.63 % Favored : 86.19 % Rotamer: Outliers : 12.39 % Allowed : 24.41 % Favored : 63.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.28 % Twisted Proline : 0.52 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.17 (0.11), residues: 5143 helix: -0.49 (0.14), residues: 1442 sheet: -2.13 (0.16), residues: 961 loop : -3.12 (0.11), residues: 2740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP N 93 HIS 0.007 0.001 HIS 1 55 PHE 0.020 0.002 PHE l 31 TYR 0.044 0.002 TYR D 53 ARG 0.008 0.001 ARG o 89 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10286 Ramachandran restraints generated. 5143 Oldfield, 0 Emsley, 5143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10286 Ramachandran restraints generated. 5143 Oldfield, 0 Emsley, 5143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1468 residues out of total 4391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 544 poor density : 924 time to evaluate : 6.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 10 MET cc_start: 0.9126 (mmm) cc_final: 0.8804 (mmt) REVERT: c 16 ARG cc_start: 0.8521 (OUTLIER) cc_final: 0.8027 (tmm160) REVERT: c 17 ASP cc_start: 0.9153 (p0) cc_final: 0.8597 (p0) REVERT: c 40 LYS cc_start: 0.9341 (OUTLIER) cc_final: 0.8939 (tmmm) REVERT: c 55 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.6912 (tm-30) REVERT: c 141 MET cc_start: 0.8094 (mmm) cc_final: 0.7610 (mmm) REVERT: d 45 SER cc_start: 0.7591 (OUTLIER) cc_final: 0.7210 (p) REVERT: d 71 LEU cc_start: 0.9324 (OUTLIER) cc_final: 0.8954 (tt) REVERT: d 88 MET cc_start: 0.8961 (mmm) cc_final: 0.8709 (mmm) REVERT: d 94 ARG cc_start: 0.8480 (OUTLIER) cc_final: 0.7759 (ptm-80) REVERT: d 162 ARG cc_start: 0.7424 (OUTLIER) cc_final: 0.7176 (mmt-90) REVERT: f 12 ILE cc_start: 0.7733 (OUTLIER) cc_final: 0.7153 (mt) REVERT: f 25 LEU cc_start: 0.9497 (tp) cc_final: 0.9192 (tp) REVERT: f 28 ARG cc_start: 0.8704 (tmm-80) cc_final: 0.8479 (tmm-80) REVERT: f 39 GLU cc_start: 0.8375 (mt-10) cc_final: 0.7802 (tm-30) REVERT: f 55 MET cc_start: 0.8857 (mmm) cc_final: 0.8360 (mmm) REVERT: f 82 ARG cc_start: 0.9031 (ttp80) cc_final: 0.8721 (ttt90) REVERT: g 24 THR cc_start: 0.8615 (OUTLIER) cc_final: 0.8380 (p) REVERT: g 31 MET cc_start: 0.8686 (ttp) cc_final: 0.8230 (ttt) REVERT: g 66 MET cc_start: 0.8273 (tpp) cc_final: 0.7862 (tmm) REVERT: g 86 GLN cc_start: 0.7951 (pt0) cc_final: 0.7659 (mp10) REVERT: g 116 MET cc_start: 0.8286 (OUTLIER) cc_final: 0.7986 (mmp) REVERT: g 126 ASP cc_start: 0.8631 (m-30) cc_final: 0.8380 (m-30) REVERT: h 5 ASP cc_start: 0.8070 (t0) cc_final: 0.7736 (p0) REVERT: h 54 ASP cc_start: 0.8350 (p0) cc_final: 0.7865 (p0) REVERT: h 76 ASN cc_start: 0.9106 (t0) cc_final: 0.8597 (t0) REVERT: i 14 ASN cc_start: 0.8725 (OUTLIER) cc_final: 0.8370 (t0) REVERT: i 81 HIS cc_start: 0.8017 (m90) cc_final: 0.6510 (t-170) REVERT: i 110 MET cc_start: 0.8111 (ptp) cc_final: 0.7762 (mtp) REVERT: i 112 GLU cc_start: 0.8792 (tp30) cc_final: 0.8290 (tp30) REVERT: j 47 SER cc_start: 0.9544 (m) cc_final: 0.9294 (p) REVERT: j 66 GLU cc_start: 0.8627 (pt0) cc_final: 0.8231 (pt0) REVERT: k 14 LYS cc_start: 0.9220 (ttpp) cc_final: 0.8885 (ttpp) REVERT: k 105 LEU cc_start: 0.8816 (mt) cc_final: 0.8166 (mp) REVERT: l 39 ASN cc_start: 0.8929 (OUTLIER) cc_final: 0.8567 (p0) REVERT: l 75 GLU cc_start: 0.7722 (mm-30) cc_final: 0.7270 (tm-30) REVERT: m 13 LYS cc_start: 0.8560 (OUTLIER) cc_final: 0.8337 (mmmm) REVERT: m 54 ASP cc_start: 0.8861 (m-30) cc_final: 0.8525 (m-30) REVERT: m 61 ASP cc_start: 0.9032 (t0) cc_final: 0.8623 (t0) REVERT: m 95 LEU cc_start: 0.6565 (OUTLIER) cc_final: 0.6337 (mm) REVERT: n 25 GLU cc_start: 0.8736 (mm-30) cc_final: 0.8416 (mm-30) REVERT: n 35 ARG cc_start: 0.8459 (OUTLIER) cc_final: 0.7952 (ptm-80) REVERT: n 36 LYS cc_start: 0.9198 (tppt) cc_final: 0.8895 (tmtt) REVERT: o 44 ARG cc_start: 0.8305 (mtm180) cc_final: 0.8101 (mtm180) REVERT: o 45 THR cc_start: 0.8692 (m) cc_final: 0.8470 (p) REVERT: p 10 MET cc_start: 0.8684 (OUTLIER) cc_final: 0.8249 (mtp) REVERT: p 30 ASP cc_start: 0.8676 (p0) cc_final: 0.8311 (t0) REVERT: q 12 GLN cc_start: 0.8311 (tt0) cc_final: 0.7477 (tp40) REVERT: q 20 MET cc_start: 0.7609 (mmm) cc_final: 0.7394 (mmt) REVERT: q 52 GLU cc_start: 0.8665 (mp0) cc_final: 0.8426 (mp0) REVERT: r 26 ASP cc_start: 0.8648 (t0) cc_final: 0.8283 (t70) REVERT: s 12 ASP cc_start: 0.7996 (m-30) cc_final: 0.7641 (m-30) REVERT: s 14 HIS cc_start: 0.8016 (OUTLIER) cc_final: 0.7230 (p-80) REVERT: s 40 ILE cc_start: 0.8512 (mm) cc_final: 0.8020 (mt) REVERT: s 73 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.6972 (tm-30) REVERT: t 44 ASP cc_start: 0.8282 (t0) cc_final: 0.7845 (p0) REVERT: C 66 ASP cc_start: 0.8630 (t0) cc_final: 0.8417 (t0) REVERT: C 108 LYS cc_start: 0.8659 (ttmt) cc_final: 0.8114 (mttt) REVERT: C 123 ASP cc_start: 0.8648 (t0) cc_final: 0.8071 (t0) REVERT: C 180 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.7674 (pm20) REVERT: C 274 ARG cc_start: 0.7837 (tpt90) cc_final: 0.7366 (tpt90) REVERT: D 168 ARG cc_start: 0.9086 (OUTLIER) cc_final: 0.8322 (ptm160) REVERT: E 12 THR cc_start: 0.7896 (OUTLIER) cc_final: 0.7663 (p) REVERT: E 46 GLN cc_start: 0.8289 (OUTLIER) cc_final: 0.7864 (tt0) REVERT: F 56 GLU cc_start: 0.8492 (mm-30) cc_final: 0.8261 (mp0) REVERT: F 83 MET cc_start: 0.8792 (mmm) cc_final: 0.8138 (mtt) REVERT: F 120 LYS cc_start: 0.9166 (mttt) cc_final: 0.8917 (tptp) REVERT: G 94 TYR cc_start: 0.8369 (m-10) cc_final: 0.8156 (m-80) REVERT: G 99 GLN cc_start: 0.8357 (pp30) cc_final: 0.7995 (pp30) REVERT: G 130 GLN cc_start: 0.8082 (OUTLIER) cc_final: 0.7537 (mp-120) REVERT: K 117 ARG cc_start: 0.8924 (mtm180) cc_final: 0.8481 (mtt180) REVERT: K 119 GLN cc_start: 0.9000 (OUTLIER) cc_final: 0.8513 (mt0) REVERT: L 2 ILE cc_start: 0.8798 (mt) cc_final: 0.8449 (tp) REVERT: L 13 ASN cc_start: 0.8902 (t0) cc_final: 0.8401 (p0) REVERT: M 84 ARG cc_start: 0.8332 (OUTLIER) cc_final: 0.7936 (mpp80) REVERT: M 101 ILE cc_start: 0.7896 (mp) cc_final: 0.7660 (mm) REVERT: N 1 MET cc_start: -0.0420 (mmm) cc_final: -0.2153 (mmm) REVERT: N 6 ARG cc_start: 0.7917 (ttm110) cc_final: 0.7370 (ttm170) REVERT: N 58 MET cc_start: 0.9099 (ttm) cc_final: 0.8740 (ttm) REVERT: N 65 TRP cc_start: 0.8451 (OUTLIER) cc_final: 0.6905 (m100) REVERT: O 24 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8661 (tt) REVERT: O 41 ARG cc_start: 0.7972 (OUTLIER) cc_final: 0.6785 (ppt90) REVERT: O 46 LYS cc_start: 0.9061 (tttt) cc_final: 0.8467 (tptp) REVERT: O 96 ARG cc_start: 0.8616 (OUTLIER) cc_final: 0.7963 (ttm170) REVERT: O 125 PHE cc_start: 0.8658 (OUTLIER) cc_final: 0.7272 (m-10) REVERT: P 62 GLU cc_start: 0.7410 (OUTLIER) cc_final: 0.7072 (mm-30) REVERT: Q 7 GLU cc_start: 0.8720 (mt-10) cc_final: 0.8441 (mt-10) REVERT: Q 106 LYS cc_start: 0.8929 (mtpt) cc_final: 0.8059 (mtpt) REVERT: Q 111 LYS cc_start: 0.9245 (mttt) cc_final: 0.8970 (mtpt) REVERT: R 89 ASP cc_start: 0.7546 (p0) cc_final: 0.7136 (p0) REVERT: S 1 MET cc_start: 0.8799 (OUTLIER) cc_final: 0.7998 (ttt) REVERT: S 2 TYR cc_start: 0.8171 (t80) cc_final: 0.7963 (t80) REVERT: S 6 LYS cc_start: 0.8574 (mttt) cc_final: 0.8149 (mttt) REVERT: S 37 GLU cc_start: 0.7924 (mt-10) cc_final: 0.7546 (mt-10) REVERT: S 81 HIS cc_start: 0.8362 (OUTLIER) cc_final: 0.7537 (m-70) REVERT: S 96 MET cc_start: 0.8870 (tmm) cc_final: 0.8614 (tmm) REVERT: T 114 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.8488 (tt0) REVERT: U 5 ASP cc_start: 0.7994 (m-30) cc_final: 0.7772 (t0) REVERT: U 7 ILE cc_start: 0.8989 (OUTLIER) cc_final: 0.8586 (mt) REVERT: V 1 MET cc_start: 0.7707 (OUTLIER) cc_final: 0.7439 (mmt) REVERT: V 7 ASP cc_start: 0.8183 (m-30) cc_final: 0.7929 (m-30) REVERT: V 20 GLU cc_start: 0.8826 (mt-10) cc_final: 0.8435 (mp0) REVERT: V 53 GLN cc_start: 0.8776 (mt0) cc_final: 0.8280 (mm-40) REVERT: W 74 MET cc_start: 0.7003 (ptp) cc_final: 0.6548 (ppp) REVERT: W 80 ASP cc_start: 0.5372 (OUTLIER) cc_final: 0.4958 (m-30) REVERT: W 86 MET cc_start: 0.5584 (mtm) cc_final: 0.4970 (ptp) REVERT: X 72 VAL cc_start: 0.8724 (t) cc_final: 0.8428 (p) REVERT: X 87 GLN cc_start: 0.8624 (mt0) cc_final: 0.8409 (mt0) REVERT: Y 22 MET cc_start: 0.7337 (OUTLIER) cc_final: 0.7091 (mmm) REVERT: Y 30 LYS cc_start: 0.9170 (mtmt) cc_final: 0.8930 (mttm) REVERT: Y 35 LYS cc_start: 0.8744 (mtpm) cc_final: 0.8361 (tttp) REVERT: Z 22 LYS cc_start: 0.9373 (mmmm) cc_final: 0.8942 (tptt) REVERT: Z 23 GLU cc_start: 0.8657 (tm-30) cc_final: 0.8404 (tm-30) REVERT: Z 24 GLU cc_start: 0.8611 (tm-30) cc_final: 0.8188 (tm-30) REVERT: Z 28 LEU cc_start: 0.8618 (mt) cc_final: 0.8194 (mp) REVERT: 0 44 LYS cc_start: 0.8470 (mttp) cc_final: 0.7990 (mptt) REVERT: 0 55 ASP cc_start: 0.7622 (m-30) cc_final: 0.7377 (m-30) REVERT: 1 12 VAL cc_start: 0.9205 (t) cc_final: 0.8889 (p) REVERT: 1 15 MET cc_start: 0.7639 (ptt) cc_final: 0.7375 (ptt) REVERT: 1 43 TYR cc_start: 0.7400 (m-80) cc_final: 0.6945 (m-10) REVERT: 1 54 SER cc_start: 0.8407 (m) cc_final: 0.7954 (p) REVERT: 1 73 ARG cc_start: 0.7852 (tmt170) cc_final: 0.7334 (ttp-170) REVERT: 1 76 LYS cc_start: 0.9460 (tttt) cc_final: 0.9160 (tptt) REVERT: 2 36 MET cc_start: 0.8927 (mmm) cc_final: 0.8504 (mmt) REVERT: 3 13 LYS cc_start: 0.8831 (mmtm) cc_final: 0.8416 (mmtm) REVERT: 3 41 LYS cc_start: 0.8760 (tppt) cc_final: 0.8391 (ptpp) REVERT: 3 44 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8225 (tm) REVERT: 4 11 LYS cc_start: 0.8470 (mttt) cc_final: 0.6737 (mmtt) REVERT: 5 57 ARG cc_start: 0.9107 (OUTLIER) cc_final: 0.8272 (ptp90) outliers start: 544 outliers final: 417 residues processed: 1316 average time/residue: 1.1862 time to fit residues: 2740.3040 Evaluate side-chains 1349 residues out of total 4391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 457 poor density : 892 time to evaluate : 7.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 15 ILE Chi-restraints excluded: chain c residue 16 ARG Chi-restraints excluded: chain c residue 40 LYS Chi-restraints excluded: chain c residue 42 ILE Chi-restraints excluded: chain c residue 55 GLU Chi-restraints excluded: chain c residue 83 VAL Chi-restraints excluded: chain c residue 85 ASN Chi-restraints excluded: chain c residue 98 VAL Chi-restraints excluded: chain c residue 127 VAL Chi-restraints excluded: chain c residue 167 TYR Chi-restraints excluded: chain c residue 176 THR Chi-restraints excluded: chain c residue 200 TRP Chi-restraints excluded: chain d residue 4 TYR Chi-restraints excluded: chain d residue 45 SER Chi-restraints excluded: chain d residue 57 LEU Chi-restraints excluded: chain d residue 60 MET Chi-restraints excluded: chain d residue 64 ASN Chi-restraints excluded: chain d residue 71 LEU Chi-restraints excluded: chain d residue 94 ARG Chi-restraints excluded: chain d residue 107 THR Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 162 ARG Chi-restraints excluded: chain d residue 184 ASP Chi-restraints excluded: chain d residue 190 ILE Chi-restraints excluded: chain d residue 195 VAL Chi-restraints excluded: chain e residue 9 LEU Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 72 VAL Chi-restraints excluded: chain e residue 105 VAL Chi-restraints excluded: chain e residue 114 VAL Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain e residue 127 SER Chi-restraints excluded: chain e residue 131 ASN Chi-restraints excluded: chain e residue 132 THR Chi-restraints excluded: chain e residue 144 LEU Chi-restraints excluded: chain e residue 159 LYS Chi-restraints excluded: chain f residue 11 TYR Chi-restraints excluded: chain f residue 12 ILE Chi-restraints excluded: chain f residue 13 ILE Chi-restraints excluded: chain f residue 14 ARG Chi-restraints excluded: chain f residue 18 ASP Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 54 GLU Chi-restraints excluded: chain f residue 56 ASN Chi-restraints excluded: chain f residue 65 ILE Chi-restraints excluded: chain f residue 66 VAL Chi-restraints excluded: chain f residue 67 ASN Chi-restraints excluded: chain f residue 98 VAL Chi-restraints excluded: chain g residue 19 ASN Chi-restraints excluded: chain g residue 24 THR Chi-restraints excluded: chain g residue 47 PHE Chi-restraints excluded: chain g residue 75 VAL Chi-restraints excluded: chain g residue 87 VAL Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain g residue 116 MET Chi-restraints excluded: chain h residue 14 ILE Chi-restraints excluded: chain h residue 20 VAL Chi-restraints excluded: chain h residue 22 HIS Chi-restraints excluded: chain h residue 32 ILE Chi-restraints excluded: chain h residue 46 ILE Chi-restraints excluded: chain h residue 59 VAL Chi-restraints excluded: chain h residue 60 ILE Chi-restraints excluded: chain h residue 69 ASN Chi-restraints excluded: chain h residue 74 ILE Chi-restraints excluded: chain h residue 89 VAL Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 98 LEU Chi-restraints excluded: chain h residue 103 ILE Chi-restraints excluded: chain h residue 106 ILE Chi-restraints excluded: chain h residue 112 VAL Chi-restraints excluded: chain h residue 127 VAL Chi-restraints excluded: chain i residue 9 THR Chi-restraints excluded: chain i residue 12 ARG Chi-restraints excluded: chain i residue 14 ASN Chi-restraints excluded: chain i residue 22 VAL Chi-restraints excluded: chain i residue 30 VAL Chi-restraints excluded: chain i residue 34 ASP Chi-restraints excluded: chain i residue 57 THR Chi-restraints excluded: chain i residue 88 LEU Chi-restraints excluded: chain i residue 91 ASP Chi-restraints excluded: chain i residue 93 ASP Chi-restraints excluded: chain j residue 51 VAL Chi-restraints excluded: chain j residue 74 ILE Chi-restraints excluded: chain j residue 90 LEU Chi-restraints excluded: chain j residue 98 ILE Chi-restraints excluded: chain k residue 18 SER Chi-restraints excluded: chain k residue 26 THR Chi-restraints excluded: chain k residue 35 THR Chi-restraints excluded: chain k residue 46 SER Chi-restraints excluded: chain k residue 55 SER Chi-restraints excluded: chain k residue 59 THR Chi-restraints excluded: chain k residue 73 VAL Chi-restraints excluded: chain k residue 76 GLU Chi-restraints excluded: chain k residue 97 ILE Chi-restraints excluded: chain k residue 99 SER Chi-restraints excluded: chain l residue 4 ILE Chi-restraints excluded: chain l residue 20 ASP Chi-restraints excluded: chain l residue 32 LYS Chi-restraints excluded: chain l residue 39 ASN Chi-restraints excluded: chain l residue 47 CYS Chi-restraints excluded: chain l residue 50 VAL Chi-restraints excluded: chain l residue 72 ASN Chi-restraints excluded: chain l residue 76 VAL Chi-restraints excluded: chain l residue 83 ILE Chi-restraints excluded: chain l residue 93 VAL Chi-restraints excluded: chain l residue 103 LEU Chi-restraints excluded: chain l residue 107 ARG Chi-restraints excluded: chain l residue 115 LEU Chi-restraints excluded: chain l residue 122 ASP Chi-restraints excluded: chain l residue 124 LYS Chi-restraints excluded: chain l residue 126 SER Chi-restraints excluded: chain l residue 132 THR Chi-restraints excluded: chain m residue 4 ILE Chi-restraints excluded: chain m residue 9 ILE Chi-restraints excluded: chain m residue 13 LYS Chi-restraints excluded: chain m residue 28 THR Chi-restraints excluded: chain m residue 40 SER Chi-restraints excluded: chain m residue 45 VAL Chi-restraints excluded: chain m residue 60 ILE Chi-restraints excluded: chain m residue 81 MET Chi-restraints excluded: chain m residue 95 LEU Chi-restraints excluded: chain m residue 101 ASN Chi-restraints excluded: chain m residue 102 THR Chi-restraints excluded: chain n residue 7 ILE Chi-restraints excluded: chain n residue 18 THR Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain n residue 35 ARG Chi-restraints excluded: chain n residue 57 LYS Chi-restraints excluded: chain o residue 11 ILE Chi-restraints excluded: chain o residue 24 SER Chi-restraints excluded: chain o residue 35 ASP Chi-restraints excluded: chain o residue 52 SER Chi-restraints excluded: chain o residue 66 LEU Chi-restraints excluded: chain o residue 73 THR Chi-restraints excluded: chain o residue 80 GLU Chi-restraints excluded: chain o residue 89 ARG Chi-restraints excluded: chain p residue 3 VAL Chi-restraints excluded: chain p residue 5 ILE Chi-restraints excluded: chain p residue 10 MET Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain p residue 39 THR Chi-restraints excluded: chain p residue 40 TYR Chi-restraints excluded: chain p residue 84 HIS Chi-restraints excluded: chain q residue 5 ARG Chi-restraints excluded: chain q residue 7 GLN Chi-restraints excluded: chain q residue 17 SER Chi-restraints excluded: chain q residue 23 THR Chi-restraints excluded: chain q residue 27 VAL Chi-restraints excluded: chain q residue 44 SER Chi-restraints excluded: chain q residue 54 ASN Chi-restraints excluded: chain q residue 58 VAL Chi-restraints excluded: chain q residue 78 LEU Chi-restraints excluded: chain r residue 16 TYR Chi-restraints excluded: chain r residue 25 ILE Chi-restraints excluded: chain r residue 29 ASP Chi-restraints excluded: chain r residue 30 THR Chi-restraints excluded: chain r residue 37 ILE Chi-restraints excluded: chain r residue 51 THR Chi-restraints excluded: chain r residue 63 ILE Chi-restraints excluded: chain s residue 7 LYS Chi-restraints excluded: chain s residue 14 HIS Chi-restraints excluded: chain s residue 33 THR Chi-restraints excluded: chain s residue 65 ASP Chi-restraints excluded: chain s residue 73 GLU Chi-restraints excluded: chain t residue 4 ILE Chi-restraints excluded: chain t residue 8 ILE Chi-restraints excluded: chain t residue 23 SER Chi-restraints excluded: chain t residue 30 THR Chi-restraints excluded: chain t residue 46 VAL Chi-restraints excluded: chain t residue 65 LEU Chi-restraints excluded: chain t residue 81 LEU Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 15 ASN Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 45 ASN Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 53 HIS Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 134 ASN Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 171 TYR Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 194 SER Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 225 MET Chi-restraints excluded: chain C residue 228 ASN Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 130 ARG Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 167 ASP Chi-restraints excluded: chain D residue 168 ARG Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 184 ASN Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 188 ILE Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain E residue 7 PHE Chi-restraints excluded: chain E residue 8 LYS Chi-restraints excluded: chain E residue 10 ASP Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain E residue 46 GLN Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 74 ARG Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 84 ARG Chi-restraints excluded: chain E residue 121 ASN Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 177 THR Chi-restraints excluded: chain E residue 179 ASP Chi-restraints excluded: chain E residue 195 THR Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 123 ASP Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 135 GLN Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 41 ILE Chi-restraints excluded: chain G residue 43 MET Chi-restraints excluded: chain G residue 65 HIS Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 90 ILE Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 128 ASN Chi-restraints excluded: chain G residue 130 GLN Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 23 ASP Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 41 ASN Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 50 ASP Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 85 LEU Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 113 ASN Chi-restraints excluded: chain K residue 115 LEU Chi-restraints excluded: chain K residue 119 GLN Chi-restraints excluded: chain K residue 142 ASP Chi-restraints excluded: chain L residue 6 SER Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 37 ASP Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 73 ASP Chi-restraints excluded: chain L residue 90 ASP Chi-restraints excluded: chain L residue 92 SER Chi-restraints excluded: chain L residue 110 ASN Chi-restraints excluded: chain M residue 3 LEU Chi-restraints excluded: chain M residue 18 ARG Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain M residue 73 ASP Chi-restraints excluded: chain M residue 76 VAL Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 79 LEU Chi-restraints excluded: chain M residue 84 ARG Chi-restraints excluded: chain M residue 89 THR Chi-restraints excluded: chain M residue 95 VAL Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain M residue 97 LYS Chi-restraints excluded: chain M residue 103 LYS Chi-restraints excluded: chain M residue 117 LEU Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 52 ILE Chi-restraints excluded: chain N residue 65 TRP Chi-restraints excluded: chain N residue 68 ILE Chi-restraints excluded: chain N residue 76 SER Chi-restraints excluded: chain N residue 113 VAL Chi-restraints excluded: chain N residue 116 GLU Chi-restraints excluded: chain N residue 120 LEU Chi-restraints excluded: chain N residue 127 VAL Chi-restraints excluded: chain O residue 24 LEU Chi-restraints excluded: chain O residue 26 ILE Chi-restraints excluded: chain O residue 27 ASN Chi-restraints excluded: chain O residue 41 ARG Chi-restraints excluded: chain O residue 42 SER Chi-restraints excluded: chain O residue 56 LEU Chi-restraints excluded: chain O residue 70 VAL Chi-restraints excluded: chain O residue 81 VAL Chi-restraints excluded: chain O residue 89 LEU Chi-restraints excluded: chain O residue 96 ARG Chi-restraints excluded: chain O residue 104 TYR Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain O residue 114 ARG Chi-restraints excluded: chain O residue 121 VAL Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain O residue 123 ILE Chi-restraints excluded: chain O residue 125 PHE Chi-restraints excluded: chain O residue 126 VAL Chi-restraints excluded: chain P residue 6 ASP Chi-restraints excluded: chain P residue 31 LEU Chi-restraints excluded: chain P residue 39 ASN Chi-restraints excluded: chain P residue 62 GLU Chi-restraints excluded: chain P residue 71 THR Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain P residue 101 HIS Chi-restraints excluded: chain P residue 104 VAL Chi-restraints excluded: chain Q residue 8 LEU Chi-restraints excluded: chain Q residue 15 THR Chi-restraints excluded: chain Q residue 16 ASP Chi-restraints excluded: chain Q residue 24 ASP Chi-restraints excluded: chain Q residue 26 VAL Chi-restraints excluded: chain Q residue 32 VAL Chi-restraints excluded: chain Q residue 48 ILE Chi-restraints excluded: chain Q residue 55 ILE Chi-restraints excluded: chain Q residue 73 THR Chi-restraints excluded: chain Q residue 76 LEU Chi-restraints excluded: chain Q residue 110 ILE Chi-restraints excluded: chain R residue 9 VAL Chi-restraints excluded: chain R residue 20 LEU Chi-restraints excluded: chain R residue 29 HIS Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 34 SER Chi-restraints excluded: chain R residue 76 TYR Chi-restraints excluded: chain R residue 85 LEU Chi-restraints excluded: chain R residue 90 ILE Chi-restraints excluded: chain R residue 102 ASP Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 22 VAL Chi-restraints excluded: chain S residue 23 GLU Chi-restraints excluded: chain S residue 27 VAL Chi-restraints excluded: chain S residue 33 VAL Chi-restraints excluded: chain S residue 81 HIS Chi-restraints excluded: chain T residue 29 ILE Chi-restraints excluded: chain T residue 67 PHE Chi-restraints excluded: chain T residue 86 THR Chi-restraints excluded: chain T residue 102 ASN Chi-restraints excluded: chain T residue 114 GLU Chi-restraints excluded: chain U residue 6 VAL Chi-restraints excluded: chain U residue 7 ILE Chi-restraints excluded: chain U residue 11 VAL Chi-restraints excluded: chain U residue 31 THR Chi-restraints excluded: chain U residue 47 ASP Chi-restraints excluded: chain U residue 53 VAL Chi-restraints excluded: chain U residue 80 VAL Chi-restraints excluded: chain U residue 89 ILE Chi-restraints excluded: chain V residue 1 MET Chi-restraints excluded: chain V residue 12 ILE Chi-restraints excluded: chain V residue 31 ASP Chi-restraints excluded: chain V residue 35 VAL Chi-restraints excluded: chain V residue 40 VAL Chi-restraints excluded: chain V residue 48 ASN Chi-restraints excluded: chain V residue 70 VAL Chi-restraints excluded: chain V residue 94 SER Chi-restraints excluded: chain W residue 13 ARG Chi-restraints excluded: chain W residue 31 VAL Chi-restraints excluded: chain W residue 38 SER Chi-restraints excluded: chain W residue 43 PHE Chi-restraints excluded: chain W residue 71 ASN Chi-restraints excluded: chain W residue 80 ASP Chi-restraints excluded: chain W residue 94 VAL Chi-restraints excluded: chain X residue 34 SER Chi-restraints excluded: chain X residue 40 VAL Chi-restraints excluded: chain X residue 66 ASP Chi-restraints excluded: chain X residue 67 THR Chi-restraints excluded: chain X residue 73 ASP Chi-restraints excluded: chain X residue 76 VAL Chi-restraints excluded: chain X residue 88 VAL Chi-restraints excluded: chain Y residue 8 THR Chi-restraints excluded: chain Y residue 12 THR Chi-restraints excluded: chain Y residue 14 SER Chi-restraints excluded: chain Y residue 16 ASN Chi-restraints excluded: chain Y residue 22 MET Chi-restraints excluded: chain Y residue 25 THR Chi-restraints excluded: chain Y residue 33 LEU Chi-restraints excluded: chain Y residue 36 VAL Chi-restraints excluded: chain Y residue 41 ASP Chi-restraints excluded: chain Y residue 55 LYS Chi-restraints excluded: chain Z residue 25 LEU Chi-restraints excluded: chain Z residue 30 PHE Chi-restraints excluded: chain Z residue 32 LEU Chi-restraints excluded: chain Z residue 62 ASN Chi-restraints excluded: chain 0 residue 13 ILE Chi-restraints excluded: chain 0 residue 22 THR Chi-restraints excluded: chain 0 residue 23 VAL Chi-restraints excluded: chain 0 residue 43 ILE Chi-restraints excluded: chain 0 residue 47 VAL Chi-restraints excluded: chain 0 residue 53 LEU Chi-restraints excluded: chain 0 residue 56 VAL Chi-restraints excluded: chain 1 residue 13 VAL Chi-restraints excluded: chain 1 residue 23 PHE Chi-restraints excluded: chain 1 residue 25 SER Chi-restraints excluded: chain 1 residue 36 GLU Chi-restraints excluded: chain 2 residue 3 VAL Chi-restraints excluded: chain 2 residue 6 ARG Chi-restraints excluded: chain 2 residue 9 SER Chi-restraints excluded: chain 2 residue 18 THR Chi-restraints excluded: chain 3 residue 5 ILE Chi-restraints excluded: chain 3 residue 8 GLU Chi-restraints excluded: chain 3 residue 11 SER Chi-restraints excluded: chain 3 residue 39 GLU Chi-restraints excluded: chain 3 residue 44 LEU Chi-restraints excluded: chain 4 residue 5 TYR Chi-restraints excluded: chain 4 residue 24 THR Chi-restraints excluded: chain 4 residue 42 ILE Chi-restraints excluded: chain 4 residue 43 SER Chi-restraints excluded: chain 5 residue 14 VAL Chi-restraints excluded: chain 5 residue 54 ASP Chi-restraints excluded: chain 5 residue 57 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 954 random chunks: chunk 310 optimal weight: 0.9990 chunk 830 optimal weight: 7.9990 chunk 182 optimal weight: 20.0000 chunk 541 optimal weight: 10.0000 chunk 227 optimal weight: 5.9990 chunk 923 optimal weight: 9.9990 chunk 766 optimal weight: 5.9990 chunk 427 optimal weight: 10.0000 chunk 76 optimal weight: 10.0000 chunk 305 optimal weight: 4.9990 chunk 484 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 10 ASN ** n 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 35 GLN ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 ASN D 157 ASN D 191 ASN ** G 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 35 GLN P 20 ASN ** P 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 46 ASN T 66 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 150747 Z= 0.263 Angle : 0.654 14.599 226044 Z= 0.335 Chirality : 0.038 0.323 28980 Planarity : 0.005 0.097 11734 Dihedral : 23.226 179.811 76751 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.17 % Allowed : 12.56 % Favored : 87.26 % Rotamer: Outliers : 11.34 % Allowed : 26.24 % Favored : 62.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.28 % Twisted Proline : 0.52 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.93 (0.11), residues: 5143 helix: -0.27 (0.14), residues: 1439 sheet: -1.92 (0.17), residues: 919 loop : -3.00 (0.11), residues: 2785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP c 200 HIS 0.007 0.001 HIS 1 55 PHE 0.018 0.002 PHE l 31 TYR 0.055 0.002 TYR D 53 ARG 0.013 0.000 ARG C 273 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10286 Ramachandran restraints generated. 5143 Oldfield, 0 Emsley, 5143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10286 Ramachandran restraints generated. 5143 Oldfield, 0 Emsley, 5143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1448 residues out of total 4391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 498 poor density : 950 time to evaluate : 6.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 10 MET cc_start: 0.9106 (mmm) cc_final: 0.8798 (mmt) REVERT: c 40 LYS cc_start: 0.9350 (OUTLIER) cc_final: 0.8943 (tmmm) REVERT: c 55 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.6951 (tm-30) REVERT: c 141 MET cc_start: 0.8080 (mmm) cc_final: 0.7609 (mmm) REVERT: d 71 LEU cc_start: 0.9304 (OUTLIER) cc_final: 0.8943 (tt) REVERT: d 88 MET cc_start: 0.9011 (mmm) cc_final: 0.8744 (mmm) REVERT: d 94 ARG cc_start: 0.8394 (OUTLIER) cc_final: 0.7665 (ptm-80) REVERT: d 162 ARG cc_start: 0.7358 (OUTLIER) cc_final: 0.7091 (mmt-90) REVERT: f 4 ASP cc_start: 0.7780 (m-30) cc_final: 0.7422 (t0) REVERT: f 25 LEU cc_start: 0.9496 (tp) cc_final: 0.9246 (tp) REVERT: f 28 ARG cc_start: 0.8691 (tmm-80) cc_final: 0.8386 (tmm-80) REVERT: f 30 ASP cc_start: 0.9053 (OUTLIER) cc_final: 0.8640 (t0) REVERT: f 39 GLU cc_start: 0.8370 (mt-10) cc_final: 0.7810 (tm-30) REVERT: f 55 MET cc_start: 0.8672 (mmm) cc_final: 0.8212 (mmm) REVERT: f 72 SER cc_start: 0.9364 (p) cc_final: 0.9057 (m) REVERT: f 82 ARG cc_start: 0.9013 (ttp80) cc_final: 0.8700 (ttt90) REVERT: g 24 THR cc_start: 0.8603 (OUTLIER) cc_final: 0.8342 (p) REVERT: g 31 MET cc_start: 0.8687 (ttp) cc_final: 0.8221 (ttt) REVERT: g 66 MET cc_start: 0.8298 (tpp) cc_final: 0.7613 (tmm) REVERT: g 70 MET cc_start: 0.7969 (mmt) cc_final: 0.7524 (mmt) REVERT: g 86 GLN cc_start: 0.7916 (pt0) cc_final: 0.7656 (mp10) REVERT: g 116 MET cc_start: 0.8219 (OUTLIER) cc_final: 0.7939 (mmp) REVERT: g 125 MET cc_start: 0.8565 (mmt) cc_final: 0.8158 (mmt) REVERT: g 126 ASP cc_start: 0.8659 (m-30) cc_final: 0.8448 (m-30) REVERT: h 54 ASP cc_start: 0.8342 (p0) cc_final: 0.7824 (p0) REVERT: h 71 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7685 (pm20) REVERT: h 76 ASN cc_start: 0.9161 (t0) cc_final: 0.8666 (t0) REVERT: i 14 ASN cc_start: 0.8711 (OUTLIER) cc_final: 0.8359 (t0) REVERT: i 81 HIS cc_start: 0.8017 (m90) cc_final: 0.6543 (t-170) REVERT: i 110 MET cc_start: 0.8014 (ptp) cc_final: 0.7665 (mtp) REVERT: i 112 GLU cc_start: 0.8770 (tp30) cc_final: 0.8299 (tp30) REVERT: j 47 SER cc_start: 0.9550 (m) cc_final: 0.9284 (p) REVERT: j 66 GLU cc_start: 0.8584 (pt0) cc_final: 0.8162 (pt0) REVERT: k 76 GLU cc_start: 0.8750 (OUTLIER) cc_final: 0.8466 (tm-30) REVERT: k 87 LYS cc_start: 0.8488 (OUTLIER) cc_final: 0.8204 (mmmm) REVERT: k 105 LEU cc_start: 0.8758 (mt) cc_final: 0.8100 (mp) REVERT: l 75 GLU cc_start: 0.7677 (mm-30) cc_final: 0.7269 (tm-30) REVERT: m 13 LYS cc_start: 0.8553 (OUTLIER) cc_final: 0.8319 (mmmm) REVERT: m 54 ASP cc_start: 0.8856 (m-30) cc_final: 0.8499 (m-30) REVERT: n 25 GLU cc_start: 0.8715 (mm-30) cc_final: 0.8377 (mm-30) REVERT: n 35 ARG cc_start: 0.8391 (OUTLIER) cc_final: 0.7894 (ptm-80) REVERT: n 36 LYS cc_start: 0.9156 (tppt) cc_final: 0.8864 (tmtt) REVERT: n 52 GLN cc_start: 0.8001 (mt0) cc_final: 0.7445 (mt0) REVERT: o 41 GLU cc_start: 0.8736 (mm-30) cc_final: 0.8442 (mm-30) REVERT: o 45 THR cc_start: 0.8643 (m) cc_final: 0.8433 (p) REVERT: p 10 MET cc_start: 0.8630 (OUTLIER) cc_final: 0.8230 (mtp) REVERT: p 30 ASP cc_start: 0.8608 (p0) cc_final: 0.8394 (t0) REVERT: p 65 GLN cc_start: 0.7186 (mp10) cc_final: 0.6975 (mp10) REVERT: q 12 GLN cc_start: 0.8290 (tt0) cc_final: 0.7449 (tp40) REVERT: q 52 GLU cc_start: 0.8692 (mp0) cc_final: 0.8447 (mp0) REVERT: r 26 ASP cc_start: 0.8625 (t0) cc_final: 0.8239 (t70) REVERT: s 12 ASP cc_start: 0.8018 (m-30) cc_final: 0.7672 (m-30) REVERT: s 14 HIS cc_start: 0.8039 (OUTLIER) cc_final: 0.7266 (p-80) REVERT: s 40 ILE cc_start: 0.8506 (mm) cc_final: 0.8008 (mt) REVERT: s 73 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.6985 (tm-30) REVERT: t 44 ASP cc_start: 0.8366 (t0) cc_final: 0.7998 (p0) REVERT: C 37 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7906 (tt) REVERT: C 66 ASP cc_start: 0.8657 (t0) cc_final: 0.8413 (t0) REVERT: C 108 LYS cc_start: 0.8671 (ttmt) cc_final: 0.8028 (mttt) REVERT: C 123 ASP cc_start: 0.8590 (t0) cc_final: 0.8030 (t0) REVERT: C 180 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7545 (pm20) REVERT: C 274 ARG cc_start: 0.7861 (tpt90) cc_final: 0.7381 (tpt90) REVERT: D 168 ARG cc_start: 0.9085 (OUTLIER) cc_final: 0.8390 (ptm160) REVERT: E 46 GLN cc_start: 0.8258 (OUTLIER) cc_final: 0.7806 (tt0) REVERT: E 74 ARG cc_start: 0.8478 (OUTLIER) cc_final: 0.7626 (ptt90) REVERT: F 96 MET cc_start: 0.8706 (tpp) cc_final: 0.8443 (tpp) REVERT: F 120 LYS cc_start: 0.9130 (mttt) cc_final: 0.8904 (tptp) REVERT: G 52 PHE cc_start: 0.6746 (OUTLIER) cc_final: 0.6096 (t80) REVERT: G 99 GLN cc_start: 0.8470 (pp30) cc_final: 0.8149 (pp30) REVERT: G 130 GLN cc_start: 0.8071 (OUTLIER) cc_final: 0.7519 (mp-120) REVERT: K 119 GLN cc_start: 0.8993 (OUTLIER) cc_final: 0.8485 (mt0) REVERT: L 2 ILE cc_start: 0.8805 (mt) cc_final: 0.8453 (tp) REVERT: L 13 ASN cc_start: 0.8904 (t0) cc_final: 0.8497 (p0) REVERT: M 84 ARG cc_start: 0.8340 (OUTLIER) cc_final: 0.7970 (mpp80) REVERT: M 90 GLU cc_start: 0.7837 (tt0) cc_final: 0.7521 (tp30) REVERT: M 101 ILE cc_start: 0.7877 (OUTLIER) cc_final: 0.7573 (mm) REVERT: N 1 MET cc_start: -0.0158 (mmm) cc_final: -0.1864 (mmm) REVERT: N 58 MET cc_start: 0.9062 (ttm) cc_final: 0.8713 (ttm) REVERT: N 65 TRP cc_start: 0.8396 (OUTLIER) cc_final: 0.6732 (m100) REVERT: N 103 MET cc_start: 0.8395 (mmm) cc_final: 0.8155 (mmm) REVERT: O 24 LEU cc_start: 0.9198 (OUTLIER) cc_final: 0.8823 (tp) REVERT: O 41 ARG cc_start: 0.7972 (OUTLIER) cc_final: 0.6825 (ppt90) REVERT: O 46 LYS cc_start: 0.9027 (tttt) cc_final: 0.8451 (tptp) REVERT: O 96 ARG cc_start: 0.8607 (OUTLIER) cc_final: 0.8050 (ttm170) REVERT: O 125 PHE cc_start: 0.8492 (OUTLIER) cc_final: 0.7515 (m-10) REVERT: P 62 GLU cc_start: 0.7368 (OUTLIER) cc_final: 0.7051 (mm-30) REVERT: Q 39 ARG cc_start: 0.8213 (OUTLIER) cc_final: 0.6847 (ttm170) REVERT: Q 106 LYS cc_start: 0.8918 (mtpt) cc_final: 0.8045 (mtpt) REVERT: Q 111 LYS cc_start: 0.9224 (mttt) cc_final: 0.8958 (mtpt) REVERT: Q 113 ILE cc_start: 0.8828 (tp) cc_final: 0.8587 (tt) REVERT: R 89 ASP cc_start: 0.7531 (p0) cc_final: 0.7066 (p0) REVERT: S 1 MET cc_start: 0.8832 (OUTLIER) cc_final: 0.8009 (ttt) REVERT: S 6 LYS cc_start: 0.8543 (mttt) cc_final: 0.8109 (mttt) REVERT: S 37 GLU cc_start: 0.7892 (mt-10) cc_final: 0.7528 (mt-10) REVERT: S 81 HIS cc_start: 0.8288 (OUTLIER) cc_final: 0.7448 (m-70) REVERT: S 96 MET cc_start: 0.8886 (tmm) cc_final: 0.8472 (tmm) REVERT: U 5 ASP cc_start: 0.7899 (m-30) cc_final: 0.7578 (t0) REVERT: U 59 ARG cc_start: 0.7573 (mtt180) cc_final: 0.7181 (mtt180) REVERT: V 1 MET cc_start: 0.7686 (OUTLIER) cc_final: 0.7390 (mmt) REVERT: V 7 ASP cc_start: 0.8171 (m-30) cc_final: 0.7952 (m-30) REVERT: V 20 GLU cc_start: 0.8786 (mt-10) cc_final: 0.8469 (mp0) REVERT: V 53 GLN cc_start: 0.8772 (mt0) cc_final: 0.8269 (mm-40) REVERT: W 80 ASP cc_start: 0.5311 (OUTLIER) cc_final: 0.4829 (m-30) REVERT: W 86 MET cc_start: 0.5628 (mtm) cc_final: 0.5015 (ptp) REVERT: X 72 VAL cc_start: 0.8710 (t) cc_final: 0.8424 (p) REVERT: X 87 GLN cc_start: 0.8620 (mt0) cc_final: 0.8419 (mt0) REVERT: Y 22 MET cc_start: 0.7285 (OUTLIER) cc_final: 0.7050 (mmm) REVERT: Y 30 LYS cc_start: 0.9165 (mtmt) cc_final: 0.8930 (mttm) REVERT: Y 35 LYS cc_start: 0.8732 (mtpm) cc_final: 0.8384 (tttp) REVERT: Z 22 LYS cc_start: 0.9355 (mmmm) cc_final: 0.8911 (tptp) REVERT: Z 23 GLU cc_start: 0.8635 (tm-30) cc_final: 0.8326 (tm-30) REVERT: Z 24 GLU cc_start: 0.8613 (tm-30) cc_final: 0.8165 (tm-30) REVERT: Z 27 ASN cc_start: 0.8128 (m-40) cc_final: 0.7881 (m110) REVERT: Z 28 LEU cc_start: 0.8579 (mt) cc_final: 0.8138 (mp) REVERT: Z 36 GLN cc_start: 0.8567 (OUTLIER) cc_final: 0.7838 (mt0) REVERT: 0 55 ASP cc_start: 0.7576 (m-30) cc_final: 0.7368 (m-30) REVERT: 0 57 GLU cc_start: 0.8490 (mt-10) cc_final: 0.8227 (tt0) REVERT: 1 12 VAL cc_start: 0.9178 (t) cc_final: 0.8836 (p) REVERT: 1 15 MET cc_start: 0.7594 (ptt) cc_final: 0.7358 (ptt) REVERT: 1 43 TYR cc_start: 0.7372 (m-80) cc_final: 0.6919 (m-10) REVERT: 1 54 SER cc_start: 0.8439 (m) cc_final: 0.8052 (p) REVERT: 1 73 ARG cc_start: 0.7860 (tmt170) cc_final: 0.7305 (ttp-170) REVERT: 1 76 LYS cc_start: 0.9456 (tttt) cc_final: 0.9158 (tptt) REVERT: 2 36 MET cc_start: 0.8974 (mmm) cc_final: 0.8648 (mmt) REVERT: 3 8 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.6889 (tp30) REVERT: 3 13 LYS cc_start: 0.8831 (mmtm) cc_final: 0.8419 (mmtm) REVERT: 3 41 LYS cc_start: 0.8764 (tppt) cc_final: 0.8396 (ptpp) REVERT: 3 44 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8226 (tm) REVERT: 5 57 ARG cc_start: 0.9129 (OUTLIER) cc_final: 0.8433 (ptp90) outliers start: 498 outliers final: 376 residues processed: 1305 average time/residue: 1.1552 time to fit residues: 2654.7726 Evaluate side-chains 1325 residues out of total 4391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 419 poor density : 906 time to evaluate : 6.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 15 ILE Chi-restraints excluded: chain c residue 40 LYS Chi-restraints excluded: chain c residue 42 ILE Chi-restraints excluded: chain c residue 55 GLU Chi-restraints excluded: chain c residue 83 VAL Chi-restraints excluded: chain c residue 85 ASN Chi-restraints excluded: chain c residue 98 VAL Chi-restraints excluded: chain c residue 102 ILE Chi-restraints excluded: chain c residue 127 VAL Chi-restraints excluded: chain c residue 200 TRP Chi-restraints excluded: chain d residue 4 TYR Chi-restraints excluded: chain d residue 57 LEU Chi-restraints excluded: chain d residue 60 MET Chi-restraints excluded: chain d residue 64 ASN Chi-restraints excluded: chain d residue 71 LEU Chi-restraints excluded: chain d residue 94 ARG Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 162 ARG Chi-restraints excluded: chain d residue 184 ASP Chi-restraints excluded: chain d residue 190 ILE Chi-restraints excluded: chain d residue 195 VAL Chi-restraints excluded: chain e residue 9 LEU Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 84 GLU Chi-restraints excluded: chain e residue 105 VAL Chi-restraints excluded: chain e residue 114 VAL Chi-restraints excluded: chain e residue 125 SER Chi-restraints excluded: chain e residue 127 SER Chi-restraints excluded: chain e residue 131 ASN Chi-restraints excluded: chain e residue 132 THR Chi-restraints excluded: chain e residue 144 LEU Chi-restraints excluded: chain e residue 159 LYS Chi-restraints excluded: chain f residue 11 TYR Chi-restraints excluded: chain f residue 18 ASP Chi-restraints excluded: chain f residue 30 ASP Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 65 ILE Chi-restraints excluded: chain f residue 66 VAL Chi-restraints excluded: chain f residue 67 ASN Chi-restraints excluded: chain f residue 98 VAL Chi-restraints excluded: chain g residue 19 ASN Chi-restraints excluded: chain g residue 24 THR Chi-restraints excluded: chain g residue 75 VAL Chi-restraints excluded: chain g residue 87 VAL Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain g residue 116 MET Chi-restraints excluded: chain h residue 20 VAL Chi-restraints excluded: chain h residue 22 HIS Chi-restraints excluded: chain h residue 32 ILE Chi-restraints excluded: chain h residue 46 ILE Chi-restraints excluded: chain h residue 59 VAL Chi-restraints excluded: chain h residue 60 ILE Chi-restraints excluded: chain h residue 69 ASN Chi-restraints excluded: chain h residue 71 GLU Chi-restraints excluded: chain h residue 74 ILE Chi-restraints excluded: chain h residue 89 VAL Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 98 LEU Chi-restraints excluded: chain h residue 103 ILE Chi-restraints excluded: chain h residue 112 VAL Chi-restraints excluded: chain h residue 127 VAL Chi-restraints excluded: chain i residue 9 THR Chi-restraints excluded: chain i residue 12 ARG Chi-restraints excluded: chain i residue 14 ASN Chi-restraints excluded: chain i residue 30 VAL Chi-restraints excluded: chain i residue 34 ASP Chi-restraints excluded: chain i residue 57 THR Chi-restraints excluded: chain i residue 66 ASN Chi-restraints excluded: chain i residue 88 LEU Chi-restraints excluded: chain i residue 91 ASP Chi-restraints excluded: chain i residue 93 ASP Chi-restraints excluded: chain j residue 51 VAL Chi-restraints excluded: chain j residue 74 ILE Chi-restraints excluded: chain j residue 90 LEU Chi-restraints excluded: chain j residue 98 ILE Chi-restraints excluded: chain k residue 26 THR Chi-restraints excluded: chain k residue 35 THR Chi-restraints excluded: chain k residue 46 SER Chi-restraints excluded: chain k residue 55 SER Chi-restraints excluded: chain k residue 73 VAL Chi-restraints excluded: chain k residue 76 GLU Chi-restraints excluded: chain k residue 87 LYS Chi-restraints excluded: chain k residue 97 ILE Chi-restraints excluded: chain k residue 99 SER Chi-restraints excluded: chain l residue 4 ILE Chi-restraints excluded: chain l residue 20 ASP Chi-restraints excluded: chain l residue 32 LYS Chi-restraints excluded: chain l residue 50 VAL Chi-restraints excluded: chain l residue 72 ASN Chi-restraints excluded: chain l residue 76 VAL Chi-restraints excluded: chain l residue 95 LEU Chi-restraints excluded: chain l residue 107 ARG Chi-restraints excluded: chain l residue 115 LEU Chi-restraints excluded: chain l residue 124 LYS Chi-restraints excluded: chain l residue 126 SER Chi-restraints excluded: chain l residue 132 THR Chi-restraints excluded: chain m residue 4 ILE Chi-restraints excluded: chain m residue 9 ILE Chi-restraints excluded: chain m residue 13 LYS Chi-restraints excluded: chain m residue 28 THR Chi-restraints excluded: chain m residue 45 VAL Chi-restraints excluded: chain m residue 68 ASP Chi-restraints excluded: chain m residue 81 MET Chi-restraints excluded: chain m residue 101 ASN Chi-restraints excluded: chain m residue 102 THR Chi-restraints excluded: chain n residue 18 THR Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain n residue 35 ARG Chi-restraints excluded: chain n residue 57 LYS Chi-restraints excluded: chain o residue 11 ILE Chi-restraints excluded: chain o residue 24 SER Chi-restraints excluded: chain o residue 35 ASP Chi-restraints excluded: chain o residue 52 SER Chi-restraints excluded: chain o residue 66 LEU Chi-restraints excluded: chain o residue 73 THR Chi-restraints excluded: chain o residue 80 GLU Chi-restraints excluded: chain o residue 89 ARG Chi-restraints excluded: chain p residue 3 VAL Chi-restraints excluded: chain p residue 5 ILE Chi-restraints excluded: chain p residue 10 MET Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain p residue 39 THR Chi-restraints excluded: chain p residue 40 TYR Chi-restraints excluded: chain p residue 84 HIS Chi-restraints excluded: chain q residue 5 ARG Chi-restraints excluded: chain q residue 7 GLN Chi-restraints excluded: chain q residue 17 SER Chi-restraints excluded: chain q residue 23 THR Chi-restraints excluded: chain q residue 27 VAL Chi-restraints excluded: chain q residue 54 ASN Chi-restraints excluded: chain q residue 58 VAL Chi-restraints excluded: chain q residue 78 LEU Chi-restraints excluded: chain r residue 16 TYR Chi-restraints excluded: chain r residue 25 ILE Chi-restraints excluded: chain r residue 29 ASP Chi-restraints excluded: chain r residue 30 THR Chi-restraints excluded: chain r residue 51 THR Chi-restraints excluded: chain r residue 63 ILE Chi-restraints excluded: chain s residue 7 LYS Chi-restraints excluded: chain s residue 14 HIS Chi-restraints excluded: chain s residue 30 VAL Chi-restraints excluded: chain s residue 48 THR Chi-restraints excluded: chain s residue 65 ASP Chi-restraints excluded: chain s residue 73 GLU Chi-restraints excluded: chain t residue 4 ILE Chi-restraints excluded: chain t residue 8 ILE Chi-restraints excluded: chain t residue 23 SER Chi-restraints excluded: chain t residue 30 THR Chi-restraints excluded: chain t residue 65 LEU Chi-restraints excluded: chain t residue 78 LEU Chi-restraints excluded: chain t residue 81 LEU Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 15 ASN Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 45 ASN Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 53 HIS Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 134 ASN Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 171 TYR Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 194 SER Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 225 MET Chi-restraints excluded: chain C residue 228 ASN Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 130 ARG Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 167 ASP Chi-restraints excluded: chain D residue 168 ARG Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 184 ASN Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 188 ILE Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain E residue 7 PHE Chi-restraints excluded: chain E residue 8 LYS Chi-restraints excluded: chain E residue 10 ASP Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain E residue 46 GLN Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 74 ARG Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 84 ARG Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 121 ASN Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain E residue 179 ASP Chi-restraints excluded: chain E residue 195 THR Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 123 ASP Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 135 GLN Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 43 MET Chi-restraints excluded: chain G residue 52 PHE Chi-restraints excluded: chain G residue 65 HIS Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 90 ILE Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 128 ASN Chi-restraints excluded: chain G residue 130 GLN Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 23 ASP Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 41 ASN Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 50 ASP Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 80 MET Chi-restraints excluded: chain K residue 85 LEU Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 113 ASN Chi-restraints excluded: chain K residue 115 LEU Chi-restraints excluded: chain K residue 119 GLN Chi-restraints excluded: chain K residue 142 ASP Chi-restraints excluded: chain L residue 6 SER Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 73 ASP Chi-restraints excluded: chain L residue 90 ASP Chi-restraints excluded: chain L residue 92 SER Chi-restraints excluded: chain L residue 110 ASN Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain M residue 3 LEU Chi-restraints excluded: chain M residue 18 ARG Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain M residue 73 ASP Chi-restraints excluded: chain M residue 76 VAL Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 84 ARG Chi-restraints excluded: chain M residue 89 THR Chi-restraints excluded: chain M residue 95 VAL Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain M residue 97 LYS Chi-restraints excluded: chain M residue 101 ILE Chi-restraints excluded: chain M residue 103 LYS Chi-restraints excluded: chain M residue 117 LEU Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 65 TRP Chi-restraints excluded: chain N residue 68 ILE Chi-restraints excluded: chain N residue 76 SER Chi-restraints excluded: chain N residue 116 GLU Chi-restraints excluded: chain N residue 120 LEU Chi-restraints excluded: chain N residue 127 VAL Chi-restraints excluded: chain N residue 133 LYS Chi-restraints excluded: chain O residue 24 LEU Chi-restraints excluded: chain O residue 26 ILE Chi-restraints excluded: chain O residue 41 ARG Chi-restraints excluded: chain O residue 42 SER Chi-restraints excluded: chain O residue 56 LEU Chi-restraints excluded: chain O residue 70 VAL Chi-restraints excluded: chain O residue 81 VAL Chi-restraints excluded: chain O residue 89 LEU Chi-restraints excluded: chain O residue 96 ARG Chi-restraints excluded: chain O residue 104 TYR Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain O residue 114 ARG Chi-restraints excluded: chain O residue 121 VAL Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain O residue 123 ILE Chi-restraints excluded: chain O residue 125 PHE Chi-restraints excluded: chain O residue 126 VAL Chi-restraints excluded: chain P residue 6 ASP Chi-restraints excluded: chain P residue 31 LEU Chi-restraints excluded: chain P residue 39 ASN Chi-restraints excluded: chain P residue 40 ILE Chi-restraints excluded: chain P residue 62 GLU Chi-restraints excluded: chain P residue 71 THR Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain P residue 101 HIS Chi-restraints excluded: chain Q residue 8 LEU Chi-restraints excluded: chain Q residue 15 THR Chi-restraints excluded: chain Q residue 16 ASP Chi-restraints excluded: chain Q residue 24 ASP Chi-restraints excluded: chain Q residue 26 VAL Chi-restraints excluded: chain Q residue 32 VAL Chi-restraints excluded: chain Q residue 39 ARG Chi-restraints excluded: chain Q residue 48 ILE Chi-restraints excluded: chain Q residue 55 ILE Chi-restraints excluded: chain Q residue 73 THR Chi-restraints excluded: chain Q residue 76 LEU Chi-restraints excluded: chain Q residue 110 ILE Chi-restraints excluded: chain R residue 9 VAL Chi-restraints excluded: chain R residue 20 LEU Chi-restraints excluded: chain R residue 29 HIS Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 34 SER Chi-restraints excluded: chain R residue 85 LEU Chi-restraints excluded: chain R residue 90 ILE Chi-restraints excluded: chain R residue 102 ASP Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 22 VAL Chi-restraints excluded: chain S residue 27 VAL Chi-restraints excluded: chain S residue 33 VAL Chi-restraints excluded: chain S residue 81 HIS Chi-restraints excluded: chain T residue 6 THR Chi-restraints excluded: chain T residue 67 PHE Chi-restraints excluded: chain T residue 68 ASP Chi-restraints excluded: chain T residue 86 THR Chi-restraints excluded: chain T residue 101 ILE Chi-restraints excluded: chain T residue 102 ASN Chi-restraints excluded: chain U residue 6 VAL Chi-restraints excluded: chain U residue 11 VAL Chi-restraints excluded: chain U residue 31 THR Chi-restraints excluded: chain U residue 47 ASP Chi-restraints excluded: chain U residue 80 VAL Chi-restraints excluded: chain V residue 1 MET Chi-restraints excluded: chain V residue 12 ILE Chi-restraints excluded: chain V residue 31 ASP Chi-restraints excluded: chain V residue 33 VAL Chi-restraints excluded: chain V residue 35 VAL Chi-restraints excluded: chain V residue 40 VAL Chi-restraints excluded: chain V residue 48 ASN Chi-restraints excluded: chain V residue 70 VAL Chi-restraints excluded: chain V residue 72 ASP Chi-restraints excluded: chain V residue 94 SER Chi-restraints excluded: chain W residue 13 ARG Chi-restraints excluded: chain W residue 31 VAL Chi-restraints excluded: chain W residue 38 SER Chi-restraints excluded: chain W residue 41 ILE Chi-restraints excluded: chain W residue 43 PHE Chi-restraints excluded: chain W residue 71 ASN Chi-restraints excluded: chain W residue 80 ASP Chi-restraints excluded: chain W residue 94 VAL Chi-restraints excluded: chain X residue 34 SER Chi-restraints excluded: chain X residue 40 VAL Chi-restraints excluded: chain X residue 66 ASP Chi-restraints excluded: chain X residue 67 THR Chi-restraints excluded: chain X residue 73 ASP Chi-restraints excluded: chain X residue 76 VAL Chi-restraints excluded: chain X residue 88 VAL Chi-restraints excluded: chain Y residue 8 THR Chi-restraints excluded: chain Y residue 12 THR Chi-restraints excluded: chain Y residue 14 SER Chi-restraints excluded: chain Y residue 22 MET Chi-restraints excluded: chain Y residue 25 THR Chi-restraints excluded: chain Y residue 36 VAL Chi-restraints excluded: chain Y residue 47 VAL Chi-restraints excluded: chain Y residue 55 LYS Chi-restraints excluded: chain Z residue 18 GLU Chi-restraints excluded: chain Z residue 30 PHE Chi-restraints excluded: chain Z residue 32 LEU Chi-restraints excluded: chain Z residue 36 GLN Chi-restraints excluded: chain Z residue 45 GLU Chi-restraints excluded: chain Z residue 62 ASN Chi-restraints excluded: chain 0 residue 13 ILE Chi-restraints excluded: chain 0 residue 47 VAL Chi-restraints excluded: chain 0 residue 53 LEU Chi-restraints excluded: chain 0 residue 56 VAL Chi-restraints excluded: chain 1 residue 13 VAL Chi-restraints excluded: chain 1 residue 23 PHE Chi-restraints excluded: chain 1 residue 25 SER Chi-restraints excluded: chain 2 residue 3 VAL Chi-restraints excluded: chain 2 residue 6 ARG Chi-restraints excluded: chain 2 residue 9 SER Chi-restraints excluded: chain 2 residue 18 THR Chi-restraints excluded: chain 3 residue 5 ILE Chi-restraints excluded: chain 3 residue 8 GLU Chi-restraints excluded: chain 3 residue 11 SER Chi-restraints excluded: chain 3 residue 39 GLU Chi-restraints excluded: chain 3 residue 44 LEU Chi-restraints excluded: chain 4 residue 5 TYR Chi-restraints excluded: chain 4 residue 24 THR Chi-restraints excluded: chain 4 residue 42 ILE Chi-restraints excluded: chain 4 residue 43 SER Chi-restraints excluded: chain 5 residue 14 VAL Chi-restraints excluded: chain 5 residue 57 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 954 random chunks: chunk 889 optimal weight: 7.9990 chunk 104 optimal weight: 20.0000 chunk 525 optimal weight: 10.0000 chunk 674 optimal weight: 0.9980 chunk 522 optimal weight: 10.0000 chunk 777 optimal weight: 6.9990 chunk 515 optimal weight: 9.9990 chunk 919 optimal weight: 9.9990 chunk 575 optimal weight: 10.0000 chunk 560 optimal weight: 10.0000 chunk 424 optimal weight: 10.0000 overall best weight: 7.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 35 GLN ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 ASN D 73 ASN D 85 ASN D 191 ASN ** G 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 35 GLN P 20 ASN P 32 ASN ** P 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 68 GLN ** S 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 66 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 150747 Z= 0.350 Angle : 0.715 14.948 226044 Z= 0.363 Chirality : 0.041 0.349 28980 Planarity : 0.005 0.098 11734 Dihedral : 23.257 179.441 76722 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.17 % Allowed : 14.31 % Favored : 85.51 % Rotamer: Outliers : 11.68 % Allowed : 26.65 % Favored : 61.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.28 % Twisted Proline : 0.52 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.01 (0.11), residues: 5143 helix: -0.38 (0.14), residues: 1446 sheet: -1.93 (0.17), residues: 932 loop : -3.04 (0.11), residues: 2765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP N 93 HIS 0.006 0.001 HIS l 109 PHE 0.023 0.002 PHE N 69 TYR 0.077 0.002 TYR D 53 ARG 0.013 0.001 ARG C 273 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10286 Ramachandran restraints generated. 5143 Oldfield, 0 Emsley, 5143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10286 Ramachandran restraints generated. 5143 Oldfield, 0 Emsley, 5143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1422 residues out of total 4391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 513 poor density : 909 time to evaluate : 5.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 16 ARG cc_start: 0.8498 (OUTLIER) cc_final: 0.8014 (tmm160) REVERT: c 17 ASP cc_start: 0.9173 (p0) cc_final: 0.8591 (p0) REVERT: c 40 LYS cc_start: 0.9356 (OUTLIER) cc_final: 0.8961 (tmmm) REVERT: c 55 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.6901 (tm-30) REVERT: c 64 ASN cc_start: 0.8361 (p0) cc_final: 0.7958 (p0) REVERT: c 141 MET cc_start: 0.8057 (mmm) cc_final: 0.7590 (mmm) REVERT: d 45 SER cc_start: 0.7536 (OUTLIER) cc_final: 0.7165 (p) REVERT: d 71 LEU cc_start: 0.9330 (OUTLIER) cc_final: 0.8980 (tt) REVERT: d 88 MET cc_start: 0.9045 (mmm) cc_final: 0.8750 (mmm) REVERT: d 94 ARG cc_start: 0.8373 (OUTLIER) cc_final: 0.7587 (ptm-80) REVERT: d 162 ARG cc_start: 0.7346 (OUTLIER) cc_final: 0.7090 (mmt-90) REVERT: f 4 ASP cc_start: 0.7820 (m-30) cc_final: 0.7463 (t0) REVERT: f 30 ASP cc_start: 0.9061 (OUTLIER) cc_final: 0.8652 (t0) REVERT: f 39 GLU cc_start: 0.8394 (mt-10) cc_final: 0.7896 (tm-30) REVERT: f 55 MET cc_start: 0.8776 (mmm) cc_final: 0.8262 (mmm) REVERT: f 82 ARG cc_start: 0.9036 (ttp80) cc_final: 0.8707 (ttt90) REVERT: g 24 THR cc_start: 0.8594 (OUTLIER) cc_final: 0.8338 (p) REVERT: g 31 MET cc_start: 0.8676 (ttp) cc_final: 0.8190 (ttt) REVERT: g 66 MET cc_start: 0.8318 (tpp) cc_final: 0.7545 (tmm) REVERT: g 86 GLN cc_start: 0.7896 (pt0) cc_final: 0.7595 (mp10) REVERT: g 116 MET cc_start: 0.8242 (OUTLIER) cc_final: 0.7946 (mmp) REVERT: g 126 ASP cc_start: 0.8616 (m-30) cc_final: 0.8357 (m-30) REVERT: h 5 ASP cc_start: 0.8058 (p0) cc_final: 0.7842 (p0) REVERT: h 54 ASP cc_start: 0.8442 (p0) cc_final: 0.8029 (p0) REVERT: h 71 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7647 (pm20) REVERT: h 76 ASN cc_start: 0.9110 (t0) cc_final: 0.8590 (t0) REVERT: i 14 ASN cc_start: 0.8715 (OUTLIER) cc_final: 0.8375 (t0) REVERT: i 81 HIS cc_start: 0.8085 (m90) cc_final: 0.6538 (t-170) REVERT: i 112 GLU cc_start: 0.8803 (tp30) cc_final: 0.8299 (tp30) REVERT: j 47 SER cc_start: 0.9554 (m) cc_final: 0.9295 (p) REVERT: j 66 GLU cc_start: 0.8605 (pt0) cc_final: 0.8200 (pt0) REVERT: k 14 LYS cc_start: 0.9146 (ttpp) cc_final: 0.8826 (ttpp) REVERT: k 87 LYS cc_start: 0.8499 (OUTLIER) cc_final: 0.8218 (mmmm) REVERT: k 105 LEU cc_start: 0.8789 (mt) cc_final: 0.8112 (mp) REVERT: l 39 ASN cc_start: 0.8920 (OUTLIER) cc_final: 0.8589 (p0) REVERT: l 75 GLU cc_start: 0.7733 (mm-30) cc_final: 0.7265 (tm-30) REVERT: m 13 LYS cc_start: 0.8564 (OUTLIER) cc_final: 0.8315 (mmmm) REVERT: m 54 ASP cc_start: 0.8848 (m-30) cc_final: 0.8494 (m-30) REVERT: n 25 GLU cc_start: 0.8748 (mm-30) cc_final: 0.8406 (mm-30) REVERT: n 27 CYS cc_start: 0.6341 (OUTLIER) cc_final: 0.6131 (p) REVERT: n 35 ARG cc_start: 0.8463 (OUTLIER) cc_final: 0.8166 (ptm160) REVERT: n 52 GLN cc_start: 0.8013 (mt0) cc_final: 0.7444 (mt0) REVERT: o 41 GLU cc_start: 0.8808 (mm-30) cc_final: 0.8280 (mm-30) REVERT: o 44 ARG cc_start: 0.8293 (mtm180) cc_final: 0.7838 (mtm180) REVERT: o 45 THR cc_start: 0.8706 (m) cc_final: 0.8493 (p) REVERT: p 10 MET cc_start: 0.8673 (OUTLIER) cc_final: 0.8264 (mtp) REVERT: p 30 ASP cc_start: 0.8628 (p0) cc_final: 0.8410 (t0) REVERT: p 65 GLN cc_start: 0.7225 (mp10) cc_final: 0.6993 (mp10) REVERT: q 12 GLN cc_start: 0.8293 (tt0) cc_final: 0.7451 (tp40) REVERT: q 40 ARG cc_start: 0.8507 (mmm160) cc_final: 0.7685 (ttt90) REVERT: q 52 GLU cc_start: 0.8704 (mp0) cc_final: 0.8328 (mp0) REVERT: q 53 ASN cc_start: 0.9153 (OUTLIER) cc_final: 0.8951 (p0) REVERT: r 26 ASP cc_start: 0.8624 (t0) cc_final: 0.8238 (t70) REVERT: r 57 ARG cc_start: 0.9286 (mtm180) cc_final: 0.9075 (mtm180) REVERT: s 12 ASP cc_start: 0.8045 (m-30) cc_final: 0.7694 (m-30) REVERT: s 14 HIS cc_start: 0.7985 (OUTLIER) cc_final: 0.7225 (p-80) REVERT: s 40 ILE cc_start: 0.8557 (mm) cc_final: 0.8087 (mt) REVERT: s 73 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7011 (tm-30) REVERT: t 44 ASP cc_start: 0.8383 (t0) cc_final: 0.7920 (p0) REVERT: C 123 ASP cc_start: 0.8559 (t0) cc_final: 0.8145 (t0) REVERT: C 180 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7617 (pm20) REVERT: C 274 ARG cc_start: 0.7929 (tpt90) cc_final: 0.7659 (tpt90) REVERT: D 168 ARG cc_start: 0.9092 (OUTLIER) cc_final: 0.8413 (ptm160) REVERT: E 13 GLN cc_start: 0.8890 (mp10) cc_final: 0.8607 (mp10) REVERT: E 46 GLN cc_start: 0.8301 (OUTLIER) cc_final: 0.7865 (tt0) REVERT: E 74 ARG cc_start: 0.8536 (OUTLIER) cc_final: 0.7743 (ptt90) REVERT: F 120 LYS cc_start: 0.9152 (mttt) cc_final: 0.8912 (tptp) REVERT: G 52 PHE cc_start: 0.6827 (OUTLIER) cc_final: 0.6080 (t80) REVERT: G 89 LEU cc_start: 0.9317 (OUTLIER) cc_final: 0.8947 (tt) REVERT: G 94 TYR cc_start: 0.8395 (m-80) cc_final: 0.8041 (m-80) REVERT: G 99 GLN cc_start: 0.8522 (pp30) cc_final: 0.8201 (pp30) REVERT: G 130 GLN cc_start: 0.8092 (OUTLIER) cc_final: 0.7540 (mp-120) REVERT: K 119 GLN cc_start: 0.9007 (OUTLIER) cc_final: 0.8499 (mt0) REVERT: L 2 ILE cc_start: 0.8823 (mt) cc_final: 0.8471 (tp) REVERT: L 13 ASN cc_start: 0.8902 (t0) cc_final: 0.8446 (p0) REVERT: M 101 ILE cc_start: 0.7963 (OUTLIER) cc_final: 0.7715 (mm) REVERT: N 1 MET cc_start: 0.0581 (mmm) cc_final: -0.0258 (mmm) REVERT: N 58 MET cc_start: 0.9131 (ttm) cc_final: 0.8750 (ttm) REVERT: N 65 TRP cc_start: 0.8371 (OUTLIER) cc_final: 0.6633 (m100) REVERT: N 134 ARG cc_start: 0.8137 (OUTLIER) cc_final: 0.7363 (ttt90) REVERT: O 24 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.8772 (tp) REVERT: O 41 ARG cc_start: 0.7967 (OUTLIER) cc_final: 0.6771 (ppt90) REVERT: O 46 LYS cc_start: 0.9063 (tttt) cc_final: 0.8466 (tptp) REVERT: O 96 ARG cc_start: 0.8627 (OUTLIER) cc_final: 0.7970 (ttm170) REVERT: O 125 PHE cc_start: 0.8600 (OUTLIER) cc_final: 0.7391 (m-10) REVERT: P 27 GLU cc_start: 0.8732 (tm-30) cc_final: 0.8479 (tm-30) REVERT: P 30 ARG cc_start: 0.8835 (OUTLIER) cc_final: 0.8420 (ttm170) REVERT: P 62 GLU cc_start: 0.7362 (OUTLIER) cc_final: 0.7015 (mm-30) REVERT: Q 7 GLU cc_start: 0.8758 (mt-10) cc_final: 0.8473 (mt-10) REVERT: Q 39 ARG cc_start: 0.8250 (OUTLIER) cc_final: 0.6895 (ttm170) REVERT: Q 106 LYS cc_start: 0.8933 (mtpt) cc_final: 0.8693 (mtpp) REVERT: Q 111 LYS cc_start: 0.9223 (mttt) cc_final: 0.8962 (mtpt) REVERT: Q 113 ILE cc_start: 0.8874 (tp) cc_final: 0.8669 (tt) REVERT: R 89 ASP cc_start: 0.7550 (p0) cc_final: 0.7085 (p0) REVERT: S 1 MET cc_start: 0.8820 (OUTLIER) cc_final: 0.7909 (ttt) REVERT: S 2 TYR cc_start: 0.8235 (t80) cc_final: 0.7960 (t80) REVERT: S 6 LYS cc_start: 0.8552 (mttt) cc_final: 0.8112 (mttt) REVERT: S 37 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7542 (mt-10) REVERT: S 81 HIS cc_start: 0.8394 (OUTLIER) cc_final: 0.7574 (m-70) REVERT: U 5 ASP cc_start: 0.8093 (m-30) cc_final: 0.7729 (t0) REVERT: U 7 ILE cc_start: 0.9024 (OUTLIER) cc_final: 0.8804 (mt) REVERT: V 1 MET cc_start: 0.7688 (OUTLIER) cc_final: 0.7413 (mmt) REVERT: V 7 ASP cc_start: 0.8167 (m-30) cc_final: 0.7935 (m-30) REVERT: V 20 GLU cc_start: 0.8825 (mt-10) cc_final: 0.8428 (mp0) REVERT: V 53 GLN cc_start: 0.8761 (mt0) cc_final: 0.8268 (mm-40) REVERT: W 74 MET cc_start: 0.7102 (ptp) cc_final: 0.6711 (ppp) REVERT: W 80 ASP cc_start: 0.5321 (OUTLIER) cc_final: 0.4837 (m-30) REVERT: W 86 MET cc_start: 0.5582 (mtm) cc_final: 0.4901 (ptp) REVERT: X 72 VAL cc_start: 0.8742 (t) cc_final: 0.8435 (p) REVERT: Y 22 MET cc_start: 0.7380 (OUTLIER) cc_final: 0.7116 (mmm) REVERT: Y 30 LYS cc_start: 0.9171 (mtmt) cc_final: 0.8947 (mttm) REVERT: Y 35 LYS cc_start: 0.8741 (mtpm) cc_final: 0.8371 (tttp) REVERT: Z 22 LYS cc_start: 0.9380 (mmmm) cc_final: 0.8939 (tptp) REVERT: Z 23 GLU cc_start: 0.8668 (tm-30) cc_final: 0.8422 (tm-30) REVERT: Z 24 GLU cc_start: 0.8648 (tm-30) cc_final: 0.8229 (tm-30) REVERT: Z 28 LEU cc_start: 0.8587 (mt) cc_final: 0.8159 (mp) REVERT: 0 30 LYS cc_start: 0.9056 (mmmt) cc_final: 0.8599 (mmmt) REVERT: 0 44 LYS cc_start: 0.8438 (mttp) cc_final: 0.8003 (mptt) REVERT: 0 57 GLU cc_start: 0.8467 (mt-10) cc_final: 0.8225 (tt0) REVERT: 1 12 VAL cc_start: 0.9221 (t) cc_final: 0.8870 (p) REVERT: 1 34 THR cc_start: 0.7190 (p) cc_final: 0.6963 (p) REVERT: 1 43 TYR cc_start: 0.7455 (m-80) cc_final: 0.7031 (m-10) REVERT: 1 54 SER cc_start: 0.8547 (m) cc_final: 0.8329 (p) REVERT: 1 73 ARG cc_start: 0.7924 (tmt170) cc_final: 0.7385 (ttp-170) REVERT: 1 76 LYS cc_start: 0.9467 (tttt) cc_final: 0.9191 (tptt) REVERT: 2 6 ARG cc_start: 0.8647 (OUTLIER) cc_final: 0.7766 (tpm-80) REVERT: 2 36 MET cc_start: 0.8877 (mmm) cc_final: 0.8382 (mmm) REVERT: 3 41 LYS cc_start: 0.8767 (tppt) cc_final: 0.8395 (ptpp) REVERT: 3 44 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8235 (tm) REVERT: 6 24 MET cc_start: 0.8501 (mmm) cc_final: 0.8240 (mmt) outliers start: 513 outliers final: 403 residues processed: 1279 average time/residue: 1.1868 time to fit residues: 2680.7257 Evaluate side-chains 1337 residues out of total 4391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 450 poor density : 887 time to evaluate : 6.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 15 ILE Chi-restraints excluded: chain c residue 16 ARG Chi-restraints excluded: chain c residue 40 LYS Chi-restraints excluded: chain c residue 42 ILE Chi-restraints excluded: chain c residue 55 GLU Chi-restraints excluded: chain c residue 83 VAL Chi-restraints excluded: chain c residue 85 ASN Chi-restraints excluded: chain c residue 98 VAL Chi-restraints excluded: chain c residue 127 VAL Chi-restraints excluded: chain c residue 176 THR Chi-restraints excluded: chain c residue 200 TRP Chi-restraints excluded: chain d residue 4 TYR Chi-restraints excluded: chain d residue 45 SER Chi-restraints excluded: chain d residue 57 LEU Chi-restraints excluded: chain d residue 64 ASN Chi-restraints excluded: chain d residue 71 LEU Chi-restraints excluded: chain d residue 94 ARG Chi-restraints excluded: chain d residue 107 THR Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 135 GLU Chi-restraints excluded: chain d residue 136 VAL Chi-restraints excluded: chain d residue 162 ARG Chi-restraints excluded: chain d residue 184 ASP Chi-restraints excluded: chain d residue 190 ILE Chi-restraints excluded: chain d residue 195 VAL Chi-restraints excluded: chain e residue 3 TYR Chi-restraints excluded: chain e residue 9 LEU Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 72 VAL Chi-restraints excluded: chain e residue 84 GLU Chi-restraints excluded: chain e residue 105 VAL Chi-restraints excluded: chain e residue 114 VAL Chi-restraints excluded: chain e residue 127 SER Chi-restraints excluded: chain e residue 131 ASN Chi-restraints excluded: chain e residue 132 THR Chi-restraints excluded: chain e residue 144 LEU Chi-restraints excluded: chain e residue 159 LYS Chi-restraints excluded: chain f residue 11 TYR Chi-restraints excluded: chain f residue 13 ILE Chi-restraints excluded: chain f residue 18 ASP Chi-restraints excluded: chain f residue 30 ASP Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 50 ARG Chi-restraints excluded: chain f residue 65 ILE Chi-restraints excluded: chain f residue 66 VAL Chi-restraints excluded: chain f residue 67 ASN Chi-restraints excluded: chain f residue 98 VAL Chi-restraints excluded: chain g residue 19 ASN Chi-restraints excluded: chain g residue 24 THR Chi-restraints excluded: chain g residue 75 VAL Chi-restraints excluded: chain g residue 87 VAL Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain g residue 116 MET Chi-restraints excluded: chain h residue 14 ILE Chi-restraints excluded: chain h residue 20 VAL Chi-restraints excluded: chain h residue 22 HIS Chi-restraints excluded: chain h residue 32 ILE Chi-restraints excluded: chain h residue 46 ILE Chi-restraints excluded: chain h residue 59 VAL Chi-restraints excluded: chain h residue 60 ILE Chi-restraints excluded: chain h residue 69 ASN Chi-restraints excluded: chain h residue 71 GLU Chi-restraints excluded: chain h residue 74 ILE Chi-restraints excluded: chain h residue 89 VAL Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 98 LEU Chi-restraints excluded: chain h residue 103 ILE Chi-restraints excluded: chain h residue 112 VAL Chi-restraints excluded: chain h residue 127 VAL Chi-restraints excluded: chain i residue 9 THR Chi-restraints excluded: chain i residue 12 ARG Chi-restraints excluded: chain i residue 14 ASN Chi-restraints excluded: chain i residue 22 VAL Chi-restraints excluded: chain i residue 30 VAL Chi-restraints excluded: chain i residue 34 ASP Chi-restraints excluded: chain i residue 57 THR Chi-restraints excluded: chain i residue 66 ASN Chi-restraints excluded: chain i residue 88 LEU Chi-restraints excluded: chain i residue 91 ASP Chi-restraints excluded: chain i residue 93 ASP Chi-restraints excluded: chain j residue 51 VAL Chi-restraints excluded: chain j residue 74 ILE Chi-restraints excluded: chain j residue 90 LEU Chi-restraints excluded: chain j residue 98 ILE Chi-restraints excluded: chain k residue 26 THR Chi-restraints excluded: chain k residue 35 THR Chi-restraints excluded: chain k residue 46 SER Chi-restraints excluded: chain k residue 55 SER Chi-restraints excluded: chain k residue 73 VAL Chi-restraints excluded: chain k residue 76 GLU Chi-restraints excluded: chain k residue 87 LYS Chi-restraints excluded: chain k residue 97 ILE Chi-restraints excluded: chain k residue 99 SER Chi-restraints excluded: chain l residue 4 ILE Chi-restraints excluded: chain l residue 20 ASP Chi-restraints excluded: chain l residue 30 SER Chi-restraints excluded: chain l residue 32 LYS Chi-restraints excluded: chain l residue 39 ASN Chi-restraints excluded: chain l residue 50 VAL Chi-restraints excluded: chain l residue 72 ASN Chi-restraints excluded: chain l residue 76 VAL Chi-restraints excluded: chain l residue 83 ILE Chi-restraints excluded: chain l residue 92 VAL Chi-restraints excluded: chain l residue 95 LEU Chi-restraints excluded: chain l residue 102 ASP Chi-restraints excluded: chain l residue 107 ARG Chi-restraints excluded: chain l residue 115 LEU Chi-restraints excluded: chain l residue 124 LYS Chi-restraints excluded: chain l residue 126 SER Chi-restraints excluded: chain l residue 132 THR Chi-restraints excluded: chain m residue 4 ILE Chi-restraints excluded: chain m residue 9 ILE Chi-restraints excluded: chain m residue 13 LYS Chi-restraints excluded: chain m residue 28 THR Chi-restraints excluded: chain m residue 45 VAL Chi-restraints excluded: chain m residue 60 ILE Chi-restraints excluded: chain m residue 68 ASP Chi-restraints excluded: chain m residue 77 ILE Chi-restraints excluded: chain m residue 81 MET Chi-restraints excluded: chain m residue 101 ASN Chi-restraints excluded: chain n residue 18 THR Chi-restraints excluded: chain n residue 27 CYS Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain n residue 35 ARG Chi-restraints excluded: chain n residue 41 ARG Chi-restraints excluded: chain n residue 57 LYS Chi-restraints excluded: chain o residue 11 ILE Chi-restraints excluded: chain o residue 24 SER Chi-restraints excluded: chain o residue 35 ASP Chi-restraints excluded: chain o residue 46 HIS Chi-restraints excluded: chain o residue 52 SER Chi-restraints excluded: chain o residue 66 LEU Chi-restraints excluded: chain o residue 73 THR Chi-restraints excluded: chain o residue 80 GLU Chi-restraints excluded: chain o residue 89 ARG Chi-restraints excluded: chain p residue 3 VAL Chi-restraints excluded: chain p residue 5 ILE Chi-restraints excluded: chain p residue 10 MET Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain p residue 39 THR Chi-restraints excluded: chain p residue 84 HIS Chi-restraints excluded: chain q residue 5 ARG Chi-restraints excluded: chain q residue 7 GLN Chi-restraints excluded: chain q residue 17 SER Chi-restraints excluded: chain q residue 23 THR Chi-restraints excluded: chain q residue 27 VAL Chi-restraints excluded: chain q residue 44 SER Chi-restraints excluded: chain q residue 53 ASN Chi-restraints excluded: chain q residue 54 ASN Chi-restraints excluded: chain q residue 58 VAL Chi-restraints excluded: chain q residue 78 LEU Chi-restraints excluded: chain r residue 16 TYR Chi-restraints excluded: chain r residue 25 ILE Chi-restraints excluded: chain r residue 29 ASP Chi-restraints excluded: chain r residue 30 THR Chi-restraints excluded: chain r residue 33 LEU Chi-restraints excluded: chain r residue 46 ARG Chi-restraints excluded: chain r residue 51 THR Chi-restraints excluded: chain r residue 63 ILE Chi-restraints excluded: chain s residue 7 LYS Chi-restraints excluded: chain s residue 14 HIS Chi-restraints excluded: chain s residue 30 VAL Chi-restraints excluded: chain s residue 33 THR Chi-restraints excluded: chain s residue 48 THR Chi-restraints excluded: chain s residue 65 ASP Chi-restraints excluded: chain s residue 73 GLU Chi-restraints excluded: chain t residue 4 ILE Chi-restraints excluded: chain t residue 8 ILE Chi-restraints excluded: chain t residue 23 SER Chi-restraints excluded: chain t residue 30 THR Chi-restraints excluded: chain t residue 65 LEU Chi-restraints excluded: chain t residue 78 LEU Chi-restraints excluded: chain t residue 81 LEU Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 15 ASN Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 20 ASP Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 45 ASN Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 53 HIS Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 134 ASN Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 171 TYR Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 194 SER Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 225 MET Chi-restraints excluded: chain C residue 228 ASN Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 130 ARG Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 167 ASP Chi-restraints excluded: chain D residue 168 ARG Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 184 ASN Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 188 ILE Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain E residue 7 PHE Chi-restraints excluded: chain E residue 8 LYS Chi-restraints excluded: chain E residue 10 ASP Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain E residue 46 GLN Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 74 ARG Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 84 ARG Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 121 ASN Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 177 THR Chi-restraints excluded: chain E residue 179 ASP Chi-restraints excluded: chain E residue 195 THR Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 123 ASP Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 135 GLN Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 43 MET Chi-restraints excluded: chain G residue 52 PHE Chi-restraints excluded: chain G residue 65 HIS Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 90 ILE Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 128 ASN Chi-restraints excluded: chain G residue 130 GLN Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 23 ASP Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 41 ASN Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 50 ASP Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 80 MET Chi-restraints excluded: chain K residue 85 LEU Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 113 ASN Chi-restraints excluded: chain K residue 115 LEU Chi-restraints excluded: chain K residue 119 GLN Chi-restraints excluded: chain K residue 142 ASP Chi-restraints excluded: chain L residue 6 SER Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 73 ASP Chi-restraints excluded: chain L residue 90 ASP Chi-restraints excluded: chain L residue 92 SER Chi-restraints excluded: chain L residue 110 ASN Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain M residue 3 LEU Chi-restraints excluded: chain M residue 18 ARG Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain M residue 73 ASP Chi-restraints excluded: chain M residue 76 VAL Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 79 LEU Chi-restraints excluded: chain M residue 95 VAL Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain M residue 97 LYS Chi-restraints excluded: chain M residue 101 ILE Chi-restraints excluded: chain M residue 103 LYS Chi-restraints excluded: chain M residue 117 LEU Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 65 TRP Chi-restraints excluded: chain N residue 68 ILE Chi-restraints excluded: chain N residue 79 ILE Chi-restraints excluded: chain N residue 116 GLU Chi-restraints excluded: chain N residue 120 LEU Chi-restraints excluded: chain N residue 127 VAL Chi-restraints excluded: chain N residue 133 LYS Chi-restraints excluded: chain N residue 134 ARG Chi-restraints excluded: chain O residue 24 LEU Chi-restraints excluded: chain O residue 26 ILE Chi-restraints excluded: chain O residue 41 ARG Chi-restraints excluded: chain O residue 42 SER Chi-restraints excluded: chain O residue 56 LEU Chi-restraints excluded: chain O residue 70 VAL Chi-restraints excluded: chain O residue 79 SER Chi-restraints excluded: chain O residue 81 VAL Chi-restraints excluded: chain O residue 89 LEU Chi-restraints excluded: chain O residue 96 ARG Chi-restraints excluded: chain O residue 104 TYR Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain O residue 114 ARG Chi-restraints excluded: chain O residue 121 VAL Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain O residue 123 ILE Chi-restraints excluded: chain O residue 125 PHE Chi-restraints excluded: chain O residue 126 VAL Chi-restraints excluded: chain P residue 6 ASP Chi-restraints excluded: chain P residue 30 ARG Chi-restraints excluded: chain P residue 31 LEU Chi-restraints excluded: chain P residue 39 ASN Chi-restraints excluded: chain P residue 40 ILE Chi-restraints excluded: chain P residue 62 GLU Chi-restraints excluded: chain P residue 71 THR Chi-restraints excluded: chain P residue 101 HIS Chi-restraints excluded: chain Q residue 8 LEU Chi-restraints excluded: chain Q residue 15 THR Chi-restraints excluded: chain Q residue 16 ASP Chi-restraints excluded: chain Q residue 24 ASP Chi-restraints excluded: chain Q residue 26 VAL Chi-restraints excluded: chain Q residue 32 VAL Chi-restraints excluded: chain Q residue 39 ARG Chi-restraints excluded: chain Q residue 48 ILE Chi-restraints excluded: chain Q residue 68 VAL Chi-restraints excluded: chain Q residue 73 THR Chi-restraints excluded: chain Q residue 76 LEU Chi-restraints excluded: chain Q residue 110 ILE Chi-restraints excluded: chain R residue 9 VAL Chi-restraints excluded: chain R residue 20 LEU Chi-restraints excluded: chain R residue 29 HIS Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 34 SER Chi-restraints excluded: chain R residue 76 TYR Chi-restraints excluded: chain R residue 85 LEU Chi-restraints excluded: chain R residue 90 ILE Chi-restraints excluded: chain R residue 102 ASP Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 22 VAL Chi-restraints excluded: chain S residue 27 VAL Chi-restraints excluded: chain S residue 33 VAL Chi-restraints excluded: chain S residue 81 HIS Chi-restraints excluded: chain T residue 6 THR Chi-restraints excluded: chain T residue 29 ILE Chi-restraints excluded: chain T residue 67 PHE Chi-restraints excluded: chain T residue 86 THR Chi-restraints excluded: chain T residue 102 ASN Chi-restraints excluded: chain U residue 6 VAL Chi-restraints excluded: chain U residue 7 ILE Chi-restraints excluded: chain U residue 11 VAL Chi-restraints excluded: chain U residue 31 THR Chi-restraints excluded: chain U residue 47 ASP Chi-restraints excluded: chain U residue 53 VAL Chi-restraints excluded: chain U residue 80 VAL Chi-restraints excluded: chain V residue 1 MET Chi-restraints excluded: chain V residue 12 ILE Chi-restraints excluded: chain V residue 31 ASP Chi-restraints excluded: chain V residue 33 VAL Chi-restraints excluded: chain V residue 35 VAL Chi-restraints excluded: chain V residue 40 VAL Chi-restraints excluded: chain V residue 48 ASN Chi-restraints excluded: chain V residue 70 VAL Chi-restraints excluded: chain V residue 94 SER Chi-restraints excluded: chain W residue 13 ARG Chi-restraints excluded: chain W residue 31 VAL Chi-restraints excluded: chain W residue 41 ILE Chi-restraints excluded: chain W residue 43 PHE Chi-restraints excluded: chain W residue 71 ASN Chi-restraints excluded: chain W residue 80 ASP Chi-restraints excluded: chain W residue 94 VAL Chi-restraints excluded: chain X residue 34 SER Chi-restraints excluded: chain X residue 40 VAL Chi-restraints excluded: chain X residue 66 ASP Chi-restraints excluded: chain X residue 67 THR Chi-restraints excluded: chain X residue 73 ASP Chi-restraints excluded: chain X residue 88 VAL Chi-restraints excluded: chain Y residue 8 THR Chi-restraints excluded: chain Y residue 12 THR Chi-restraints excluded: chain Y residue 14 SER Chi-restraints excluded: chain Y residue 16 ASN Chi-restraints excluded: chain Y residue 22 MET Chi-restraints excluded: chain Y residue 25 THR Chi-restraints excluded: chain Y residue 36 VAL Chi-restraints excluded: chain Y residue 55 LYS Chi-restraints excluded: chain Z residue 30 PHE Chi-restraints excluded: chain Z residue 32 LEU Chi-restraints excluded: chain Z residue 45 GLU Chi-restraints excluded: chain 0 residue 13 ILE Chi-restraints excluded: chain 0 residue 22 THR Chi-restraints excluded: chain 0 residue 43 ILE Chi-restraints excluded: chain 0 residue 47 VAL Chi-restraints excluded: chain 0 residue 53 LEU Chi-restraints excluded: chain 0 residue 56 VAL Chi-restraints excluded: chain 1 residue 13 VAL Chi-restraints excluded: chain 1 residue 23 PHE Chi-restraints excluded: chain 1 residue 25 SER Chi-restraints excluded: chain 2 residue 3 VAL Chi-restraints excluded: chain 2 residue 6 ARG Chi-restraints excluded: chain 2 residue 9 SER Chi-restraints excluded: chain 2 residue 18 THR Chi-restraints excluded: chain 3 residue 5 ILE Chi-restraints excluded: chain 3 residue 8 GLU Chi-restraints excluded: chain 3 residue 11 SER Chi-restraints excluded: chain 3 residue 39 GLU Chi-restraints excluded: chain 3 residue 44 LEU Chi-restraints excluded: chain 4 residue 5 TYR Chi-restraints excluded: chain 4 residue 24 THR Chi-restraints excluded: chain 4 residue 42 ILE Chi-restraints excluded: chain 4 residue 43 SER Chi-restraints excluded: chain 5 residue 14 VAL Chi-restraints excluded: chain 5 residue 54 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 954 random chunks: chunk 568 optimal weight: 50.0000 chunk 367 optimal weight: 20.0000 chunk 549 optimal weight: 10.0000 chunk 276 optimal weight: 20.0000 chunk 180 optimal weight: 10.0000 chunk 178 optimal weight: 7.9990 chunk 584 optimal weight: 10.0000 chunk 626 optimal weight: 10.0000 chunk 454 optimal weight: 10.0000 chunk 85 optimal weight: 10.0000 chunk 722 optimal weight: 9.9990 overall best weight: 9.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 22 HIS ** j 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 18 ASN t 24 GLN C 35 GLN ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 ASN D 191 ASN ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 115 HIS ** G 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 35 GLN P 20 ASN ** P 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 66 ASN ** 2 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.106 150747 Z= 0.456 Angle : 0.814 15.643 226044 Z= 0.409 Chirality : 0.045 0.363 28980 Planarity : 0.006 0.101 11734 Dihedral : 23.370 178.563 76706 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 16.48 Ramachandran Plot: Outliers : 0.17 % Allowed : 14.91 % Favored : 84.91 % Rotamer: Outliers : 11.89 % Allowed : 26.80 % Favored : 61.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.28 % Twisted Proline : 0.52 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.17 (0.11), residues: 5143 helix: -0.58 (0.14), residues: 1429 sheet: -1.98 (0.17), residues: 897 loop : -3.10 (0.10), residues: 2817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP N 93 HIS 0.008 0.001 HIS l 109 PHE 0.025 0.002 PHE l 31 TYR 0.099 0.003 TYR D 53 ARG 0.014 0.001 ARG N 6 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10286 Ramachandran restraints generated. 5143 Oldfield, 0 Emsley, 5143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10286 Ramachandran restraints generated. 5143 Oldfield, 0 Emsley, 5143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1406 residues out of total 4391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 522 poor density : 884 time to evaluate : 6.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 10 MET cc_start: 0.8955 (mmm) cc_final: 0.8610 (mmt) REVERT: c 16 ARG cc_start: 0.8534 (OUTLIER) cc_final: 0.8040 (tmm160) REVERT: c 17 ASP cc_start: 0.9124 (p0) cc_final: 0.8578 (p0) REVERT: c 40 LYS cc_start: 0.9357 (OUTLIER) cc_final: 0.8944 (tmmm) REVERT: c 55 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7339 (mp0) REVERT: c 82 GLU cc_start: 0.9237 (OUTLIER) cc_final: 0.8763 (mp0) REVERT: c 141 MET cc_start: 0.8105 (mmm) cc_final: 0.7638 (mmm) REVERT: d 45 SER cc_start: 0.7367 (OUTLIER) cc_final: 0.7030 (p) REVERT: d 71 LEU cc_start: 0.9355 (OUTLIER) cc_final: 0.8996 (tt) REVERT: d 88 MET cc_start: 0.8950 (mmm) cc_final: 0.8717 (mmm) REVERT: d 162 ARG cc_start: 0.7372 (OUTLIER) cc_final: 0.7162 (mmt-90) REVERT: d 201 GLN cc_start: 0.7987 (mt0) cc_final: 0.7680 (mt0) REVERT: f 4 ASP cc_start: 0.7811 (m-30) cc_final: 0.7452 (t0) REVERT: f 30 ASP cc_start: 0.9052 (OUTLIER) cc_final: 0.8633 (t0) REVERT: f 39 GLU cc_start: 0.8355 (mt-10) cc_final: 0.7940 (tm-30) REVERT: f 55 MET cc_start: 0.8839 (mmm) cc_final: 0.8342 (mmm) REVERT: f 82 ARG cc_start: 0.9055 (ttp80) cc_final: 0.8744 (ttt90) REVERT: g 24 THR cc_start: 0.8581 (OUTLIER) cc_final: 0.8322 (p) REVERT: g 31 MET cc_start: 0.8667 (ttp) cc_final: 0.8231 (ttt) REVERT: g 51 LYS cc_start: 0.8777 (OUTLIER) cc_final: 0.8310 (tmmt) REVERT: g 66 MET cc_start: 0.8283 (tpp) cc_final: 0.7811 (tmm) REVERT: g 86 GLN cc_start: 0.7904 (pt0) cc_final: 0.7614 (mp10) REVERT: g 116 MET cc_start: 0.8262 (OUTLIER) cc_final: 0.7950 (mmp) REVERT: g 126 ASP cc_start: 0.8551 (m-30) cc_final: 0.8282 (m-30) REVERT: h 7 ILE cc_start: 0.9065 (OUTLIER) cc_final: 0.8848 (mt) REVERT: h 54 ASP cc_start: 0.8476 (p0) cc_final: 0.8145 (p0) REVERT: h 71 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7594 (mp0) REVERT: i 14 ASN cc_start: 0.8697 (OUTLIER) cc_final: 0.8356 (t0) REVERT: i 110 MET cc_start: 0.8327 (mtp) cc_final: 0.8087 (mtm) REVERT: i 112 GLU cc_start: 0.8854 (tp30) cc_final: 0.8374 (tp30) REVERT: j 47 SER cc_start: 0.9570 (m) cc_final: 0.9298 (p) REVERT: j 66 GLU cc_start: 0.8713 (pt0) cc_final: 0.8290 (pt0) REVERT: k 14 LYS cc_start: 0.9146 (ttpp) cc_final: 0.8941 (ttpp) REVERT: k 87 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.8310 (mmmm) REVERT: k 105 LEU cc_start: 0.8863 (mt) cc_final: 0.8156 (mp) REVERT: l 39 ASN cc_start: 0.8868 (OUTLIER) cc_final: 0.8555 (p0) REVERT: l 86 ASN cc_start: 0.9384 (p0) cc_final: 0.8969 (p0) REVERT: m 13 LYS cc_start: 0.8612 (OUTLIER) cc_final: 0.8407 (mmmm) REVERT: m 54 ASP cc_start: 0.8864 (m-30) cc_final: 0.8502 (m-30) REVERT: n 25 GLU cc_start: 0.8813 (mm-30) cc_final: 0.8467 (mm-30) REVERT: n 27 CYS cc_start: 0.6332 (OUTLIER) cc_final: 0.6108 (p) REVERT: n 35 ARG cc_start: 0.8524 (OUTLIER) cc_final: 0.7956 (ptm-80) REVERT: o 41 GLU cc_start: 0.8881 (mm-30) cc_final: 0.8274 (mm-30) REVERT: o 44 ARG cc_start: 0.8280 (mtm180) cc_final: 0.7844 (mtm180) REVERT: o 45 THR cc_start: 0.8837 (m) cc_final: 0.8623 (p) REVERT: p 10 MET cc_start: 0.8758 (OUTLIER) cc_final: 0.8327 (mtp) REVERT: p 80 MET cc_start: 0.8755 (mtp) cc_final: 0.8455 (mtp) REVERT: q 40 ARG cc_start: 0.8506 (mmm160) cc_final: 0.8301 (mmm160) REVERT: q 52 GLU cc_start: 0.8705 (mp0) cc_final: 0.8325 (mp0) REVERT: q 53 ASN cc_start: 0.9161 (OUTLIER) cc_final: 0.8958 (p0) REVERT: r 26 ASP cc_start: 0.8623 (t0) cc_final: 0.8215 (t70) REVERT: s 12 ASP cc_start: 0.8042 (m-30) cc_final: 0.7760 (m-30) REVERT: s 14 HIS cc_start: 0.8073 (OUTLIER) cc_final: 0.7326 (p-80) REVERT: s 40 ILE cc_start: 0.8545 (mm) cc_final: 0.8121 (mt) REVERT: s 73 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7048 (tm-30) REVERT: t 44 ASP cc_start: 0.8375 (t0) cc_final: 0.7930 (p0) REVERT: C 123 ASP cc_start: 0.8628 (t0) cc_final: 0.8217 (t0) REVERT: C 180 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7694 (pm20) REVERT: C 274 ARG cc_start: 0.8107 (tpt90) cc_final: 0.7798 (tpt90) REVERT: D 168 ARG cc_start: 0.9115 (OUTLIER) cc_final: 0.8364 (ptm160) REVERT: E 46 GLN cc_start: 0.8381 (OUTLIER) cc_final: 0.7981 (tt0) REVERT: E 67 GLN cc_start: 0.8703 (tp40) cc_final: 0.8195 (tp-100) REVERT: E 74 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.8187 (mtm180) REVERT: F 120 LYS cc_start: 0.9147 (mttt) cc_final: 0.8910 (tptp) REVERT: G 52 PHE cc_start: 0.6902 (OUTLIER) cc_final: 0.6055 (t80) REVERT: G 89 LEU cc_start: 0.9293 (OUTLIER) cc_final: 0.8927 (tt) REVERT: G 94 TYR cc_start: 0.8397 (m-80) cc_final: 0.8139 (m-80) REVERT: G 99 GLN cc_start: 0.8621 (pp30) cc_final: 0.8309 (pp30) REVERT: G 130 GLN cc_start: 0.8105 (OUTLIER) cc_final: 0.7560 (mp-120) REVERT: K 103 GLU cc_start: 0.8434 (mt-10) cc_final: 0.8020 (mt-10) REVERT: K 119 GLN cc_start: 0.9040 (OUTLIER) cc_final: 0.8528 (mt0) REVERT: L 2 ILE cc_start: 0.8798 (mt) cc_final: 0.8487 (tp) REVERT: L 13 ASN cc_start: 0.9053 (t0) cc_final: 0.8552 (p0) REVERT: N 1 MET cc_start: 0.1082 (mmm) cc_final: 0.0065 (mmm) REVERT: N 58 MET cc_start: 0.9185 (ttm) cc_final: 0.8931 (ttm) REVERT: N 65 TRP cc_start: 0.8357 (OUTLIER) cc_final: 0.6744 (m100) REVERT: N 134 ARG cc_start: 0.8119 (OUTLIER) cc_final: 0.7369 (ttt90) REVERT: O 24 LEU cc_start: 0.9311 (OUTLIER) cc_final: 0.8835 (tp) REVERT: O 41 ARG cc_start: 0.8095 (OUTLIER) cc_final: 0.6893 (ppt90) REVERT: O 46 LYS cc_start: 0.9128 (tttt) cc_final: 0.8504 (tptp) REVERT: O 96 ARG cc_start: 0.8648 (OUTLIER) cc_final: 0.7916 (ttm170) REVERT: O 125 PHE cc_start: 0.8707 (OUTLIER) cc_final: 0.7294 (m-10) REVERT: P 27 GLU cc_start: 0.8721 (tm-30) cc_final: 0.8496 (tm-30) REVERT: P 30 ARG cc_start: 0.8841 (OUTLIER) cc_final: 0.8360 (ttm170) REVERT: P 62 GLU cc_start: 0.7317 (OUTLIER) cc_final: 0.7004 (mm-30) REVERT: Q 39 ARG cc_start: 0.8365 (OUTLIER) cc_final: 0.7066 (ttm170) REVERT: Q 106 LYS cc_start: 0.8951 (mtpt) cc_final: 0.8037 (mtpt) REVERT: Q 111 LYS cc_start: 0.9285 (mttt) cc_final: 0.9007 (mtpt) REVERT: Q 113 ILE cc_start: 0.8809 (tp) cc_final: 0.8602 (tt) REVERT: R 89 ASP cc_start: 0.7726 (p0) cc_final: 0.7441 (p0) REVERT: S 1 MET cc_start: 0.8747 (OUTLIER) cc_final: 0.7991 (ttt) REVERT: S 2 TYR cc_start: 0.8332 (t80) cc_final: 0.7998 (t80) REVERT: S 6 LYS cc_start: 0.8659 (mttt) cc_final: 0.8214 (mttt) REVERT: S 37 GLU cc_start: 0.7966 (mt-10) cc_final: 0.7622 (mt-10) REVERT: S 81 HIS cc_start: 0.8570 (OUTLIER) cc_final: 0.7830 (m-70) REVERT: S 96 MET cc_start: 0.8958 (tmm) cc_final: 0.8644 (tmm) REVERT: T 67 PHE cc_start: 0.7937 (OUTLIER) cc_final: 0.6285 (p90) REVERT: U 5 ASP cc_start: 0.8286 (m-30) cc_final: 0.7830 (t0) REVERT: U 7 ILE cc_start: 0.9087 (OUTLIER) cc_final: 0.8840 (mt) REVERT: V 1 MET cc_start: 0.7681 (OUTLIER) cc_final: 0.7414 (mmm) REVERT: V 7 ASP cc_start: 0.8222 (m-30) cc_final: 0.7999 (m-30) REVERT: V 20 GLU cc_start: 0.8808 (mt-10) cc_final: 0.8308 (mp0) REVERT: V 53 GLN cc_start: 0.8821 (mt0) cc_final: 0.8313 (mm-40) REVERT: W 80 ASP cc_start: 0.5414 (OUTLIER) cc_final: 0.4985 (m-30) REVERT: W 86 MET cc_start: 0.5413 (mtm) cc_final: 0.4614 (ptp) REVERT: Y 22 MET cc_start: 0.7307 (OUTLIER) cc_final: 0.7051 (mmm) REVERT: Y 30 LYS cc_start: 0.9179 (mtmt) cc_final: 0.8957 (mttm) REVERT: Z 22 LYS cc_start: 0.9404 (mmmm) cc_final: 0.8971 (tptp) REVERT: Z 24 GLU cc_start: 0.8710 (tm-30) cc_final: 0.8396 (tm-30) REVERT: Z 28 LEU cc_start: 0.8603 (mt) cc_final: 0.8206 (mp) REVERT: Z 29 ARG cc_start: 0.8795 (mtm-85) cc_final: 0.8587 (mtp-110) REVERT: 0 30 LYS cc_start: 0.9094 (mmmt) cc_final: 0.8667 (mmmt) REVERT: 0 41 GLU cc_start: 0.8825 (tp30) cc_final: 0.8486 (tp30) REVERT: 1 12 VAL cc_start: 0.9158 (OUTLIER) cc_final: 0.8702 (p) REVERT: 1 14 PHE cc_start: 0.7645 (m-80) cc_final: 0.7261 (m-80) REVERT: 1 34 THR cc_start: 0.7000 (p) cc_final: 0.6758 (p) REVERT: 1 43 TYR cc_start: 0.7625 (m-80) cc_final: 0.7234 (m-10) REVERT: 1 54 SER cc_start: 0.8576 (m) cc_final: 0.8365 (p) REVERT: 1 73 ARG cc_start: 0.7978 (tmt170) cc_final: 0.7745 (ttt180) REVERT: 1 76 LYS cc_start: 0.9495 (tttt) cc_final: 0.9195 (tptt) REVERT: 2 6 ARG cc_start: 0.8717 (OUTLIER) cc_final: 0.7868 (tpm-80) REVERT: 3 41 LYS cc_start: 0.8770 (tppt) cc_final: 0.8392 (ptpp) REVERT: 3 44 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8263 (tm) REVERT: 6 24 MET cc_start: 0.8524 (mmm) cc_final: 0.8240 (mmt) outliers start: 522 outliers final: 415 residues processed: 1267 average time/residue: 1.1577 time to fit residues: 2572.1530 Evaluate side-chains 1332 residues out of total 4391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 465 poor density : 867 time to evaluate : 7.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 15 ILE Chi-restraints excluded: chain c residue 16 ARG Chi-restraints excluded: chain c residue 40 LYS Chi-restraints excluded: chain c residue 42 ILE Chi-restraints excluded: chain c residue 55 GLU Chi-restraints excluded: chain c residue 82 GLU Chi-restraints excluded: chain c residue 85 ASN Chi-restraints excluded: chain c residue 98 VAL Chi-restraints excluded: chain c residue 127 VAL Chi-restraints excluded: chain c residue 176 THR Chi-restraints excluded: chain c residue 200 TRP Chi-restraints excluded: chain d residue 4 TYR Chi-restraints excluded: chain d residue 45 SER Chi-restraints excluded: chain d residue 57 LEU Chi-restraints excluded: chain d residue 60 MET Chi-restraints excluded: chain d residue 64 ASN Chi-restraints excluded: chain d residue 71 LEU Chi-restraints excluded: chain d residue 107 THR Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 136 VAL Chi-restraints excluded: chain d residue 162 ARG Chi-restraints excluded: chain d residue 184 ASP Chi-restraints excluded: chain d residue 195 VAL Chi-restraints excluded: chain e residue 3 TYR Chi-restraints excluded: chain e residue 9 LEU Chi-restraints excluded: chain e residue 22 THR Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 42 LYS Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 72 VAL Chi-restraints excluded: chain e residue 105 VAL Chi-restraints excluded: chain e residue 114 VAL Chi-restraints excluded: chain e residue 125 SER Chi-restraints excluded: chain e residue 127 SER Chi-restraints excluded: chain e residue 131 ASN Chi-restraints excluded: chain e residue 132 THR Chi-restraints excluded: chain e residue 144 LEU Chi-restraints excluded: chain e residue 159 LYS Chi-restraints excluded: chain f residue 11 TYR Chi-restraints excluded: chain f residue 13 ILE Chi-restraints excluded: chain f residue 18 ASP Chi-restraints excluded: chain f residue 30 ASP Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 50 ARG Chi-restraints excluded: chain f residue 54 GLU Chi-restraints excluded: chain f residue 56 ASN Chi-restraints excluded: chain f residue 65 ILE Chi-restraints excluded: chain f residue 66 VAL Chi-restraints excluded: chain f residue 67 ASN Chi-restraints excluded: chain f residue 98 VAL Chi-restraints excluded: chain g residue 19 ASN Chi-restraints excluded: chain g residue 24 THR Chi-restraints excluded: chain g residue 51 LYS Chi-restraints excluded: chain g residue 75 VAL Chi-restraints excluded: chain g residue 87 VAL Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain g residue 116 MET Chi-restraints excluded: chain h residue 7 ILE Chi-restraints excluded: chain h residue 14 ILE Chi-restraints excluded: chain h residue 20 VAL Chi-restraints excluded: chain h residue 22 HIS Chi-restraints excluded: chain h residue 32 ILE Chi-restraints excluded: chain h residue 46 ILE Chi-restraints excluded: chain h residue 59 VAL Chi-restraints excluded: chain h residue 60 ILE Chi-restraints excluded: chain h residue 69 ASN Chi-restraints excluded: chain h residue 71 GLU Chi-restraints excluded: chain h residue 74 ILE Chi-restraints excluded: chain h residue 89 VAL Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 98 LEU Chi-restraints excluded: chain h residue 103 ILE Chi-restraints excluded: chain h residue 112 VAL Chi-restraints excluded: chain h residue 127 VAL Chi-restraints excluded: chain i residue 9 THR Chi-restraints excluded: chain i residue 12 ARG Chi-restraints excluded: chain i residue 14 ASN Chi-restraints excluded: chain i residue 22 VAL Chi-restraints excluded: chain i residue 30 VAL Chi-restraints excluded: chain i residue 34 ASP Chi-restraints excluded: chain i residue 57 THR Chi-restraints excluded: chain i residue 66 ASN Chi-restraints excluded: chain i residue 88 LEU Chi-restraints excluded: chain i residue 91 ASP Chi-restraints excluded: chain i residue 93 ASP Chi-restraints excluded: chain j residue 51 VAL Chi-restraints excluded: chain j residue 74 ILE Chi-restraints excluded: chain j residue 90 LEU Chi-restraints excluded: chain j residue 96 VAL Chi-restraints excluded: chain j residue 98 ILE Chi-restraints excluded: chain k residue 26 THR Chi-restraints excluded: chain k residue 35 THR Chi-restraints excluded: chain k residue 46 SER Chi-restraints excluded: chain k residue 55 SER Chi-restraints excluded: chain k residue 59 THR Chi-restraints excluded: chain k residue 65 MET Chi-restraints excluded: chain k residue 73 VAL Chi-restraints excluded: chain k residue 76 GLU Chi-restraints excluded: chain k residue 87 LYS Chi-restraints excluded: chain k residue 91 SER Chi-restraints excluded: chain k residue 97 ILE Chi-restraints excluded: chain k residue 99 SER Chi-restraints excluded: chain k residue 119 ASN Chi-restraints excluded: chain l residue 4 ILE Chi-restraints excluded: chain l residue 20 ASP Chi-restraints excluded: chain l residue 30 SER Chi-restraints excluded: chain l residue 32 LYS Chi-restraints excluded: chain l residue 34 THR Chi-restraints excluded: chain l residue 39 ASN Chi-restraints excluded: chain l residue 40 SER Chi-restraints excluded: chain l residue 50 VAL Chi-restraints excluded: chain l residue 72 ASN Chi-restraints excluded: chain l residue 76 VAL Chi-restraints excluded: chain l residue 83 ILE Chi-restraints excluded: chain l residue 95 LEU Chi-restraints excluded: chain l residue 102 ASP Chi-restraints excluded: chain l residue 107 ARG Chi-restraints excluded: chain l residue 115 LEU Chi-restraints excluded: chain l residue 124 LYS Chi-restraints excluded: chain l residue 126 SER Chi-restraints excluded: chain l residue 132 THR Chi-restraints excluded: chain m residue 4 ILE Chi-restraints excluded: chain m residue 9 ILE Chi-restraints excluded: chain m residue 13 LYS Chi-restraints excluded: chain m residue 28 THR Chi-restraints excluded: chain m residue 45 VAL Chi-restraints excluded: chain m residue 60 ILE Chi-restraints excluded: chain m residue 75 LEU Chi-restraints excluded: chain m residue 77 ILE Chi-restraints excluded: chain m residue 81 MET Chi-restraints excluded: chain m residue 101 ASN Chi-restraints excluded: chain n residue 7 ILE Chi-restraints excluded: chain n residue 18 THR Chi-restraints excluded: chain n residue 27 CYS Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain n residue 35 ARG Chi-restraints excluded: chain n residue 41 ARG Chi-restraints excluded: chain n residue 57 LYS Chi-restraints excluded: chain o residue 11 ILE Chi-restraints excluded: chain o residue 24 SER Chi-restraints excluded: chain o residue 46 HIS Chi-restraints excluded: chain o residue 52 SER Chi-restraints excluded: chain o residue 73 THR Chi-restraints excluded: chain o residue 80 GLU Chi-restraints excluded: chain o residue 89 ARG Chi-restraints excluded: chain p residue 3 VAL Chi-restraints excluded: chain p residue 5 ILE Chi-restraints excluded: chain p residue 10 MET Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain p residue 39 THR Chi-restraints excluded: chain p residue 84 HIS Chi-restraints excluded: chain q residue 5 ARG Chi-restraints excluded: chain q residue 7 GLN Chi-restraints excluded: chain q residue 17 SER Chi-restraints excluded: chain q residue 21 ASP Chi-restraints excluded: chain q residue 23 THR Chi-restraints excluded: chain q residue 27 VAL Chi-restraints excluded: chain q residue 44 SER Chi-restraints excluded: chain q residue 53 ASN Chi-restraints excluded: chain q residue 54 ASN Chi-restraints excluded: chain q residue 58 VAL Chi-restraints excluded: chain q residue 78 LEU Chi-restraints excluded: chain r residue 16 TYR Chi-restraints excluded: chain r residue 25 ILE Chi-restraints excluded: chain r residue 29 ASP Chi-restraints excluded: chain r residue 30 THR Chi-restraints excluded: chain r residue 33 LEU Chi-restraints excluded: chain r residue 46 ARG Chi-restraints excluded: chain r residue 51 THR Chi-restraints excluded: chain r residue 63 ILE Chi-restraints excluded: chain s residue 7 LYS Chi-restraints excluded: chain s residue 14 HIS Chi-restraints excluded: chain s residue 30 VAL Chi-restraints excluded: chain s residue 33 THR Chi-restraints excluded: chain s residue 48 THR Chi-restraints excluded: chain s residue 65 ASP Chi-restraints excluded: chain s residue 73 GLU Chi-restraints excluded: chain t residue 4 ILE Chi-restraints excluded: chain t residue 8 ILE Chi-restraints excluded: chain t residue 23 SER Chi-restraints excluded: chain t residue 30 THR Chi-restraints excluded: chain t residue 65 LEU Chi-restraints excluded: chain t residue 78 LEU Chi-restraints excluded: chain t residue 81 LEU Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 15 ASN Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 20 ASP Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 45 ASN Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 53 HIS Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 134 ASN Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 171 TYR Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 194 SER Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 225 MET Chi-restraints excluded: chain C residue 228 ASN Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain D residue 12 MET Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 130 ARG Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 167 ASP Chi-restraints excluded: chain D residue 168 ARG Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 184 ASN Chi-restraints excluded: chain D residue 188 ILE Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain E residue 7 PHE Chi-restraints excluded: chain E residue 8 LYS Chi-restraints excluded: chain E residue 10 ASP Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain E residue 46 GLN Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 74 ARG Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 84 ARG Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 121 ASN Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 177 THR Chi-restraints excluded: chain E residue 179 ASP Chi-restraints excluded: chain E residue 195 THR Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 123 ASP Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 43 MET Chi-restraints excluded: chain G residue 52 PHE Chi-restraints excluded: chain G residue 65 HIS Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 128 ASN Chi-restraints excluded: chain G residue 130 GLN Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 23 ASP Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 41 ASN Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 50 ASP Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 80 MET Chi-restraints excluded: chain K residue 85 LEU Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 113 ASN Chi-restraints excluded: chain K residue 115 LEU Chi-restraints excluded: chain K residue 119 GLN Chi-restraints excluded: chain K residue 142 ASP Chi-restraints excluded: chain L residue 6 SER Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 73 ASP Chi-restraints excluded: chain L residue 90 ASP Chi-restraints excluded: chain L residue 92 SER Chi-restraints excluded: chain L residue 110 ASN Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain M residue 3 LEU Chi-restraints excluded: chain M residue 18 ARG Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain M residue 73 ASP Chi-restraints excluded: chain M residue 76 VAL Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 79 LEU Chi-restraints excluded: chain M residue 89 THR Chi-restraints excluded: chain M residue 95 VAL Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain M residue 97 LYS Chi-restraints excluded: chain M residue 103 LYS Chi-restraints excluded: chain M residue 117 LEU Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 65 TRP Chi-restraints excluded: chain N residue 68 ILE Chi-restraints excluded: chain N residue 79 ILE Chi-restraints excluded: chain N residue 116 GLU Chi-restraints excluded: chain N residue 120 LEU Chi-restraints excluded: chain N residue 127 VAL Chi-restraints excluded: chain N residue 133 LYS Chi-restraints excluded: chain N residue 134 ARG Chi-restraints excluded: chain O residue 6 LEU Chi-restraints excluded: chain O residue 24 LEU Chi-restraints excluded: chain O residue 26 ILE Chi-restraints excluded: chain O residue 27 ASN Chi-restraints excluded: chain O residue 41 ARG Chi-restraints excluded: chain O residue 42 SER Chi-restraints excluded: chain O residue 56 LEU Chi-restraints excluded: chain O residue 70 VAL Chi-restraints excluded: chain O residue 75 GLU Chi-restraints excluded: chain O residue 81 VAL Chi-restraints excluded: chain O residue 89 LEU Chi-restraints excluded: chain O residue 96 ARG Chi-restraints excluded: chain O residue 104 TYR Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain O residue 114 ARG Chi-restraints excluded: chain O residue 121 VAL Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain O residue 123 ILE Chi-restraints excluded: chain O residue 125 PHE Chi-restraints excluded: chain O residue 126 VAL Chi-restraints excluded: chain P residue 3 THR Chi-restraints excluded: chain P residue 6 ASP Chi-restraints excluded: chain P residue 30 ARG Chi-restraints excluded: chain P residue 31 LEU Chi-restraints excluded: chain P residue 39 ASN Chi-restraints excluded: chain P residue 40 ILE Chi-restraints excluded: chain P residue 62 GLU Chi-restraints excluded: chain P residue 71 THR Chi-restraints excluded: chain P residue 101 HIS Chi-restraints excluded: chain Q residue 8 LEU Chi-restraints excluded: chain Q residue 15 THR Chi-restraints excluded: chain Q residue 16 ASP Chi-restraints excluded: chain Q residue 24 ASP Chi-restraints excluded: chain Q residue 26 VAL Chi-restraints excluded: chain Q residue 32 VAL Chi-restraints excluded: chain Q residue 39 ARG Chi-restraints excluded: chain Q residue 48 ILE Chi-restraints excluded: chain Q residue 68 VAL Chi-restraints excluded: chain Q residue 73 THR Chi-restraints excluded: chain Q residue 76 LEU Chi-restraints excluded: chain Q residue 110 ILE Chi-restraints excluded: chain R residue 9 VAL Chi-restraints excluded: chain R residue 20 LEU Chi-restraints excluded: chain R residue 29 HIS Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 34 SER Chi-restraints excluded: chain R residue 85 LEU Chi-restraints excluded: chain R residue 90 ILE Chi-restraints excluded: chain R residue 102 ASP Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 27 VAL Chi-restraints excluded: chain S residue 33 VAL Chi-restraints excluded: chain S residue 81 HIS Chi-restraints excluded: chain T residue 6 THR Chi-restraints excluded: chain T residue 29 ILE Chi-restraints excluded: chain T residue 67 PHE Chi-restraints excluded: chain T residue 86 THR Chi-restraints excluded: chain T residue 101 ILE Chi-restraints excluded: chain T residue 102 ASN Chi-restraints excluded: chain U residue 6 VAL Chi-restraints excluded: chain U residue 7 ILE Chi-restraints excluded: chain U residue 11 VAL Chi-restraints excluded: chain U residue 31 THR Chi-restraints excluded: chain U residue 43 GLU Chi-restraints excluded: chain U residue 47 ASP Chi-restraints excluded: chain U residue 53 VAL Chi-restraints excluded: chain U residue 80 VAL Chi-restraints excluded: chain V residue 1 MET Chi-restraints excluded: chain V residue 12 ILE Chi-restraints excluded: chain V residue 31 ASP Chi-restraints excluded: chain V residue 35 VAL Chi-restraints excluded: chain V residue 40 VAL Chi-restraints excluded: chain V residue 48 ASN Chi-restraints excluded: chain V residue 70 VAL Chi-restraints excluded: chain V residue 94 SER Chi-restraints excluded: chain W residue 13 ARG Chi-restraints excluded: chain W residue 31 VAL Chi-restraints excluded: chain W residue 41 ILE Chi-restraints excluded: chain W residue 43 PHE Chi-restraints excluded: chain W residue 71 ASN Chi-restraints excluded: chain W residue 80 ASP Chi-restraints excluded: chain W residue 94 VAL Chi-restraints excluded: chain X residue 34 SER Chi-restraints excluded: chain X residue 40 VAL Chi-restraints excluded: chain X residue 60 VAL Chi-restraints excluded: chain X residue 66 ASP Chi-restraints excluded: chain X residue 67 THR Chi-restraints excluded: chain X residue 73 ASP Chi-restraints excluded: chain X residue 88 VAL Chi-restraints excluded: chain Y residue 8 THR Chi-restraints excluded: chain Y residue 12 THR Chi-restraints excluded: chain Y residue 14 SER Chi-restraints excluded: chain Y residue 16 ASN Chi-restraints excluded: chain Y residue 22 MET Chi-restraints excluded: chain Y residue 25 THR Chi-restraints excluded: chain Y residue 36 VAL Chi-restraints excluded: chain Y residue 55 LYS Chi-restraints excluded: chain Z residue 30 PHE Chi-restraints excluded: chain Z residue 32 LEU Chi-restraints excluded: chain Z residue 45 GLU Chi-restraints excluded: chain 0 residue 13 ILE Chi-restraints excluded: chain 0 residue 22 THR Chi-restraints excluded: chain 0 residue 43 ILE Chi-restraints excluded: chain 0 residue 47 VAL Chi-restraints excluded: chain 0 residue 53 LEU Chi-restraints excluded: chain 0 residue 56 VAL Chi-restraints excluded: chain 1 residue 12 VAL Chi-restraints excluded: chain 1 residue 13 VAL Chi-restraints excluded: chain 1 residue 23 PHE Chi-restraints excluded: chain 1 residue 25 SER Chi-restraints excluded: chain 2 residue 3 VAL Chi-restraints excluded: chain 2 residue 6 ARG Chi-restraints excluded: chain 2 residue 9 SER Chi-restraints excluded: chain 2 residue 18 THR Chi-restraints excluded: chain 3 residue 5 ILE Chi-restraints excluded: chain 3 residue 8 GLU Chi-restraints excluded: chain 3 residue 11 SER Chi-restraints excluded: chain 3 residue 39 GLU Chi-restraints excluded: chain 3 residue 44 LEU Chi-restraints excluded: chain 4 residue 5 TYR Chi-restraints excluded: chain 4 residue 24 THR Chi-restraints excluded: chain 4 residue 42 ILE Chi-restraints excluded: chain 4 residue 43 SER Chi-restraints excluded: chain 5 residue 14 VAL Chi-restraints excluded: chain 5 residue 54 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 954 random chunks: chunk 836 optimal weight: 5.9990 chunk 880 optimal weight: 0.6980 chunk 803 optimal weight: 6.9990 chunk 856 optimal weight: 7.9990 chunk 515 optimal weight: 10.0000 chunk 373 optimal weight: 10.0000 chunk 672 optimal weight: 4.9990 chunk 262 optimal weight: 0.3980 chunk 774 optimal weight: 3.9990 chunk 810 optimal weight: 0.7980 chunk 853 optimal weight: 0.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 97 ASN ** j 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 46 HIS q 34 HIS ** q 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 24 GLN C 35 GLN ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 ASN D 191 ASN E 160 ASN F 49 ASN F 135 GLN F 172 GLN G 44 ASN N 35 GLN P 20 ASN ** P 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 29 HIS R 38 GLN ** R 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 90 GLN Y 23 ASN 0 52 HIS ** 1 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 150747 Z= 0.140 Angle : 0.599 14.706 226044 Z= 0.308 Chirality : 0.034 0.305 28980 Planarity : 0.005 0.093 11734 Dihedral : 23.149 179.578 76703 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.66 % Favored : 90.18 % Rotamer: Outliers : 7.65 % Allowed : 31.09 % Favored : 61.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.28 % Twisted Proline : 0.52 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.68 (0.11), residues: 5143 helix: -0.06 (0.14), residues: 1445 sheet: -1.73 (0.17), residues: 899 loop : -2.86 (0.11), residues: 2799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 65 HIS 0.009 0.001 HIS k 118 PHE 0.016 0.001 PHE f 80 TYR 0.053 0.002 TYR D 53 ARG 0.014 0.001 ARG C 273 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10286 Ramachandran restraints generated. 5143 Oldfield, 0 Emsley, 5143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10286 Ramachandran restraints generated. 5143 Oldfield, 0 Emsley, 5143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1327 residues out of total 4391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 336 poor density : 991 time to evaluate : 6.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 10 MET cc_start: 0.8968 (mmm) cc_final: 0.8610 (mmt) REVERT: c 17 ASP cc_start: 0.9120 (p0) cc_final: 0.8523 (p0) REVERT: c 40 LYS cc_start: 0.9365 (OUTLIER) cc_final: 0.8926 (tmmm) REVERT: c 55 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7368 (tm-30) REVERT: c 82 GLU cc_start: 0.9245 (OUTLIER) cc_final: 0.8750 (mp0) REVERT: c 141 MET cc_start: 0.7856 (mmm) cc_final: 0.7377 (mmm) REVERT: c 168 SER cc_start: 0.8115 (p) cc_final: 0.7515 (t) REVERT: c 200 TRP cc_start: 0.7805 (OUTLIER) cc_final: 0.6215 (m100) REVERT: d 71 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.8688 (tt) REVERT: d 88 MET cc_start: 0.8976 (mmm) cc_final: 0.8734 (mmm) REVERT: d 94 ARG cc_start: 0.8390 (OUTLIER) cc_final: 0.7767 (ptm-80) REVERT: f 4 ASP cc_start: 0.7720 (m-30) cc_final: 0.7349 (t0) REVERT: f 39 GLU cc_start: 0.8344 (mt-10) cc_final: 0.7871 (tm-30) REVERT: f 50 ARG cc_start: 0.7291 (OUTLIER) cc_final: 0.6036 (tmm-80) REVERT: f 55 MET cc_start: 0.8634 (mmm) cc_final: 0.8196 (mmm) REVERT: f 59 ARG cc_start: 0.8070 (mmm-85) cc_final: 0.7413 (mmm160) REVERT: f 72 SER cc_start: 0.9319 (p) cc_final: 0.9021 (m) REVERT: f 82 ARG cc_start: 0.8972 (ttp80) cc_final: 0.8668 (ttt90) REVERT: g 31 MET cc_start: 0.8685 (ttp) cc_final: 0.8164 (ttt) REVERT: g 66 MET cc_start: 0.8436 (tpp) cc_final: 0.8226 (tpp) REVERT: g 86 GLN cc_start: 0.7950 (pt0) cc_final: 0.7710 (mp10) REVERT: g 116 MET cc_start: 0.7934 (OUTLIER) cc_final: 0.7644 (mmp) REVERT: g 126 ASP cc_start: 0.8610 (m-30) cc_final: 0.8402 (m-30) REVERT: h 54 ASP cc_start: 0.8391 (p0) cc_final: 0.7963 (p0) REVERT: h 76 ASN cc_start: 0.9139 (t0) cc_final: 0.8669 (t0) REVERT: i 14 ASN cc_start: 0.8700 (OUTLIER) cc_final: 0.8326 (t0) REVERT: i 81 HIS cc_start: 0.8094 (m90) cc_final: 0.6671 (t-170) REVERT: j 31 ARG cc_start: 0.7951 (ttp-170) cc_final: 0.7588 (ptt90) REVERT: j 47 SER cc_start: 0.9506 (m) cc_final: 0.9278 (p) REVERT: j 66 GLU cc_start: 0.8536 (pt0) cc_final: 0.8128 (pt0) REVERT: k 76 GLU cc_start: 0.8772 (tt0) cc_final: 0.8472 (tm-30) REVERT: k 87 LYS cc_start: 0.8320 (OUTLIER) cc_final: 0.8092 (mmmm) REVERT: k 105 LEU cc_start: 0.8844 (mt) cc_final: 0.8146 (mp) REVERT: k 106 GLU cc_start: 0.8615 (mm-30) cc_final: 0.8356 (mm-30) REVERT: l 75 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7463 (tm-30) REVERT: l 124 LYS cc_start: 0.9334 (OUTLIER) cc_final: 0.8678 (mtmm) REVERT: m 54 ASP cc_start: 0.8872 (m-30) cc_final: 0.8507 (m-30) REVERT: n 25 GLU cc_start: 0.8730 (mm-30) cc_final: 0.8354 (mm-30) REVERT: n 35 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.7454 (ptm-80) REVERT: n 36 LYS cc_start: 0.8846 (tmtt) cc_final: 0.8615 (tmtt) REVERT: o 41 GLU cc_start: 0.8811 (mm-30) cc_final: 0.8536 (mm-30) REVERT: o 44 ARG cc_start: 0.8275 (mtm180) cc_final: 0.7776 (mtm180) REVERT: p 80 MET cc_start: 0.8668 (mtp) cc_final: 0.8253 (mtp) REVERT: q 12 GLN cc_start: 0.8347 (tt0) cc_final: 0.7560 (tp40) REVERT: q 40 ARG cc_start: 0.8468 (mmm160) cc_final: 0.7647 (ttt90) REVERT: q 52 GLU cc_start: 0.8754 (mp0) cc_final: 0.8429 (mp0) REVERT: r 26 ASP cc_start: 0.8672 (t0) cc_final: 0.8287 (t70) REVERT: r 40 ARG cc_start: 0.8514 (mtp-110) cc_final: 0.8217 (tmm160) REVERT: s 12 ASP cc_start: 0.8039 (m-30) cc_final: 0.7747 (m-30) REVERT: s 14 HIS cc_start: 0.7893 (OUTLIER) cc_final: 0.7181 (p-80) REVERT: s 40 ILE cc_start: 0.8452 (mm) cc_final: 0.7915 (mt) REVERT: t 44 ASP cc_start: 0.8392 (t0) cc_final: 0.7934 (p0) REVERT: t 80 LYS cc_start: 0.9386 (mtpt) cc_final: 0.9028 (mtmm) REVERT: C 14 ARG cc_start: 0.9043 (OUTLIER) cc_final: 0.7931 (mmt90) REVERT: C 108 LYS cc_start: 0.8471 (ttmt) cc_final: 0.8139 (mttm) REVERT: C 123 ASP cc_start: 0.8462 (t0) cc_final: 0.7939 (t0) REVERT: C 180 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7543 (pm20) REVERT: C 274 ARG cc_start: 0.7760 (tpt90) cc_final: 0.7266 (tpt90) REVERT: D 168 ARG cc_start: 0.9067 (OUTLIER) cc_final: 0.8330 (ptm160) REVERT: E 75 GLN cc_start: 0.8647 (mm-40) cc_final: 0.8397 (mm-40) REVERT: F 38 MET cc_start: 0.8171 (tmm) cc_final: 0.7944 (tmm) REVERT: F 83 MET cc_start: 0.8651 (mmm) cc_final: 0.8129 (mtt) REVERT: F 114 PHE cc_start: 0.8317 (t80) cc_final: 0.8074 (t80) REVERT: F 120 LYS cc_start: 0.9105 (mttt) cc_final: 0.8893 (tptp) REVERT: F 135 GLN cc_start: 0.8028 (OUTLIER) cc_final: 0.7760 (pp30) REVERT: G 52 PHE cc_start: 0.6828 (OUTLIER) cc_final: 0.6021 (t80) REVERT: G 99 GLN cc_start: 0.8466 (pp30) cc_final: 0.8232 (pp30) REVERT: G 130 GLN cc_start: 0.8102 (OUTLIER) cc_final: 0.7546 (mp-120) REVERT: K 119 GLN cc_start: 0.8955 (OUTLIER) cc_final: 0.8390 (mt0) REVERT: L 1 MET cc_start: 0.8269 (mmt) cc_final: 0.7992 (mmt) REVERT: L 2 ILE cc_start: 0.8827 (mt) cc_final: 0.8473 (tp) REVERT: L 13 ASN cc_start: 0.8816 (t0) cc_final: 0.8583 (p0) REVERT: L 25 LEU cc_start: 0.8651 (mp) cc_final: 0.8298 (mt) REVERT: M 101 ILE cc_start: 0.7852 (mp) cc_final: 0.7543 (pt) REVERT: N 14 ARG cc_start: 0.7640 (mmt180) cc_final: 0.7287 (tpp-160) REVERT: N 58 MET cc_start: 0.8973 (ttm) cc_final: 0.8636 (ttm) REVERT: N 103 MET cc_start: 0.8375 (mmm) cc_final: 0.8138 (mmm) REVERT: N 106 ILE cc_start: 0.8931 (mm) cc_final: 0.8574 (tp) REVERT: N 134 ARG cc_start: 0.8167 (OUTLIER) cc_final: 0.7283 (ttt90) REVERT: O 24 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8663 (tt) REVERT: O 41 ARG cc_start: 0.7799 (OUTLIER) cc_final: 0.6639 (ppt90) REVERT: O 46 LYS cc_start: 0.8900 (tttt) cc_final: 0.8367 (tptp) REVERT: O 96 ARG cc_start: 0.8585 (OUTLIER) cc_final: 0.8123 (ttm170) REVERT: O 125 PHE cc_start: 0.8410 (OUTLIER) cc_final: 0.7341 (m-80) REVERT: P 30 ARG cc_start: 0.8671 (OUTLIER) cc_final: 0.8439 (ttm170) REVERT: Q 39 ARG cc_start: 0.8043 (OUTLIER) cc_final: 0.6662 (ttm170) REVERT: Q 106 LYS cc_start: 0.8868 (mtpt) cc_final: 0.8024 (mtpt) REVERT: Q 111 LYS cc_start: 0.9242 (mttt) cc_final: 0.8984 (mtpt) REVERT: Q 113 ILE cc_start: 0.8808 (tp) cc_final: 0.8549 (tt) REVERT: R 59 LYS cc_start: 0.7852 (mttt) cc_final: 0.7475 (mmtt) REVERT: R 89 ASP cc_start: 0.7420 (p0) cc_final: 0.7198 (p0) REVERT: S 1 MET cc_start: 0.8568 (OUTLIER) cc_final: 0.7662 (ttt) REVERT: S 37 GLU cc_start: 0.7924 (mt-10) cc_final: 0.7503 (mt-10) REVERT: T 67 PHE cc_start: 0.7855 (OUTLIER) cc_final: 0.6361 (p90) REVERT: T 89 ARG cc_start: 0.8923 (OUTLIER) cc_final: 0.8103 (mtt90) REVERT: U 59 ARG cc_start: 0.7495 (mtt180) cc_final: 0.7170 (mtt180) REVERT: V 1 MET cc_start: 0.7543 (OUTLIER) cc_final: 0.7285 (mmt) REVERT: V 53 GLN cc_start: 0.8768 (mt0) cc_final: 0.8262 (mm-40) REVERT: W 86 MET cc_start: 0.5384 (mtm) cc_final: 0.4552 (ptp) REVERT: X 47 TYR cc_start: 0.8383 (t80) cc_final: 0.7914 (t80) REVERT: Y 17 ASN cc_start: 0.8103 (t0) cc_final: 0.7834 (t0) REVERT: Y 22 MET cc_start: 0.7381 (OUTLIER) cc_final: 0.7131 (mmm) REVERT: Y 35 LYS cc_start: 0.8715 (mtpm) cc_final: 0.8450 (tttp) REVERT: Z 22 LYS cc_start: 0.9342 (mmmm) cc_final: 0.8968 (tptp) REVERT: Z 24 GLU cc_start: 0.8709 (tm-30) cc_final: 0.8142 (tm-30) REVERT: Z 27 ASN cc_start: 0.8188 (m-40) cc_final: 0.7861 (m110) REVERT: Z 28 LEU cc_start: 0.8634 (mt) cc_final: 0.8213 (mp) REVERT: Z 29 ARG cc_start: 0.8832 (mtm-85) cc_final: 0.8442 (mtp-110) REVERT: 0 41 GLU cc_start: 0.8634 (tp30) cc_final: 0.8402 (tp30) REVERT: 0 44 LYS cc_start: 0.8271 (mttp) cc_final: 0.7871 (mptt) REVERT: 0 57 GLU cc_start: 0.8397 (mt-10) cc_final: 0.8193 (tt0) REVERT: 1 1 MET cc_start: 0.8382 (mmm) cc_final: 0.8077 (mmp) REVERT: 1 12 VAL cc_start: 0.9071 (t) cc_final: 0.8601 (p) REVERT: 1 14 PHE cc_start: 0.7413 (m-80) cc_final: 0.7037 (m-80) REVERT: 1 43 TYR cc_start: 0.7546 (m-80) cc_final: 0.7299 (m-10) REVERT: 1 54 SER cc_start: 0.8695 (m) cc_final: 0.8317 (p) REVERT: 1 73 ARG cc_start: 0.7867 (tmt170) cc_final: 0.7253 (ttp-170) REVERT: 1 76 LYS cc_start: 0.9466 (tttt) cc_final: 0.9181 (tptt) REVERT: 3 8 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7003 (tp30) REVERT: 3 13 LYS cc_start: 0.8683 (mmtm) cc_final: 0.8146 (mmtm) REVERT: 3 41 LYS cc_start: 0.8776 (tppt) cc_final: 0.8505 (ptpp) REVERT: 3 44 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8199 (tm) REVERT: 4 6 GLN cc_start: 0.7997 (mm-40) cc_final: 0.7741 (mp10) REVERT: 6 24 MET cc_start: 0.8305 (mmm) cc_final: 0.8006 (mmt) outliers start: 336 outliers final: 232 residues processed: 1231 average time/residue: 1.1787 time to fit residues: 2538.3796 Evaluate side-chains 1186 residues out of total 4391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 266 poor density : 920 time to evaluate : 6.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 15 ILE Chi-restraints excluded: chain c residue 40 LYS Chi-restraints excluded: chain c residue 55 GLU Chi-restraints excluded: chain c residue 82 GLU Chi-restraints excluded: chain c residue 85 ASN Chi-restraints excluded: chain c residue 98 VAL Chi-restraints excluded: chain c residue 127 VAL Chi-restraints excluded: chain c residue 199 VAL Chi-restraints excluded: chain c residue 200 TRP Chi-restraints excluded: chain d residue 4 TYR Chi-restraints excluded: chain d residue 57 LEU Chi-restraints excluded: chain d residue 71 LEU Chi-restraints excluded: chain d residue 94 ARG Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 135 GLU Chi-restraints excluded: chain d residue 136 VAL Chi-restraints excluded: chain e residue 9 LEU Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 31 LEU Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 105 VAL Chi-restraints excluded: chain e residue 125 SER Chi-restraints excluded: chain e residue 127 SER Chi-restraints excluded: chain e residue 131 ASN Chi-restraints excluded: chain e residue 132 THR Chi-restraints excluded: chain e residue 144 LEU Chi-restraints excluded: chain e residue 159 LYS Chi-restraints excluded: chain f residue 11 TYR Chi-restraints excluded: chain f residue 13 ILE Chi-restraints excluded: chain f residue 18 ASP Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 50 ARG Chi-restraints excluded: chain f residue 65 ILE Chi-restraints excluded: chain f residue 66 VAL Chi-restraints excluded: chain f residue 98 VAL Chi-restraints excluded: chain g residue 75 VAL Chi-restraints excluded: chain g residue 87 VAL Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain g residue 116 MET Chi-restraints excluded: chain h residue 20 VAL Chi-restraints excluded: chain h residue 22 HIS Chi-restraints excluded: chain h residue 32 ILE Chi-restraints excluded: chain h residue 59 VAL Chi-restraints excluded: chain h residue 60 ILE Chi-restraints excluded: chain h residue 69 ASN Chi-restraints excluded: chain h residue 74 ILE Chi-restraints excluded: chain h residue 89 VAL Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 103 ILE Chi-restraints excluded: chain h residue 106 ILE Chi-restraints excluded: chain h residue 127 VAL Chi-restraints excluded: chain i residue 12 ARG Chi-restraints excluded: chain i residue 14 ASN Chi-restraints excluded: chain i residue 30 VAL Chi-restraints excluded: chain i residue 34 ASP Chi-restraints excluded: chain i residue 57 THR Chi-restraints excluded: chain i residue 88 LEU Chi-restraints excluded: chain i residue 91 ASP Chi-restraints excluded: chain i residue 93 ASP Chi-restraints excluded: chain j residue 98 ILE Chi-restraints excluded: chain k residue 35 THR Chi-restraints excluded: chain k residue 46 SER Chi-restraints excluded: chain k residue 55 SER Chi-restraints excluded: chain k residue 87 LYS Chi-restraints excluded: chain k residue 91 SER Chi-restraints excluded: chain k residue 97 ILE Chi-restraints excluded: chain k residue 99 SER Chi-restraints excluded: chain l residue 4 ILE Chi-restraints excluded: chain l residue 20 ASP Chi-restraints excluded: chain l residue 32 LYS Chi-restraints excluded: chain l residue 34 THR Chi-restraints excluded: chain l residue 48 THR Chi-restraints excluded: chain l residue 50 VAL Chi-restraints excluded: chain l residue 72 ASN Chi-restraints excluded: chain l residue 124 LYS Chi-restraints excluded: chain m residue 4 ILE Chi-restraints excluded: chain m residue 28 THR Chi-restraints excluded: chain m residue 45 VAL Chi-restraints excluded: chain m residue 101 ASN Chi-restraints excluded: chain m residue 102 THR Chi-restraints excluded: chain n residue 5 SER Chi-restraints excluded: chain n residue 18 THR Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain n residue 35 ARG Chi-restraints excluded: chain n residue 41 ARG Chi-restraints excluded: chain n residue 57 LYS Chi-restraints excluded: chain o residue 89 ARG Chi-restraints excluded: chain p residue 3 VAL Chi-restraints excluded: chain p residue 5 ILE Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain q residue 5 ARG Chi-restraints excluded: chain q residue 7 GLN Chi-restraints excluded: chain q residue 23 THR Chi-restraints excluded: chain q residue 27 VAL Chi-restraints excluded: chain q residue 78 LEU Chi-restraints excluded: chain r residue 16 TYR Chi-restraints excluded: chain r residue 30 THR Chi-restraints excluded: chain r residue 33 LEU Chi-restraints excluded: chain r residue 46 ARG Chi-restraints excluded: chain s residue 14 HIS Chi-restraints excluded: chain s residue 30 VAL Chi-restraints excluded: chain s residue 33 THR Chi-restraints excluded: chain s residue 48 THR Chi-restraints excluded: chain s residue 65 ASP Chi-restraints excluded: chain t residue 8 ILE Chi-restraints excluded: chain t residue 23 SER Chi-restraints excluded: chain t residue 30 THR Chi-restraints excluded: chain t residue 65 LEU Chi-restraints excluded: chain t residue 81 LEU Chi-restraints excluded: chain C residue 14 ARG Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 171 TYR Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 225 MET Chi-restraints excluded: chain C residue 228 ASN Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 85 ASN Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 130 ARG Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 167 ASP Chi-restraints excluded: chain D residue 168 ARG Chi-restraints excluded: chain D residue 188 ILE Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain E residue 7 PHE Chi-restraints excluded: chain E residue 10 ASP Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 121 ASN Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 177 THR Chi-restraints excluded: chain E residue 179 ASP Chi-restraints excluded: chain E residue 195 THR Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 123 ASP Chi-restraints excluded: chain F residue 135 GLN Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 52 PHE Chi-restraints excluded: chain G residue 65 HIS Chi-restraints excluded: chain G residue 128 ASN Chi-restraints excluded: chain G residue 130 GLN Chi-restraints excluded: chain K residue 23 ASP Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 50 ASP Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 113 ASN Chi-restraints excluded: chain K residue 115 LEU Chi-restraints excluded: chain K residue 119 GLN Chi-restraints excluded: chain L residue 6 SER Chi-restraints excluded: chain L residue 19 ILE Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 73 ASP Chi-restraints excluded: chain M residue 18 ARG Chi-restraints excluded: chain M residue 76 VAL Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 89 THR Chi-restraints excluded: chain M residue 95 VAL Chi-restraints excluded: chain M residue 97 LYS Chi-restraints excluded: chain M residue 117 LEU Chi-restraints excluded: chain N residue 68 ILE Chi-restraints excluded: chain N residue 109 VAL Chi-restraints excluded: chain N residue 116 GLU Chi-restraints excluded: chain N residue 120 LEU Chi-restraints excluded: chain N residue 134 ARG Chi-restraints excluded: chain O residue 24 LEU Chi-restraints excluded: chain O residue 26 ILE Chi-restraints excluded: chain O residue 41 ARG Chi-restraints excluded: chain O residue 56 LEU Chi-restraints excluded: chain O residue 70 VAL Chi-restraints excluded: chain O residue 81 VAL Chi-restraints excluded: chain O residue 96 ARG Chi-restraints excluded: chain O residue 104 TYR Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain O residue 114 ARG Chi-restraints excluded: chain O residue 121 VAL Chi-restraints excluded: chain O residue 125 PHE Chi-restraints excluded: chain P residue 20 ASN Chi-restraints excluded: chain P residue 30 ARG Chi-restraints excluded: chain P residue 31 LEU Chi-restraints excluded: chain P residue 71 THR Chi-restraints excluded: chain P residue 101 HIS Chi-restraints excluded: chain Q residue 32 VAL Chi-restraints excluded: chain Q residue 39 ARG Chi-restraints excluded: chain Q residue 48 ILE Chi-restraints excluded: chain Q residue 68 VAL Chi-restraints excluded: chain Q residue 73 THR Chi-restraints excluded: chain Q residue 76 LEU Chi-restraints excluded: chain R residue 9 VAL Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 85 LEU Chi-restraints excluded: chain R residue 102 ASP Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 27 VAL Chi-restraints excluded: chain S residue 81 HIS Chi-restraints excluded: chain T residue 6 THR Chi-restraints excluded: chain T residue 67 PHE Chi-restraints excluded: chain T residue 86 THR Chi-restraints excluded: chain T residue 89 ARG Chi-restraints excluded: chain T residue 102 ASN Chi-restraints excluded: chain U residue 31 THR Chi-restraints excluded: chain U residue 47 ASP Chi-restraints excluded: chain V residue 1 MET Chi-restraints excluded: chain V residue 12 ILE Chi-restraints excluded: chain V residue 35 VAL Chi-restraints excluded: chain V residue 40 VAL Chi-restraints excluded: chain V residue 48 ASN Chi-restraints excluded: chain V residue 70 VAL Chi-restraints excluded: chain V residue 94 SER Chi-restraints excluded: chain W residue 43 PHE Chi-restraints excluded: chain W residue 94 VAL Chi-restraints excluded: chain X residue 34 SER Chi-restraints excluded: chain X residue 67 THR Chi-restraints excluded: chain X residue 73 ASP Chi-restraints excluded: chain X residue 88 VAL Chi-restraints excluded: chain Y residue 12 THR Chi-restraints excluded: chain Y residue 14 SER Chi-restraints excluded: chain Y residue 22 MET Chi-restraints excluded: chain Y residue 25 THR Chi-restraints excluded: chain Y residue 55 LYS Chi-restraints excluded: chain Z residue 18 GLU Chi-restraints excluded: chain Z residue 30 PHE Chi-restraints excluded: chain Z residue 45 GLU Chi-restraints excluded: chain 0 residue 53 LEU Chi-restraints excluded: chain 0 residue 56 VAL Chi-restraints excluded: chain 1 residue 13 VAL Chi-restraints excluded: chain 1 residue 23 PHE Chi-restraints excluded: chain 2 residue 6 ARG Chi-restraints excluded: chain 2 residue 18 THR Chi-restraints excluded: chain 3 residue 5 ILE Chi-restraints excluded: chain 3 residue 8 GLU Chi-restraints excluded: chain 3 residue 11 SER Chi-restraints excluded: chain 3 residue 39 GLU Chi-restraints excluded: chain 3 residue 44 LEU Chi-restraints excluded: chain 4 residue 24 THR Chi-restraints excluded: chain 4 residue 42 ILE Chi-restraints excluded: chain 5 residue 14 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 954 random chunks: chunk 562 optimal weight: 20.0000 chunk 906 optimal weight: 1.9990 chunk 553 optimal weight: 10.0000 chunk 429 optimal weight: 10.0000 chunk 629 optimal weight: 10.0000 chunk 950 optimal weight: 0.9980 chunk 874 optimal weight: 0.0370 chunk 756 optimal weight: 0.8980 chunk 78 optimal weight: 10.0000 chunk 584 optimal weight: 10.0000 chunk 464 optimal weight: 50.0000 overall best weight: 2.7864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 114 HIS ** j 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 119 ASN l 86 ASN m 104 ASN ** q 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 35 GLN C 45 ASN C 153 GLN ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 191 ASN ** E 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 172 GLN L 110 ASN N 35 GLN P 20 ASN ** P 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 150747 Z= 0.173 Angle : 0.592 16.113 226044 Z= 0.304 Chirality : 0.034 0.320 28980 Planarity : 0.004 0.095 11734 Dihedral : 23.080 179.309 76592 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.16 % Allowed : 11.02 % Favored : 88.82 % Rotamer: Outliers : 6.10 % Allowed : 32.29 % Favored : 61.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.28 % Twisted Proline : 0.52 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.56 (0.11), residues: 5143 helix: -0.01 (0.14), residues: 1443 sheet: -1.66 (0.17), residues: 910 loop : -2.75 (0.11), residues: 2790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP c 200 HIS 0.008 0.001 HIS F 115 PHE 0.029 0.001 PHE N 69 TYR 0.048 0.002 TYR R 76 ARG 0.015 0.000 ARG C 273 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10286 Ramachandran restraints generated. 5143 Oldfield, 0 Emsley, 5143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10286 Ramachandran restraints generated. 5143 Oldfield, 0 Emsley, 5143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1200 residues out of total 4391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 268 poor density : 932 time to evaluate : 6.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 10 MET cc_start: 0.8964 (mmm) cc_final: 0.8621 (mmt) REVERT: c 17 ASP cc_start: 0.9145 (p0) cc_final: 0.8559 (p0) REVERT: c 40 LYS cc_start: 0.9349 (OUTLIER) cc_final: 0.8906 (tmmm) REVERT: c 55 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7042 (tm-30) REVERT: c 141 MET cc_start: 0.7883 (mmm) cc_final: 0.7397 (mmm) REVERT: c 200 TRP cc_start: 0.7822 (OUTLIER) cc_final: 0.6111 (m100) REVERT: d 88 MET cc_start: 0.8978 (mmm) cc_final: 0.8684 (mmm) REVERT: d 186 LEU cc_start: 0.9047 (tt) cc_final: 0.8241 (mt) REVERT: f 4 ASP cc_start: 0.7745 (m-30) cc_final: 0.7365 (t0) REVERT: f 28 ARG cc_start: 0.8679 (tmm-80) cc_final: 0.8472 (tmm-80) REVERT: f 39 GLU cc_start: 0.8353 (mt-10) cc_final: 0.7857 (tm-30) REVERT: f 55 MET cc_start: 0.8643 (mmm) cc_final: 0.8230 (mmm) REVERT: f 82 ARG cc_start: 0.8956 (ttp80) cc_final: 0.8679 (ttt90) REVERT: g 31 MET cc_start: 0.8683 (ttp) cc_final: 0.8125 (ttt) REVERT: g 66 MET cc_start: 0.8460 (tpp) cc_final: 0.7650 (tmm) REVERT: g 86 GLN cc_start: 0.7878 (pt0) cc_final: 0.7623 (mp10) REVERT: g 126 ASP cc_start: 0.8623 (m-30) cc_final: 0.8394 (m-30) REVERT: h 76 ASN cc_start: 0.9141 (t0) cc_final: 0.8663 (t0) REVERT: i 14 ASN cc_start: 0.8691 (OUTLIER) cc_final: 0.8310 (t0) REVERT: i 81 HIS cc_start: 0.8118 (m90) cc_final: 0.6661 (t-170) REVERT: j 31 ARG cc_start: 0.7910 (ttp-170) cc_final: 0.7544 (ptt90) REVERT: j 47 SER cc_start: 0.9489 (m) cc_final: 0.9261 (p) REVERT: j 66 GLU cc_start: 0.8533 (pt0) cc_final: 0.8249 (pt0) REVERT: k 76 GLU cc_start: 0.8704 (tt0) cc_final: 0.8473 (tm-30) REVERT: k 87 LYS cc_start: 0.8283 (OUTLIER) cc_final: 0.8020 (mmmm) REVERT: k 105 LEU cc_start: 0.8856 (mt) cc_final: 0.8153 (mp) REVERT: k 106 GLU cc_start: 0.8608 (mm-30) cc_final: 0.8397 (mm-30) REVERT: l 75 GLU cc_start: 0.8053 (mm-30) cc_final: 0.7505 (tm-30) REVERT: l 86 ASN cc_start: 0.9361 (OUTLIER) cc_final: 0.8800 (p0) REVERT: l 124 LYS cc_start: 0.9318 (OUTLIER) cc_final: 0.8612 (mtmm) REVERT: m 54 ASP cc_start: 0.8827 (m-30) cc_final: 0.8451 (m-30) REVERT: m 104 ASN cc_start: 0.6449 (OUTLIER) cc_final: 0.5719 (m-40) REVERT: n 25 GLU cc_start: 0.8747 (mm-30) cc_final: 0.8379 (mm-30) REVERT: n 35 ARG cc_start: 0.8076 (OUTLIER) cc_final: 0.7860 (ptm160) REVERT: o 48 LYS cc_start: 0.8532 (mppt) cc_final: 0.8198 (mppt) REVERT: q 12 GLN cc_start: 0.8271 (tt0) cc_final: 0.7519 (tp40) REVERT: q 40 ARG cc_start: 0.8461 (mmm160) cc_final: 0.7632 (ttt90) REVERT: q 52 GLU cc_start: 0.8591 (mp0) cc_final: 0.8376 (mp0) REVERT: r 26 ASP cc_start: 0.8688 (t0) cc_final: 0.8339 (t70) REVERT: r 40 ARG cc_start: 0.8535 (mtp-110) cc_final: 0.8215 (tmm160) REVERT: s 12 ASP cc_start: 0.7961 (m-30) cc_final: 0.7682 (m-30) REVERT: s 14 HIS cc_start: 0.7879 (OUTLIER) cc_final: 0.7202 (p-80) REVERT: s 40 ILE cc_start: 0.8499 (mm) cc_final: 0.7969 (mt) REVERT: s 66 MET cc_start: 0.7767 (ttp) cc_final: 0.7105 (ptp) REVERT: t 44 ASP cc_start: 0.8468 (t0) cc_final: 0.8011 (p0) REVERT: t 80 LYS cc_start: 0.9387 (mtpt) cc_final: 0.9032 (mtmm) REVERT: C 108 LYS cc_start: 0.8579 (ttmt) cc_final: 0.8161 (mttm) REVERT: C 123 ASP cc_start: 0.8528 (t0) cc_final: 0.7906 (t0) REVERT: C 180 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7507 (pm20) REVERT: C 274 ARG cc_start: 0.7779 (tpt90) cc_final: 0.7443 (tpt90) REVERT: D 168 ARG cc_start: 0.9071 (OUTLIER) cc_final: 0.8225 (ptm160) REVERT: E 67 GLN cc_start: 0.8633 (tp40) cc_final: 0.8339 (tp-100) REVERT: E 75 GLN cc_start: 0.8650 (mm-40) cc_final: 0.8401 (mm-40) REVERT: F 38 MET cc_start: 0.8178 (tmm) cc_final: 0.7955 (tmm) REVERT: F 83 MET cc_start: 0.8636 (mmm) cc_final: 0.8091 (mtt) REVERT: F 114 PHE cc_start: 0.8260 (t80) cc_final: 0.8024 (t80) REVERT: F 120 LYS cc_start: 0.9106 (mttt) cc_final: 0.8886 (tptp) REVERT: G 52 PHE cc_start: 0.6773 (OUTLIER) cc_final: 0.6133 (t80) REVERT: G 99 GLN cc_start: 0.8507 (pp30) cc_final: 0.8241 (pp30) REVERT: G 130 GLN cc_start: 0.8103 (OUTLIER) cc_final: 0.7554 (mp-120) REVERT: K 119 GLN cc_start: 0.8982 (OUTLIER) cc_final: 0.8445 (mt0) REVERT: L 1 MET cc_start: 0.8382 (mmt) cc_final: 0.8082 (mmt) REVERT: L 2 ILE cc_start: 0.8786 (mt) cc_final: 0.8396 (tp) REVERT: L 13 ASN cc_start: 0.8836 (t0) cc_final: 0.8551 (p0) REVERT: L 25 LEU cc_start: 0.8757 (mp) cc_final: 0.8350 (mt) REVERT: M 95 VAL cc_start: 0.8602 (OUTLIER) cc_final: 0.8402 (p) REVERT: M 101 ILE cc_start: 0.7826 (mp) cc_final: 0.7508 (pt) REVERT: N 58 MET cc_start: 0.8984 (ttm) cc_final: 0.8613 (ttm) REVERT: N 103 MET cc_start: 0.8355 (mmm) cc_final: 0.8039 (mmm) REVERT: N 106 ILE cc_start: 0.8974 (mm) cc_final: 0.8715 (tp) REVERT: N 134 ARG cc_start: 0.8041 (OUTLIER) cc_final: 0.7142 (ttt90) REVERT: O 24 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8802 (tp) REVERT: O 41 ARG cc_start: 0.7832 (OUTLIER) cc_final: 0.6694 (ppt90) REVERT: O 46 LYS cc_start: 0.8898 (tttt) cc_final: 0.8429 (tptp) REVERT: O 96 ARG cc_start: 0.8612 (OUTLIER) cc_final: 0.8185 (ttm170) REVERT: O 125 PHE cc_start: 0.8495 (OUTLIER) cc_final: 0.7478 (m-10) REVERT: P 30 ARG cc_start: 0.8668 (OUTLIER) cc_final: 0.8435 (ttm170) REVERT: Q 39 ARG cc_start: 0.8107 (OUTLIER) cc_final: 0.6699 (ttm170) REVERT: Q 71 GLU cc_start: 0.8184 (mp0) cc_final: 0.7846 (mp0) REVERT: Q 106 LYS cc_start: 0.8900 (mtpt) cc_final: 0.8077 (mtpt) REVERT: Q 111 LYS cc_start: 0.9264 (mttt) cc_final: 0.8987 (mtpt) REVERT: Q 115 ARG cc_start: 0.7543 (mmt-90) cc_final: 0.7236 (mmp80) REVERT: R 60 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8415 (tt) REVERT: R 89 ASP cc_start: 0.7337 (p0) cc_final: 0.7079 (p0) REVERT: S 1 MET cc_start: 0.8466 (OUTLIER) cc_final: 0.7473 (ttt) REVERT: T 67 PHE cc_start: 0.7888 (OUTLIER) cc_final: 0.6263 (p90) REVERT: T 89 ARG cc_start: 0.8946 (OUTLIER) cc_final: 0.8056 (mtt90) REVERT: U 59 ARG cc_start: 0.7550 (mtt180) cc_final: 0.7222 (mtt180) REVERT: V 1 MET cc_start: 0.7534 (OUTLIER) cc_final: 0.7281 (mmt) REVERT: V 53 GLN cc_start: 0.8777 (mt0) cc_final: 0.8275 (mm-40) REVERT: W 74 MET cc_start: 0.7930 (ppp) cc_final: 0.6019 (ptp) REVERT: X 47 TYR cc_start: 0.8415 (t80) cc_final: 0.7944 (t80) REVERT: Y 17 ASN cc_start: 0.8194 (t0) cc_final: 0.7924 (t0) REVERT: Y 22 MET cc_start: 0.7377 (OUTLIER) cc_final: 0.7115 (mmm) REVERT: Z 22 LYS cc_start: 0.9343 (mmmm) cc_final: 0.8917 (tptp) REVERT: Z 24 GLU cc_start: 0.8624 (tm-30) cc_final: 0.8113 (tm-30) REVERT: Z 28 LEU cc_start: 0.8627 (mt) cc_final: 0.8211 (mp) REVERT: Z 29 ARG cc_start: 0.8803 (mtm-85) cc_final: 0.8410 (mtp-110) REVERT: Z 36 GLN cc_start: 0.8634 (OUTLIER) cc_final: 0.7524 (mt0) REVERT: 0 44 LYS cc_start: 0.8295 (mttp) cc_final: 0.7868 (mptt) REVERT: 0 57 GLU cc_start: 0.8360 (mt-10) cc_final: 0.8149 (tt0) REVERT: 1 1 MET cc_start: 0.8359 (mmm) cc_final: 0.8144 (mmp) REVERT: 1 12 VAL cc_start: 0.9113 (t) cc_final: 0.8659 (p) REVERT: 1 14 PHE cc_start: 0.7423 (m-80) cc_final: 0.7119 (m-80) REVERT: 1 43 TYR cc_start: 0.7701 (m-80) cc_final: 0.7414 (m-10) REVERT: 1 54 SER cc_start: 0.8543 (m) cc_final: 0.8206 (p) REVERT: 1 73 ARG cc_start: 0.7834 (tmt170) cc_final: 0.7224 (ttp-170) REVERT: 1 76 LYS cc_start: 0.9477 (tttt) cc_final: 0.9189 (tptt) REVERT: 3 8 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7185 (tp30) REVERT: 3 13 LYS cc_start: 0.8665 (mmtm) cc_final: 0.8109 (mmtm) REVERT: 3 20 ASN cc_start: 0.9032 (p0) cc_final: 0.8716 (p0) REVERT: 3 32 LYS cc_start: 0.8105 (mmtt) cc_final: 0.7900 (mmtt) REVERT: 3 41 LYS cc_start: 0.8773 (tppt) cc_final: 0.8464 (ptpp) REVERT: 3 44 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8155 (tm) REVERT: 4 4 THR cc_start: 0.8816 (p) cc_final: 0.8503 (p) REVERT: 4 5 TYR cc_start: 0.6203 (m-10) cc_final: 0.5981 (m-80) REVERT: 6 24 MET cc_start: 0.8228 (mmm) cc_final: 0.7950 (mmt) outliers start: 268 outliers final: 209 residues processed: 1125 average time/residue: 1.1656 time to fit residues: 2293.4729 Evaluate side-chains 1152 residues out of total 4391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 241 poor density : 911 time to evaluate : 5.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 40 LYS Chi-restraints excluded: chain c residue 55 GLU Chi-restraints excluded: chain c residue 85 ASN Chi-restraints excluded: chain c residue 127 VAL Chi-restraints excluded: chain c residue 199 VAL Chi-restraints excluded: chain c residue 200 TRP Chi-restraints excluded: chain d residue 4 TYR Chi-restraints excluded: chain d residue 57 LEU Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 190 ILE Chi-restraints excluded: chain d residue 194 LEU Chi-restraints excluded: chain e residue 9 LEU Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 31 LEU Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 105 VAL Chi-restraints excluded: chain e residue 125 SER Chi-restraints excluded: chain e residue 131 ASN Chi-restraints excluded: chain e residue 132 THR Chi-restraints excluded: chain e residue 144 LEU Chi-restraints excluded: chain e residue 159 LYS Chi-restraints excluded: chain f residue 11 TYR Chi-restraints excluded: chain f residue 13 ILE Chi-restraints excluded: chain f residue 18 ASP Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 50 ARG Chi-restraints excluded: chain f residue 65 ILE Chi-restraints excluded: chain f residue 66 VAL Chi-restraints excluded: chain f residue 98 VAL Chi-restraints excluded: chain g residue 75 VAL Chi-restraints excluded: chain g residue 87 VAL Chi-restraints excluded: chain h residue 20 VAL Chi-restraints excluded: chain h residue 22 HIS Chi-restraints excluded: chain h residue 32 ILE Chi-restraints excluded: chain h residue 59 VAL Chi-restraints excluded: chain h residue 69 ASN Chi-restraints excluded: chain h residue 74 ILE Chi-restraints excluded: chain h residue 89 VAL Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 103 ILE Chi-restraints excluded: chain h residue 127 VAL Chi-restraints excluded: chain i residue 12 ARG Chi-restraints excluded: chain i residue 14 ASN Chi-restraints excluded: chain i residue 30 VAL Chi-restraints excluded: chain i residue 34 ASP Chi-restraints excluded: chain i residue 57 THR Chi-restraints excluded: chain i residue 88 LEU Chi-restraints excluded: chain i residue 91 ASP Chi-restraints excluded: chain i residue 93 ASP Chi-restraints excluded: chain j residue 98 ILE Chi-restraints excluded: chain k residue 35 THR Chi-restraints excluded: chain k residue 46 SER Chi-restraints excluded: chain k residue 55 SER Chi-restraints excluded: chain k residue 87 LYS Chi-restraints excluded: chain k residue 97 ILE Chi-restraints excluded: chain k residue 99 SER Chi-restraints excluded: chain k residue 119 ASN Chi-restraints excluded: chain l residue 4 ILE Chi-restraints excluded: chain l residue 20 ASP Chi-restraints excluded: chain l residue 32 LYS Chi-restraints excluded: chain l residue 34 THR Chi-restraints excluded: chain l residue 50 VAL Chi-restraints excluded: chain l residue 72 ASN Chi-restraints excluded: chain l residue 86 ASN Chi-restraints excluded: chain l residue 124 LYS Chi-restraints excluded: chain m residue 4 ILE Chi-restraints excluded: chain m residue 9 ILE Chi-restraints excluded: chain m residue 28 THR Chi-restraints excluded: chain m residue 45 VAL Chi-restraints excluded: chain m residue 101 ASN Chi-restraints excluded: chain m residue 104 ASN Chi-restraints excluded: chain n residue 5 SER Chi-restraints excluded: chain n residue 18 THR Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain n residue 35 ARG Chi-restraints excluded: chain n residue 41 ARG Chi-restraints excluded: chain n residue 57 LYS Chi-restraints excluded: chain o residue 89 ARG Chi-restraints excluded: chain p residue 3 VAL Chi-restraints excluded: chain p residue 5 ILE Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain p residue 39 THR Chi-restraints excluded: chain q residue 5 ARG Chi-restraints excluded: chain q residue 7 GLN Chi-restraints excluded: chain q residue 23 THR Chi-restraints excluded: chain q residue 27 VAL Chi-restraints excluded: chain q residue 78 LEU Chi-restraints excluded: chain r residue 16 TYR Chi-restraints excluded: chain r residue 29 ASP Chi-restraints excluded: chain s residue 14 HIS Chi-restraints excluded: chain s residue 33 THR Chi-restraints excluded: chain s residue 48 THR Chi-restraints excluded: chain s residue 65 ASP Chi-restraints excluded: chain t residue 8 ILE Chi-restraints excluded: chain t residue 23 SER Chi-restraints excluded: chain t residue 30 THR Chi-restraints excluded: chain t residue 65 LEU Chi-restraints excluded: chain t residue 81 LEU Chi-restraints excluded: chain C residue 45 ASN Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 171 TYR Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 228 ASN Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 53 TYR Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 130 ARG Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 168 ARG Chi-restraints excluded: chain D residue 188 ILE Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain E residue 7 PHE Chi-restraints excluded: chain E residue 10 ASP Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 121 ASN Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 123 ASP Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 172 GLN Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 52 PHE Chi-restraints excluded: chain G residue 65 HIS Chi-restraints excluded: chain G residue 128 ASN Chi-restraints excluded: chain G residue 130 GLN Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 50 ASP Chi-restraints excluded: chain K residue 85 LEU Chi-restraints excluded: chain K residue 113 ASN Chi-restraints excluded: chain K residue 115 LEU Chi-restraints excluded: chain K residue 119 GLN Chi-restraints excluded: chain K residue 142 ASP Chi-restraints excluded: chain L residue 6 SER Chi-restraints excluded: chain L residue 19 ILE Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 73 ASP Chi-restraints excluded: chain M residue 18 ARG Chi-restraints excluded: chain M residue 76 VAL Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 95 VAL Chi-restraints excluded: chain N residue 68 ILE Chi-restraints excluded: chain N residue 116 GLU Chi-restraints excluded: chain N residue 120 LEU Chi-restraints excluded: chain N residue 134 ARG Chi-restraints excluded: chain O residue 24 LEU Chi-restraints excluded: chain O residue 26 ILE Chi-restraints excluded: chain O residue 41 ARG Chi-restraints excluded: chain O residue 56 LEU Chi-restraints excluded: chain O residue 81 VAL Chi-restraints excluded: chain O residue 96 ARG Chi-restraints excluded: chain O residue 104 TYR Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain O residue 114 ARG Chi-restraints excluded: chain O residue 121 VAL Chi-restraints excluded: chain O residue 125 PHE Chi-restraints excluded: chain P residue 30 ARG Chi-restraints excluded: chain P residue 31 LEU Chi-restraints excluded: chain P residue 71 THR Chi-restraints excluded: chain P residue 101 HIS Chi-restraints excluded: chain Q residue 32 VAL Chi-restraints excluded: chain Q residue 39 ARG Chi-restraints excluded: chain Q residue 48 ILE Chi-restraints excluded: chain Q residue 73 THR Chi-restraints excluded: chain Q residue 76 LEU Chi-restraints excluded: chain R residue 9 VAL Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 85 LEU Chi-restraints excluded: chain R residue 102 ASP Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 27 VAL Chi-restraints excluded: chain S residue 81 HIS Chi-restraints excluded: chain T residue 6 THR Chi-restraints excluded: chain T residue 67 PHE Chi-restraints excluded: chain T residue 86 THR Chi-restraints excluded: chain T residue 89 ARG Chi-restraints excluded: chain T residue 102 ASN Chi-restraints excluded: chain U residue 31 THR Chi-restraints excluded: chain U residue 43 GLU Chi-restraints excluded: chain U residue 47 ASP Chi-restraints excluded: chain V residue 1 MET Chi-restraints excluded: chain V residue 12 ILE Chi-restraints excluded: chain V residue 35 VAL Chi-restraints excluded: chain V residue 40 VAL Chi-restraints excluded: chain V residue 70 VAL Chi-restraints excluded: chain V residue 94 SER Chi-restraints excluded: chain W residue 43 PHE Chi-restraints excluded: chain W residue 94 VAL Chi-restraints excluded: chain X residue 34 SER Chi-restraints excluded: chain X residue 67 THR Chi-restraints excluded: chain X residue 73 ASP Chi-restraints excluded: chain X residue 88 VAL Chi-restraints excluded: chain Y residue 12 THR Chi-restraints excluded: chain Y residue 14 SER Chi-restraints excluded: chain Y residue 22 MET Chi-restraints excluded: chain Y residue 25 THR Chi-restraints excluded: chain Y residue 55 LYS Chi-restraints excluded: chain Z residue 18 GLU Chi-restraints excluded: chain Z residue 25 LEU Chi-restraints excluded: chain Z residue 30 PHE Chi-restraints excluded: chain Z residue 36 GLN Chi-restraints excluded: chain Z residue 45 GLU Chi-restraints excluded: chain 0 residue 56 VAL Chi-restraints excluded: chain 1 residue 13 VAL Chi-restraints excluded: chain 1 residue 23 PHE Chi-restraints excluded: chain 1 residue 25 SER Chi-restraints excluded: chain 2 residue 6 ARG Chi-restraints excluded: chain 2 residue 18 THR Chi-restraints excluded: chain 3 residue 5 ILE Chi-restraints excluded: chain 3 residue 8 GLU Chi-restraints excluded: chain 3 residue 39 GLU Chi-restraints excluded: chain 3 residue 44 LEU Chi-restraints excluded: chain 4 residue 24 THR Chi-restraints excluded: chain 4 residue 42 ILE Chi-restraints excluded: chain 5 residue 14 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 954 random chunks: chunk 601 optimal weight: 10.0000 chunk 806 optimal weight: 0.6980 chunk 231 optimal weight: 7.9990 chunk 697 optimal weight: 0.5980 chunk 111 optimal weight: 20.0000 chunk 210 optimal weight: 2.9990 chunk 758 optimal weight: 2.9990 chunk 317 optimal weight: 0.8980 chunk 778 optimal weight: 4.9990 chunk 95 optimal weight: 20.0000 chunk 139 optimal weight: 20.0000 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 104 ASN ** q 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 35 GLN ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 172 GLN N 35 GLN P 20 ASN ** P 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 27 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.072247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.057257 restraints weight = 569715.896| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 1.88 r_work: 0.3084 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.211 150747 Z= 0.197 Angle : 0.688 59.133 226044 Z= 0.382 Chirality : 0.035 1.155 28980 Planarity : 0.005 0.095 11734 Dihedral : 23.079 179.317 76565 Min Nonbonded Distance : 1.678 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.17 % Allowed : 11.10 % Favored : 88.72 % Rotamer: Outliers : 5.88 % Allowed : 32.86 % Favored : 61.26 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.28 % Twisted Proline : 0.52 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.56 (0.11), residues: 5143 helix: -0.02 (0.14), residues: 1443 sheet: -1.66 (0.17), residues: 910 loop : -2.74 (0.11), residues: 2790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP c 200 HIS 0.025 0.001 HIS Q 77 PHE 0.021 0.001 PHE N 69 TYR 0.043 0.002 TYR D 53 ARG 0.015 0.000 ARG F 167 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 38360.71 seconds wall clock time: 667 minutes 58.99 seconds (40078.99 seconds total)