Starting phenix.real_space_refine on Sat Mar 16 16:32:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w6p_21562/03_2024/6w6p_21562.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w6p_21562/03_2024/6w6p_21562.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w6p_21562/03_2024/6w6p_21562.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w6p_21562/03_2024/6w6p_21562.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w6p_21562/03_2024/6w6p_21562.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w6p_21562/03_2024/6w6p_21562.pdb" } resolution = 2.9 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= 0.003 sd= 0.007 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 4378 5.49 5 S 124 5.16 5 C 66715 2.51 5 N 24762 2.21 5 O 37571 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "c GLU 25": "OE1" <-> "OE2" Residue "d GLU 25": "OE1" <-> "OE2" Residue "d ASP 169": "OD1" <-> "OD2" Residue "d GLU 182": "OE1" <-> "OE2" Residue "f GLU 8": "OE1" <-> "OE2" Residue "g TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 23": "OE1" <-> "OE2" Residue "k GLU 94": "OE1" <-> "OE2" Residue "l ASP 122": "OD1" <-> "OD2" Residue "n GLU 46": "OE1" <-> "OE2" Residue "o ARG 89": "NH1" <-> "NH2" Residue "p PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p GLU 53": "OE1" <-> "OE2" Residue "q GLU 4": "OE1" <-> "OE2" Residue "q GLU 66": "OE1" <-> "OE2" Residue "r TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s GLU 20": "OE1" <-> "OE2" Residue "C GLU 121": "OE1" <-> "OE2" Residue "F ASP 153": "OD1" <-> "OD2" Residue "G GLU 49": "OE1" <-> "OE2" Residue "G GLU 173": "OE1" <-> "OE2" Residue "L GLU 5": "OE1" <-> "OE2" Residue "L GLU 56": "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 ARG 60": "NH1" <-> "NH2" Residue "M GLU 90": "OE1" <-> "OE2" Residue "N GLU 31": "OE1" <-> "OE2" Residue "N PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 119": "NH1" <-> "NH2" Residue "O ARG 114": "NH1" <-> "NH2" Residue "Q ARG 21": "NH1" <-> "NH2" Residue "T ARG 16": "NH1" <-> "NH2" Residue "U PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 80": "NH1" <-> "NH2" Residue "Y ARG 52": "NH1" <-> "NH2" 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: 133554 Number of models: 1 Model: "" Number of chains: 51 Chain: "a" Number of atoms: 32646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1523, 32646 Classifications: {'RNA': 1523} Modifications used: {'rna2p_pur': 118, 'rna2p_pyr': 89, 'rna3p_pur': 739, 'rna3p_pyr': 577} 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: {'PTRANS': 8, 'TRANS': 192} 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: {'PTRANS': 6, 'TRANS': 110} Chain: "l" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1065 Classifications: {'peptide': 136} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 127} Chain: "m" Number of atoms: 870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 870 Classifications: {'peptide': 110} Link IDs: {'CIS': 3, 'PTRANS': 2, 'TRANS': 104} 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: {'PTRANS': 5, '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: 617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 617 Classifications: {'peptide': 82} Link IDs: {'TRANS': 81} Chain: "A" Number of atoms: 58793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2739, 58793 Classifications: {'RNA': 2739} Modifications used: {'rna2p_pur': 287, 'rna2p_pyr': 144, 'rna3p_pur': 1306, 'rna3p_pyr': 1002} Link IDs: {'rna2p': 431, 'rna3p': 2307} Chain breaks: 5 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': 6, 'rna3p_pur': 56, 'rna3p_pyr': 48} Link IDs: {'rna2p': 12, 'rna3p': 103} Chain: "C" Number of atoms: 2115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2115 Classifications: {'peptide': 275} Link IDs: {'PTRANS': 16, 'TRANS': 258} 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: {'CIS': 1, 'PTRANS': 6, 'TRANS': 133} Chain: "O" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 991 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "P" Number of atoms: 899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 899 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 2, 'TRANS': 114} 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: "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: "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 44914 SG CYS n 24 57.908 133.754 121.752 1.00 17.98 S ATOM 44940 SG CYS n 27 61.128 134.929 121.159 1.00 19.90 S ATOM 45052 SG CYS n 40 60.686 133.396 124.429 1.00 18.14 S ATOM 45077 SG CYS n 43 59.723 136.904 123.952 1.00 17.83 S ATOM A0OHE SG CYS 2 30 251.494 140.306 86.693 1.00 11.93 S ATOM A0OHY SG CYS 2 33 253.995 137.507 88.840 1.00 15.95 S ATOM A0OK4 SG CYS 2 43 250.324 138.566 90.028 1.00 7.68 S ATOM A0OKM SG CYS 2 46 253.404 140.813 90.534 1.00 11.63 S ATOM A0OOZ SG CYS 3 9 139.886 42.693 136.022 1.00 17.23 S ATOM A0OPI SG CYS 3 12 143.582 41.685 137.123 1.00 19.37 S ATOM A0OVF SG CYS 3 36 142.569 40.855 133.529 1.00 12.53 S ATOM A0PPV SG CYS 6 11 141.849 124.568 49.335 1.00 16.19 S ATOM A0PQK SG CYS 6 14 145.338 122.889 50.457 1.00 14.26 S ATOM A0PTI SG CYS 6 27 145.147 126.153 48.919 1.00 10.76 S Time building chain proxies: 49.76, per 1000 atoms: 0.37 Number of scatterers: 133554 At special positions: 0 Unit cell: (288.511, 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 124 16.00 P 4378 15.00 O 37571 8.00 N 24762 7.00 C 66715 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: 45.84 Conformation dependent library (CDL) restraints added in 6.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 2 101 " pdb="ZN ZN 2 101 " - pdb=" SG CYS 2 33 " pdb="ZN ZN 2 101 " - pdb=" SG CYS 2 43 " pdb="ZN ZN 2 101 " - pdb=" SG CYS 2 46 " pdb="ZN ZN 2 101 " - pdb=" SG CYS 2 30 " pdb=" ZN 3 101 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 9 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 12 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 36 " pdb=" ZN 6 101 " pdb="ZN ZN 6 101 " - pdb=" ND1 HIS 6 33 " pdb="ZN ZN 6 101 " - pdb=" SG CYS 6 11 " pdb="ZN ZN 6 101 " - pdb=" SG CYS 6 27 " pdb="ZN ZN 6 101 " - pdb=" SG CYS 6 14 " pdb=" ZN n 101 " pdb="ZN ZN n 101 " - pdb=" SG CYS n 27 " pdb="ZN ZN n 101 " - pdb=" SG CYS n 43 " pdb="ZN ZN n 101 " - pdb=" SG CYS n 40 " pdb="ZN ZN n 101 " - pdb=" SG CYS n 24 " Number of angles added : 15 9940 Ramachandran restraints generated. 4970 Oldfield, 0 Emsley, 4970 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9278 Finding SS restraints... Secondary structure from input PDB file: 153 helices and 67 sheets defined 31.6% alpha, 20.3% beta 1427 base pairs and 2363 stacking pairs defined. Time for finding SS restraints: 41.66 Creating SS restraints... Processing helix chain 'c' and resid 28 through 42 Processing helix chain 'c' and resid 45 through 50 Processing helix chain 'c' and resid 72 through 77 Processing helix chain 'c' and resid 82 through 95 removed outlier: 4.201A pdb=" N LYS c 92 " --> pdb=" O LYS c 88 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU c 93 " --> pdb=" O GLU c 89 " (cutoff:3.500A) Processing helix chain 'c' and resid 107 through 110 Processing helix chain 'c' and resid 111 through 119 Processing helix chain 'c' and resid 122 through 126 removed outlier: 3.565A pdb=" N ARG c 126 " --> pdb=" O LEU c 123 " (cutoff:3.500A) Processing helix chain 'c' and resid 128 through 142 removed outlier: 3.662A pdb=" N ALA c 132 " --> pdb=" O ALA c 128 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS c 134 " --> pdb=" O ARG c 130 " (cutoff:3.500A) Processing helix chain 'c' and resid 155 through 159 removed outlier: 3.635A pdb=" N GLY c 158 " --> pdb=" O ARG c 155 " (cutoff:3.500A) Processing helix chain 'd' and resid 9 through 16 Processing helix chain 'd' and resid 45 through 61 removed outlier: 3.510A pdb=" N MET d 49 " --> pdb=" O SER d 45 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLN d 50 " --> pdb=" O GLU d 46 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N TYR d 61 " --> pdb=" O LEU d 57 " (cutoff:3.500A) Processing helix chain 'd' and resid 64 through 76 Processing helix chain 'd' and resid 83 through 91 removed outlier: 3.589A pdb=" N PHE d 87 " --> pdb=" O HIS d 83 " (cutoff:3.500A) Processing helix chain 'd' and resid 94 through 103 Processing helix chain 'd' and resid 107 through 117 removed outlier: 3.806A pdb=" N ALA d 111 " --> pdb=" O THR d 107 " (cutoff:3.500A) Processing helix chain 'd' and resid 149 through 158 removed outlier: 3.586A pdb=" N GLU d 157 " --> pdb=" O LYS d 153 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA d 158 " --> pdb=" O GLU d 154 " (cutoff:3.500A) Processing helix chain 'd' and resid 182 through 186 Processing helix chain 'd' and resid 193 through 199 removed outlier: 3.540A pdb=" N TYR d 199 " --> pdb=" O VAL d 195 " (cutoff:3.500A) Processing helix chain 'e' and resid 55 through 69 removed outlier: 3.838A pdb=" N LYS e 69 " --> pdb=" O GLU e 65 " (cutoff:3.500A) Processing helix chain 'e' and resid 108 through 117 removed outlier: 3.643A pdb=" N ALA e 113 " --> pdb=" O GLY e 109 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL e 114 " --> pdb=" O PRO e 110 " (cutoff:3.500A) Processing helix chain 'e' and resid 132 through 145 Processing helix chain 'e' and resid 149 through 157 removed outlier: 3.666A pdb=" N VAL e 153 " --> pdb=" O ARG e 149 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA e 154 " --> pdb=" O ALA e 150 " (cutoff:3.500A) Processing helix chain 'f' and resid 20 through 35 Processing helix chain 'f' and resid 76 through 85 removed outlier: 3.738A pdb=" N ASP f 81 " --> pdb=" O ILE f 77 " (cutoff:3.500A) Processing helix chain 'g' and resid 20 through 31 Processing helix chain 'g' and resid 35 through 53 removed outlier: 3.704A pdb=" N ALA g 39 " --> pdb=" O LYS g 35 " (cutoff:3.500A) Processing helix chain 'g' and resid 57 through 70 removed outlier: 3.515A pdb=" N VAL g 61 " --> pdb=" O ASP g 57 " (cutoff:3.500A) Processing helix chain 'g' and resid 92 through 109 Processing helix chain 'g' and resid 115 through 128 removed outlier: 4.082A pdb=" N LYS g 122 " --> pdb=" O GLU g 118 " (cutoff:3.500A) Processing helix chain 'g' and resid 132 through 145 Processing helix chain 'g' and resid 149 through 153 removed outlier: 3.674A pdb=" N HIS g 153 " --> pdb=" O ALA g 150 " (cutoff:3.500A) Processing helix chain 'h' and resid 5 through 20 Processing helix chain 'h' and resid 30 through 43 Processing helix chain 'h' and resid 115 through 122 Processing helix chain 'i' and resid 35 through 39 removed outlier: 3.556A 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 44 through 49 Processing helix chain 'i' and resid 49 through 55 Processing helix chain 'i' and resid 73 through 91 removed outlier: 3.741A pdb=" N GLY i 77 " --> pdb=" O ALA i 73 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ILE i 79 " --> pdb=" O GLN i 75 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP i 91 " --> pdb=" O LEU i 87 " (cutoff:3.500A) Processing helix chain 'i' and resid 92 through 95 Processing helix chain 'i' and resid 96 through 101 removed outlier: 3.601A pdb=" N ALA i 101 " --> pdb=" O ALA i 97 " (cutoff:3.500A) Processing helix chain 'j' and resid 14 through 31 Processing helix chain 'j' and resid 82 through 89 removed outlier: 3.711A pdb=" N LYS j 89 " --> pdb=" O ASP j 85 " (cutoff:3.500A) Processing helix chain 'k' and resid 48 through 51 Processing helix chain 'k' and resid 53 through 58 Processing helix chain 'k' and resid 59 through 75 removed outlier: 3.747A pdb=" N ALA k 63 " --> pdb=" O THR k 59 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N VAL k 73 " --> pdb=" O ALA k 69 " (cutoff:3.500A) Processing helix chain 'k' and resid 92 through 102 removed outlier: 3.667A pdb=" N ILE k 97 " --> pdb=" O ARG k 93 " (cutoff:3.500A) Processing helix chain 'l' and resid 3 through 10 Processing helix chain 'l' and resid 21 through 25 Processing helix chain 'm' and resid 14 through 19 Processing helix chain 'm' and resid 20 through 22 No H-bonds generated for 'chain 'm' and resid 20 through 22' Processing helix chain 'm' and resid 27 through 38 removed outlier: 3.703A pdb=" N VAL m 37 " --> pdb=" O VAL m 33 " (cutoff:3.500A) Processing helix chain 'm' and resid 49 through 59 removed outlier: 3.557A pdb=" N ASP m 54 " --> pdb=" O ASN m 50 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU m 59 " --> pdb=" O ALA m 55 " (cutoff:3.500A) Processing helix chain 'm' and resid 60 through 63 Processing helix chain 'm' and resid 68 through 81 removed outlier: 3.840A pdb=" N GLU m 72 " --> pdb=" O ASP m 68 " (cutoff:3.500A) Processing helix chain 'm' and resid 85 through 92 Processing helix chain 'm' and resid 106 through 111 Processing helix chain 'n' and resid 4 through 12 removed outlier: 3.751A pdb=" N ALA n 8 " --> pdb=" O LYS n 4 " (cutoff:3.500A) Processing helix chain 'n' and resid 16 through 20 removed outlier: 3.796A pdb=" N ALA n 20 " --> pdb=" O SER n 17 " (cutoff:3.500A) Processing helix chain 'n' and resid 41 through 49 removed outlier: 3.985A pdb=" N ARG n 45 " --> pdb=" O ARG n 41 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N GLU n 46 " --> pdb=" O ILE n 42 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N TYR n 49 " --> pdb=" O ARG n 45 " (cutoff:3.500A) Processing helix chain 'o' and resid 4 through 13 removed outlier: 3.901A pdb=" N ASN o 9 " --> pdb=" O GLN o 5 " (cutoff:3.500A) Processing helix chain 'o' and resid 24 through 46 removed outlier: 3.938A pdb=" N GLN o 28 " --> pdb=" O SER o 24 " (cutoff:3.500A) Processing helix chain 'o' and resid 49 through 74 removed outlier: 3.667A pdb=" N ARG o 54 " --> pdb=" O HIS o 50 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N GLY o 55 " --> pdb=" O HIS o 51 " (cutoff:3.500A) Processing helix chain 'o' and resid 74 through 86 removed outlier: 3.713A pdb=" N GLY o 86 " --> pdb=" O ILE o 82 " (cutoff:3.500A) Processing helix chain 'p' and resid 55 through 61 removed outlier: 3.551A pdb=" N SER p 61 " --> pdb=" O LEU p 57 " (cutoff:3.500A) Processing helix chain 'p' and resid 67 through 76 Processing helix chain 'p' and resid 78 through 88 removed outlier: 3.937A pdb=" N LYS p 82 " --> pdb=" O GLY p 78 " (cutoff:3.500A) Processing helix chain 'r' and resid 15 through 20 removed outlier: 3.722A pdb=" N ASN r 20 " --> pdb=" O TYR r 16 " (cutoff:3.500A) Processing helix chain 'r' and resid 29 through 34 Processing helix chain 'r' and resid 45 through 50 removed outlier: 3.643A pdb=" N THR r 49 " --> pdb=" O PRO r 45 " (cutoff:3.500A) Processing helix chain 'r' and resid 52 through 69 removed outlier: 3.565A pdb=" N ARG r 57 " --> pdb=" O ALA r 53 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE r 68 " --> pdb=" O LYS r 64 " (cutoff:3.500A) Processing helix chain 's' and resid 12 through 23 Processing helix chain 's' and resid 70 through 75 removed outlier: 3.801A pdb=" N PHE s 74 " --> pdb=" O LEU s 71 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA s 75 " --> pdb=" O GLY s 72 " (cutoff:3.500A) Processing helix chain 't' and resid 4 through 40 removed outlier: 3.524A pdb=" N ILE t 8 " --> pdb=" O ILE t 4 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS t 9 " --> pdb=" O GLU t 5 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG t 10 " --> pdb=" O SER t 6 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL t 11 " --> pdb=" O ALA t 7 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ARG t 12 " --> pdb=" O ILE t 8 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA t 38 " --> pdb=" O LYS t 34 " (cutoff:3.500A) Processing helix chain 't' and resid 46 through 63 removed outlier: 3.648A pdb=" N TYR t 50 " --> pdb=" O VAL t 46 " (cutoff:3.500A) Processing helix chain 't' and resid 68 through 80 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 198 through 203 removed outlier: 3.893A pdb=" N GLU C 201 " --> pdb=" O GLU C 198 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE C 203 " --> pdb=" O HIS C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 214 Processing helix chain 'C' and resid 221 through 225 removed outlier: 3.661A pdb=" N MET C 225 " --> pdb=" O GLY C 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 71 removed outlier: 4.319A pdb=" N LYS D 71 " --> pdb=" O GLY D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 102 Processing helix chain 'D' and resid 121 through 127 Processing helix chain 'E' and resid 29 through 43 removed outlier: 3.512A pdb=" N VAL E 33 " --> pdb=" O ASN E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 119 Processing helix chain 'E' and resid 135 through 146 Processing helix chain 'E' and resid 160 through 168 Processing helix chain 'E' and resid 182 through 189 removed outlier: 3.722A pdb=" N VAL E 186 " --> pdb=" O SER E 182 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER E 188 " --> pdb=" O LEU E 184 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA E 189 " --> pdb=" O ASP E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 196 through 207 removed outlier: 3.592A pdb=" N VAL E 205 " --> pdb=" O GLN E 201 " (cutoff:3.500A) Processing helix chain 'F' and resid 4 through 20 removed outlier: 6.122A 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 49 through 61 Processing helix chain 'F' and resid 74 through 78 removed outlier: 3.662A pdb=" N PHE F 77 " --> pdb=" O ILE F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 106 removed outlier: 3.682A pdb=" N TYR F 97 " --> pdb=" O GLY F 93 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL F 106 " --> pdb=" O LYS F 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 111 Processing helix chain 'F' and resid 162 through 172 removed outlier: 3.706A pdb=" N SER F 166 " --> pdb=" O THR F 162 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 81 removed outlier: 4.030A pdb=" N PHE G 72 " --> pdb=" O THR G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 149 removed outlier: 3.840A pdb=" N VAL G 141 " --> pdb=" O ASN G 137 " (cutoff:3.500A) Processing helix chain 'K' and resid 25 through 38 Processing helix chain 'K' and resid 60 through 63 Processing helix chain 'K' and resid 68 through 73 Processing helix chain 'K' and resid 91 through 96 removed outlier: 3.866A pdb=" N ASP K 95 " --> pdb=" O GLY K 91 " (cutoff:3.500A) Processing helix chain 'K' and resid 97 through 108 removed outlier: 4.016A pdb=" N LEU K 101 " --> pdb=" O ASN K 97 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE K 102 " --> pdb=" O SER K 98 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLY K 108 " --> pdb=" O THR K 104 " (cutoff:3.500A) Processing helix chain 'K' and resid 113 through 120 removed outlier: 3.570A pdb=" N LYS K 118 " --> pdb=" O THR K 114 " (cutoff:3.500A) Processing helix chain 'K' and resid 133 through 137 removed outlier: 3.643A pdb=" N GLN K 136 " --> pdb=" O HIS K 133 " (cutoff:3.500A) Processing helix chain 'L' and resid 104 through 109 removed outlier: 4.451A pdb=" N GLU L 108 " --> pdb=" O ARG L 104 " (cutoff:3.500A) Processing helix chain 'M' and resid 37 through 41 removed outlier: 3.602A pdb=" N ARG M 41 " --> pdb=" O GLN M 38 " (cutoff:3.500A) Processing helix chain 'M' and resid 56 through 61 removed outlier: 3.557A pdb=" N ARG M 60 " --> pdb=" O PRO M 56 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU M 61 " --> pdb=" O LEU M 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 56 through 61' Processing helix chain 'M' and resid 80 through 84 removed outlier: 3.671A pdb=" N ARG M 84 " --> pdb=" O THR M 81 " (cutoff:3.500A) Processing helix chain 'M' and resid 92 through 97 Processing helix chain 'M' and resid 129 through 140 Processing helix chain 'N' and resid 44 through 57 removed outlier: 3.755A pdb=" N TYR N 57 " --> pdb=" O ALA N 53 " (cutoff:3.500A) Processing helix chain 'N' and resid 110 through 123 removed outlier: 3.832A pdb=" N HIS N 123 " --> pdb=" O ARG N 119 " (cutoff:3.500A) Processing helix chain 'O' and resid 9 through 26 removed outlier: 3.632A pdb=" N LYS O 14 " --> pdb=" O SER O 10 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR O 22 " --> pdb=" O ARG O 18 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N LEU O 24 " --> pdb=" O ILE O 20 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE O 25 " --> pdb=" O THR O 21 " (cutoff:3.500A) Processing helix chain 'O' and resid 34 through 52 removed outlier: 3.636A pdb=" N LYS O 38 " --> pdb=" O GLU O 34 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU O 50 " --> pdb=" O LYS O 46 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 63 Processing helix chain 'O' and resid 86 through 92 Processing helix chain 'O' and resid 92 through 97 Processing helix chain 'P' and resid 6 through 19 removed outlier: 3.741A pdb=" N THR P 10 " --> pdb=" O ASP P 6 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG P 14 " --> pdb=" O THR P 10 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ARG P 17 " --> pdb=" O LYS P 13 " (cutoff:3.500A) Processing helix chain 'P' and resid 69 through 86 removed outlier: 4.029A pdb=" N ALA P 73 " --> pdb=" O THR P 69 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA P 74 " --> pdb=" O GLU P 70 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL P 75 " --> pdb=" O THR P 71 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS P 86 " --> pdb=" O ARG P 82 " (cutoff:3.500A) Processing helix chain 'P' and resid 102 through 114 removed outlier: 3.707A pdb=" N ALA P 106 " --> pdb=" O GLY P 102 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU P 107 " --> pdb=" O ARG P 103 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASN P 114 " --> pdb=" O ALA P 110 " (cutoff:3.500A) Processing helix chain 'Q' and resid 3 through 11 removed outlier: 4.655A pdb=" N GLU Q 11 " --> pdb=" O GLU Q 7 " (cutoff:3.500A) Processing helix chain 'Q' and resid 53 through 56 removed outlier: 4.097A pdb=" N SER Q 56 " --> pdb=" O ALA Q 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 53 through 56' Processing helix chain 'Q' and resid 97 through 103 removed outlier: 3.675A pdb=" N ALA Q 102 " --> pdb=" O TYR Q 99 " (cutoff:3.500A) Processing helix chain 'R' and resid 8 through 20 removed outlier: 3.747A pdb=" N LYS R 12 " --> pdb=" O THR R 8 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU R 20 " --> pdb=" O LYS R 16 " (cutoff:3.500A) Processing helix chain 'R' and resid 25 through 29 Processing helix chain 'R' and resid 31 through 70 removed outlier: 3.913A pdb=" N ARG R 51 " --> pdb=" O PHE R 47 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LYS R 54 " --> pdb=" O ARG R 50 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ARG R 55 " --> pdb=" O ARG R 51 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ARG R 58 " --> pdb=" O LYS R 54 " (cutoff:3.500A) Processing helix chain 'R' and resid 71 through 73 No H-bonds generated for 'chain 'R' and resid 71 through 73' Processing helix chain 'R' and resid 75 through 86 Processing helix chain 'R' and resid 91 through 102 Processing helix chain 'R' and resid 102 through 117 Processing helix chain 'T' and resid 18 through 27 removed outlier: 3.635A pdb=" N ARG T 23 " --> pdb=" O PRO T 19 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU T 24 " --> pdb=" O ARG T 20 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL T 25 " --> pdb=" O LYS T 21 " (cutoff:3.500A) Processing helix chain 'T' and resid 33 through 43 removed outlier: 3.645A pdb=" N ILE T 38 " --> pdb=" O VAL T 34 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N SER T 39 " --> pdb=" O ALA T 35 " (cutoff:3.500A) Processing helix chain 'T' and resid 48 through 66 removed outlier: 3.553A pdb=" N LYS T 54 " --> pdb=" O GLY T 50 " (cutoff:3.500A) Processing helix chain 'T' and resid 94 through 96 No H-bonds generated for 'chain 'T' and resid 94 through 96' Processing helix chain 'U' and resid 13 through 20 removed outlier: 3.870A pdb=" N LEU U 18 " --> pdb=" O GLU U 14 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA U 19 " --> pdb=" O LYS U 15 " (cutoff:3.500A) Processing helix chain 'U' and resid 34 through 47 Processing helix chain 'Y' and resid 51 through 55 Processing helix chain 'Z' and resid 3 through 7 Processing helix chain 'Z' and resid 10 through 34 removed outlier: 3.719A pdb=" N LEU Z 15 " --> pdb=" O THR Z 11 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA Z 33 " --> pdb=" O ARG Z 29 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR Z 34 " --> pdb=" O PHE Z 30 " (cutoff:3.500A) Processing helix chain 'Z' and resid 41 through 61 removed outlier: 3.706A pdb=" N GLU Z 45 " --> pdb=" O ALA Z 41 " (cutoff:3.500A) Processing helix chain '0' and resid 16 through 27 Processing helix chain '0' and resid 40 through 51 removed outlier: 3.519A pdb=" N LYS 0 44 " --> pdb=" O ASN 0 40 " (cutoff:3.500A) Processing helix chain '2' and resid 9 through 17 Processing helix chain '2' and resid 18 through 20 No H-bonds generated for 'chain '2' and resid 18 through 20' Processing helix chain '4' and resid 8 through 17 removed outlier: 3.650A pdb=" N ARG 4 12 " --> pdb=" O ASN 4 8 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN 4 13 " --> pdb=" O LYS 4 9 " (cutoff:3.500A) Processing helix chain '4' and resid 17 through 23 Processing helix chain '4' and resid 24 through 36 removed outlier: 3.631A pdb=" N ARG 4 28 " --> pdb=" O THR 4 24 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG 4 29 " --> pdb=" O LYS 4 25 " (cutoff:3.500A) Processing helix chain '5' and resid 7 through 12 removed outlier: 3.637A pdb=" N LYS 5 12 " --> pdb=" O ARG 5 8 " (cutoff:3.500A) Processing helix chain '5' and resid 32 through 36 Processing helix chain '5' and resid 37 through 44 Processing helix chain '5' and resid 51 through 59 removed outlier: 3.570A pdb=" N ARG 5 57 " --> pdb=" O GLY 5 53 " (cutoff:3.500A) Processing helix chain '5' and resid 60 through 63 removed outlier: 3.873A pdb=" N ALA 5 63 " --> pdb=" O GLN 5 60 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 60 through 63' Processing helix chain '6' and resid 30 through 33 Processing sheet with id=AA1, first strand: chain 'c' and resid 51 through 58 removed outlier: 3.958A pdb=" N THR c 53 " --> pdb=" O HIS c 68 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'c' and resid 51 through 58 removed outlier: 3.958A pdb=" N THR c 53 " --> pdb=" O HIS c 68 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N VAL c 103 " --> pdb=" O ILE c 65 " (cutoff:3.500A) removed outlier: 6.033A 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 165 Processing sheet with id=AA4, first strand: chain 'c' and resid 163 through 165 removed outlier: 3.552A pdb=" N GLY c 147 " --> pdb=" O TYR c 202 " (cutoff:3.500A) removed outlier: 3.540A 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 Processing sheet with id=AA6, first strand: chain 'd' and resid 166 through 169 Processing sheet with id=AA7, first strand: chain 'e' and resid 14 through 24 removed outlier: 5.688A pdb=" N VAL e 15 " --> pdb=" O VAL e 38 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N VAL e 38 " --> pdb=" O VAL e 15 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA e 17 " --> pdb=" O LEU e 36 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'e' and resid 85 through 88 Processing sheet with id=AA9, first strand: chain 'f' and resid 39 through 50 removed outlier: 6.062A pdb=" N ASN f 67 " --> pdb=" O ILE f 41 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N SER f 43 " --> pdb=" O ILE f 65 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ILE f 65 " --> pdb=" O SER f 43 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N ASP f 45 " --> pdb=" O TYR f 63 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N TYR f 63 " --> pdb=" O ASP f 45 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N GLU f 47 " --> pdb=" O GLY f 61 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N GLY f 61 " --> pdb=" O GLU f 47 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL f 68 " --> pdb=" O TYR f 7 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N MET f 10 " --> pdb=" O HIS f 93 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N HIS f 93 " --> pdb=" O MET f 10 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE f 12 " --> pdb=" O ILE f 91 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'f' and resid 39 through 50 removed outlier: 6.062A pdb=" N ASN f 67 " --> pdb=" O ILE f 41 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N SER f 43 " --> pdb=" O ILE f 65 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ILE f 65 " --> pdb=" O SER f 43 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N ASP f 45 " --> pdb=" O TYR f 63 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N TYR f 63 " --> pdb=" O ASP f 45 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N GLU f 47 " --> pdb=" O GLY f 61 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N GLY f 61 " --> pdb=" O GLU f 47 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL f 68 " --> pdb=" O TYR f 7 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N LYS f 6 " --> pdb=" O VAL f 98 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'g' and resid 74 through 79 removed outlier: 3.580A pdb=" N GLU g 74 " --> pdb=" O VAL g 89 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'h' and resid 25 through 27 removed outlier: 3.650A pdb=" N ASP h 48 " --> pdb=" O PHE h 63 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'h' and resid 77 through 79 removed outlier: 6.805A pdb=" N ILE h 105 " --> pdb=" O ILE h 128 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N TYR h 130 " --> pdb=" O ILE h 103 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ILE h 103 " --> pdb=" O TYR h 130 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY h 111 " --> pdb=" O THR h 108 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'i' and resid 6 through 12 removed outlier: 6.540A pdb=" N LYS i 27 " --> pdb=" O VAL i 63 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N VAL i 65 " --> pdb=" O LYS i 27 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N THR i 29 " --> pdb=" O VAL i 65 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N VAL i 67 " --> pdb=" O THR i 29 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'j' and resid 40 through 52 removed outlier: 6.457A pdb=" N LEU j 73 " --> pdb=" O PRO j 41 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N LYS j 71 " --> pdb=" O PRO j 43 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU j 45 " --> pdb=" O THR j 69 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER j 47 " --> pdb=" O MET j 67 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET j 67 " --> pdb=" O SER j 47 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE j 74 " --> pdb=" O ILE j 8 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'j' and resid 40 through 52 removed outlier: 6.457A pdb=" N LEU j 73 " --> pdb=" O PRO j 41 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N LYS j 71 " --> pdb=" O PRO j 43 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU j 45 " --> pdb=" O THR j 69 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER j 47 " --> pdb=" O MET j 67 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET j 67 " --> pdb=" O SER j 47 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'k' and resid 41 through 46 removed outlier: 6.344A pdb=" N VAL k 82 " --> pdb=" O VAL k 107 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ALA k 109 " --> pdb=" O VAL k 82 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'l' and resid 43 through 53 removed outlier: 5.875A pdb=" N CYS l 47 " --> pdb=" O ARG l 69 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ARG l 69 " --> pdb=" O CYS l 47 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARG l 49 " --> pdb=" O ARG l 67 " (cutoff:3.500A) removed outlier: 13.538A pdb=" N GLU l 75 " --> pdb=" O VAL l 106 " (cutoff:3.500A) removed outlier: 10.192A pdb=" N TYR l 108 " --> pdb=" O GLU l 75 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N THR l 77 " --> pdb=" O TYR l 108 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N ILE l 110 " --> pdb=" O THR l 77 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N TYR l 79 " --> pdb=" O ILE l 110 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'n' and resid 33 through 34 Processing sheet with id=AC2, first strand: chain 'p' and resid 48 through 50 removed outlier: 3.595A pdb=" N GLU p 48 " --> pdb=" O ASN p 41 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU p 35 " --> pdb=" O VAL p 22 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ILE p 20 " --> pdb=" O VAL p 37 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N THR p 39 " --> pdb=" O TYR p 18 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N TYR p 18 " --> pdb=" O THR p 39 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'q' and resid 10 through 17 removed outlier: 17.366A pdb=" N VAL q 10 " --> pdb=" O LYS q 31 " (cutoff:3.500A) removed outlier: 14.270A pdb=" N LYS q 31 " --> pdb=" O VAL q 10 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N GLN q 12 " --> pdb=" O GLU q 29 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N GLU q 29 " --> pdb=" O GLN q 12 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N THR q 25 " --> pdb=" O VAL q 16 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N LEU q 78 " --> pdb=" O MET q 65 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N MET q 65 " --> pdb=" O LEU q 78 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU q 80 " --> pdb=" O LYS q 63 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ILE q 61 " --> pdb=" O VAL q 82 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 's' and resid 32 through 33 removed outlier: 3.684A pdb=" N TYR s 52 " --> pdb=" O THR s 33 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 3 through 5 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: 3.749A pdb=" N THR C 80 " --> pdb=" O LEU C 93 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N HIS C 95 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N VAL C 78 " --> pdb=" O HIS C 95 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 129 through 131 removed outlier: 5.823A pdb=" N VAL C 164 " --> pdb=" O ARG C 175 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ARG C 175 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY C 166 " --> pdb=" O LEU C 173 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 247 through 248 Processing sheet with id=AD1, first strand: chain 'D' and resid 4 through 16 removed outlier: 6.813A pdb=" N VAL D 27 " --> pdb=" O VAL D 10 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N MET D 12 " --> pdb=" O VAL D 25 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N VAL D 25 " --> pdb=" O MET D 12 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N GLN D 14 " --> pdb=" O ILE D 23 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ILE D 23 " --> pdb=" O GLN D 14 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS D 178 " --> pdb=" O LEU D 187 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LYS D 189 " --> pdb=" O VAL D 176 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N VAL D 176 " --> pdb=" O LYS D 189 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N VAL D 108 " --> pdb=" O ASN D 173 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N GLU D 175 " --> pdb=" O ASP D 106 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N ASP D 106 " --> pdb=" O GLU D 175 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N THR D 113 " --> pdb=" O LEU D 199 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N LEU D 199 " --> pdb=" O THR D 113 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 77 through 84 removed outlier: 6.460A pdb=" N LYS D 77 " --> pdb=" O ASP D 55 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ASP D 55 " --> pdb=" O LYS D 77 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ALA D 48 " --> pdb=" O VAL D 38 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N VAL D 38 " --> pdb=" O ALA D 48 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N GLN D 50 " --> pdb=" O LEU D 36 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 116 through 120 removed outlier: 3.569A pdb=" N GLY D 118 " --> pdb=" O MET D 164 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 16 through 18 removed outlier: 10.091A pdb=" N ASN E 3 " --> pdb=" O LEU E 123 " (cutoff:3.500A) removed outlier: 9.371A pdb=" N ALA E 125 " --> pdb=" O ASN E 3 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ALA E 5 " --> pdb=" O ALA E 125 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LEU E 153 " --> pdb=" O LEU E 193 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N THR E 195 " --> pdb=" O LEU E 153 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N VAL E 155 " --> pdb=" O THR E 195 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 87 through 91 removed outlier: 3.640A pdb=" N ALA F 87 " --> pdb=" O MET F 38 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 16 through 20 removed outlier: 3.881A pdb=" N LYS G 18 " --> pdb=" O THR G 25 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR G 25 " --> pdb=" O LYS G 18 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP G 20 " --> pdb=" O ASN G 23 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 83 through 87 removed outlier: 3.573A pdb=" N PHE G 83 " --> pdb=" O GLY G 135 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLY G 135 " --> pdb=" O PHE G 83 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS G 134 " --> pdb=" O THR G 122 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 95 through 99 removed outlier: 3.525A pdb=" N ARG G 95 " --> pdb=" O ASN G 106 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'K' and resid 123 through 126 removed outlier: 6.620A pdb=" N VAL K 55 " --> pdb=" O ASN K 124 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N TYR K 126 " --> pdb=" O VAL K 55 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N VAL K 57 " --> pdb=" O TYR K 126 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N TRP K 16 " --> pdb=" O GLU K 139 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'K' and resid 75 through 78 removed outlier: 7.039A pdb=" N TYR K 75 " --> pdb=" O VAL K 88 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N VAL K 88 " --> pdb=" O TYR K 75 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'L' and resid 7 through 10 removed outlier: 6.251A pdb=" N ARG L 17 " --> pdb=" O VAL L 10 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N ALA L 16 " --> pdb=" O ALA L 46 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ALA L 46 " --> pdb=" O ALA L 16 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N GLU L 18 " --> pdb=" O LYS L 44 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL L 40 " --> pdb=" O ILE L 22 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA L 83 " --> pdb=" O VAL L 63 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N ALA L 84 " --> pdb=" O ARG L 7 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ARG L 9 " --> pdb=" O ALA L 84 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N ILE L 86 " --> pdb=" O ARG L 9 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'L' and resid 69 through 70 removed outlier: 6.928A pdb=" N THR Q 58 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ARG Q 50 " --> pdb=" O THR Q 58 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N THR Q 60 " --> pdb=" O ILE Q 48 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N VAL Q 64 " --> pdb=" O GLU Q 44 " (cutoff:3.500A) removed outlier: 9.076A pdb=" N GLU Q 44 " --> pdb=" O VAL Q 64 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N THR Q 25 " --> pdb=" O VAL Q 87 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'M' and resid 110 through 111 Processing sheet with id=AE5, first strand: chain 'M' and resid 122 through 125 removed outlier: 3.675A pdb=" N ALA M 125 " --> pdb=" O GLU M 144 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'N' and resid 63 through 66 removed outlier: 6.873A pdb=" N LEU N 34 " --> pdb=" O MET N 103 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLU N 105 " --> pdb=" O TRP N 32 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N TRP N 32 " --> pdb=" O GLU N 105 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'N' and resid 40 through 43 Processing sheet with id=AE8, first strand: chain 'O' and resid 29 through 33 removed outlier: 6.585A pdb=" N MET O 120 " --> pdb=" O THR O 110 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'P' and resid 34 through 35 removed outlier: 6.994A pdb=" N ILE P 40 " --> pdb=" O SER P 57 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N SER P 57 " --> pdb=" O ILE P 40 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N ALA P 42 " --> pdb=" O SER P 55 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N SER P 55 " --> pdb=" O ALA P 42 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N VAL P 44 " --> pdb=" O LEU P 53 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'P' and resid 34 through 35 Processing sheet with id=AF2, first strand: chain 'Q' and resid 32 through 34 removed outlier: 3.636A pdb=" N ARG Q 37 " --> pdb=" O GLU Q 34 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'S' and resid 10 through 14 removed outlier: 3.564A pdb=" N ALA S 3 " --> pdb=" O VAL S 14 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILE S 4 " --> pdb=" O ILE S 39 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL S 41 " --> pdb=" O LYS S 47 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'S' and resid 19 through 22 removed outlier: 6.682A pdb=" N TYR S 92 " --> pdb=" O HIS S 65 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N HIS S 65 " --> pdb=" O TYR S 92 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LYS S 94 " --> pdb=" O GLU S 63 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU S 59 " --> pdb=" O GLU S 98 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'S' and resid 71 through 76 Processing sheet with id=AF6, first strand: chain 'T' and resid 7 through 15 removed outlier: 5.611A pdb=" N LYS T 9 " --> pdb=" O VAL T 112 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N VAL T 112 " --> pdb=" O LYS T 9 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N THR T 11 " --> pdb=" O VAL T 110 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N VAL T 110 " --> pdb=" O THR T 11 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N LYS T 13 " --> pdb=" O ILE T 108 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ILE T 108 " --> pdb=" O LYS T 13 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU T 78 " --> pdb=" O VAL T 111 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N THR T 113 " --> pdb=" O VAL T 76 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N VAL T 76 " --> pdb=" O THR T 113 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'T' and resid 87 through 92 Processing sheet with id=AF8, first strand: chain 'U' and resid 7 through 10 removed outlier: 3.541A pdb=" N ARG U 9 " --> pdb=" O GLU U 28 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ARG U 76 " --> pdb=" O VAL U 29 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR U 81 " --> pdb=" O ASN U 52 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ASN U 52 " --> pdb=" O THR U 81 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'U' and resid 62 through 64 Processing sheet with id=AG1, first strand: chain 'V' and resid 63 through 64 removed outlier: 7.173A pdb=" N LYS V 32 " --> pdb=" O ALA V 26 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N ALA V 26 " --> pdb=" O LYS V 32 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE V 34 " --> pdb=" O LEU V 24 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N LYS V 8 " --> pdb=" O ILE V 71 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N VAL V 70 " --> pdb=" O THR V 79 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'V' and resid 40 through 42 Processing sheet with id=AG3, first strand: chain 'V' and resid 81 through 83 Processing sheet with id=AG4, first strand: chain 'X' and resid 31 through 32 removed outlier: 6.623A pdb=" N LEU X 68 " --> pdb=" O LEU X 46 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'X' and resid 39 through 40 removed outlier: 3.516A pdb=" N LYS X 85 " --> pdb=" O LYS X 81 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'Y' and resid 13 through 18 removed outlier: 3.637A pdb=" N THR Y 25 " --> pdb=" O ASN Y 17 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'Y' and resid 33 through 39 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 removed outlier: 3.523A pdb=" N LYS 2 52 " --> pdb=" O TYR 2 49 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain '3' and resid 15 through 22 removed outlier: 6.452A pdb=" N ARG 3 15 " --> pdb=" O CYS 3 9 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N CYS 3 9 " --> pdb=" O ARG 3 15 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR 3 17 " --> pdb=" O LEU 3 7 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain '5' and resid 14 through 16 Processing sheet with id=AH4, first strand: chain '6' and resid 2 through 4 removed outlier: 6.099A pdb=" N LYS 6 2 " --> pdb=" O ARG 6 36 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N VAL 6 23 " --> pdb=" O GLN 6 37 " (cutoff:3.500A) 1418 hydrogen bonds defined for protein. 3942 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3582 hydrogen bonds 5722 hydrogen bond angles 0 basepair planarities 1427 basepair parallelities 2363 stacking parallelities Total time for adding SS restraints: 201.47 Time building geometry restraints manager: 50.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 13575 1.31 - 1.44: 64147 1.44 - 1.57: 58657 1.57 - 1.70: 8745 1.70 - 1.83: 229 Bond restraints: 145353 Sorted by residual: bond pdb=" C6 G A 903 " pdb=" N1 G A 903 " ideal model delta sigma weight residual 1.391 1.308 0.083 2.00e-02 2.50e+03 1.72e+01 bond pdb=" N9 G A 769 " pdb=" C4 G A 769 " ideal model delta sigma weight residual 1.375 1.306 0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" N9 G A1492 " pdb=" C4 G A1492 " ideal model delta sigma weight residual 1.375 1.310 0.065 2.00e-02 2.50e+03 1.05e+01 bond pdb=" C4 C A 956 " pdb=" N4 C A 956 " ideal model delta sigma weight residual 1.335 1.271 0.064 2.00e-02 2.50e+03 1.01e+01 bond pdb=" C ARG M 60 " pdb=" N LEU M 61 " ideal model delta sigma weight residual 1.339 1.179 0.160 5.57e-02 3.22e+02 8.28e+00 ... (remaining 145348 not shown) Histogram of bond angle deviations from ideal: 94.45 - 103.92: 13740 103.92 - 113.39: 97270 113.39 - 122.86: 80966 122.86 - 132.34: 25386 132.34 - 141.81: 572 Bond angle restraints: 217934 Sorted by residual: angle pdb=" N3 C A 956 " pdb=" C4 C A 956 " pdb=" N4 C A 956 " ideal model delta sigma weight residual 118.00 96.38 21.62 3.00e+00 1.11e-01 5.19e+01 angle pdb=" N GLY Q 52 " pdb=" CA GLY Q 52 " pdb=" C GLY Q 52 " ideal model delta sigma weight residual 110.77 121.30 -10.53 1.59e+00 3.96e-01 4.39e+01 angle pdb=" O3' U a 34 " pdb=" P G a 35 " pdb=" O5' G a 35 " ideal model delta sigma weight residual 104.00 112.98 -8.98 1.50e+00 4.44e-01 3.59e+01 angle pdb=" N4 C A 956 " pdb=" C4 C A 956 " pdb=" C5 C A 956 " ideal model delta sigma weight residual 120.20 138.03 -17.83 3.00e+00 1.11e-01 3.53e+01 angle pdb=" C3' U a 34 " pdb=" O3' U a 34 " pdb=" P G a 35 " ideal model delta sigma weight residual 120.20 111.59 8.61 1.50e+00 4.44e-01 3.29e+01 ... (remaining 217929 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.82: 81668 35.82 - 71.65: 10213 71.65 - 107.47: 1061 107.47 - 143.30: 20 143.30 - 179.12: 24 Dihedral angle restraints: 92986 sinusoidal: 78565 harmonic: 14421 Sorted by residual: 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 180.00 116.80 63.20 0 5.00e+00 4.00e-02 1.60e+02 dihedral pdb=" C5' U A2811 " pdb=" C4' U A2811 " pdb=" C3' U A2811 " pdb=" O3' U A2811 " ideal model delta sinusoidal sigma weight residual 147.00 76.16 70.84 1 8.00e+00 1.56e-02 1.01e+02 dihedral pdb=" CA ALA S 50 " pdb=" C ALA S 50 " pdb=" N PRO S 51 " pdb=" CA PRO S 51 " ideal model delta harmonic sigma weight residual -180.00 -130.42 -49.58 0 5.00e+00 4.00e-02 9.83e+01 ... (remaining 92983 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 24252 0.082 - 0.165: 3348 0.165 - 0.247: 291 0.247 - 0.329: 45 0.329 - 0.411: 9 Chirality restraints: 27945 Sorted by residual: chirality pdb=" C1' C a 201 " pdb=" O4' C a 201 " pdb=" C2' C a 201 " pdb=" N1 C a 201 " both_signs ideal model delta sigma weight residual False 2.47 2.05 0.41 2.00e-01 2.50e+01 4.23e+00 chirality pdb=" C1' A A 654 " pdb=" O4' A A 654 " pdb=" C2' A A 654 " pdb=" N9 A A 654 " both_signs ideal model delta sigma weight residual False 2.44 2.05 0.39 2.00e-01 2.50e+01 3.77e+00 chirality pdb=" C1' U A1093 " pdb=" O4' U A1093 " pdb=" C2' U A1093 " pdb=" N1 U A1093 " both_signs ideal model delta sigma weight residual False 2.47 2.08 0.38 2.00e-01 2.50e+01 3.64e+00 ... (remaining 27942 not shown) Planarity restraints: 11316 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G A 992 " 0.079 2.00e-02 2.50e+03 3.41e-02 3.48e+01 pdb=" N9 G A 992 " -0.082 2.00e-02 2.50e+03 pdb=" C8 G A 992 " -0.012 2.00e-02 2.50e+03 pdb=" N7 G A 992 " 0.003 2.00e-02 2.50e+03 pdb=" C5 G A 992 " -0.003 2.00e-02 2.50e+03 pdb=" C6 G A 992 " 0.019 2.00e-02 2.50e+03 pdb=" O6 G A 992 " 0.012 2.00e-02 2.50e+03 pdb=" N1 G A 992 " 0.012 2.00e-02 2.50e+03 pdb=" C2 G A 992 " -0.003 2.00e-02 2.50e+03 pdb=" N2 G A 992 " -0.005 2.00e-02 2.50e+03 pdb=" N3 G A 992 " -0.009 2.00e-02 2.50e+03 pdb=" C4 G A 992 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C A2454 " -0.065 2.00e-02 2.50e+03 3.74e-02 3.15e+01 pdb=" N1 C A2454 " 0.089 2.00e-02 2.50e+03 pdb=" C2 C A2454 " -0.006 2.00e-02 2.50e+03 pdb=" O2 C A2454 " 0.005 2.00e-02 2.50e+03 pdb=" N3 C A2454 " -0.002 2.00e-02 2.50e+03 pdb=" C4 C A2454 " -0.011 2.00e-02 2.50e+03 pdb=" N4 C A2454 " -0.014 2.00e-02 2.50e+03 pdb=" C5 C A2454 " -0.003 2.00e-02 2.50e+03 pdb=" C6 C A2454 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C a 31 " -0.068 2.00e-02 2.50e+03 3.64e-02 2.99e+01 pdb=" N1 C a 31 " 0.081 2.00e-02 2.50e+03 pdb=" C2 C a 31 " 0.005 2.00e-02 2.50e+03 pdb=" O2 C a 31 " 0.004 2.00e-02 2.50e+03 pdb=" N3 C a 31 " -0.005 2.00e-02 2.50e+03 pdb=" C4 C a 31 " -0.016 2.00e-02 2.50e+03 pdb=" N4 C a 31 " -0.013 2.00e-02 2.50e+03 pdb=" C5 C a 31 " -0.004 2.00e-02 2.50e+03 pdb=" C6 C a 31 " 0.016 2.00e-02 2.50e+03 ... (remaining 11313 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 979 2.57 - 3.15: 92598 3.15 - 3.74: 236802 3.74 - 4.32: 358494 4.32 - 4.90: 477735 Nonbonded interactions: 1166608 Sorted by model distance: nonbonded pdb=" OG SER V 94 " pdb=" O LYS V 95 " model vdw 1.989 2.440 nonbonded pdb=" O2 U a 976 " pdb=" O2' G a1237 " model vdw 1.992 2.440 nonbonded pdb=" OE2 GLU 3 39 " pdb="ZN ZN 3 101 " model vdw 1.992 2.230 nonbonded pdb=" O2' C A2454 " pdb=" O5' C A2455 " model vdw 2.017 2.440 nonbonded pdb=" O2' U A1832 " pdb=" O LEU C 154 " model vdw 2.029 2.440 ... (remaining 1166603 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: 3.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.080 Extract box with map and model: 21.980 Check model and map are aligned: 1.430 Set scattering table: 0.880 Process input model: 447.190 Find NCS groups from input model: 2.390 Set up NCS constraints: 0.290 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:11.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 489.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 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 0.160 145353 Z= 0.596 Angle : 1.072 21.620 217934 Z= 0.530 Chirality : 0.057 0.411 27945 Planarity : 0.007 0.081 11316 Dihedral : 23.451 179.124 83708 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.32 % Allowed : 12.07 % Favored : 87.61 % Rotamer: Outliers : 16.52 % Allowed : 14.35 % Favored : 69.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.17 % Twisted Proline : 0.54 % Twisted General : 0.21 % 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: -4.00 (0.10), residues: 4970 helix: -2.37 (0.11), residues: 1415 sheet: -1.85 (0.15), residues: 975 loop : -3.21 (0.10), residues: 2580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP d 9 HIS 0.010 0.002 HIS h 22 PHE 0.033 0.004 PHE V 2 TYR 0.029 0.003 TYR l 28 ARG 0.011 0.001 ARG 5 45 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9940 Ramachandran restraints generated. 4970 Oldfield, 0 Emsley, 4970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9940 Ramachandran restraints generated. 4970 Oldfield, 0 Emsley, 4970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1583 residues out of total 4231 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 699 poor density : 884 time to evaluate : 5.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 39 ARG cc_start: 0.8154 (OUTLIER) cc_final: 0.7924 (ttp-170) REVERT: c 200 TRP cc_start: 0.7997 (OUTLIER) cc_final: 0.7488 (m100) REVERT: d 29 ARG cc_start: 0.7831 (OUTLIER) cc_final: 0.7204 (ptt180) REVERT: d 65 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7410 (mm-30) REVERT: d 114 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8539 (mt) REVERT: d 143 ARG cc_start: 0.7501 (OUTLIER) cc_final: 0.6683 (ttt-90) REVERT: d 190 ILE cc_start: 0.6730 (OUTLIER) cc_final: 0.6425 (mt) REVERT: e 112 ARG cc_start: 0.7779 (OUTLIER) cc_final: 0.7522 (ttm-80) REVERT: f 3 GLN cc_start: 0.6112 (OUTLIER) cc_final: 0.5166 (mm110) REVERT: g 10 ARG cc_start: 0.7231 (OUTLIER) cc_final: 0.5169 (tpm170) REVERT: g 117 GLU cc_start: 0.7521 (pm20) cc_final: 0.6174 (mt-10) REVERT: h 49 VAL cc_start: 0.8717 (OUTLIER) cc_final: 0.8446 (t) REVERT: i 89 GLN cc_start: 0.7676 (tt0) cc_final: 0.7400 (tt0) REVERT: j 4 GLN cc_start: 0.4872 (OUTLIER) cc_final: 0.4501 (tm-30) REVERT: j 85 ASP cc_start: 0.6106 (OUTLIER) cc_final: 0.5727 (m-30) REVERT: k 40 ASN cc_start: 0.7278 (OUTLIER) cc_final: 0.7043 (m110) REVERT: l 42 GLN cc_start: 0.8348 (OUTLIER) cc_final: 0.8035 (mp10) REVERT: l 63 ARG cc_start: 0.8538 (OUTLIER) cc_final: 0.7883 (mtt90) REVERT: l 86 ASN cc_start: 0.7740 (p0) cc_final: 0.7516 (p0) REVERT: m 11 ARG cc_start: 0.6063 (mmm-85) cc_final: 0.5694 (tmt170) REVERT: m 100 GLN cc_start: 0.8134 (OUTLIER) cc_final: 0.7724 (mp10) REVERT: m 109 ARG cc_start: 0.8174 (OUTLIER) cc_final: 0.7660 (tpt-90) REVERT: o 67 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8640 (mt) REVERT: q 41 MET cc_start: 0.7276 (mmm) cc_final: 0.6978 (mmt) REVERT: s 7 LYS cc_start: 0.5396 (OUTLIER) cc_final: 0.3739 (pttt) REVERT: s 36 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.6833 (mtm110) REVERT: C 30 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7082 (tm-30) REVERT: C 38 LYS cc_start: 0.8100 (OUTLIER) cc_final: 0.7826 (tttt) REVERT: D 3 LYS cc_start: 0.8337 (mttt) cc_final: 0.8126 (mtpt) REVERT: D 90 GLU cc_start: 0.6970 (OUTLIER) cc_final: 0.5878 (tm-30) REVERT: E 45 ARG cc_start: 0.8869 (OUTLIER) cc_final: 0.7255 (mtt180) REVERT: E 66 ARG cc_start: 0.5869 (mtm110) cc_final: 0.5401 (mtt-85) REVERT: E 78 ILE cc_start: 0.8278 (OUTLIER) cc_final: 0.7834 (mp) REVERT: E 147 SER cc_start: 0.8242 (p) cc_final: 0.8002 (m) REVERT: E 190 ASN cc_start: 0.8687 (OUTLIER) cc_final: 0.8341 (t0) REVERT: G 44 ASN cc_start: 0.4729 (OUTLIER) cc_final: 0.4345 (t0) REVERT: G 171 ARG cc_start: 0.7879 (OUTLIER) cc_final: 0.7223 (mmm160) REVERT: K 14 ARG cc_start: 0.8184 (OUTLIER) cc_final: 0.6526 (mtt180) REVERT: K 26 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8330 (tp) REVERT: K 123 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8681 (tp) REVERT: L 19 ILE cc_start: 0.8168 (OUTLIER) cc_final: 0.7778 (pt) REVERT: L 105 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7622 (mm-30) REVERT: L 110 ASN cc_start: 0.6477 (OUTLIER) cc_final: 0.6098 (m110) REVERT: M 79 LEU cc_start: 0.7484 (OUTLIER) cc_final: 0.6820 (mp) REVERT: N 11 ARG cc_start: 0.8548 (OUTLIER) cc_final: 0.6257 (mmt90) REVERT: N 26 GLU cc_start: 0.7324 (OUTLIER) cc_final: 0.6814 (mm-30) REVERT: N 51 ARG cc_start: 0.7790 (OUTLIER) cc_final: 0.6765 (ttm110) REVERT: O 19 ASP cc_start: 0.7594 (m-30) cc_final: 0.7187 (m-30) REVERT: P 22 ILE cc_start: 0.8651 (OUTLIER) cc_final: 0.8225 (mp) REVERT: P 35 ARG cc_start: 0.8310 (OUTLIER) cc_final: 0.6727 (ttt180) REVERT: Q 104 HIS cc_start: 0.6381 (m-70) cc_final: 0.6175 (m90) REVERT: R 56 ASP cc_start: 0.7413 (m-30) cc_final: 0.7114 (m-30) REVERT: S 96 MET cc_start: 0.7625 (mmm) cc_final: 0.7231 (tpt) REVERT: S 101 ASN cc_start: 0.5655 (OUTLIER) cc_final: 0.5453 (t0) REVERT: T 27 ASP cc_start: 0.7604 (m-30) cc_final: 0.7278 (m-30) REVERT: T 93 ARG cc_start: 0.8502 (OUTLIER) cc_final: 0.5843 (mpt-90) REVERT: U 30 ASP cc_start: 0.7606 (t70) cc_final: 0.7362 (t70) REVERT: U 75 ARG cc_start: 0.8285 (OUTLIER) cc_final: 0.7674 (mtt90) REVERT: V 5 LYS cc_start: 0.7917 (OUTLIER) cc_final: 0.6929 (tttm) REVERT: V 17 LYS cc_start: 0.8391 (OUTLIER) cc_final: 0.8145 (ttmp) REVERT: V 29 LYS cc_start: 0.7327 (OUTLIER) cc_final: 0.6979 (pttt) REVERT: V 58 GLU cc_start: 0.7374 (OUTLIER) cc_final: 0.7096 (mt-10) REVERT: X 23 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.8000 (mtm-85) REVERT: Y 22 MET cc_start: 0.7541 (OUTLIER) cc_final: 0.7034 (mmp) REVERT: Y 37 ARG cc_start: 0.7268 (mtt90) cc_final: 0.6993 (mtt-85) REVERT: Z 15 LEU cc_start: 0.7609 (OUTLIER) cc_final: 0.7264 (mp) REVERT: Z 44 LYS cc_start: 0.8397 (tttt) cc_final: 0.8075 (ttmt) REVERT: 3 5 ILE cc_start: 0.7702 (OUTLIER) cc_final: 0.7327 (pt) REVERT: 5 57 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.6617 (ttp80) REVERT: 6 36 ARG cc_start: 0.8717 (OUTLIER) cc_final: 0.7947 (ptt90) outliers start: 699 outliers final: 358 residues processed: 1413 average time/residue: 1.9858 time to fit residues: 3981.8293 Evaluate side-chains 1116 residues out of total 4231 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 412 poor density : 704 time to evaluate : 5.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 21 LYS Chi-restraints excluded: chain c residue 25 GLU Chi-restraints excluded: chain c residue 39 ARG Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 45 LYS Chi-restraints excluded: chain c residue 51 VAL Chi-restraints excluded: chain c residue 67 ILE Chi-restraints excluded: chain c residue 69 THR Chi-restraints excluded: chain c residue 81 SER Chi-restraints excluded: chain c residue 98 VAL Chi-restraints excluded: chain c residue 100 ILE Chi-restraints excluded: chain c residue 103 VAL Chi-restraints excluded: chain c residue 171 THR Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain c residue 199 VAL Chi-restraints excluded: chain c residue 200 TRP Chi-restraints excluded: chain d residue 14 ARG Chi-restraints excluded: chain d residue 25 GLU Chi-restraints excluded: chain d residue 29 ARG Chi-restraints excluded: chain d residue 57 LEU Chi-restraints excluded: chain d residue 58 ARG Chi-restraints excluded: chain d residue 63 MET Chi-restraints excluded: chain d residue 65 GLU Chi-restraints excluded: chain d residue 71 LEU Chi-restraints excluded: chain d residue 114 LEU Chi-restraints excluded: chain d residue 139 VAL Chi-restraints excluded: chain d residue 140 ILE Chi-restraints excluded: chain d residue 143 ARG Chi-restraints excluded: chain d residue 159 THR Chi-restraints excluded: chain d residue 186 LEU Chi-restraints excluded: chain d residue 189 GLU Chi-restraints excluded: chain d residue 190 ILE Chi-restraints excluded: chain d residue 202 LYS Chi-restraints excluded: chain e residue 22 THR Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 76 MET Chi-restraints excluded: chain e residue 95 LEU Chi-restraints excluded: chain e residue 100 VAL Chi-restraints excluded: chain e residue 105 VAL Chi-restraints excluded: chain e residue 111 VAL Chi-restraints excluded: chain e residue 112 ARG Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain e residue 128 LEU Chi-restraints excluded: chain e residue 144 LEU Chi-restraints excluded: chain e residue 147 LEU Chi-restraints excluded: chain e residue 160 SER Chi-restraints excluded: chain e residue 165 ILE Chi-restraints excluded: chain f residue 3 GLN Chi-restraints excluded: chain f residue 4 ASP Chi-restraints excluded: chain f residue 5 THR Chi-restraints excluded: chain f residue 33 LEU Chi-restraints excluded: chain f residue 36 ASN Chi-restraints excluded: chain f residue 45 ASP Chi-restraints excluded: chain f residue 65 ILE Chi-restraints excluded: chain f residue 68 VAL Chi-restraints excluded: chain f residue 77 ILE Chi-restraints excluded: chain f residue 96 VAL Chi-restraints excluded: chain g residue 10 ARG Chi-restraints excluded: chain g residue 43 ILE Chi-restraints excluded: chain g residue 52 GLU Chi-restraints excluded: chain g residue 56 ASN Chi-restraints excluded: chain g residue 64 GLN Chi-restraints excluded: chain g residue 72 VAL Chi-restraints excluded: chain g residue 75 VAL Chi-restraints excluded: chain g residue 85 TYR Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain g residue 120 LEU Chi-restraints excluded: chain g residue 131 THR Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain h residue 2 VAL Chi-restraints excluded: chain h residue 11 LEU Chi-restraints excluded: chain h residue 25 LEU Chi-restraints excluded: chain h residue 27 VAL Chi-restraints excluded: chain h residue 49 VAL Chi-restraints excluded: chain h residue 52 ILE Chi-restraints excluded: chain h residue 54 ASP Chi-restraints excluded: chain h residue 57 GLN Chi-restraints excluded: chain h residue 69 ASN Chi-restraints excluded: chain h residue 73 VAL Chi-restraints excluded: chain h residue 75 THR Chi-restraints excluded: chain h residue 89 VAL Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 113 ILE Chi-restraints excluded: chain h residue 131 VAL Chi-restraints excluded: chain i residue 16 VAL Chi-restraints excluded: chain i residue 29 THR Chi-restraints excluded: chain i residue 35 VAL Chi-restraints excluded: chain i residue 47 VAL Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain i residue 83 ILE Chi-restraints excluded: chain i residue 130 ARG Chi-restraints excluded: chain j residue 4 GLN Chi-restraints excluded: chain j residue 18 LEU Chi-restraints excluded: chain j residue 25 ILE Chi-restraints excluded: chain j residue 32 THR Chi-restraints excluded: chain j residue 48 LEU Chi-restraints excluded: chain j residue 51 VAL Chi-restraints excluded: chain j residue 85 ASP Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 35 THR Chi-restraints excluded: chain k residue 37 THR Chi-restraints excluded: chain k residue 40 ASN Chi-restraints excluded: chain k residue 45 SER Chi-restraints excluded: chain k residue 55 SER Chi-restraints excluded: chain k residue 65 MET Chi-restraints excluded: chain k residue 81 THR Chi-restraints excluded: chain k residue 82 VAL Chi-restraints excluded: chain k residue 85 THR Chi-restraints excluded: chain k residue 86 VAL Chi-restraints excluded: chain l residue 8 VAL Chi-restraints excluded: chain l residue 24 LEU Chi-restraints excluded: chain l residue 25 ASN Chi-restraints excluded: chain l residue 36 THR Chi-restraints excluded: chain l residue 42 GLN Chi-restraints excluded: chain l residue 54 THR Chi-restraints excluded: chain l residue 63 ARG Chi-restraints excluded: chain l residue 64 LYS Chi-restraints excluded: chain l residue 72 ASN Chi-restraints excluded: chain l residue 77 THR Chi-restraints excluded: chain l residue 80 ILE Chi-restraints excluded: chain l residue 92 VAL Chi-restraints excluded: chain l residue 106 VAL Chi-restraints excluded: chain l residue 111 VAL Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain l residue 122 ASP Chi-restraints excluded: chain m residue 14 ARG Chi-restraints excluded: chain m residue 28 THR Chi-restraints excluded: chain m residue 34 LEU Chi-restraints excluded: chain m residue 80 LEU Chi-restraints excluded: chain m residue 100 GLN Chi-restraints excluded: chain m residue 102 THR Chi-restraints excluded: chain m residue 103 LYS Chi-restraints excluded: chain m residue 109 ARG Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain o residue 56 LEU Chi-restraints excluded: chain o residue 67 LEU Chi-restraints excluded: chain o residue 75 ILE Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain p residue 32 ARG Chi-restraints excluded: chain p residue 36 THR Chi-restraints excluded: chain p residue 39 THR Chi-restraints excluded: chain p residue 73 ILE Chi-restraints excluded: chain q residue 10 VAL Chi-restraints excluded: chain q residue 14 ARG Chi-restraints excluded: chain q residue 16 VAL Chi-restraints excluded: chain q residue 18 ASP Chi-restraints excluded: chain q residue 21 ASP Chi-restraints excluded: chain q residue 30 THR Chi-restraints excluded: chain q residue 42 LYS Chi-restraints excluded: chain q residue 55 THR Chi-restraints excluded: chain q residue 81 VAL Chi-restraints excluded: chain r residue 20 ASN Chi-restraints excluded: chain r residue 22 ILE Chi-restraints excluded: chain r residue 63 ILE Chi-restraints excluded: chain s residue 7 LYS Chi-restraints excluded: chain s residue 11 VAL Chi-restraints excluded: chain s residue 14 HIS Chi-restraints excluded: chain s residue 17 LYS Chi-restraints excluded: chain s residue 27 LYS Chi-restraints excluded: chain s residue 36 ARG Chi-restraints excluded: chain s residue 39 THR Chi-restraints excluded: chain s residue 45 VAL Chi-restraints excluded: chain t residue 13 THR Chi-restraints excluded: chain t residue 20 LYS Chi-restraints excluded: chain t residue 39 VAL Chi-restraints excluded: chain t residue 44 ASP Chi-restraints excluded: chain t residue 49 LEU Chi-restraints excluded: chain t residue 62 THR Chi-restraints excluded: chain t residue 81 LEU Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 38 LYS Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 177 ASN Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 260 ARG Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 71 LYS Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 158 LYS Chi-restraints excluded: chain D residue 167 ASP Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 191 ASN Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain E residue 6 LEU Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain E residue 65 TRP Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 80 SER Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 105 VAL Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 190 ASN Chi-restraints excluded: chain E residue 195 THR Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 88 LYS Chi-restraints excluded: chain F residue 127 ASN Chi-restraints excluded: chain F residue 133 LYS Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 152 MET Chi-restraints excluded: chain F residue 154 ILE Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 44 ASN Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 84 GLN Chi-restraints excluded: chain G residue 101 ASN Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 165 VAL Chi-restraints excluded: chain G residue 171 ARG Chi-restraints excluded: chain K residue 2 ARG Chi-restraints excluded: chain K residue 14 ARG Chi-restraints excluded: chain K residue 22 THR Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 58 ILE Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 114 THR Chi-restraints excluded: chain K residue 115 LEU Chi-restraints excluded: chain K residue 123 LEU Chi-restraints excluded: chain K residue 145 ASN Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 19 ILE Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 53 LYS Chi-restraints excluded: chain L residue 54 LYS Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 87 ILE Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain L residue 110 ASN Chi-restraints excluded: chain M residue 16 ARG Chi-restraints excluded: chain M residue 42 SER Chi-restraints excluded: chain M residue 60 ARG Chi-restraints excluded: chain M residue 67 THR Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 79 LEU Chi-restraints excluded: chain M residue 81 THR Chi-restraints excluded: chain M residue 87 ASP Chi-restraints excluded: chain M residue 122 THR Chi-restraints excluded: chain M residue 131 SER Chi-restraints excluded: chain N residue 5 LYS Chi-restraints excluded: chain N residue 11 ARG Chi-restraints excluded: chain N residue 26 GLU Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 51 ARG Chi-restraints excluded: chain N residue 76 SER Chi-restraints excluded: chain N residue 85 LYS Chi-restraints excluded: chain N residue 111 GLU Chi-restraints excluded: chain N residue 127 VAL Chi-restraints excluded: chain N residue 133 LYS Chi-restraints excluded: chain O residue 23 ASP Chi-restraints excluded: chain O residue 24 LEU Chi-restraints excluded: chain O residue 48 ILE Chi-restraints excluded: chain O residue 49 THR Chi-restraints excluded: chain O residue 84 SER Chi-restraints excluded: chain O residue 121 VAL Chi-restraints excluded: chain O residue 124 GLU Chi-restraints excluded: chain P residue 2 ILE Chi-restraints excluded: chain P residue 6 ASP Chi-restraints excluded: chain P residue 13 LYS Chi-restraints excluded: chain P residue 22 ILE Chi-restraints excluded: chain P residue 31 LEU Chi-restraints excluded: chain P residue 35 ARG Chi-restraints excluded: chain P residue 46 ASP Chi-restraints excluded: chain P residue 51 VAL Chi-restraints excluded: chain P residue 57 SER Chi-restraints excluded: chain P residue 63 ILE Chi-restraints excluded: chain P residue 67 THR Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain P residue 95 ARG Chi-restraints excluded: chain P residue 104 VAL Chi-restraints excluded: chain Q residue 36 THR Chi-restraints excluded: chain Q residue 55 ILE Chi-restraints excluded: chain Q residue 60 THR Chi-restraints excluded: chain Q residue 78 THR Chi-restraints excluded: chain Q residue 109 ARG Chi-restraints excluded: chain R residue 9 VAL Chi-restraints excluded: chain R residue 10 THR Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 79 LEU Chi-restraints excluded: chain R residue 90 ILE Chi-restraints excluded: chain S residue 10 LYS Chi-restraints excluded: chain S residue 14 VAL Chi-restraints excluded: chain S residue 22 VAL Chi-restraints excluded: chain S residue 33 VAL Chi-restraints excluded: chain S residue 61 THR Chi-restraints excluded: chain S residue 73 THR Chi-restraints excluded: chain S residue 75 GLN Chi-restraints excluded: chain S residue 101 ASN Chi-restraints excluded: chain T residue 4 GLN Chi-restraints excluded: chain T residue 11 THR Chi-restraints excluded: chain T residue 14 THR Chi-restraints excluded: chain T residue 26 ILE Chi-restraints excluded: chain T residue 29 ILE Chi-restraints excluded: chain T residue 75 VAL Chi-restraints excluded: chain T residue 93 ARG Chi-restraints excluded: chain T residue 105 THR Chi-restraints excluded: chain T residue 109 THR Chi-restraints excluded: chain T residue 115 LYS Chi-restraints excluded: chain U residue 2 GLU Chi-restraints excluded: chain U residue 3 LEU Chi-restraints excluded: chain U residue 16 SER Chi-restraints excluded: chain U residue 26 THR Chi-restraints excluded: chain U residue 42 VAL Chi-restraints excluded: chain U residue 55 ILE Chi-restraints excluded: chain U residue 56 LEU Chi-restraints excluded: chain U residue 75 ARG Chi-restraints excluded: chain U residue 84 GLU Chi-restraints excluded: chain V residue 2 PHE Chi-restraints excluded: chain V residue 5 LYS Chi-restraints excluded: chain V residue 9 VAL Chi-restraints excluded: chain V residue 13 THR Chi-restraints excluded: chain V residue 17 LYS Chi-restraints excluded: chain V residue 29 LYS Chi-restraints excluded: chain V residue 33 VAL Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain V residue 58 GLU Chi-restraints excluded: chain V residue 59 VAL Chi-restraints excluded: chain V residue 68 VAL Chi-restraints excluded: chain V residue 91 VAL Chi-restraints excluded: chain V residue 94 SER Chi-restraints excluded: chain V residue 99 GLU Chi-restraints excluded: chain X residue 18 SER Chi-restraints excluded: chain X residue 19 THR Chi-restraints excluded: chain X residue 20 SER Chi-restraints excluded: chain X residue 23 ARG Chi-restraints excluded: chain X residue 39 THR Chi-restraints excluded: chain X residue 40 VAL Chi-restraints excluded: chain X residue 58 VAL Chi-restraints excluded: chain X residue 67 THR Chi-restraints excluded: chain X residue 79 GLU Chi-restraints excluded: chain X residue 88 VAL Chi-restraints excluded: chain X residue 93 VAL Chi-restraints excluded: chain Y residue 12 THR Chi-restraints excluded: chain Y residue 22 MET Chi-restraints excluded: chain Y residue 24 SER Chi-restraints excluded: chain Y residue 40 ILE Chi-restraints excluded: chain Z residue 3 VAL Chi-restraints excluded: chain Z residue 10 THR Chi-restraints excluded: chain Z residue 15 LEU Chi-restraints excluded: chain Z residue 24 GLU Chi-restraints excluded: chain Z residue 32 LEU Chi-restraints excluded: chain Z residue 37 LEU Chi-restraints excluded: chain Z residue 55 THR Chi-restraints excluded: chain 0 residue 8 LEU Chi-restraints excluded: chain 0 residue 35 VAL Chi-restraints excluded: chain 0 residue 54 VAL Chi-restraints excluded: chain 0 residue 59 VAL Chi-restraints excluded: chain 2 residue 3 VAL Chi-restraints excluded: chain 2 residue 8 THR Chi-restraints excluded: chain 2 residue 18 THR Chi-restraints excluded: chain 2 residue 23 THR Chi-restraints excluded: chain 2 residue 56 SER 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 44 LEU Chi-restraints excluded: chain 4 residue 10 ARG Chi-restraints excluded: chain 4 residue 20 LYS Chi-restraints excluded: chain 4 residue 24 THR Chi-restraints excluded: chain 4 residue 43 SER Chi-restraints excluded: chain 5 residue 14 VAL Chi-restraints excluded: chain 5 residue 31 HIS Chi-restraints excluded: chain 5 residue 32 ARG Chi-restraints excluded: chain 5 residue 57 ARG Chi-restraints excluded: chain 5 residue 60 GLN Chi-restraints excluded: chain 6 residue 4 ARG Chi-restraints excluded: chain 6 residue 26 ILE Chi-restraints excluded: chain 6 residue 36 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 920 random chunks: chunk 776 optimal weight: 5.9990 chunk 697 optimal weight: 3.9990 chunk 386 optimal weight: 7.9990 chunk 238 optimal weight: 5.9990 chunk 470 optimal weight: 5.9990 chunk 372 optimal weight: 5.9990 chunk 721 optimal weight: 30.0000 chunk 279 optimal weight: 4.9990 chunk 438 optimal weight: 3.9990 chunk 536 optimal weight: 30.0000 chunk 835 optimal weight: 3.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 85 ASN d 50 GLN d 55 GLN d 59 HIS d 113 GLN ** e 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 43 ASN f 67 ASN g 28 ASN g 64 GLN ** g 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 57 GLN i 3 GLN i 5 GLN i 66 ASN i 81 HIS l 5 ASN l 109 HIS l 125 GLN ** m 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 9 ASN o 38 GLN o 42 HIS o 46 HIS p 72 ASN q 34 HIS q 53 ASN ** s 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 45 ASN C 35 GLN C 90 ASN C 143 ASN C 261 ASN D 37 GLN D 68 HIS D 103 GLN E 13 GLN E 75 GLN E 82 GLN E 160 ASN E 196 GLN ** F 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 59 ASN K 131 HIS M 4 HIS M 17 ASN M 38 GLN M 133 GLN O 61 GLN ** O 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 12 GLN P 15 HIS P 20 ASN Q 6 GLN Q 41 GLN ** R 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 83 HIS S 86 GLN S 88 HIS T 4 GLN T 46 ASN X 49 GLN X 87 GLN Y 17 ASN Y 23 ASN Y 32 ASN Z 36 GLN 2 40 HIS 4 8 ASN 5 4 GLN 5 31 HIS Total number of N/Q/H flips: 64 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.1016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 145353 Z= 0.273 Angle : 0.738 10.586 217934 Z= 0.381 Chirality : 0.043 0.317 27945 Planarity : 0.006 0.066 11316 Dihedral : 23.227 179.838 74363 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.15 % Favored : 90.78 % Rotamer: Outliers : 11.79 % Allowed : 22.45 % Favored : 65.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.17 % Twisted Proline : 0.54 % Twisted General : 0.10 % 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: -2.90 (0.11), residues: 4970 helix: -1.01 (0.13), residues: 1458 sheet: -1.29 (0.15), residues: 1011 loop : -2.82 (0.11), residues: 2501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP d 9 HIS 0.007 0.001 HIS R 29 PHE 0.026 0.002 PHE V 2 TYR 0.023 0.002 TYR l 28 ARG 0.007 0.001 ARG l 12 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9940 Ramachandran restraints generated. 4970 Oldfield, 0 Emsley, 4970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9940 Ramachandran restraints generated. 4970 Oldfield, 0 Emsley, 4970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1227 residues out of total 4231 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 499 poor density : 728 time to evaluate : 5.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 39 ARG cc_start: 0.8086 (OUTLIER) cc_final: 0.7774 (ttp-170) REVERT: c 200 TRP cc_start: 0.7992 (OUTLIER) cc_final: 0.7219 (m100) REVERT: d 53 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7472 (tp30) REVERT: d 74 LYS cc_start: 0.8514 (OUTLIER) cc_final: 0.8033 (ttmm) REVERT: d 114 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8526 (mt) REVERT: d 143 ARG cc_start: 0.7445 (OUTLIER) cc_final: 0.6282 (ttt-90) REVERT: f 3 GLN cc_start: 0.6069 (OUTLIER) cc_final: 0.5122 (mm110) REVERT: g 10 ARG cc_start: 0.7187 (OUTLIER) cc_final: 0.6940 (ttm-80) REVERT: h 49 VAL cc_start: 0.8763 (OUTLIER) cc_final: 0.8269 (t) REVERT: i 66 ASN cc_start: 0.8026 (t0) cc_final: 0.7786 (t0) REVERT: j 85 ASP cc_start: 0.5747 (OUTLIER) cc_final: 0.5323 (m-30) REVERT: k 32 VAL cc_start: 0.8385 (OUTLIER) cc_final: 0.8131 (t) REVERT: k 72 LYS cc_start: 0.6698 (OUTLIER) cc_final: 0.6460 (ttpp) REVERT: l 63 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.7466 (mtt90) REVERT: l 80 ILE cc_start: 0.8280 (OUTLIER) cc_final: 0.7716 (tp) REVERT: m 100 GLN cc_start: 0.8118 (OUTLIER) cc_final: 0.7648 (mp10) REVERT: o 56 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8123 (tp) REVERT: p 10 MET cc_start: 0.7510 (mtp) cc_final: 0.7302 (mtp) REVERT: s 7 LYS cc_start: 0.4989 (OUTLIER) cc_final: 0.3667 (pttt) REVERT: s 27 LYS cc_start: 0.5377 (OUTLIER) cc_final: 0.4626 (mptt) REVERT: C 30 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7238 (tm-30) REVERT: C 38 LYS cc_start: 0.8032 (OUTLIER) cc_final: 0.7757 (tmtt) REVERT: D 90 GLU cc_start: 0.6827 (OUTLIER) cc_final: 0.5882 (tm-30) REVERT: D 138 ARG cc_start: 0.8115 (OUTLIER) cc_final: 0.7594 (mtt180) REVERT: D 168 ARG cc_start: 0.8387 (OUTLIER) cc_final: 0.7896 (ptt180) REVERT: E 45 ARG cc_start: 0.8865 (OUTLIER) cc_final: 0.7180 (mtt180) REVERT: E 66 ARG cc_start: 0.5747 (mtm110) cc_final: 0.5445 (mtt-85) REVERT: E 147 SER cc_start: 0.8231 (p) cc_final: 0.7936 (m) REVERT: E 190 ASN cc_start: 0.8649 (OUTLIER) cc_final: 0.8291 (t0) REVERT: F 169 LEU cc_start: 0.6958 (OUTLIER) cc_final: 0.6614 (tp) REVERT: G 44 ASN cc_start: 0.4731 (OUTLIER) cc_final: 0.4440 (t0) REVERT: G 171 ARG cc_start: 0.7771 (OUTLIER) cc_final: 0.7171 (mmm160) REVERT: K 14 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.6621 (mtp180) REVERT: K 101 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8171 (tt) REVERT: L 19 ILE cc_start: 0.8061 (OUTLIER) cc_final: 0.7591 (pt) REVERT: L 87 ILE cc_start: 0.8643 (OUTLIER) cc_final: 0.8333 (mp) REVERT: L 110 ASN cc_start: 0.6438 (OUTLIER) cc_final: 0.6047 (m110) REVERT: M 16 ARG cc_start: 0.6996 (OUTLIER) cc_final: 0.6787 (mtt180) REVERT: M 79 LEU cc_start: 0.7342 (OUTLIER) cc_final: 0.6671 (mp) REVERT: M 133 GLN cc_start: 0.7143 (tt0) cc_final: 0.6821 (tt0) REVERT: N 26 GLU cc_start: 0.7132 (OUTLIER) cc_final: 0.6581 (mm-30) REVERT: O 19 ASP cc_start: 0.7559 (m-30) cc_final: 0.7192 (m-30) REVERT: O 108 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8516 (mp) REVERT: P 22 ILE cc_start: 0.8634 (OUTLIER) cc_final: 0.8126 (mp) REVERT: P 35 ARG cc_start: 0.8279 (OUTLIER) cc_final: 0.6823 (ttm170) REVERT: Q 6 GLN cc_start: 0.7334 (mt0) cc_final: 0.7077 (mt0) REVERT: R 56 ASP cc_start: 0.7427 (m-30) cc_final: 0.7169 (m-30) REVERT: S 73 THR cc_start: 0.8363 (OUTLIER) cc_final: 0.8135 (m) REVERT: S 96 MET cc_start: 0.7631 (mmm) cc_final: 0.7385 (tpp) REVERT: S 101 ASN cc_start: 0.5452 (OUTLIER) cc_final: 0.5219 (t0) REVERT: T 17 THR cc_start: 0.8437 (p) cc_final: 0.8190 (t) REVERT: U 75 ARG cc_start: 0.8131 (OUTLIER) cc_final: 0.7490 (mtt90) REVERT: U 84 GLU cc_start: 0.5802 (OUTLIER) cc_final: 0.4891 (mp0) REVERT: V 5 LYS cc_start: 0.7917 (OUTLIER) cc_final: 0.7019 (tttm) REVERT: V 17 LYS cc_start: 0.8294 (OUTLIER) cc_final: 0.8059 (ttmt) REVERT: X 23 ARG cc_start: 0.8423 (OUTLIER) cc_final: 0.7577 (ptt90) REVERT: Y 22 MET cc_start: 0.7418 (OUTLIER) cc_final: 0.6961 (mmp) REVERT: 3 24 ARG cc_start: 0.6986 (OUTLIER) cc_final: 0.6696 (ttm170) REVERT: 3 32 LYS cc_start: 0.7714 (mmtt) cc_final: 0.7410 (mtpp) outliers start: 499 outliers final: 309 residues processed: 1102 average time/residue: 1.9093 time to fit residues: 3020.3408 Evaluate side-chains 1043 residues out of total 4231 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 357 poor density : 686 time to evaluate : 5.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 21 LYS Chi-restraints excluded: chain c residue 25 GLU Chi-restraints excluded: chain c residue 39 ARG Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 51 VAL Chi-restraints excluded: chain c residue 66 SER Chi-restraints excluded: chain c residue 67 ILE Chi-restraints excluded: chain c residue 98 VAL Chi-restraints excluded: chain c residue 100 ILE Chi-restraints excluded: chain c residue 103 VAL Chi-restraints excluded: chain c residue 168 SER Chi-restraints excluded: chain c residue 171 THR Chi-restraints excluded: chain c residue 200 TRP Chi-restraints excluded: chain d residue 14 ARG Chi-restraints excluded: chain d residue 22 THR Chi-restraints excluded: chain d residue 25 GLU Chi-restraints excluded: chain d residue 53 GLU Chi-restraints excluded: chain d residue 63 MET Chi-restraints excluded: chain d residue 71 LEU Chi-restraints excluded: chain d residue 74 LYS Chi-restraints excluded: chain d residue 114 LEU Chi-restraints excluded: chain d residue 139 VAL Chi-restraints excluded: chain d residue 140 ILE Chi-restraints excluded: chain d residue 143 ARG Chi-restraints excluded: chain d residue 159 THR Chi-restraints excluded: chain d residue 186 LEU Chi-restraints excluded: chain d residue 202 LYS 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 39 VAL Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 84 GLU Chi-restraints excluded: chain e residue 95 LEU Chi-restraints excluded: chain e residue 100 VAL Chi-restraints excluded: chain e residue 105 VAL Chi-restraints excluded: chain e residue 111 VAL Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain e residue 128 LEU Chi-restraints excluded: chain e residue 144 LEU Chi-restraints excluded: chain e residue 147 LEU Chi-restraints excluded: chain e residue 160 SER Chi-restraints excluded: chain e residue 164 ILE Chi-restraints excluded: chain f residue 3 GLN Chi-restraints excluded: chain f residue 5 THR Chi-restraints excluded: chain f residue 33 LEU Chi-restraints excluded: chain f residue 36 ASN Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 45 ASP Chi-restraints excluded: chain f residue 65 ILE Chi-restraints excluded: chain f residue 66 VAL Chi-restraints excluded: chain f residue 68 VAL Chi-restraints excluded: chain f residue 77 ILE Chi-restraints excluded: chain g residue 10 ARG Chi-restraints excluded: chain g residue 43 ILE Chi-restraints excluded: chain g residue 52 GLU Chi-restraints excluded: chain g residue 56 ASN Chi-restraints excluded: chain g residue 75 VAL Chi-restraints excluded: chain g residue 85 TYR Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain g residue 120 LEU Chi-restraints excluded: chain g residue 131 THR Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain h residue 2 VAL Chi-restraints excluded: chain h residue 25 LEU Chi-restraints excluded: chain h residue 27 VAL Chi-restraints excluded: chain h residue 49 VAL Chi-restraints excluded: chain h residue 52 ILE Chi-restraints excluded: chain h residue 54 ASP Chi-restraints excluded: chain h residue 62 VAL Chi-restraints excluded: chain h residue 69 ASN Chi-restraints excluded: chain h residue 75 THR Chi-restraints excluded: chain h residue 89 VAL Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 99 ASN Chi-restraints excluded: chain h residue 131 VAL Chi-restraints excluded: chain i residue 35 VAL Chi-restraints excluded: chain i residue 47 VAL Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain i residue 83 ILE Chi-restraints excluded: chain i residue 130 ARG Chi-restraints excluded: chain j residue 18 LEU Chi-restraints excluded: chain j residue 25 ILE Chi-restraints excluded: chain j residue 51 VAL Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain j residue 84 VAL Chi-restraints excluded: chain j residue 85 ASP Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 32 VAL Chi-restraints excluded: chain k residue 35 THR Chi-restraints excluded: chain k residue 37 THR Chi-restraints excluded: chain k residue 45 SER Chi-restraints excluded: chain k residue 46 SER Chi-restraints excluded: chain k residue 65 MET Chi-restraints excluded: chain k residue 72 LYS Chi-restraints excluded: chain k residue 81 THR Chi-restraints excluded: chain k residue 82 VAL Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain k residue 85 THR Chi-restraints excluded: chain k residue 86 VAL Chi-restraints excluded: chain l residue 8 VAL Chi-restraints excluded: chain l residue 24 LEU Chi-restraints excluded: chain l residue 25 ASN Chi-restraints excluded: chain l residue 28 TYR Chi-restraints excluded: chain l residue 36 THR Chi-restraints excluded: chain l residue 54 THR Chi-restraints excluded: chain l residue 63 ARG Chi-restraints excluded: chain l residue 72 ASN Chi-restraints excluded: chain l residue 77 THR Chi-restraints excluded: chain l residue 80 ILE Chi-restraints excluded: chain l residue 92 VAL Chi-restraints excluded: chain l residue 111 VAL Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain l residue 121 ASN Chi-restraints excluded: chain l residue 122 ASP Chi-restraints excluded: chain m residue 14 ARG Chi-restraints excluded: chain m residue 15 VAL Chi-restraints excluded: chain m residue 34 LEU Chi-restraints excluded: chain m residue 68 ASP Chi-restraints excluded: chain m residue 100 GLN Chi-restraints excluded: chain m residue 102 THR Chi-restraints excluded: chain m residue 103 LYS Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain n residue 42 ILE Chi-restraints excluded: chain o residue 56 LEU Chi-restraints excluded: chain o residue 67 LEU Chi-restraints excluded: chain o residue 75 ILE Chi-restraints excluded: chain o residue 89 ARG Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain p residue 32 ARG Chi-restraints excluded: chain p residue 36 THR Chi-restraints excluded: chain p residue 39 THR Chi-restraints excluded: chain q residue 10 VAL Chi-restraints excluded: chain q residue 18 ASP Chi-restraints excluded: chain q residue 21 ASP Chi-restraints excluded: chain q residue 30 THR Chi-restraints excluded: chain q residue 55 THR Chi-restraints excluded: chain q residue 81 VAL Chi-restraints excluded: chain r residue 20 ASN Chi-restraints excluded: chain r residue 22 ILE Chi-restraints excluded: chain r residue 48 VAL Chi-restraints excluded: chain r residue 63 ILE Chi-restraints excluded: chain s residue 7 LYS Chi-restraints excluded: chain s residue 11 VAL Chi-restraints excluded: chain s residue 14 HIS Chi-restraints excluded: chain s residue 26 GLU Chi-restraints excluded: chain s residue 27 LYS Chi-restraints excluded: chain s residue 39 THR Chi-restraints excluded: chain s residue 45 VAL Chi-restraints excluded: chain s residue 67 VAL Chi-restraints excluded: chain t residue 12 ARG Chi-restraints excluded: chain t residue 39 VAL Chi-restraints excluded: chain t residue 44 ASP Chi-restraints excluded: chain t residue 49 LEU Chi-restraints excluded: chain t residue 62 THR Chi-restraints excluded: chain t residue 81 LEU Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 38 LYS Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 177 ASN Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 138 ARG Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 167 ASP Chi-restraints excluded: chain D residue 168 ARG Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 191 ASN Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain E residue 6 LEU Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 105 VAL Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 190 ASN Chi-restraints excluded: chain F residue 15 SER Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 32 ASP Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 88 LYS Chi-restraints excluded: chain F residue 127 ASN Chi-restraints excluded: chain F residue 133 LYS Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain G residue 2 SER Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 44 ASN Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 84 GLN Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 101 ASN Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 171 ARG Chi-restraints excluded: chain K residue 2 ARG Chi-restraints excluded: chain K residue 14 ARG Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 58 ILE Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 114 THR Chi-restraints excluded: chain K residue 115 LEU Chi-restraints excluded: chain K residue 145 ASN Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 19 ILE Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 53 LYS Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 87 ILE Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain L residue 110 ASN Chi-restraints excluded: chain M residue 16 ARG Chi-restraints excluded: chain M residue 36 LYS Chi-restraints excluded: chain M residue 42 SER Chi-restraints excluded: chain M residue 67 THR Chi-restraints excluded: chain M residue 79 LEU Chi-restraints excluded: chain M residue 81 THR Chi-restraints excluded: chain M residue 87 ASP Chi-restraints excluded: chain M residue 105 GLU Chi-restraints excluded: chain M residue 122 THR Chi-restraints excluded: chain N residue 5 LYS Chi-restraints excluded: chain N residue 26 GLU Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 76 SER Chi-restraints excluded: chain N residue 85 LYS Chi-restraints excluded: chain N residue 111 GLU 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 48 ILE Chi-restraints excluded: chain O residue 49 THR Chi-restraints excluded: chain O residue 84 SER Chi-restraints excluded: chain O residue 108 LEU Chi-restraints excluded: chain O residue 121 VAL Chi-restraints excluded: chain P residue 2 ILE Chi-restraints excluded: chain P residue 6 ASP Chi-restraints excluded: chain P residue 22 ILE Chi-restraints excluded: chain P residue 28 CYS Chi-restraints excluded: chain P residue 31 LEU Chi-restraints excluded: chain P residue 35 ARG Chi-restraints excluded: chain P residue 51 VAL Chi-restraints excluded: chain P residue 63 ILE Chi-restraints excluded: chain P residue 67 THR Chi-restraints excluded: chain P residue 86 LYS Chi-restraints excluded: chain P residue 95 ARG Chi-restraints excluded: chain Q residue 36 THR Chi-restraints excluded: chain Q residue 60 THR Chi-restraints excluded: chain Q residue 78 THR Chi-restraints excluded: chain Q residue 80 ARG Chi-restraints excluded: chain Q residue 109 ARG Chi-restraints excluded: chain R residue 10 THR Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 79 LEU Chi-restraints excluded: chain R residue 112 GLN Chi-restraints excluded: chain S residue 10 LYS Chi-restraints excluded: chain S residue 14 VAL Chi-restraints excluded: chain S residue 22 VAL Chi-restraints excluded: chain S residue 33 VAL Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 73 THR Chi-restraints excluded: chain S residue 75 GLN Chi-restraints excluded: chain S residue 101 ASN Chi-restraints excluded: chain T residue 11 THR Chi-restraints excluded: chain T residue 14 THR Chi-restraints excluded: chain T residue 26 ILE Chi-restraints excluded: chain T residue 29 ILE Chi-restraints excluded: chain T residue 106 SER Chi-restraints excluded: chain T residue 109 THR Chi-restraints excluded: chain U residue 3 LEU Chi-restraints excluded: chain U residue 16 SER Chi-restraints excluded: chain U residue 36 THR Chi-restraints excluded: chain U residue 42 VAL Chi-restraints excluded: chain U residue 56 LEU Chi-restraints excluded: chain U residue 75 ARG Chi-restraints excluded: chain U residue 84 GLU Chi-restraints excluded: chain V residue 2 PHE Chi-restraints excluded: chain V residue 5 LYS Chi-restraints excluded: chain V residue 9 VAL Chi-restraints excluded: chain V residue 13 THR Chi-restraints excluded: chain V residue 17 LYS Chi-restraints excluded: chain V residue 33 VAL Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain V residue 68 VAL Chi-restraints excluded: chain V residue 91 VAL Chi-restraints excluded: chain V residue 99 GLU Chi-restraints excluded: chain X residue 18 SER Chi-restraints excluded: chain X residue 19 THR Chi-restraints excluded: chain X residue 20 SER Chi-restraints excluded: chain X residue 23 ARG Chi-restraints excluded: chain X residue 24 ASP Chi-restraints excluded: chain X residue 40 VAL Chi-restraints excluded: chain X residue 58 VAL Chi-restraints excluded: chain X residue 67 THR Chi-restraints excluded: chain X residue 79 GLU Chi-restraints excluded: chain X residue 88 VAL Chi-restraints excluded: chain X residue 93 VAL Chi-restraints excluded: chain Y residue 12 THR Chi-restraints excluded: chain Y residue 22 MET Chi-restraints excluded: chain Y residue 24 SER Chi-restraints excluded: chain Z residue 3 VAL Chi-restraints excluded: chain Z residue 10 THR Chi-restraints excluded: chain Z residue 37 LEU Chi-restraints excluded: chain 0 residue 30 LYS Chi-restraints excluded: chain 0 residue 35 VAL Chi-restraints excluded: chain 0 residue 54 VAL Chi-restraints excluded: chain 0 residue 59 VAL Chi-restraints excluded: chain 2 residue 3 VAL Chi-restraints excluded: chain 2 residue 8 THR Chi-restraints excluded: chain 2 residue 18 THR Chi-restraints excluded: chain 2 residue 23 THR Chi-restraints excluded: chain 2 residue 56 SER Chi-restraints excluded: chain 3 residue 8 GLU Chi-restraints excluded: chain 3 residue 10 THR Chi-restraints excluded: chain 3 residue 24 ARG Chi-restraints excluded: chain 3 residue 44 LEU Chi-restraints excluded: chain 4 residue 20 LYS Chi-restraints excluded: chain 4 residue 24 THR Chi-restraints excluded: chain 4 residue 43 SER Chi-restraints excluded: chain 5 residue 14 VAL Chi-restraints excluded: chain 5 residue 17 THR Chi-restraints excluded: chain 5 residue 32 ARG Chi-restraints excluded: chain 5 residue 58 ILE Chi-restraints excluded: chain 6 residue 4 ARG Chi-restraints excluded: chain 6 residue 11 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 920 random chunks: chunk 464 optimal weight: 10.0000 chunk 259 optimal weight: 10.0000 chunk 695 optimal weight: 9.9990 chunk 568 optimal weight: 10.0000 chunk 230 optimal weight: 5.9990 chunk 836 optimal weight: 2.9990 chunk 904 optimal weight: 9.9990 chunk 745 optimal weight: 5.9990 chunk 829 optimal weight: 1.9990 chunk 285 optimal weight: 2.9990 chunk 671 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 67 ASN ** g 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 9 ASN o 38 GLN ** s 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 199 GLN ** F 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 44 ASN O 61 GLN ** R 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 59 ASN X 87 GLN Z 60 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 145353 Z= 0.240 Angle : 0.679 10.130 217934 Z= 0.351 Chirality : 0.041 0.297 27945 Planarity : 0.006 0.071 11316 Dihedral : 23.013 179.560 74108 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.48 % Favored : 90.46 % Rotamer: Outliers : 11.49 % Allowed : 23.73 % Favored : 64.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.17 % Twisted Proline : 0.54 % Twisted General : 0.08 % 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: -2.25 (0.11), residues: 4970 helix: -0.31 (0.13), residues: 1457 sheet: -0.82 (0.16), residues: 1027 loop : -2.60 (0.11), residues: 2486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP d 9 HIS 0.007 0.001 HIS h 22 PHE 0.025 0.002 PHE V 2 TYR 0.020 0.002 TYR l 28 ARG 0.005 0.001 ARG l 12 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9940 Ramachandran restraints generated. 4970 Oldfield, 0 Emsley, 4970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9940 Ramachandran restraints generated. 4970 Oldfield, 0 Emsley, 4970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1169 residues out of total 4231 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 486 poor density : 683 time to evaluate : 5.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 200 TRP cc_start: 0.7989 (OUTLIER) cc_final: 0.7512 (m100) REVERT: d 50 GLN cc_start: 0.7687 (mt0) cc_final: 0.7455 (mt0) REVERT: d 53 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.7443 (tp30) REVERT: d 114 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8481 (mt) REVERT: d 143 ARG cc_start: 0.7457 (OUTLIER) cc_final: 0.6367 (ttt-90) REVERT: f 3 GLN cc_start: 0.6169 (OUTLIER) cc_final: 0.5189 (mm110) REVERT: h 49 VAL cc_start: 0.8781 (OUTLIER) cc_final: 0.8298 (t) REVERT: j 85 ASP cc_start: 0.5886 (OUTLIER) cc_final: 0.5579 (m-30) REVERT: k 72 LYS cc_start: 0.6741 (OUTLIER) cc_final: 0.6517 (ttpp) REVERT: l 72 ASN cc_start: 0.5310 (OUTLIER) cc_final: 0.4936 (t0) REVERT: l 80 ILE cc_start: 0.8143 (OUTLIER) cc_final: 0.7702 (tp) REVERT: m 100 GLN cc_start: 0.8040 (OUTLIER) cc_final: 0.7593 (mp10) REVERT: m 109 ARG cc_start: 0.7902 (OUTLIER) cc_final: 0.7316 (tpt-90) REVERT: o 56 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8192 (tp) REVERT: o 84 ARG cc_start: 0.8450 (OUTLIER) cc_final: 0.8079 (ttp-170) REVERT: C 30 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7164 (tm-30) REVERT: C 38 LYS cc_start: 0.8064 (OUTLIER) cc_final: 0.7832 (tmtt) REVERT: C 175 ARG cc_start: 0.7710 (OUTLIER) cc_final: 0.7093 (ttp-110) REVERT: D 90 GLU cc_start: 0.6797 (OUTLIER) cc_final: 0.5888 (tm-30) REVERT: D 138 ARG cc_start: 0.8046 (OUTLIER) cc_final: 0.7622 (mtt180) REVERT: D 168 ARG cc_start: 0.8392 (OUTLIER) cc_final: 0.7899 (ptt180) REVERT: E 45 ARG cc_start: 0.8868 (OUTLIER) cc_final: 0.7175 (mtt180) REVERT: E 66 ARG cc_start: 0.5704 (mtm110) cc_final: 0.5233 (mtt-85) REVERT: E 147 SER cc_start: 0.8228 (p) cc_final: 0.7923 (m) REVERT: E 190 ASN cc_start: 0.8633 (OUTLIER) cc_final: 0.8282 (t0) REVERT: F 8 TYR cc_start: 0.4272 (OUTLIER) cc_final: 0.3959 (m-10) REVERT: F 36 ILE cc_start: 0.8072 (OUTLIER) cc_final: 0.7675 (mp) REVERT: F 169 LEU cc_start: 0.7344 (OUTLIER) cc_final: 0.7077 (tp) REVERT: F 172 GLN cc_start: 0.6155 (OUTLIER) cc_final: 0.5815 (mm110) REVERT: G 44 ASN cc_start: 0.4647 (OUTLIER) cc_final: 0.4430 (t0) REVERT: G 144 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7543 (mp) REVERT: G 171 ARG cc_start: 0.7845 (OUTLIER) cc_final: 0.7289 (mmm160) REVERT: K 14 ARG cc_start: 0.8168 (OUTLIER) cc_final: 0.6713 (mtp180) REVERT: K 109 MET cc_start: 0.9142 (mtt) cc_final: 0.8912 (mtt) REVERT: L 19 ILE cc_start: 0.8032 (OUTLIER) cc_final: 0.7584 (pt) REVERT: L 71 ARG cc_start: 0.7875 (OUTLIER) cc_final: 0.7648 (mpt-90) REVERT: L 87 ILE cc_start: 0.8613 (OUTLIER) cc_final: 0.8397 (mm) REVERT: L 110 ASN cc_start: 0.6471 (OUTLIER) cc_final: 0.6032 (m110) REVERT: M 39 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.8516 (mtpm) REVERT: M 133 GLN cc_start: 0.7352 (tt0) cc_final: 0.6800 (tt0) REVERT: N 130 LYS cc_start: 0.7765 (OUTLIER) cc_final: 0.7446 (mtmm) REVERT: O 19 ASP cc_start: 0.7567 (m-30) cc_final: 0.7213 (m-30) REVERT: P 22 ILE cc_start: 0.8619 (OUTLIER) cc_final: 0.8100 (mp) REVERT: P 35 ARG cc_start: 0.8246 (OUTLIER) cc_final: 0.7128 (ttm170) REVERT: P 113 GLU cc_start: 0.5986 (OUTLIER) cc_final: 0.5724 (mt-10) REVERT: Q 6 GLN cc_start: 0.7361 (mt0) cc_final: 0.7104 (mt0) REVERT: Q 38 GLU cc_start: 0.6405 (OUTLIER) cc_final: 0.5829 (tp30) REVERT: Q 60 THR cc_start: 0.8556 (OUTLIER) cc_final: 0.8209 (m) REVERT: R 56 ASP cc_start: 0.7356 (m-30) cc_final: 0.7106 (m-30) REVERT: R 90 ILE cc_start: 0.8504 (OUTLIER) cc_final: 0.8250 (tt) REVERT: S 96 MET cc_start: 0.7607 (mmm) cc_final: 0.7360 (tpp) REVERT: U 17 MET cc_start: 0.8240 (mmm) cc_final: 0.8031 (mmm) REVERT: U 75 ARG cc_start: 0.8199 (OUTLIER) cc_final: 0.7577 (mtt90) REVERT: V 5 LYS cc_start: 0.7973 (OUTLIER) cc_final: 0.6874 (tptm) REVERT: V 17 LYS cc_start: 0.8244 (OUTLIER) cc_final: 0.8000 (ttmt) REVERT: X 23 ARG cc_start: 0.8415 (OUTLIER) cc_final: 0.7516 (ptt90) REVERT: Y 22 MET cc_start: 0.7529 (OUTLIER) cc_final: 0.7085 (mmp) REVERT: 0 40 ASN cc_start: 0.7620 (m-40) cc_final: 0.7330 (m-40) REVERT: 0 58 GLU cc_start: 0.7038 (mm-30) cc_final: 0.6766 (tp30) REVERT: 3 24 ARG cc_start: 0.6974 (OUTLIER) cc_final: 0.6698 (ttm170) REVERT: 3 32 LYS cc_start: 0.7675 (mmtt) cc_final: 0.7384 (mtpp) REVERT: 5 32 ARG cc_start: 0.8068 (OUTLIER) cc_final: 0.7665 (ptt180) outliers start: 486 outliers final: 310 residues processed: 1035 average time/residue: 1.8515 time to fit residues: 2770.6639 Evaluate side-chains 1013 residues out of total 4231 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 359 poor density : 654 time to evaluate : 5.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 21 LYS Chi-restraints excluded: chain c residue 25 GLU Chi-restraints excluded: chain c residue 51 VAL Chi-restraints excluded: chain c residue 67 ILE Chi-restraints excluded: chain c residue 69 THR Chi-restraints excluded: chain c residue 98 VAL Chi-restraints excluded: chain c residue 100 ILE Chi-restraints excluded: chain c residue 153 SER Chi-restraints excluded: chain c residue 168 SER Chi-restraints excluded: chain c residue 171 THR Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain c residue 200 TRP Chi-restraints excluded: chain d residue 14 ARG Chi-restraints excluded: chain d residue 22 THR Chi-restraints excluded: chain d residue 53 GLU Chi-restraints excluded: chain d residue 71 LEU Chi-restraints excluded: chain d residue 114 LEU Chi-restraints excluded: chain d residue 139 VAL Chi-restraints excluded: chain d residue 140 ILE Chi-restraints excluded: chain d residue 143 ARG Chi-restraints excluded: chain d residue 150 SER Chi-restraints excluded: chain d residue 159 THR Chi-restraints excluded: chain d residue 186 LEU Chi-restraints excluded: chain d residue 189 GLU Chi-restraints excluded: chain d residue 192 GLU Chi-restraints excluded: chain e residue 22 THR Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 76 MET Chi-restraints excluded: chain e residue 84 GLU Chi-restraints excluded: chain e residue 94 ILE Chi-restraints excluded: chain e residue 100 VAL Chi-restraints excluded: chain e residue 105 VAL Chi-restraints excluded: chain e residue 111 VAL Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain e residue 128 LEU Chi-restraints excluded: chain e residue 144 LEU Chi-restraints excluded: chain e residue 147 LEU Chi-restraints excluded: chain e residue 160 SER Chi-restraints excluded: chain e residue 164 ILE Chi-restraints excluded: chain f residue 3 GLN Chi-restraints excluded: chain f residue 5 THR Chi-restraints excluded: chain f residue 36 ASN Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 45 ASP Chi-restraints excluded: chain f residue 65 ILE Chi-restraints excluded: chain f residue 66 VAL Chi-restraints excluded: chain g residue 27 ILE Chi-restraints excluded: chain g residue 43 ILE Chi-restraints excluded: chain g residue 75 VAL Chi-restraints excluded: chain g residue 85 TYR Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain g residue 131 THR Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain h residue 2 VAL Chi-restraints excluded: chain h residue 27 VAL Chi-restraints excluded: chain h residue 49 VAL Chi-restraints excluded: chain h residue 52 ILE Chi-restraints excluded: chain h residue 54 ASP Chi-restraints excluded: chain h residue 62 VAL Chi-restraints excluded: chain h residue 69 ASN Chi-restraints excluded: chain h residue 73 VAL Chi-restraints excluded: chain h residue 75 THR Chi-restraints excluded: chain h residue 89 VAL Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 99 ASN Chi-restraints excluded: chain h residue 114 THR Chi-restraints excluded: chain h residue 131 VAL Chi-restraints excluded: chain i residue 29 THR Chi-restraints excluded: chain i residue 35 VAL Chi-restraints excluded: chain i residue 47 VAL Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain j residue 18 LEU Chi-restraints excluded: chain j residue 25 ILE Chi-restraints excluded: chain j residue 32 THR Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain j residue 51 VAL Chi-restraints excluded: chain j residue 84 VAL Chi-restraints excluded: chain j residue 85 ASP Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 35 THR Chi-restraints excluded: chain k residue 37 THR Chi-restraints excluded: chain k residue 46 SER Chi-restraints excluded: chain k residue 65 MET Chi-restraints excluded: chain k residue 72 LYS Chi-restraints excluded: chain k residue 81 THR Chi-restraints excluded: chain k residue 82 VAL Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain k residue 85 THR Chi-restraints excluded: chain k residue 86 VAL Chi-restraints excluded: chain k residue 107 VAL Chi-restraints excluded: chain l residue 8 VAL Chi-restraints excluded: chain l residue 21 SER Chi-restraints excluded: chain l residue 25 ASN Chi-restraints excluded: chain l residue 28 TYR Chi-restraints excluded: chain l residue 36 THR Chi-restraints excluded: chain l residue 54 THR Chi-restraints excluded: chain l residue 72 ASN Chi-restraints excluded: chain l residue 77 THR Chi-restraints excluded: chain l residue 80 ILE Chi-restraints excluded: chain l residue 92 VAL Chi-restraints excluded: chain l residue 107 ARG Chi-restraints excluded: chain l residue 111 VAL Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain l residue 121 ASN Chi-restraints excluded: chain l residue 122 ASP Chi-restraints excluded: chain m residue 14 ARG Chi-restraints excluded: chain m residue 15 VAL Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 28 THR Chi-restraints excluded: chain m residue 39 VAL Chi-restraints excluded: chain m residue 68 ASP Chi-restraints excluded: chain m residue 100 GLN Chi-restraints excluded: chain m residue 102 THR Chi-restraints excluded: chain m residue 103 LYS Chi-restraints excluded: chain m residue 109 ARG Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain o residue 22 THR Chi-restraints excluded: chain o residue 56 LEU Chi-restraints excluded: chain o residue 67 LEU Chi-restraints excluded: chain o residue 73 THR Chi-restraints excluded: chain o residue 75 ILE Chi-restraints excluded: chain o residue 84 ARG Chi-restraints excluded: chain o residue 89 ARG Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain p residue 32 ARG Chi-restraints excluded: chain p residue 36 THR Chi-restraints excluded: chain p residue 44 LYS Chi-restraints excluded: chain p residue 73 ILE Chi-restraints excluded: chain q residue 10 VAL Chi-restraints excluded: chain q residue 16 VAL Chi-restraints excluded: chain q residue 21 ASP Chi-restraints excluded: chain q residue 32 LYS Chi-restraints excluded: chain q residue 55 THR Chi-restraints excluded: chain q residue 80 GLU Chi-restraints excluded: chain q residue 81 VAL Chi-restraints excluded: chain r residue 20 ASN Chi-restraints excluded: chain r residue 22 ILE Chi-restraints excluded: chain r residue 48 VAL Chi-restraints excluded: chain r residue 49 THR Chi-restraints excluded: chain r residue 63 ILE Chi-restraints excluded: chain s residue 11 VAL Chi-restraints excluded: chain s residue 14 HIS Chi-restraints excluded: chain s residue 26 GLU Chi-restraints excluded: chain s residue 27 LYS Chi-restraints excluded: chain s residue 39 THR Chi-restraints excluded: chain s residue 45 VAL Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain s residue 73 GLU Chi-restraints excluded: chain t residue 12 ARG Chi-restraints excluded: chain t residue 39 VAL Chi-restraints excluded: chain t residue 49 LEU Chi-restraints excluded: chain t residue 62 THR Chi-restraints excluded: chain t residue 81 LEU Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 38 LYS Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 175 ARG Chi-restraints excluded: chain C residue 177 ASN Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 138 ARG Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 167 ASP Chi-restraints excluded: chain D residue 168 ARG Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 184 ASN Chi-restraints excluded: chain D residue 191 ASN Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain E residue 6 LEU Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 105 VAL Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 190 ASN Chi-restraints excluded: chain E residue 195 THR Chi-restraints excluded: chain F residue 8 TYR Chi-restraints excluded: chain F residue 15 SER Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 88 LYS Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 127 ASN Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 172 GLN Chi-restraints excluded: chain G residue 2 SER Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 44 ASN Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 101 ASN Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 125 VAL Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 144 LEU Chi-restraints excluded: chain G residue 171 ARG Chi-restraints excluded: chain K residue 14 ARG Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 58 ILE Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 114 THR Chi-restraints excluded: chain K residue 115 LEU Chi-restraints excluded: chain K residue 145 ASN Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 19 ILE Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 53 LYS Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 71 ARG Chi-restraints excluded: chain L residue 87 ILE Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain L residue 110 ASN Chi-restraints excluded: chain M residue 36 LYS Chi-restraints excluded: chain M residue 39 LYS Chi-restraints excluded: chain M residue 42 SER Chi-restraints excluded: chain M residue 81 THR Chi-restraints excluded: chain M residue 87 ASP Chi-restraints excluded: chain M residue 105 GLU Chi-restraints excluded: chain M residue 122 THR Chi-restraints excluded: chain M residue 131 SER Chi-restraints excluded: chain N residue 5 LYS Chi-restraints excluded: chain N residue 26 GLU Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 76 SER Chi-restraints excluded: chain N residue 85 LYS Chi-restraints excluded: chain N residue 111 GLU Chi-restraints excluded: chain N residue 122 SER Chi-restraints excluded: chain N residue 127 VAL Chi-restraints excluded: chain N residue 130 LYS Chi-restraints excluded: chain N residue 133 LYS Chi-restraints excluded: chain O residue 24 LEU Chi-restraints excluded: chain O residue 121 VAL Chi-restraints excluded: chain P residue 2 ILE Chi-restraints excluded: chain P residue 6 ASP Chi-restraints excluded: chain P residue 22 ILE Chi-restraints excluded: chain P residue 28 CYS Chi-restraints excluded: chain P residue 35 ARG Chi-restraints excluded: chain P residue 51 VAL Chi-restraints excluded: chain P residue 63 ILE Chi-restraints excluded: chain P residue 67 THR Chi-restraints excluded: chain P residue 70 GLU Chi-restraints excluded: chain P residue 86 LYS Chi-restraints excluded: chain P residue 95 ARG Chi-restraints excluded: chain P residue 113 GLU Chi-restraints excluded: chain Q residue 2 ASN Chi-restraints excluded: chain Q residue 36 THR Chi-restraints excluded: chain Q residue 38 GLU Chi-restraints excluded: chain Q residue 60 THR Chi-restraints excluded: chain Q residue 78 THR Chi-restraints excluded: chain Q residue 80 ARG Chi-restraints excluded: chain Q residue 109 ARG Chi-restraints excluded: chain R residue 10 THR Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 42 SER Chi-restraints excluded: chain R residue 90 ILE Chi-restraints excluded: chain R residue 112 GLN Chi-restraints excluded: chain S residue 10 LYS Chi-restraints excluded: chain S residue 14 VAL Chi-restraints excluded: chain S residue 22 VAL Chi-restraints excluded: chain S residue 28 GLU Chi-restraints excluded: chain S residue 33 VAL Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 75 GLN Chi-restraints excluded: chain T residue 11 THR Chi-restraints excluded: chain T residue 14 THR Chi-restraints excluded: chain T residue 26 ILE Chi-restraints excluded: chain T residue 29 ILE Chi-restraints excluded: chain T residue 70 ASP Chi-restraints excluded: chain T residue 75 VAL Chi-restraints excluded: chain T residue 105 THR Chi-restraints excluded: chain T residue 109 THR Chi-restraints excluded: chain U residue 3 LEU Chi-restraints excluded: chain U residue 16 SER Chi-restraints excluded: chain U residue 36 THR Chi-restraints excluded: chain U residue 42 VAL Chi-restraints excluded: chain U residue 55 ILE Chi-restraints excluded: chain U residue 56 LEU Chi-restraints excluded: chain U residue 75 ARG Chi-restraints excluded: chain U residue 84 GLU Chi-restraints excluded: chain V residue 2 PHE Chi-restraints excluded: chain V residue 5 LYS Chi-restraints excluded: chain V residue 7 ASP Chi-restraints excluded: chain V residue 9 VAL Chi-restraints excluded: chain V residue 13 THR Chi-restraints excluded: chain V residue 17 LYS Chi-restraints excluded: chain V residue 33 VAL Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain V residue 68 VAL Chi-restraints excluded: chain V residue 91 VAL Chi-restraints excluded: chain V residue 99 GLU Chi-restraints excluded: chain X residue 18 SER Chi-restraints excluded: chain X residue 19 THR Chi-restraints excluded: chain X residue 23 ARG Chi-restraints excluded: chain X residue 24 ASP Chi-restraints excluded: chain X residue 39 THR Chi-restraints excluded: chain X residue 40 VAL Chi-restraints excluded: chain X residue 67 THR Chi-restraints excluded: chain X residue 75 VAL Chi-restraints excluded: chain X residue 79 GLU Chi-restraints excluded: chain X residue 88 VAL Chi-restraints excluded: chain X residue 93 VAL Chi-restraints excluded: chain Y residue 12 THR Chi-restraints excluded: chain Y residue 22 MET Chi-restraints excluded: chain Y residue 24 SER Chi-restraints excluded: chain Y residue 28 THR Chi-restraints excluded: chain Z residue 3 VAL Chi-restraints excluded: chain Z residue 37 LEU Chi-restraints excluded: chain Z residue 49 SER Chi-restraints excluded: chain 0 residue 35 VAL Chi-restraints excluded: chain 0 residue 54 VAL Chi-restraints excluded: chain 0 residue 59 VAL Chi-restraints excluded: chain 2 residue 3 VAL Chi-restraints excluded: chain 2 residue 8 THR Chi-restraints excluded: chain 2 residue 18 THR Chi-restraints excluded: chain 2 residue 23 THR Chi-restraints excluded: chain 2 residue 56 SER Chi-restraints excluded: chain 3 residue 24 ARG Chi-restraints excluded: chain 3 residue 44 LEU Chi-restraints excluded: chain 4 residue 20 LYS Chi-restraints excluded: chain 4 residue 24 THR Chi-restraints excluded: chain 4 residue 43 SER Chi-restraints excluded: chain 5 residue 14 VAL Chi-restraints excluded: chain 5 residue 17 THR Chi-restraints excluded: chain 5 residue 32 ARG Chi-restraints excluded: chain 5 residue 58 ILE Chi-restraints excluded: chain 5 residue 60 GLN Chi-restraints excluded: chain 6 residue 11 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 920 random chunks: chunk 826 optimal weight: 5.9990 chunk 629 optimal weight: 20.0000 chunk 434 optimal weight: 10.0000 chunk 92 optimal weight: 20.0000 chunk 399 optimal weight: 10.0000 chunk 562 optimal weight: 10.0000 chunk 839 optimal weight: 0.3980 chunk 889 optimal weight: 2.9990 chunk 438 optimal weight: 10.0000 chunk 796 optimal weight: 5.9990 chunk 239 optimal weight: 0.9980 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 135 GLN ** e 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 67 ASN ** g 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 9 ASN o 38 GLN ** s 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 199 GLN ** F 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 44 ASN O 61 GLN ** O 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 87 GLN Z 60 GLN 0 17 GLN 2 41 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 145353 Z= 0.205 Angle : 0.643 9.967 217934 Z= 0.335 Chirality : 0.039 0.288 27945 Planarity : 0.005 0.071 11316 Dihedral : 22.956 179.430 74000 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.73 % Favored : 91.21 % Rotamer: Outliers : 10.45 % Allowed : 25.29 % Favored : 64.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.17 % Twisted Proline : 0.54 % Twisted General : 0.06 % 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: -1.95 (0.11), residues: 4970 helix: -0.00 (0.14), residues: 1451 sheet: -0.57 (0.16), residues: 1000 loop : -2.47 (0.11), residues: 2519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP d 9 HIS 0.006 0.001 HIS h 22 PHE 0.018 0.002 PHE V 2 TYR 0.020 0.002 TYR l 28 ARG 0.006 0.000 ARG j 31 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9940 Ramachandran restraints generated. 4970 Oldfield, 0 Emsley, 4970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9940 Ramachandran restraints generated. 4970 Oldfield, 0 Emsley, 4970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1111 residues out of total 4231 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 442 poor density : 669 time to evaluate : 5.543 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: c 200 TRP cc_start: 0.7975 (OUTLIER) cc_final: 0.7421 (m100) REVERT: d 114 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8466 (mt) REVERT: d 143 ARG cc_start: 0.7365 (OUTLIER) cc_final: 0.6143 (ttt-90) REVERT: d 186 LEU cc_start: 0.7068 (OUTLIER) cc_final: 0.6816 (mt) REVERT: f 3 GLN cc_start: 0.6137 (OUTLIER) cc_final: 0.5139 (mm110) REVERT: f 33 LEU cc_start: 0.7315 (OUTLIER) cc_final: 0.6910 (tp) REVERT: h 49 VAL cc_start: 0.8779 (OUTLIER) cc_final: 0.8302 (t) REVERT: j 4 GLN cc_start: 0.4582 (OUTLIER) cc_final: 0.4276 (tm-30) REVERT: j 85 ASP cc_start: 0.5940 (OUTLIER) cc_final: 0.5668 (m-30) REVERT: l 62 LEU cc_start: 0.8783 (mt) cc_final: 0.8511 (mt) REVERT: l 72 ASN cc_start: 0.5250 (OUTLIER) cc_final: 0.4876 (t0) REVERT: m 64 LYS cc_start: 0.7287 (mttt) cc_final: 0.7027 (mtpt) REVERT: m 100 GLN cc_start: 0.8044 (OUTLIER) cc_final: 0.7606 (mp10) REVERT: m 103 LYS cc_start: 0.4933 (OUTLIER) cc_final: 0.2857 (mmtp) REVERT: m 109 ARG cc_start: 0.7901 (OUTLIER) cc_final: 0.7298 (tpt-90) REVERT: o 56 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8178 (tp) REVERT: o 84 ARG cc_start: 0.8468 (OUTLIER) cc_final: 0.8063 (ttp-170) REVERT: p 53 GLU cc_start: 0.6387 (pt0) cc_final: 0.6157 (pt0) REVERT: s 7 LYS cc_start: 0.4902 (OUTLIER) cc_final: 0.3751 (pttt) REVERT: s 37 ARG cc_start: 0.8069 (OUTLIER) cc_final: 0.7004 (ptp-170) REVERT: C 30 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7090 (tm-30) REVERT: C 38 LYS cc_start: 0.7993 (OUTLIER) cc_final: 0.7691 (tmtt) REVERT: C 69 ARG cc_start: 0.8664 (OUTLIER) cc_final: 0.8440 (mmm-85) REVERT: C 175 ARG cc_start: 0.7673 (OUTLIER) cc_final: 0.7065 (ttp-110) REVERT: D 90 GLU cc_start: 0.6767 (OUTLIER) cc_final: 0.5883 (tm-30) REVERT: D 138 ARG cc_start: 0.8021 (OUTLIER) cc_final: 0.7588 (mtt180) REVERT: D 168 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.7885 (ptt180) REVERT: E 45 ARG cc_start: 0.8879 (OUTLIER) cc_final: 0.7184 (mtt180) REVERT: E 66 ARG cc_start: 0.5695 (mtm110) cc_final: 0.5156 (mtt-85) REVERT: E 147 SER cc_start: 0.8194 (p) cc_final: 0.7952 (m) REVERT: F 8 TYR cc_start: 0.4276 (OUTLIER) cc_final: 0.3956 (m-10) REVERT: F 36 ILE cc_start: 0.8084 (OUTLIER) cc_final: 0.7710 (mp) REVERT: F 169 LEU cc_start: 0.7146 (OUTLIER) cc_final: 0.6837 (tp) REVERT: G 144 LEU cc_start: 0.8004 (OUTLIER) cc_final: 0.7522 (mp) REVERT: G 171 ARG cc_start: 0.7846 (OUTLIER) cc_final: 0.7296 (mmm160) REVERT: L 19 ILE cc_start: 0.8010 (OUTLIER) cc_final: 0.7618 (pt) REVERT: L 71 ARG cc_start: 0.7900 (OUTLIER) cc_final: 0.7656 (mpt-90) REVERT: M 39 LYS cc_start: 0.8727 (OUTLIER) cc_final: 0.8489 (mttm) REVERT: M 133 GLN cc_start: 0.7316 (tt0) cc_final: 0.6950 (tt0) REVERT: N 130 LYS cc_start: 0.7789 (OUTLIER) cc_final: 0.7487 (mtmm) REVERT: O 19 ASP cc_start: 0.7516 (m-30) cc_final: 0.7163 (m-30) REVERT: O 41 ARG cc_start: 0.8470 (OUTLIER) cc_final: 0.8218 (ptt180) REVERT: O 108 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8481 (mp) REVERT: P 22 ILE cc_start: 0.8607 (OUTLIER) cc_final: 0.8088 (mp) REVERT: P 113 GLU cc_start: 0.5922 (OUTLIER) cc_final: 0.5664 (mt-10) REVERT: Q 6 GLN cc_start: 0.7301 (mt0) cc_final: 0.7057 (mt0) REVERT: Q 60 THR cc_start: 0.8537 (OUTLIER) cc_final: 0.8233 (m) REVERT: R 56 ASP cc_start: 0.7336 (m-30) cc_final: 0.7081 (m-30) REVERT: R 90 ILE cc_start: 0.8505 (OUTLIER) cc_final: 0.8268 (tt) REVERT: S 96 MET cc_start: 0.7576 (mmm) cc_final: 0.7335 (tpp) REVERT: S 98 GLU cc_start: 0.7378 (OUTLIER) cc_final: 0.7076 (mt-10) REVERT: U 75 ARG cc_start: 0.8167 (OUTLIER) cc_final: 0.7522 (mtt90) REVERT: V 5 LYS cc_start: 0.7960 (OUTLIER) cc_final: 0.6982 (tptm) REVERT: V 17 LYS cc_start: 0.8186 (OUTLIER) cc_final: 0.7947 (ttmt) REVERT: X 23 ARG cc_start: 0.8379 (OUTLIER) cc_final: 0.7506 (ptt90) REVERT: Y 22 MET cc_start: 0.7524 (OUTLIER) cc_final: 0.7101 (mmp) REVERT: Y 35 LYS cc_start: 0.7814 (ttmt) cc_final: 0.7580 (ttmm) REVERT: 0 40 ASN cc_start: 0.7600 (m-40) cc_final: 0.7312 (m-40) REVERT: 0 58 GLU cc_start: 0.7050 (mm-30) cc_final: 0.6786 (tp30) REVERT: 3 24 ARG cc_start: 0.6866 (OUTLIER) cc_final: 0.6603 (ttm170) REVERT: 3 32 LYS cc_start: 0.7683 (mmtt) cc_final: 0.7370 (mtpp) REVERT: 3 38 ARG cc_start: 0.7533 (OUTLIER) cc_final: 0.6533 (ttp80) outliers start: 442 outliers final: 306 residues processed: 994 average time/residue: 1.9091 time to fit residues: 2725.3018 Evaluate side-chains 1004 residues out of total 4231 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 354 poor density : 650 time to evaluate : 5.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 21 LYS Chi-restraints excluded: chain c residue 25 GLU Chi-restraints excluded: chain c residue 51 VAL Chi-restraints excluded: chain c residue 66 SER Chi-restraints excluded: chain c residue 67 ILE Chi-restraints excluded: chain c residue 69 THR Chi-restraints excluded: chain c residue 98 VAL Chi-restraints excluded: chain c residue 100 ILE Chi-restraints excluded: chain c residue 153 SER Chi-restraints excluded: chain c residue 164 SER Chi-restraints excluded: chain c residue 168 SER Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain c residue 200 TRP Chi-restraints excluded: chain d residue 14 ARG Chi-restraints excluded: chain d residue 22 THR Chi-restraints excluded: chain d residue 71 LEU Chi-restraints excluded: chain d residue 114 LEU Chi-restraints excluded: chain d residue 139 VAL Chi-restraints excluded: chain d residue 140 ILE Chi-restraints excluded: chain d residue 143 ARG Chi-restraints excluded: chain d residue 150 SER Chi-restraints excluded: chain d residue 159 THR Chi-restraints excluded: chain d residue 186 LEU Chi-restraints excluded: chain e residue 9 LEU Chi-restraints excluded: chain e residue 21 VAL Chi-restraints excluded: chain e residue 22 THR Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 76 MET Chi-restraints excluded: chain e residue 84 GLU Chi-restraints excluded: chain e residue 95 LEU Chi-restraints excluded: chain e residue 96 MET Chi-restraints excluded: chain e residue 100 VAL Chi-restraints excluded: chain e residue 111 VAL Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain e residue 125 SER Chi-restraints excluded: chain e residue 128 LEU Chi-restraints excluded: chain e residue 144 LEU Chi-restraints excluded: chain e residue 147 LEU Chi-restraints excluded: chain e residue 160 SER Chi-restraints excluded: chain e residue 164 ILE Chi-restraints excluded: chain e residue 165 ILE Chi-restraints excluded: chain f residue 3 GLN Chi-restraints excluded: chain f residue 5 THR Chi-restraints excluded: chain f residue 33 LEU Chi-restraints excluded: chain f residue 36 ASN Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 45 ASP Chi-restraints excluded: chain f residue 65 ILE Chi-restraints excluded: chain f residue 66 VAL Chi-restraints excluded: chain f residue 68 VAL Chi-restraints excluded: chain g residue 43 ILE Chi-restraints excluded: chain g residue 56 ASN Chi-restraints excluded: chain g residue 75 VAL Chi-restraints excluded: chain g residue 85 TYR Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain g residue 131 THR Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain h residue 24 THR Chi-restraints excluded: chain h residue 27 VAL Chi-restraints excluded: chain h residue 49 VAL Chi-restraints excluded: chain h residue 52 ILE Chi-restraints excluded: chain h residue 54 ASP Chi-restraints excluded: chain h residue 62 VAL Chi-restraints excluded: chain h residue 69 ASN Chi-restraints excluded: chain h residue 73 VAL Chi-restraints excluded: chain h residue 75 THR Chi-restraints excluded: chain h residue 89 VAL Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 99 ASN Chi-restraints excluded: chain h residue 126 GLU Chi-restraints excluded: chain h residue 131 VAL Chi-restraints excluded: chain i residue 16 VAL Chi-restraints excluded: chain i residue 28 ILE Chi-restraints excluded: chain i residue 29 THR Chi-restraints excluded: chain i residue 35 VAL Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain j residue 4 GLN Chi-restraints excluded: chain j residue 18 LEU Chi-restraints excluded: chain j residue 32 THR Chi-restraints excluded: chain j residue 51 VAL Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain j residue 84 VAL Chi-restraints excluded: chain j residue 85 ASP Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 35 THR Chi-restraints excluded: chain k residue 37 THR Chi-restraints excluded: chain k residue 45 SER Chi-restraints excluded: chain k residue 46 SER Chi-restraints excluded: chain k residue 81 THR Chi-restraints excluded: chain k residue 82 VAL Chi-restraints excluded: chain k residue 85 THR Chi-restraints excluded: chain k residue 86 VAL Chi-restraints excluded: chain k residue 107 VAL Chi-restraints excluded: chain l residue 8 VAL Chi-restraints excluded: chain l residue 21 SER Chi-restraints excluded: chain l residue 25 ASN Chi-restraints excluded: chain l residue 28 TYR Chi-restraints excluded: chain l residue 54 THR Chi-restraints excluded: chain l residue 72 ASN Chi-restraints excluded: chain l residue 77 THR Chi-restraints excluded: chain l residue 92 VAL Chi-restraints excluded: chain l residue 107 ARG Chi-restraints excluded: chain l residue 111 VAL Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain l residue 121 ASN Chi-restraints excluded: chain l residue 122 ASP Chi-restraints excluded: chain m residue 14 ARG Chi-restraints excluded: chain m residue 28 THR Chi-restraints excluded: chain m residue 68 ASP Chi-restraints excluded: chain m residue 80 LEU Chi-restraints excluded: chain m residue 100 GLN Chi-restraints excluded: chain m residue 102 THR Chi-restraints excluded: chain m residue 103 LYS Chi-restraints excluded: chain m residue 109 ARG Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain n residue 42 ILE Chi-restraints excluded: chain o residue 56 LEU Chi-restraints excluded: chain o residue 67 LEU Chi-restraints excluded: chain o residue 75 ILE Chi-restraints excluded: chain o residue 84 ARG Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain p residue 32 ARG Chi-restraints excluded: chain p residue 36 THR Chi-restraints excluded: chain p residue 73 ILE Chi-restraints excluded: chain q residue 10 VAL Chi-restraints excluded: chain q residue 16 VAL Chi-restraints excluded: chain q residue 21 ASP Chi-restraints excluded: chain q residue 32 LYS Chi-restraints excluded: chain q residue 55 THR Chi-restraints excluded: chain q residue 81 VAL Chi-restraints excluded: chain r residue 20 ASN Chi-restraints excluded: chain r residue 22 ILE Chi-restraints excluded: chain r residue 34 LYS Chi-restraints excluded: chain r residue 48 VAL 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 11 VAL Chi-restraints excluded: chain s residue 14 HIS Chi-restraints excluded: chain s residue 26 GLU Chi-restraints excluded: chain s residue 27 LYS Chi-restraints excluded: chain s residue 28 LYS Chi-restraints excluded: chain s residue 37 ARG Chi-restraints excluded: chain s residue 39 THR Chi-restraints excluded: chain s residue 45 VAL Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain s residue 73 GLU Chi-restraints excluded: chain t residue 12 ARG Chi-restraints excluded: chain t residue 39 VAL Chi-restraints excluded: chain t residue 49 LEU Chi-restraints excluded: chain t residue 81 LEU Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 38 LYS Chi-restraints excluded: chain C residue 69 ARG Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 175 ARG Chi-restraints excluded: chain C residue 177 ASN Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 138 ARG Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 167 ASP Chi-restraints excluded: chain D residue 168 ARG Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 184 ASN Chi-restraints excluded: chain D residue 191 ASN Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain E residue 6 LEU Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 105 VAL Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 195 THR Chi-restraints excluded: chain F residue 8 TYR Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 23 SER Chi-restraints excluded: chain F residue 32 ASP Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 88 LYS Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 127 ASN Chi-restraints excluded: chain F residue 133 LYS Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain G residue 2 SER Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 101 ASN Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 125 VAL Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 144 LEU Chi-restraints excluded: chain G residue 171 ARG Chi-restraints excluded: chain K residue 2 ARG Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 14 ARG Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 58 ILE Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 114 THR Chi-restraints excluded: chain K residue 115 LEU Chi-restraints excluded: chain K residue 145 ASN Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 19 ILE Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 53 LYS Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 71 ARG Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain M residue 36 LYS Chi-restraints excluded: chain M residue 39 LYS Chi-restraints excluded: chain M residue 42 SER Chi-restraints excluded: chain M residue 81 THR Chi-restraints excluded: chain M residue 87 ASP Chi-restraints excluded: chain M residue 105 GLU Chi-restraints excluded: chain M residue 122 THR Chi-restraints excluded: chain M residue 131 SER Chi-restraints excluded: chain N residue 5 LYS Chi-restraints excluded: chain N residue 11 ARG Chi-restraints excluded: chain N residue 26 GLU Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 75 THR Chi-restraints excluded: chain N residue 76 SER Chi-restraints excluded: chain N residue 85 LYS Chi-restraints excluded: chain N residue 122 SER Chi-restraints excluded: chain N residue 127 VAL Chi-restraints excluded: chain N residue 130 LYS Chi-restraints excluded: chain N residue 133 LYS Chi-restraints excluded: chain O residue 24 LEU Chi-restraints excluded: chain O residue 41 ARG Chi-restraints excluded: chain O residue 108 LEU Chi-restraints excluded: chain O residue 124 GLU Chi-restraints excluded: chain P residue 2 ILE Chi-restraints excluded: chain P residue 6 ASP Chi-restraints excluded: chain P residue 11 ARG Chi-restraints excluded: chain P residue 13 LYS Chi-restraints excluded: chain P residue 22 ILE Chi-restraints excluded: chain P residue 28 CYS Chi-restraints excluded: chain P residue 51 VAL Chi-restraints excluded: chain P residue 63 ILE Chi-restraints excluded: chain P residue 86 LYS Chi-restraints excluded: chain P residue 95 ARG Chi-restraints excluded: chain P residue 113 GLU Chi-restraints excluded: chain Q residue 2 ASN Chi-restraints excluded: chain Q residue 36 THR Chi-restraints excluded: chain Q residue 60 THR Chi-restraints excluded: chain Q residue 78 THR Chi-restraints excluded: chain Q residue 80 ARG Chi-restraints excluded: chain Q residue 109 ARG Chi-restraints excluded: chain R residue 10 THR Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 79 LEU Chi-restraints excluded: chain R residue 90 ILE Chi-restraints excluded: chain S residue 10 LYS Chi-restraints excluded: chain S residue 14 VAL Chi-restraints excluded: chain S residue 22 VAL Chi-restraints excluded: chain S residue 28 GLU Chi-restraints excluded: chain S residue 33 VAL Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 75 GLN Chi-restraints excluded: chain S residue 98 GLU Chi-restraints excluded: chain S residue 101 ASN Chi-restraints excluded: chain T residue 11 THR Chi-restraints excluded: chain T residue 14 THR Chi-restraints excluded: chain T residue 29 ILE Chi-restraints excluded: chain T residue 106 SER Chi-restraints excluded: chain T residue 109 THR Chi-restraints excluded: chain U residue 3 LEU Chi-restraints excluded: chain U residue 16 SER Chi-restraints excluded: chain U residue 36 THR Chi-restraints excluded: chain U residue 55 ILE Chi-restraints excluded: chain U residue 56 LEU Chi-restraints excluded: chain U residue 75 ARG Chi-restraints excluded: chain U residue 84 GLU Chi-restraints excluded: chain V residue 5 LYS Chi-restraints excluded: chain V residue 7 ASP Chi-restraints excluded: chain V residue 9 VAL Chi-restraints excluded: chain V residue 13 THR Chi-restraints excluded: chain V residue 17 LYS Chi-restraints excluded: chain V residue 33 VAL Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain V residue 68 VAL Chi-restraints excluded: chain V residue 90 LYS Chi-restraints excluded: chain V residue 91 VAL Chi-restraints excluded: chain V residue 99 GLU Chi-restraints excluded: chain X residue 18 SER Chi-restraints excluded: chain X residue 19 THR Chi-restraints excluded: chain X residue 23 ARG Chi-restraints excluded: chain X residue 24 ASP Chi-restraints excluded: chain X residue 39 THR Chi-restraints excluded: chain X residue 40 VAL Chi-restraints excluded: chain X residue 67 THR Chi-restraints excluded: chain X residue 75 VAL Chi-restraints excluded: chain X residue 79 GLU Chi-restraints excluded: chain X residue 88 VAL Chi-restraints excluded: chain X residue 93 VAL Chi-restraints excluded: chain Y residue 12 THR Chi-restraints excluded: chain Y residue 22 MET Chi-restraints excluded: chain Y residue 24 SER Chi-restraints excluded: chain Y residue 28 THR Chi-restraints excluded: chain Y residue 40 ILE Chi-restraints excluded: chain Z residue 3 VAL Chi-restraints excluded: chain Z residue 37 LEU Chi-restraints excluded: chain 0 residue 30 LYS Chi-restraints excluded: chain 0 residue 35 VAL Chi-restraints excluded: chain 0 residue 54 VAL Chi-restraints excluded: chain 0 residue 59 VAL Chi-restraints excluded: chain 2 residue 3 VAL Chi-restraints excluded: chain 2 residue 8 THR Chi-restraints excluded: chain 2 residue 18 THR Chi-restraints excluded: chain 2 residue 23 THR Chi-restraints excluded: chain 2 residue 56 SER Chi-restraints excluded: chain 3 residue 24 ARG Chi-restraints excluded: chain 3 residue 38 ARG Chi-restraints excluded: chain 4 residue 20 LYS Chi-restraints excluded: chain 5 residue 17 THR Chi-restraints excluded: chain 5 residue 32 ARG Chi-restraints excluded: chain 5 residue 58 ILE Chi-restraints excluded: chain 5 residue 60 GLN Chi-restraints excluded: chain 6 residue 11 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 920 random chunks: chunk 740 optimal weight: 7.9990 chunk 504 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 chunk 662 optimal weight: 5.9990 chunk 366 optimal weight: 10.0000 chunk 758 optimal weight: 9.9990 chunk 614 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 454 optimal weight: 10.0000 chunk 798 optimal weight: 2.9990 chunk 224 optimal weight: 20.0000 overall best weight: 7.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 67 ASN ** g 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 9 ASN o 37 ASN o 38 GLN ** s 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 ASN ** F 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 54 GLN N 44 ASN O 61 GLN ** O 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 87 GLN Z 48 GLN Z 60 GLN 0 17 GLN 3 20 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.120 145353 Z= 0.408 Angle : 0.849 12.063 217934 Z= 0.425 Chirality : 0.048 0.334 27945 Planarity : 0.007 0.076 11316 Dihedral : 23.107 179.753 73958 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.00 % Favored : 89.92 % Rotamer: Outliers : 11.44 % Allowed : 24.70 % Favored : 63.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.17 % Twisted Proline : 0.54 % Twisted General : 0.08 % 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: -2.10 (0.11), residues: 4970 helix: -0.26 (0.13), residues: 1460 sheet: -0.59 (0.16), residues: 998 loop : -2.50 (0.11), residues: 2512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP d 9 HIS 0.007 0.002 HIS h 22 PHE 0.025 0.003 PHE V 2 TYR 0.024 0.003 TYR r 27 ARG 0.009 0.001 ARG 2 6 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9940 Ramachandran restraints generated. 4970 Oldfield, 0 Emsley, 4970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9940 Ramachandran restraints generated. 4970 Oldfield, 0 Emsley, 4970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1140 residues out of total 4231 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 484 poor density : 656 time to evaluate : 5.627 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: c 200 TRP cc_start: 0.7999 (OUTLIER) cc_final: 0.7393 (m100) REVERT: d 114 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8528 (mt) REVERT: d 143 ARG cc_start: 0.7503 (OUTLIER) cc_final: 0.6518 (ttt-90) REVERT: f 3 GLN cc_start: 0.6267 (OUTLIER) cc_final: 0.5266 (mm110) REVERT: h 49 VAL cc_start: 0.8809 (OUTLIER) cc_final: 0.8372 (t) REVERT: j 4 GLN cc_start: 0.4672 (OUTLIER) cc_final: 0.4390 (tm-30) REVERT: j 85 ASP cc_start: 0.6072 (OUTLIER) cc_final: 0.5705 (m-30) REVERT: k 72 LYS cc_start: 0.6657 (OUTLIER) cc_final: 0.6364 (ttpp) REVERT: m 100 GLN cc_start: 0.8101 (OUTLIER) cc_final: 0.7671 (mp10) REVERT: m 103 LYS cc_start: 0.5065 (OUTLIER) cc_final: 0.2922 (mmtp) REVERT: m 109 ARG cc_start: 0.8019 (OUTLIER) cc_final: 0.7359 (tpt-90) REVERT: n 3 LYS cc_start: 0.8082 (OUTLIER) cc_final: 0.7874 (tptm) REVERT: o 56 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8197 (tp) REVERT: o 84 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.8115 (ttp-170) REVERT: s 7 LYS cc_start: 0.5103 (OUTLIER) cc_final: 0.3700 (pttt) REVERT: s 37 ARG cc_start: 0.8123 (OUTLIER) cc_final: 0.7024 (ptp-170) REVERT: C 30 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7278 (tm-30) REVERT: C 69 ARG cc_start: 0.8712 (OUTLIER) cc_final: 0.8454 (mmm-85) REVERT: C 175 ARG cc_start: 0.7828 (OUTLIER) cc_final: 0.7146 (ttp-110) REVERT: C 182 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.8292 (mtp85) REVERT: D 90 GLU cc_start: 0.6880 (OUTLIER) cc_final: 0.5882 (tm-30) REVERT: D 138 ARG cc_start: 0.8104 (OUTLIER) cc_final: 0.7719 (mtt180) REVERT: D 168 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.8031 (ptt180) REVERT: E 30 GLU cc_start: 0.6984 (OUTLIER) cc_final: 0.6289 (mp0) REVERT: E 45 ARG cc_start: 0.8880 (OUTLIER) cc_final: 0.7178 (mtt180) REVERT: E 66 ARG cc_start: 0.5668 (mtm110) cc_final: 0.5201 (mtt-85) REVERT: E 147 SER cc_start: 0.8146 (p) cc_final: 0.7888 (m) REVERT: E 190 ASN cc_start: 0.8617 (OUTLIER) cc_final: 0.8282 (t0) REVERT: F 8 TYR cc_start: 0.4173 (OUTLIER) cc_final: 0.3668 (m-10) REVERT: F 36 ILE cc_start: 0.8091 (OUTLIER) cc_final: 0.7675 (mp) REVERT: F 169 LEU cc_start: 0.6977 (OUTLIER) cc_final: 0.6683 (tp) REVERT: G 144 LEU cc_start: 0.8052 (OUTLIER) cc_final: 0.7541 (mp) REVERT: G 171 ARG cc_start: 0.7698 (OUTLIER) cc_final: 0.7174 (mmm160) REVERT: K 14 ARG cc_start: 0.8193 (OUTLIER) cc_final: 0.6342 (mtt-85) REVERT: L 19 ILE cc_start: 0.8060 (OUTLIER) cc_final: 0.7683 (pt) REVERT: L 71 ARG cc_start: 0.7918 (OUTLIER) cc_final: 0.7684 (mpt-90) REVERT: M 39 LYS cc_start: 0.8718 (OUTLIER) cc_final: 0.8447 (mtpm) REVERT: M 79 LEU cc_start: 0.7414 (OUTLIER) cc_final: 0.6726 (mp) REVERT: M 103 LYS cc_start: 0.8307 (OUTLIER) cc_final: 0.8105 (pttm) REVERT: M 133 GLN cc_start: 0.7259 (tt0) cc_final: 0.6925 (tt0) REVERT: N 11 ARG cc_start: 0.8590 (OUTLIER) cc_final: 0.7903 (mpt180) REVERT: N 130 LYS cc_start: 0.7870 (OUTLIER) cc_final: 0.7575 (mtmm) REVERT: O 19 ASP cc_start: 0.7561 (m-30) cc_final: 0.7227 (m-30) REVERT: O 108 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8508 (mp) REVERT: P 22 ILE cc_start: 0.8578 (OUTLIER) cc_final: 0.8081 (mp) REVERT: P 35 ARG cc_start: 0.8326 (OUTLIER) cc_final: 0.7116 (ttm170) REVERT: P 113 GLU cc_start: 0.5986 (OUTLIER) cc_final: 0.5739 (mt-10) REVERT: Q 6 GLN cc_start: 0.7504 (mt0) cc_final: 0.7249 (mt0) REVERT: Q 38 GLU cc_start: 0.6497 (OUTLIER) cc_final: 0.5923 (tp30) REVERT: Q 60 THR cc_start: 0.8506 (OUTLIER) cc_final: 0.8272 (m) REVERT: R 56 ASP cc_start: 0.7448 (m-30) cc_final: 0.7182 (m-30) REVERT: S 96 MET cc_start: 0.7677 (mmm) cc_final: 0.7429 (tpp) REVERT: S 98 GLU cc_start: 0.7430 (OUTLIER) cc_final: 0.7100 (mt-10) REVERT: U 75 ARG cc_start: 0.8213 (OUTLIER) cc_final: 0.7624 (mtt90) REVERT: V 5 LYS cc_start: 0.7840 (OUTLIER) cc_final: 0.7006 (tttm) REVERT: V 17 LYS cc_start: 0.8274 (OUTLIER) cc_final: 0.8063 (ttmt) REVERT: X 23 ARG cc_start: 0.8452 (OUTLIER) cc_final: 0.7535 (ptt90) REVERT: Y 22 MET cc_start: 0.7601 (OUTLIER) cc_final: 0.6928 (mmp) REVERT: Y 35 LYS cc_start: 0.7887 (ttmt) cc_final: 0.7667 (ttmm) REVERT: Z 15 LEU cc_start: 0.7593 (OUTLIER) cc_final: 0.7040 (mt) REVERT: 0 58 GLU cc_start: 0.7058 (mm-30) cc_final: 0.6806 (tp30) REVERT: 3 24 ARG cc_start: 0.6871 (OUTLIER) cc_final: 0.6592 (ttm170) REVERT: 3 32 LYS cc_start: 0.7728 (mmtt) cc_final: 0.7394 (mtpp) outliers start: 484 outliers final: 358 residues processed: 1015 average time/residue: 1.9394 time to fit residues: 2825.9088 Evaluate side-chains 1061 residues out of total 4231 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 411 poor density : 650 time to evaluate : 5.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 21 LYS Chi-restraints excluded: chain c residue 25 GLU Chi-restraints excluded: chain c residue 51 VAL Chi-restraints excluded: chain c residue 66 SER Chi-restraints excluded: chain c residue 67 ILE Chi-restraints excluded: chain c residue 69 THR Chi-restraints excluded: chain c residue 75 VAL Chi-restraints excluded: chain c residue 98 VAL Chi-restraints excluded: chain c residue 100 ILE Chi-restraints excluded: chain c residue 103 VAL Chi-restraints excluded: chain c residue 153 SER Chi-restraints excluded: chain c residue 164 SER Chi-restraints excluded: chain c residue 168 SER Chi-restraints excluded: chain c residue 171 THR Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain c residue 200 TRP Chi-restraints excluded: chain d residue 14 ARG Chi-restraints excluded: chain d residue 22 THR Chi-restraints excluded: chain d residue 58 ARG Chi-restraints excluded: chain d residue 63 MET Chi-restraints excluded: chain d residue 71 LEU Chi-restraints excluded: chain d residue 114 LEU Chi-restraints excluded: chain d residue 139 VAL Chi-restraints excluded: chain d residue 140 ILE Chi-restraints excluded: chain d residue 143 ARG Chi-restraints excluded: chain d residue 150 SER Chi-restraints excluded: chain d residue 159 THR Chi-restraints excluded: chain d residue 186 LEU Chi-restraints excluded: chain d residue 189 GLU Chi-restraints excluded: chain e residue 4 ILE 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 39 VAL Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 76 MET Chi-restraints excluded: chain e residue 84 GLU Chi-restraints excluded: chain e residue 95 LEU Chi-restraints excluded: chain e residue 96 MET Chi-restraints excluded: chain e residue 100 VAL Chi-restraints excluded: chain e residue 111 VAL Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain e residue 125 SER Chi-restraints excluded: chain e residue 128 LEU Chi-restraints excluded: chain e residue 144 LEU Chi-restraints excluded: chain e residue 147 LEU Chi-restraints excluded: chain e residue 160 SER Chi-restraints excluded: chain e residue 164 ILE Chi-restraints excluded: chain e residue 165 ILE Chi-restraints excluded: chain f residue 3 GLN Chi-restraints excluded: chain f residue 4 ASP Chi-restraints excluded: chain f residue 5 THR Chi-restraints excluded: chain f residue 33 LEU Chi-restraints excluded: chain f residue 36 ASN Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 41 ILE Chi-restraints excluded: chain f residue 45 ASP Chi-restraints excluded: chain f residue 65 ILE Chi-restraints excluded: chain f residue 66 VAL Chi-restraints excluded: chain g residue 43 ILE Chi-restraints excluded: chain g residue 56 ASN Chi-restraints excluded: chain g residue 75 VAL Chi-restraints excluded: chain g residue 85 TYR Chi-restraints excluded: chain g residue 91 VAL Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain g residue 131 THR Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain h residue 2 VAL Chi-restraints excluded: chain h residue 24 THR Chi-restraints excluded: chain h residue 27 VAL Chi-restraints excluded: chain h residue 49 VAL Chi-restraints excluded: chain h residue 52 ILE Chi-restraints excluded: chain h residue 54 ASP Chi-restraints excluded: chain h residue 62 VAL Chi-restraints excluded: chain h residue 69 ASN Chi-restraints excluded: chain h residue 73 VAL Chi-restraints excluded: chain h residue 75 THR Chi-restraints excluded: chain h residue 89 VAL Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 99 ASN Chi-restraints excluded: chain h residue 131 VAL Chi-restraints excluded: chain i residue 29 THR Chi-restraints excluded: chain i residue 35 VAL Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain i residue 83 ILE Chi-restraints excluded: chain j residue 4 GLN Chi-restraints excluded: chain j residue 18 LEU Chi-restraints excluded: chain j residue 25 ILE Chi-restraints excluded: chain j residue 51 VAL Chi-restraints excluded: chain j residue 84 VAL Chi-restraints excluded: chain j residue 85 ASP Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 35 THR Chi-restraints excluded: chain k residue 37 THR Chi-restraints excluded: chain k residue 45 SER Chi-restraints excluded: chain k residue 46 SER Chi-restraints excluded: chain k residue 65 MET Chi-restraints excluded: chain k residue 72 LYS Chi-restraints excluded: chain k residue 81 THR Chi-restraints excluded: chain k residue 82 VAL Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain k residue 85 THR Chi-restraints excluded: chain k residue 86 VAL Chi-restraints excluded: chain k residue 107 VAL Chi-restraints excluded: chain l residue 8 VAL Chi-restraints excluded: chain l residue 14 SER Chi-restraints excluded: chain l residue 21 SER Chi-restraints excluded: chain l residue 25 ASN Chi-restraints excluded: chain l residue 54 THR Chi-restraints excluded: chain l residue 72 ASN Chi-restraints excluded: chain l residue 77 THR Chi-restraints excluded: chain l residue 92 VAL Chi-restraints excluded: chain l residue 107 ARG Chi-restraints excluded: chain l residue 111 VAL Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain l residue 122 ASP Chi-restraints excluded: chain m residue 14 ARG Chi-restraints excluded: chain m residue 15 VAL Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 28 THR Chi-restraints excluded: chain m residue 39 VAL Chi-restraints excluded: chain m residue 80 LEU Chi-restraints excluded: chain m residue 100 GLN Chi-restraints excluded: chain m residue 102 THR Chi-restraints excluded: chain m residue 103 LYS Chi-restraints excluded: chain m residue 109 ARG Chi-restraints excluded: chain n residue 3 LYS Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain n residue 42 ILE Chi-restraints excluded: chain o residue 22 THR Chi-restraints excluded: chain o residue 56 LEU Chi-restraints excluded: chain o residue 67 LEU Chi-restraints excluded: chain o residue 73 THR Chi-restraints excluded: chain o residue 75 ILE Chi-restraints excluded: chain o residue 84 ARG Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain p residue 32 ARG Chi-restraints excluded: chain p residue 36 THR Chi-restraints excluded: chain p residue 44 LYS Chi-restraints excluded: chain p residue 73 ILE Chi-restraints excluded: chain q residue 10 VAL Chi-restraints excluded: chain q residue 16 VAL Chi-restraints excluded: chain q residue 21 ASP Chi-restraints excluded: chain q residue 25 THR Chi-restraints excluded: chain q residue 32 LYS Chi-restraints excluded: chain q residue 55 THR Chi-restraints excluded: chain q residue 80 GLU Chi-restraints excluded: chain q residue 81 VAL Chi-restraints excluded: chain r residue 20 ASN Chi-restraints excluded: chain r residue 22 ILE Chi-restraints excluded: chain r residue 32 LEU Chi-restraints excluded: chain r residue 48 VAL 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 11 VAL Chi-restraints excluded: chain s residue 14 HIS Chi-restraints excluded: chain s residue 26 GLU Chi-restraints excluded: chain s residue 27 LYS Chi-restraints excluded: chain s residue 37 ARG Chi-restraints excluded: chain s residue 39 THR Chi-restraints excluded: chain s residue 45 VAL Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain s residue 73 GLU Chi-restraints excluded: chain s residue 78 ARG Chi-restraints excluded: chain t residue 13 THR Chi-restraints excluded: chain t residue 39 VAL Chi-restraints excluded: chain t residue 49 LEU Chi-restraints excluded: chain t residue 59 MET Chi-restraints excluded: chain t residue 81 LEU Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 38 LYS Chi-restraints excluded: chain C residue 69 ARG Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 108 LYS Chi-restraints excluded: chain C residue 175 ARG Chi-restraints excluded: chain C residue 177 ASN Chi-restraints excluded: chain C residue 182 ARG Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 138 ARG Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 167 ASP Chi-restraints excluded: chain D residue 168 ARG Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 184 ASN Chi-restraints excluded: chain D residue 191 ASN Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain E residue 6 LEU Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 30 GLU Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 105 VAL Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 190 ASN Chi-restraints excluded: chain E residue 195 THR Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain F residue 8 TYR Chi-restraints excluded: chain F residue 15 SER Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 23 SER Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 88 LYS Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 123 ASP Chi-restraints excluded: chain F residue 127 ASN Chi-restraints excluded: chain F residue 133 LYS Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain G residue 2 SER Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 101 ASN Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 144 LEU Chi-restraints excluded: chain G residue 165 VAL Chi-restraints excluded: chain G residue 171 ARG Chi-restraints excluded: chain K residue 2 ARG Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 14 ARG Chi-restraints excluded: chain K residue 15 LYS Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 58 ILE Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 114 THR Chi-restraints excluded: chain K residue 115 LEU Chi-restraints excluded: chain K residue 145 ASN Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 19 ILE Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 53 LYS Chi-restraints excluded: chain L residue 54 LYS Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 71 ARG Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain M residue 36 LYS Chi-restraints excluded: chain M residue 39 LYS Chi-restraints excluded: chain M residue 42 SER Chi-restraints excluded: chain M residue 79 LEU Chi-restraints excluded: chain M residue 81 THR Chi-restraints excluded: chain M residue 87 ASP Chi-restraints excluded: chain M residue 103 LYS Chi-restraints excluded: chain M residue 105 GLU Chi-restraints excluded: chain M residue 122 THR Chi-restraints excluded: chain M residue 131 SER Chi-restraints excluded: chain N residue 5 LYS Chi-restraints excluded: chain N residue 11 ARG Chi-restraints excluded: chain N residue 26 GLU Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 75 THR Chi-restraints excluded: chain N residue 76 SER Chi-restraints excluded: chain N residue 85 LYS Chi-restraints excluded: chain N residue 122 SER Chi-restraints excluded: chain N residue 127 VAL Chi-restraints excluded: chain N residue 130 LYS Chi-restraints excluded: chain N residue 133 LYS Chi-restraints excluded: chain O residue 24 LEU Chi-restraints excluded: chain O residue 108 LEU Chi-restraints excluded: chain O residue 121 VAL Chi-restraints excluded: chain O residue 124 GLU Chi-restraints excluded: chain P residue 2 ILE Chi-restraints excluded: chain P residue 6 ASP Chi-restraints excluded: chain P residue 11 ARG Chi-restraints excluded: chain P residue 13 LYS Chi-restraints excluded: chain P residue 18 VAL Chi-restraints excluded: chain P residue 22 ILE Chi-restraints excluded: chain P residue 28 CYS Chi-restraints excluded: chain P residue 35 ARG Chi-restraints excluded: chain P residue 51 VAL Chi-restraints excluded: chain P residue 63 ILE Chi-restraints excluded: chain P residue 67 THR Chi-restraints excluded: chain P residue 70 GLU Chi-restraints excluded: chain P residue 86 LYS Chi-restraints excluded: chain P residue 95 ARG Chi-restraints excluded: chain P residue 113 GLU Chi-restraints excluded: chain Q residue 2 ASN Chi-restraints excluded: chain Q residue 36 THR Chi-restraints excluded: chain Q residue 38 GLU Chi-restraints excluded: chain Q residue 60 THR Chi-restraints excluded: chain Q residue 78 THR Chi-restraints excluded: chain Q residue 80 ARG Chi-restraints excluded: chain Q residue 109 ARG Chi-restraints excluded: chain R residue 10 THR Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 42 SER Chi-restraints excluded: chain R residue 79 LEU Chi-restraints excluded: chain R residue 112 GLN Chi-restraints excluded: chain S residue 10 LYS Chi-restraints excluded: chain S residue 14 VAL Chi-restraints excluded: chain S residue 22 VAL Chi-restraints excluded: chain S residue 28 GLU Chi-restraints excluded: chain S residue 33 VAL Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 61 THR Chi-restraints excluded: chain S residue 75 GLN Chi-restraints excluded: chain S residue 98 GLU Chi-restraints excluded: chain S residue 101 ASN Chi-restraints excluded: chain T residue 11 THR Chi-restraints excluded: chain T residue 14 THR Chi-restraints excluded: chain T residue 26 ILE Chi-restraints excluded: chain T residue 29 ILE Chi-restraints excluded: chain T residue 70 ASP Chi-restraints excluded: chain T residue 75 VAL Chi-restraints excluded: chain T residue 105 THR Chi-restraints excluded: chain T residue 106 SER Chi-restraints excluded: chain T residue 109 THR Chi-restraints excluded: chain U residue 3 LEU Chi-restraints excluded: chain U residue 16 SER Chi-restraints excluded: chain U residue 36 THR Chi-restraints excluded: chain U residue 42 VAL Chi-restraints excluded: chain U residue 55 ILE Chi-restraints excluded: chain U residue 56 LEU Chi-restraints excluded: chain U residue 75 ARG Chi-restraints excluded: chain U residue 84 GLU Chi-restraints excluded: chain V residue 2 PHE Chi-restraints excluded: chain V residue 5 LYS Chi-restraints excluded: chain V residue 9 VAL Chi-restraints excluded: chain V residue 13 THR Chi-restraints excluded: chain V residue 17 LYS Chi-restraints excluded: chain V residue 33 VAL Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain V residue 68 VAL Chi-restraints excluded: chain V residue 90 LYS Chi-restraints excluded: chain V residue 91 VAL Chi-restraints excluded: chain V residue 94 SER Chi-restraints excluded: chain V residue 99 GLU Chi-restraints excluded: chain X residue 18 SER Chi-restraints excluded: chain X residue 19 THR Chi-restraints excluded: chain X residue 23 ARG Chi-restraints excluded: chain X residue 24 ASP Chi-restraints excluded: chain X residue 39 THR Chi-restraints excluded: chain X residue 40 VAL Chi-restraints excluded: chain X residue 67 THR Chi-restraints excluded: chain X residue 75 VAL Chi-restraints excluded: chain X residue 79 GLU Chi-restraints excluded: chain X residue 88 VAL Chi-restraints excluded: chain X residue 93 VAL Chi-restraints excluded: chain Y residue 12 THR Chi-restraints excluded: chain Y residue 22 MET Chi-restraints excluded: chain Y residue 24 SER Chi-restraints excluded: chain Y residue 28 THR Chi-restraints excluded: chain Y residue 40 ILE Chi-restraints excluded: chain Z residue 3 VAL Chi-restraints excluded: chain Z residue 10 THR Chi-restraints excluded: chain Z residue 15 LEU Chi-restraints excluded: chain Z residue 18 GLU Chi-restraints excluded: chain Z residue 24 GLU Chi-restraints excluded: chain Z residue 37 LEU Chi-restraints excluded: chain Z residue 49 SER Chi-restraints excluded: chain 0 residue 30 LYS Chi-restraints excluded: chain 0 residue 35 VAL Chi-restraints excluded: chain 0 residue 54 VAL Chi-restraints excluded: chain 0 residue 59 VAL Chi-restraints excluded: chain 2 residue 3 VAL Chi-restraints excluded: chain 2 residue 8 THR Chi-restraints excluded: chain 2 residue 18 THR Chi-restraints excluded: chain 2 residue 23 THR Chi-restraints excluded: chain 2 residue 56 SER Chi-restraints excluded: chain 3 residue 24 ARG Chi-restraints excluded: chain 3 residue 38 ARG Chi-restraints excluded: chain 3 residue 44 LEU Chi-restraints excluded: chain 4 residue 1 MET Chi-restraints excluded: chain 4 residue 20 LYS Chi-restraints excluded: chain 5 residue 14 VAL Chi-restraints excluded: chain 5 residue 17 THR Chi-restraints excluded: chain 5 residue 32 ARG Chi-restraints excluded: chain 5 residue 58 ILE Chi-restraints excluded: chain 5 residue 60 GLN Chi-restraints excluded: chain 6 residue 4 ARG Chi-restraints excluded: chain 6 residue 11 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 920 random chunks: chunk 299 optimal weight: 0.9990 chunk 800 optimal weight: 5.9990 chunk 175 optimal weight: 9.9990 chunk 522 optimal weight: 7.9990 chunk 219 optimal weight: 8.9990 chunk 890 optimal weight: 0.0270 chunk 738 optimal weight: 1.9990 chunk 412 optimal weight: 10.0000 chunk 74 optimal weight: 10.0000 chunk 294 optimal weight: 20.0000 chunk 467 optimal weight: 10.0000 overall best weight: 3.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 50 GLN e 8 HIS f 67 ASN ** g 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 77 HIS ** m 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 9 ASN o 38 GLN ** s 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 103 GLN ** F 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 44 ASN O 61 GLN ** O 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 87 GLN Z 60 GLN 0 17 GLN 3 20 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 145353 Z= 0.214 Angle : 0.657 10.102 217934 Z= 0.342 Chirality : 0.040 0.289 27945 Planarity : 0.005 0.068 11316 Dihedral : 22.943 179.947 73958 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.51 % Favored : 91.43 % Rotamer: Outliers : 10.45 % Allowed : 25.88 % Favored : 63.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.17 % Twisted Proline : 0.54 % Twisted General : 0.06 % 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: -1.82 (0.11), residues: 4970 helix: 0.08 (0.14), residues: 1453 sheet: -0.50 (0.16), residues: 1019 loop : -2.37 (0.11), residues: 2498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP d 9 HIS 0.006 0.001 HIS h 22 PHE 0.019 0.002 PHE V 2 TYR 0.020 0.002 TYR l 28 ARG 0.005 0.000 ARG j 31 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9940 Ramachandran restraints generated. 4970 Oldfield, 0 Emsley, 4970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9940 Ramachandran restraints generated. 4970 Oldfield, 0 Emsley, 4970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1106 residues out of total 4231 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 442 poor density : 664 time to evaluate : 5.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 200 TRP cc_start: 0.7975 (OUTLIER) cc_final: 0.7435 (m100) REVERT: d 114 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8474 (mt) REVERT: d 143 ARG cc_start: 0.7425 (OUTLIER) cc_final: 0.6012 (ttm-80) REVERT: f 3 GLN cc_start: 0.6213 (OUTLIER) cc_final: 0.5202 (mm110) REVERT: h 49 VAL cc_start: 0.8790 (OUTLIER) cc_final: 0.8339 (t) REVERT: i 113 ARG cc_start: 0.8505 (OUTLIER) cc_final: 0.8133 (ttt180) REVERT: j 4 GLN cc_start: 0.4576 (OUTLIER) cc_final: 0.4322 (tm-30) REVERT: j 85 ASP cc_start: 0.5897 (OUTLIER) cc_final: 0.5552 (m-30) REVERT: k 72 LYS cc_start: 0.6820 (OUTLIER) cc_final: 0.6595 (mtpp) REVERT: l 63 ARG cc_start: 0.8450 (OUTLIER) cc_final: 0.6753 (mtt90) REVERT: l 72 ASN cc_start: 0.5275 (OUTLIER) cc_final: 0.4935 (t0) REVERT: m 100 GLN cc_start: 0.8034 (OUTLIER) cc_final: 0.7594 (mp10) REVERT: m 103 LYS cc_start: 0.4903 (OUTLIER) cc_final: 0.2858 (mmtp) REVERT: m 109 ARG cc_start: 0.7928 (OUTLIER) cc_final: 0.7288 (tpt-90) REVERT: o 56 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8152 (tp) REVERT: o 84 ARG cc_start: 0.8442 (OUTLIER) cc_final: 0.8080 (ttp-170) REVERT: s 7 LYS cc_start: 0.4855 (OUTLIER) cc_final: 0.3723 (pttt) REVERT: s 37 ARG cc_start: 0.8101 (OUTLIER) cc_final: 0.7055 (ptp-170) REVERT: C 30 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7161 (tm-30) REVERT: C 38 LYS cc_start: 0.8019 (OUTLIER) cc_final: 0.7739 (tmtt) REVERT: C 69 ARG cc_start: 0.8694 (OUTLIER) cc_final: 0.8478 (mmm-85) REVERT: C 175 ARG cc_start: 0.7707 (OUTLIER) cc_final: 0.7103 (ttp-110) REVERT: D 90 GLU cc_start: 0.6774 (OUTLIER) cc_final: 0.5878 (tm-30) REVERT: D 138 ARG cc_start: 0.8025 (OUTLIER) cc_final: 0.7599 (mtt180) REVERT: D 168 ARG cc_start: 0.8414 (OUTLIER) cc_final: 0.7906 (ptt180) REVERT: E 45 ARG cc_start: 0.8880 (OUTLIER) cc_final: 0.7159 (mtt180) REVERT: E 66 ARG cc_start: 0.5662 (mtm110) cc_final: 0.5102 (mtt-85) REVERT: E 147 SER cc_start: 0.8167 (p) cc_final: 0.7925 (m) REVERT: E 190 ASN cc_start: 0.8593 (OUTLIER) cc_final: 0.8256 (t0) REVERT: F 8 TYR cc_start: 0.4187 (OUTLIER) cc_final: 0.3628 (m-10) REVERT: F 36 ILE cc_start: 0.8084 (OUTLIER) cc_final: 0.7700 (mp) REVERT: F 169 LEU cc_start: 0.7136 (OUTLIER) cc_final: 0.6844 (tp) REVERT: G 144 LEU cc_start: 0.7981 (OUTLIER) cc_final: 0.7501 (mp) REVERT: G 171 ARG cc_start: 0.7850 (OUTLIER) cc_final: 0.7298 (mmm160) REVERT: L 19 ILE cc_start: 0.8014 (OUTLIER) cc_final: 0.7635 (pt) REVERT: L 71 ARG cc_start: 0.7906 (OUTLIER) cc_final: 0.7623 (mpt-90) REVERT: L 105 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7494 (mm-30) REVERT: M 39 LYS cc_start: 0.8729 (OUTLIER) cc_final: 0.8519 (mtpm) REVERT: M 133 GLN cc_start: 0.7289 (tt0) cc_final: 0.6986 (tt0) REVERT: N 130 LYS cc_start: 0.7802 (OUTLIER) cc_final: 0.7498 (mtmm) REVERT: O 19 ASP cc_start: 0.7510 (m-30) cc_final: 0.7172 (m-30) REVERT: P 22 ILE cc_start: 0.8605 (OUTLIER) cc_final: 0.8090 (mp) REVERT: P 113 GLU cc_start: 0.6007 (OUTLIER) cc_final: 0.5768 (mt-10) REVERT: Q 6 GLN cc_start: 0.7395 (mt0) cc_final: 0.7127 (mt0) REVERT: Q 38 GLU cc_start: 0.6435 (OUTLIER) cc_final: 0.5859 (tp30) REVERT: R 56 ASP cc_start: 0.7349 (m-30) cc_final: 0.7090 (m-30) REVERT: S 96 MET cc_start: 0.7603 (mmm) cc_final: 0.7329 (tpp) REVERT: S 98 GLU cc_start: 0.7363 (OUTLIER) cc_final: 0.7012 (mt-10) REVERT: U 75 ARG cc_start: 0.8201 (OUTLIER) cc_final: 0.7546 (mtt90) REVERT: V 5 LYS cc_start: 0.7948 (OUTLIER) cc_final: 0.6994 (tptm) REVERT: V 17 LYS cc_start: 0.8226 (OUTLIER) cc_final: 0.7993 (ttmt) REVERT: X 23 ARG cc_start: 0.8382 (OUTLIER) cc_final: 0.7517 (ptt90) REVERT: Y 22 MET cc_start: 0.7556 (OUTLIER) cc_final: 0.7188 (mmp) REVERT: 0 40 ASN cc_start: 0.7562 (m-40) cc_final: 0.7275 (m-40) REVERT: 0 58 GLU cc_start: 0.7042 (mm-30) cc_final: 0.6768 (tp30) REVERT: 3 24 ARG cc_start: 0.6856 (OUTLIER) cc_final: 0.6600 (ttm170) REVERT: 3 32 LYS cc_start: 0.7725 (mmtt) cc_final: 0.7370 (mtpp) REVERT: 3 38 ARG cc_start: 0.7595 (OUTLIER) cc_final: 0.6601 (ttp80) REVERT: 5 32 ARG cc_start: 0.8097 (OUTLIER) cc_final: 0.7706 (ptt180) REVERT: 6 4 ARG cc_start: 0.8696 (OUTLIER) cc_final: 0.8243 (ptp-170) outliers start: 442 outliers final: 327 residues processed: 993 average time/residue: 1.9584 time to fit residues: 2795.1676 Evaluate side-chains 1026 residues out of total 4231 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 377 poor density : 649 time to evaluate : 5.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 21 LYS Chi-restraints excluded: chain c residue 25 GLU Chi-restraints excluded: chain c residue 51 VAL Chi-restraints excluded: chain c residue 67 ILE Chi-restraints excluded: chain c residue 69 THR Chi-restraints excluded: chain c residue 75 VAL Chi-restraints excluded: chain c residue 98 VAL Chi-restraints excluded: chain c residue 100 ILE Chi-restraints excluded: chain c residue 164 SER Chi-restraints excluded: chain c residue 168 SER Chi-restraints excluded: chain c residue 171 THR Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain c residue 200 TRP Chi-restraints excluded: chain d residue 14 ARG Chi-restraints excluded: chain d residue 22 THR Chi-restraints excluded: chain d residue 63 MET Chi-restraints excluded: chain d residue 71 LEU Chi-restraints excluded: chain d residue 114 LEU Chi-restraints excluded: chain d residue 139 VAL Chi-restraints excluded: chain d residue 140 ILE Chi-restraints excluded: chain d residue 143 ARG Chi-restraints excluded: chain d residue 150 SER Chi-restraints excluded: chain d residue 159 THR Chi-restraints excluded: chain d residue 186 LEU Chi-restraints excluded: chain d residue 192 GLU Chi-restraints excluded: chain e residue 9 LEU Chi-restraints excluded: chain e residue 21 VAL Chi-restraints excluded: chain e residue 22 THR Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 52 LYS Chi-restraints excluded: chain e residue 76 MET Chi-restraints excluded: chain e residue 84 GLU Chi-restraints excluded: chain e residue 94 ILE Chi-restraints excluded: chain e residue 95 LEU Chi-restraints excluded: chain e residue 100 VAL Chi-restraints excluded: chain e residue 111 VAL Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain e residue 125 SER Chi-restraints excluded: chain e residue 128 LEU Chi-restraints excluded: chain e residue 144 LEU Chi-restraints excluded: chain e residue 147 LEU Chi-restraints excluded: chain e residue 160 SER Chi-restraints excluded: chain e residue 164 ILE Chi-restraints excluded: chain f residue 3 GLN Chi-restraints excluded: chain f residue 5 THR Chi-restraints excluded: chain f residue 36 ASN Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 41 ILE Chi-restraints excluded: chain f residue 45 ASP Chi-restraints excluded: chain f residue 65 ILE Chi-restraints excluded: chain f residue 66 VAL Chi-restraints excluded: chain f residue 68 VAL Chi-restraints excluded: chain g residue 43 ILE Chi-restraints excluded: chain g residue 56 ASN Chi-restraints excluded: chain g residue 75 VAL Chi-restraints excluded: chain g residue 85 TYR Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain g residue 131 THR Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain h residue 24 THR Chi-restraints excluded: chain h residue 27 VAL Chi-restraints excluded: chain h residue 49 VAL Chi-restraints excluded: chain h residue 52 ILE Chi-restraints excluded: chain h residue 54 ASP Chi-restraints excluded: chain h residue 62 VAL Chi-restraints excluded: chain h residue 69 ASN Chi-restraints excluded: chain h residue 73 VAL Chi-restraints excluded: chain h residue 75 THR Chi-restraints excluded: chain h residue 89 VAL Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 99 ASN Chi-restraints excluded: chain h residue 126 GLU Chi-restraints excluded: chain h residue 131 VAL Chi-restraints excluded: chain i residue 29 THR Chi-restraints excluded: chain i residue 35 VAL Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain i residue 113 ARG Chi-restraints excluded: chain j residue 4 GLN Chi-restraints excluded: chain j residue 18 LEU Chi-restraints excluded: chain j residue 25 ILE Chi-restraints excluded: chain j residue 51 VAL Chi-restraints excluded: chain j residue 84 VAL Chi-restraints excluded: chain j residue 85 ASP Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 35 THR Chi-restraints excluded: chain k residue 37 THR Chi-restraints excluded: chain k residue 45 SER Chi-restraints excluded: chain k residue 46 SER Chi-restraints excluded: chain k residue 65 MET Chi-restraints excluded: chain k residue 72 LYS Chi-restraints excluded: chain k residue 81 THR Chi-restraints excluded: chain k residue 82 VAL Chi-restraints excluded: chain k residue 85 THR Chi-restraints excluded: chain k residue 86 VAL Chi-restraints excluded: chain k residue 107 VAL Chi-restraints excluded: chain l residue 8 VAL Chi-restraints excluded: chain l residue 21 SER Chi-restraints excluded: chain l residue 25 ASN Chi-restraints excluded: chain l residue 54 THR Chi-restraints excluded: chain l residue 63 ARG Chi-restraints excluded: chain l residue 72 ASN Chi-restraints excluded: chain l residue 77 THR Chi-restraints excluded: chain l residue 92 VAL Chi-restraints excluded: chain l residue 107 ARG Chi-restraints excluded: chain l residue 110 ILE Chi-restraints excluded: chain l residue 111 VAL Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain l residue 121 ASN Chi-restraints excluded: chain l residue 122 ASP Chi-restraints excluded: chain m residue 14 ARG Chi-restraints excluded: chain m residue 28 THR Chi-restraints excluded: chain m residue 100 GLN Chi-restraints excluded: chain m residue 102 THR Chi-restraints excluded: chain m residue 103 LYS Chi-restraints excluded: chain m residue 109 ARG Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain n residue 42 ILE Chi-restraints excluded: chain o residue 22 THR Chi-restraints excluded: chain o residue 56 LEU Chi-restraints excluded: chain o residue 67 LEU Chi-restraints excluded: chain o residue 75 ILE Chi-restraints excluded: chain o residue 84 ARG Chi-restraints excluded: chain o residue 89 ARG Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain p residue 32 ARG Chi-restraints excluded: chain p residue 36 THR Chi-restraints excluded: chain p residue 73 ILE Chi-restraints excluded: chain q residue 10 VAL Chi-restraints excluded: chain q residue 16 VAL Chi-restraints excluded: chain q residue 21 ASP Chi-restraints excluded: chain q residue 32 LYS Chi-restraints excluded: chain q residue 55 THR Chi-restraints excluded: chain q residue 81 VAL Chi-restraints excluded: chain r residue 20 ASN Chi-restraints excluded: chain r residue 22 ILE Chi-restraints excluded: chain r residue 32 LEU Chi-restraints excluded: chain r residue 34 LYS Chi-restraints excluded: chain r residue 48 VAL 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 11 VAL Chi-restraints excluded: chain s residue 14 HIS Chi-restraints excluded: chain s residue 26 GLU Chi-restraints excluded: chain s residue 27 LYS Chi-restraints excluded: chain s residue 37 ARG Chi-restraints excluded: chain s residue 39 THR Chi-restraints excluded: chain s residue 45 VAL Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain s residue 73 GLU Chi-restraints excluded: chain s residue 78 ARG Chi-restraints excluded: chain t residue 39 VAL Chi-restraints excluded: chain t residue 49 LEU Chi-restraints excluded: chain t residue 81 LEU Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 38 LYS Chi-restraints excluded: chain C residue 69 ARG Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 108 LYS Chi-restraints excluded: chain C residue 175 ARG Chi-restraints excluded: chain C residue 177 ASN Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 103 GLN Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 138 ARG Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 167 ASP Chi-restraints excluded: chain D residue 168 ARG Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 184 ASN Chi-restraints excluded: chain D residue 191 ASN Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain E residue 6 LEU Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 80 SER Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 105 VAL Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 190 ASN Chi-restraints excluded: chain E residue 195 THR Chi-restraints excluded: chain F residue 8 TYR Chi-restraints excluded: chain F residue 15 SER Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 23 SER Chi-restraints excluded: chain F residue 32 ASP Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 88 LYS Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 127 ASN Chi-restraints excluded: chain F residue 133 LYS Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain G residue 2 SER Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 101 ASN Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 144 LEU Chi-restraints excluded: chain G residue 165 VAL Chi-restraints excluded: chain G residue 171 ARG Chi-restraints excluded: chain K residue 2 ARG Chi-restraints excluded: chain K residue 3 THR Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 14 ARG Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 58 ILE Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 114 THR Chi-restraints excluded: chain K residue 115 LEU Chi-restraints excluded: chain K residue 145 ASN Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 19 ILE Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 53 LYS Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 71 ARG Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain L residue 112 MET Chi-restraints excluded: chain M residue 36 LYS Chi-restraints excluded: chain M residue 39 LYS Chi-restraints excluded: chain M residue 42 SER Chi-restraints excluded: chain M residue 81 THR Chi-restraints excluded: chain M residue 87 ASP Chi-restraints excluded: chain M residue 105 GLU Chi-restraints excluded: chain M residue 122 THR Chi-restraints excluded: chain M residue 131 SER Chi-restraints excluded: chain N residue 5 LYS Chi-restraints excluded: chain N residue 11 ARG Chi-restraints excluded: chain N residue 26 GLU Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 85 LYS Chi-restraints excluded: chain N residue 122 SER Chi-restraints excluded: chain N residue 127 VAL Chi-restraints excluded: chain N residue 130 LYS Chi-restraints excluded: chain N residue 133 LYS Chi-restraints excluded: chain O residue 24 LEU Chi-restraints excluded: chain O residue 48 ILE Chi-restraints excluded: chain O residue 72 SER Chi-restraints excluded: chain O residue 121 VAL Chi-restraints excluded: chain O residue 124 GLU Chi-restraints excluded: chain P residue 2 ILE Chi-restraints excluded: chain P residue 6 ASP Chi-restraints excluded: chain P residue 11 ARG Chi-restraints excluded: chain P residue 13 LYS Chi-restraints excluded: chain P residue 22 ILE Chi-restraints excluded: chain P residue 28 CYS Chi-restraints excluded: chain P residue 51 VAL Chi-restraints excluded: chain P residue 63 ILE Chi-restraints excluded: chain P residue 67 THR Chi-restraints excluded: chain P residue 70 GLU Chi-restraints excluded: chain P residue 86 LYS Chi-restraints excluded: chain P residue 95 ARG Chi-restraints excluded: chain P residue 113 GLU Chi-restraints excluded: chain Q residue 2 ASN Chi-restraints excluded: chain Q residue 36 THR Chi-restraints excluded: chain Q residue 38 GLU Chi-restraints excluded: chain Q residue 78 THR Chi-restraints excluded: chain Q residue 80 ARG Chi-restraints excluded: chain Q residue 109 ARG Chi-restraints excluded: chain R residue 10 THR Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 42 SER Chi-restraints excluded: chain R residue 79 LEU Chi-restraints excluded: chain R residue 112 GLN Chi-restraints excluded: chain S residue 10 LYS Chi-restraints excluded: chain S residue 14 VAL Chi-restraints excluded: chain S residue 28 GLU Chi-restraints excluded: chain S residue 33 VAL Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 75 GLN Chi-restraints excluded: chain S residue 98 GLU Chi-restraints excluded: chain S residue 101 ASN Chi-restraints excluded: chain T residue 11 THR Chi-restraints excluded: chain T residue 14 THR Chi-restraints excluded: chain T residue 26 ILE Chi-restraints excluded: chain T residue 29 ILE Chi-restraints excluded: chain T residue 70 ASP Chi-restraints excluded: chain T residue 75 VAL Chi-restraints excluded: chain T residue 105 THR Chi-restraints excluded: chain T residue 106 SER Chi-restraints excluded: chain T residue 109 THR Chi-restraints excluded: chain U residue 3 LEU Chi-restraints excluded: chain U residue 16 SER Chi-restraints excluded: chain U residue 36 THR Chi-restraints excluded: chain U residue 55 ILE Chi-restraints excluded: chain U residue 56 LEU Chi-restraints excluded: chain U residue 75 ARG Chi-restraints excluded: chain U residue 84 GLU Chi-restraints excluded: chain V residue 5 LYS Chi-restraints excluded: chain V residue 7 ASP Chi-restraints excluded: chain V residue 9 VAL Chi-restraints excluded: chain V residue 13 THR Chi-restraints excluded: chain V residue 17 LYS Chi-restraints excluded: chain V residue 33 VAL Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain V residue 68 VAL Chi-restraints excluded: chain V residue 90 LYS Chi-restraints excluded: chain V residue 91 VAL Chi-restraints excluded: chain V residue 94 SER Chi-restraints excluded: chain V residue 99 GLU Chi-restraints excluded: chain X residue 18 SER Chi-restraints excluded: chain X residue 19 THR Chi-restraints excluded: chain X residue 23 ARG Chi-restraints excluded: chain X residue 24 ASP Chi-restraints excluded: chain X residue 40 VAL Chi-restraints excluded: chain X residue 58 VAL Chi-restraints excluded: chain X residue 67 THR Chi-restraints excluded: chain X residue 75 VAL Chi-restraints excluded: chain X residue 79 GLU Chi-restraints excluded: chain X residue 88 VAL Chi-restraints excluded: chain X residue 93 VAL Chi-restraints excluded: chain Y residue 12 THR Chi-restraints excluded: chain Y residue 22 MET Chi-restraints excluded: chain Y residue 24 SER Chi-restraints excluded: chain Y residue 28 THR Chi-restraints excluded: chain Y residue 40 ILE Chi-restraints excluded: chain Z residue 3 VAL Chi-restraints excluded: chain Z residue 18 GLU Chi-restraints excluded: chain Z residue 24 GLU Chi-restraints excluded: chain Z residue 37 LEU Chi-restraints excluded: chain 0 residue 30 LYS Chi-restraints excluded: chain 0 residue 35 VAL Chi-restraints excluded: chain 0 residue 54 VAL Chi-restraints excluded: chain 0 residue 59 VAL Chi-restraints excluded: chain 2 residue 3 VAL Chi-restraints excluded: chain 2 residue 8 THR Chi-restraints excluded: chain 2 residue 18 THR Chi-restraints excluded: chain 2 residue 23 THR Chi-restraints excluded: chain 2 residue 56 SER Chi-restraints excluded: chain 3 residue 24 ARG Chi-restraints excluded: chain 3 residue 38 ARG Chi-restraints excluded: chain 3 residue 44 LEU Chi-restraints excluded: chain 4 residue 1 MET Chi-restraints excluded: chain 4 residue 20 LYS Chi-restraints excluded: chain 5 residue 14 VAL Chi-restraints excluded: chain 5 residue 17 THR Chi-restraints excluded: chain 5 residue 32 ARG Chi-restraints excluded: chain 5 residue 58 ILE Chi-restraints excluded: chain 5 residue 60 GLN Chi-restraints excluded: chain 6 residue 4 ARG Chi-restraints excluded: chain 6 residue 11 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 920 random chunks: chunk 858 optimal weight: 9.9990 chunk 100 optimal weight: 20.0000 chunk 507 optimal weight: 10.0000 chunk 650 optimal weight: 0.9990 chunk 503 optimal weight: 10.0000 chunk 749 optimal weight: 9.9990 chunk 497 optimal weight: 10.0000 chunk 886 optimal weight: 0.9990 chunk 554 optimal weight: 10.0000 chunk 540 optimal weight: 10.0000 chunk 409 optimal weight: 10.0000 overall best weight: 6.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 67 ASN ** g 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 77 HIS ** m 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 9 ASN o 38 GLN ** s 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 44 ASN O 61 GLN ** O 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 48 GLN Z 60 GLN 0 17 GLN 3 20 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.110 145353 Z= 0.355 Angle : 0.788 10.979 217934 Z= 0.399 Chirality : 0.045 0.318 27945 Planarity : 0.006 0.077 11316 Dihedral : 23.024 179.865 73954 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.70 % Favored : 90.24 % Rotamer: Outliers : 11.01 % Allowed : 25.43 % Favored : 63.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.17 % Twisted Proline : 0.54 % Twisted General : 0.08 % 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: -1.92 (0.11), residues: 4970 helix: -0.06 (0.13), residues: 1462 sheet: -0.49 (0.16), residues: 1010 loop : -2.43 (0.11), residues: 2498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP d 9 HIS 0.007 0.002 HIS h 22 PHE 0.024 0.003 PHE V 2 TYR 0.024 0.002 TYR l 28 ARG 0.008 0.001 ARG 2 6 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9940 Ramachandran restraints generated. 4970 Oldfield, 0 Emsley, 4970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9940 Ramachandran restraints generated. 4970 Oldfield, 0 Emsley, 4970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1121 residues out of total 4231 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 466 poor density : 655 time to evaluate : 5.628 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: c 200 TRP cc_start: 0.7973 (OUTLIER) cc_final: 0.7372 (m100) REVERT: d 114 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8488 (mt) REVERT: d 143 ARG cc_start: 0.7542 (OUTLIER) cc_final: 0.6390 (ttt-90) REVERT: f 3 GLN cc_start: 0.6154 (OUTLIER) cc_final: 0.5207 (mm110) REVERT: h 49 VAL cc_start: 0.8810 (OUTLIER) cc_final: 0.8384 (t) REVERT: i 113 ARG cc_start: 0.8514 (OUTLIER) cc_final: 0.8162 (ttt180) REVERT: j 4 GLN cc_start: 0.4644 (OUTLIER) cc_final: 0.4374 (tm-30) REVERT: j 85 ASP cc_start: 0.6003 (OUTLIER) cc_final: 0.5711 (m-30) REVERT: k 72 LYS cc_start: 0.6837 (OUTLIER) cc_final: 0.6544 (ttpp) REVERT: l 28 TYR cc_start: 0.4802 (OUTLIER) cc_final: 0.3646 (p90) REVERT: l 63 ARG cc_start: 0.8503 (OUTLIER) cc_final: 0.6761 (mtt90) REVERT: m 11 ARG cc_start: 0.4456 (OUTLIER) cc_final: 0.3846 (mmt180) REVERT: m 100 GLN cc_start: 0.8094 (OUTLIER) cc_final: 0.7664 (mp10) REVERT: m 103 LYS cc_start: 0.5020 (OUTLIER) cc_final: 0.2868 (mmtp) REVERT: m 109 ARG cc_start: 0.7983 (OUTLIER) cc_final: 0.7324 (tpt-90) REVERT: o 56 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8206 (tp) REVERT: o 84 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.8137 (ttp-170) REVERT: s 7 LYS cc_start: 0.5073 (OUTLIER) cc_final: 0.3768 (pttt) REVERT: s 37 ARG cc_start: 0.8121 (OUTLIER) cc_final: 0.7025 (ptp-170) REVERT: C 30 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7261 (tm-30) REVERT: C 69 ARG cc_start: 0.8695 (OUTLIER) cc_final: 0.8441 (mmm-85) REVERT: C 175 ARG cc_start: 0.7803 (OUTLIER) cc_final: 0.7118 (ttp-110) REVERT: D 90 GLU cc_start: 0.6833 (OUTLIER) cc_final: 0.5875 (tm-30) REVERT: D 103 GLN cc_start: 0.7336 (pm20) cc_final: 0.6857 (pm20) REVERT: D 138 ARG cc_start: 0.8108 (OUTLIER) cc_final: 0.7706 (mtt180) REVERT: D 168 ARG cc_start: 0.8454 (OUTLIER) cc_final: 0.7996 (ptt180) REVERT: E 30 GLU cc_start: 0.7102 (OUTLIER) cc_final: 0.6343 (mp0) REVERT: E 45 ARG cc_start: 0.8874 (OUTLIER) cc_final: 0.7149 (mtt180) REVERT: E 66 ARG cc_start: 0.5637 (mtm110) cc_final: 0.5087 (mtt-85) REVERT: E 147 SER cc_start: 0.8131 (p) cc_final: 0.7883 (m) REVERT: E 190 ASN cc_start: 0.8605 (OUTLIER) cc_final: 0.8255 (t0) REVERT: F 8 TYR cc_start: 0.4261 (OUTLIER) cc_final: 0.3678 (m-10) REVERT: F 36 ILE cc_start: 0.8089 (OUTLIER) cc_final: 0.7687 (mp) REVERT: F 169 LEU cc_start: 0.6868 (OUTLIER) cc_final: 0.6590 (tp) REVERT: G 144 LEU cc_start: 0.8010 (OUTLIER) cc_final: 0.7511 (mp) REVERT: G 171 ARG cc_start: 0.7860 (OUTLIER) cc_final: 0.7300 (mmm160) REVERT: K 14 ARG cc_start: 0.8207 (OUTLIER) cc_final: 0.6732 (mtp180) REVERT: L 19 ILE cc_start: 0.8055 (OUTLIER) cc_final: 0.7677 (pt) REVERT: L 71 ARG cc_start: 0.7918 (OUTLIER) cc_final: 0.7656 (mpt-90) REVERT: M 16 ARG cc_start: 0.6982 (OUTLIER) cc_final: 0.6760 (mtt180) REVERT: M 39 LYS cc_start: 0.8719 (OUTLIER) cc_final: 0.8465 (mtpm) REVERT: M 103 LYS cc_start: 0.8302 (OUTLIER) cc_final: 0.8022 (pttm) REVERT: M 133 GLN cc_start: 0.7260 (tt0) cc_final: 0.6917 (tt0) REVERT: N 11 ARG cc_start: 0.8570 (OUTLIER) cc_final: 0.7886 (mpt180) REVERT: N 74 TYR cc_start: 0.5565 (OUTLIER) cc_final: 0.5321 (m-80) REVERT: N 130 LYS cc_start: 0.7857 (OUTLIER) cc_final: 0.7562 (mtmm) REVERT: O 19 ASP cc_start: 0.7565 (m-30) cc_final: 0.7219 (m-30) REVERT: P 22 ILE cc_start: 0.8612 (OUTLIER) cc_final: 0.8094 (mp) REVERT: P 35 ARG cc_start: 0.8364 (OUTLIER) cc_final: 0.7270 (ttm170) REVERT: P 113 GLU cc_start: 0.6040 (OUTLIER) cc_final: 0.5802 (mt-10) REVERT: Q 6 GLN cc_start: 0.7403 (mt0) cc_final: 0.7154 (mt0) REVERT: Q 38 GLU cc_start: 0.6448 (OUTLIER) cc_final: 0.5868 (tp30) REVERT: R 56 ASP cc_start: 0.7424 (m-30) cc_final: 0.7169 (m-30) REVERT: S 96 MET cc_start: 0.7569 (mmm) cc_final: 0.7349 (tpp) REVERT: S 98 GLU cc_start: 0.7328 (OUTLIER) cc_final: 0.6992 (mt-10) REVERT: U 22 GLU cc_start: 0.6757 (tm-30) cc_final: 0.6528 (tm-30) REVERT: U 75 ARG cc_start: 0.8197 (OUTLIER) cc_final: 0.7584 (mtt90) REVERT: V 5 LYS cc_start: 0.7925 (OUTLIER) cc_final: 0.7084 (tttm) REVERT: V 17 LYS cc_start: 0.8263 (OUTLIER) cc_final: 0.8052 (ttmt) REVERT: X 23 ARG cc_start: 0.8443 (OUTLIER) cc_final: 0.7537 (ptt90) REVERT: Y 22 MET cc_start: 0.7615 (OUTLIER) cc_final: 0.7078 (mmp) REVERT: Y 35 LYS cc_start: 0.8147 (OUTLIER) cc_final: 0.7853 (ttmm) REVERT: Z 2 LYS cc_start: 0.7196 (OUTLIER) cc_final: 0.5499 (pptt) REVERT: 0 40 ASN cc_start: 0.7639 (m-40) cc_final: 0.7358 (m-40) REVERT: 0 58 GLU cc_start: 0.7087 (mm-30) cc_final: 0.6827 (tp30) REVERT: 3 24 ARG cc_start: 0.6880 (OUTLIER) cc_final: 0.6617 (ttm170) REVERT: 3 32 LYS cc_start: 0.7732 (mmtt) cc_final: 0.7393 (mtpp) REVERT: 4 24 THR cc_start: 0.8181 (OUTLIER) cc_final: 0.7972 (t) outliers start: 466 outliers final: 355 residues processed: 1003 average time/residue: 1.9470 time to fit residues: 2806.2414 Evaluate side-chains 1062 residues out of total 4231 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 411 poor density : 651 time to evaluate : 5.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 21 LYS Chi-restraints excluded: chain c residue 25 GLU Chi-restraints excluded: chain c residue 51 VAL Chi-restraints excluded: chain c residue 67 ILE Chi-restraints excluded: chain c residue 69 THR Chi-restraints excluded: chain c residue 75 VAL Chi-restraints excluded: chain c residue 98 VAL Chi-restraints excluded: chain c residue 100 ILE Chi-restraints excluded: chain c residue 103 VAL Chi-restraints excluded: chain c residue 153 SER Chi-restraints excluded: chain c residue 164 SER Chi-restraints excluded: chain c residue 168 SER Chi-restraints excluded: chain c residue 171 THR Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain c residue 200 TRP Chi-restraints excluded: chain d residue 14 ARG Chi-restraints excluded: chain d residue 22 THR Chi-restraints excluded: chain d residue 63 MET Chi-restraints excluded: chain d residue 71 LEU Chi-restraints excluded: chain d residue 114 LEU Chi-restraints excluded: chain d residue 120 ILE Chi-restraints excluded: chain d residue 139 VAL Chi-restraints excluded: chain d residue 140 ILE Chi-restraints excluded: chain d residue 143 ARG Chi-restraints excluded: chain d residue 150 SER Chi-restraints excluded: chain d residue 159 THR Chi-restraints excluded: chain d residue 186 LEU 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 39 VAL Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 52 LYS Chi-restraints excluded: chain e residue 76 MET Chi-restraints excluded: chain e residue 84 GLU Chi-restraints excluded: chain e residue 94 ILE Chi-restraints excluded: chain e residue 95 LEU Chi-restraints excluded: chain e residue 96 MET Chi-restraints excluded: chain e residue 100 VAL Chi-restraints excluded: chain e residue 111 VAL Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain e residue 125 SER Chi-restraints excluded: chain e residue 128 LEU Chi-restraints excluded: chain e residue 144 LEU Chi-restraints excluded: chain e residue 147 LEU Chi-restraints excluded: chain e residue 160 SER Chi-restraints excluded: chain e residue 164 ILE Chi-restraints excluded: chain f residue 3 GLN Chi-restraints excluded: chain f residue 5 THR Chi-restraints excluded: chain f residue 33 LEU Chi-restraints excluded: chain f residue 36 ASN Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 41 ILE Chi-restraints excluded: chain f residue 45 ASP Chi-restraints excluded: chain f residue 65 ILE Chi-restraints excluded: chain f residue 66 VAL Chi-restraints excluded: chain f residue 68 VAL Chi-restraints excluded: chain g residue 43 ILE Chi-restraints excluded: chain g residue 56 ASN Chi-restraints excluded: chain g residue 75 VAL Chi-restraints excluded: chain g residue 85 TYR Chi-restraints excluded: chain g residue 91 VAL Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain g residue 131 THR Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain h residue 2 VAL Chi-restraints excluded: chain h residue 24 THR Chi-restraints excluded: chain h residue 27 VAL Chi-restraints excluded: chain h residue 49 VAL Chi-restraints excluded: chain h residue 52 ILE Chi-restraints excluded: chain h residue 54 ASP Chi-restraints excluded: chain h residue 62 VAL Chi-restraints excluded: chain h residue 69 ASN Chi-restraints excluded: chain h residue 73 VAL Chi-restraints excluded: chain h residue 75 THR Chi-restraints excluded: chain h residue 89 VAL Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 99 ASN Chi-restraints excluded: chain h residue 126 GLU Chi-restraints excluded: chain h residue 131 VAL Chi-restraints excluded: chain i residue 16 VAL Chi-restraints excluded: chain i residue 29 THR Chi-restraints excluded: chain i residue 35 VAL Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain i residue 83 ILE Chi-restraints excluded: chain i residue 113 ARG Chi-restraints excluded: chain j residue 4 GLN Chi-restraints excluded: chain j residue 18 LEU Chi-restraints excluded: chain j residue 25 ILE Chi-restraints excluded: chain j residue 51 VAL Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain j residue 84 VAL Chi-restraints excluded: chain j residue 85 ASP Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 35 THR Chi-restraints excluded: chain k residue 37 THR Chi-restraints excluded: chain k residue 45 SER Chi-restraints excluded: chain k residue 46 SER Chi-restraints excluded: chain k residue 65 MET Chi-restraints excluded: chain k residue 72 LYS Chi-restraints excluded: chain k residue 81 THR Chi-restraints excluded: chain k residue 82 VAL Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain k residue 85 THR Chi-restraints excluded: chain k residue 86 VAL Chi-restraints excluded: chain k residue 107 VAL Chi-restraints excluded: chain l residue 8 VAL Chi-restraints excluded: chain l residue 17 GLU Chi-restraints excluded: chain l residue 21 SER Chi-restraints excluded: chain l residue 25 ASN Chi-restraints excluded: chain l residue 28 TYR Chi-restraints excluded: chain l residue 54 THR Chi-restraints excluded: chain l residue 63 ARG Chi-restraints excluded: chain l residue 72 ASN Chi-restraints excluded: chain l residue 77 THR Chi-restraints excluded: chain l residue 92 VAL Chi-restraints excluded: chain l residue 107 ARG Chi-restraints excluded: chain l residue 111 VAL Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain l residue 121 ASN Chi-restraints excluded: chain l residue 122 ASP Chi-restraints excluded: chain m residue 11 ARG Chi-restraints excluded: chain m residue 14 ARG Chi-restraints excluded: chain m residue 15 VAL Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 25 ILE Chi-restraints excluded: chain m residue 28 THR Chi-restraints excluded: chain m residue 39 VAL Chi-restraints excluded: chain m residue 100 GLN Chi-restraints excluded: chain m residue 102 THR Chi-restraints excluded: chain m residue 103 LYS Chi-restraints excluded: chain m residue 109 ARG Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain n residue 42 ILE Chi-restraints excluded: chain o residue 22 THR Chi-restraints excluded: chain o residue 56 LEU Chi-restraints excluded: chain o residue 67 LEU Chi-restraints excluded: chain o residue 75 ILE Chi-restraints excluded: chain o residue 84 ARG Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain p residue 32 ARG Chi-restraints excluded: chain p residue 36 THR Chi-restraints excluded: chain p residue 73 ILE Chi-restraints excluded: chain q residue 10 VAL Chi-restraints excluded: chain q residue 16 VAL Chi-restraints excluded: chain q residue 21 ASP Chi-restraints excluded: chain q residue 32 LYS Chi-restraints excluded: chain q residue 55 THR Chi-restraints excluded: chain q residue 80 GLU Chi-restraints excluded: chain q residue 81 VAL Chi-restraints excluded: chain r residue 20 ASN Chi-restraints excluded: chain r residue 22 ILE Chi-restraints excluded: chain r residue 32 LEU Chi-restraints excluded: chain r residue 34 LYS Chi-restraints excluded: chain r residue 48 VAL 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 11 VAL Chi-restraints excluded: chain s residue 14 HIS Chi-restraints excluded: chain s residue 26 GLU Chi-restraints excluded: chain s residue 27 LYS Chi-restraints excluded: chain s residue 37 ARG Chi-restraints excluded: chain s residue 39 THR Chi-restraints excluded: chain s residue 45 VAL Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain s residue 73 GLU Chi-restraints excluded: chain s residue 78 ARG Chi-restraints excluded: chain t residue 13 THR Chi-restraints excluded: chain t residue 39 VAL Chi-restraints excluded: chain t residue 49 LEU Chi-restraints excluded: chain t residue 59 MET Chi-restraints excluded: chain t residue 81 LEU Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 38 LYS Chi-restraints excluded: chain C residue 69 ARG Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 108 LYS Chi-restraints excluded: chain C residue 175 ARG Chi-restraints excluded: chain C residue 177 ASN Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 138 ARG Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 167 ASP Chi-restraints excluded: chain D residue 168 ARG Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 184 ASN Chi-restraints excluded: chain D residue 191 ASN Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain E residue 6 LEU Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 30 GLU Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 80 SER Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 105 VAL Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 190 ASN Chi-restraints excluded: chain E residue 195 THR Chi-restraints excluded: chain F residue 8 TYR Chi-restraints excluded: chain F residue 15 SER Chi-restraints excluded: chain F residue 23 SER Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 32 ASP Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 88 LYS Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 123 ASP Chi-restraints excluded: chain F residue 127 ASN Chi-restraints excluded: chain F residue 133 LYS Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain G residue 2 SER Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 101 ASN Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 144 LEU Chi-restraints excluded: chain G residue 165 VAL Chi-restraints excluded: chain G residue 171 ARG Chi-restraints excluded: chain K residue 2 ARG Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 14 ARG Chi-restraints excluded: chain K residue 15 LYS Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 58 ILE Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 114 THR Chi-restraints excluded: chain K residue 115 LEU Chi-restraints excluded: chain K residue 145 ASN Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 19 ILE Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 53 LYS Chi-restraints excluded: chain L residue 54 LYS Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 71 ARG Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain L residue 112 MET Chi-restraints excluded: chain M residue 16 ARG Chi-restraints excluded: chain M residue 36 LYS Chi-restraints excluded: chain M residue 39 LYS Chi-restraints excluded: chain M residue 42 SER Chi-restraints excluded: chain M residue 81 THR Chi-restraints excluded: chain M residue 87 ASP Chi-restraints excluded: chain M residue 103 LYS Chi-restraints excluded: chain M residue 105 GLU Chi-restraints excluded: chain M residue 122 THR Chi-restraints excluded: chain M residue 131 SER Chi-restraints excluded: chain N residue 5 LYS Chi-restraints excluded: chain N residue 11 ARG Chi-restraints excluded: chain N residue 26 GLU Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 74 TYR Chi-restraints excluded: chain N residue 75 THR Chi-restraints excluded: chain N residue 85 LYS Chi-restraints excluded: chain N residue 122 SER Chi-restraints excluded: chain N residue 127 VAL Chi-restraints excluded: chain N residue 130 LYS Chi-restraints excluded: chain N residue 133 LYS Chi-restraints excluded: chain O residue 24 LEU Chi-restraints excluded: chain O residue 72 SER Chi-restraints excluded: chain O residue 121 VAL Chi-restraints excluded: chain O residue 124 GLU Chi-restraints excluded: chain P residue 2 ILE Chi-restraints excluded: chain P residue 6 ASP Chi-restraints excluded: chain P residue 11 ARG Chi-restraints excluded: chain P residue 13 LYS Chi-restraints excluded: chain P residue 18 VAL Chi-restraints excluded: chain P residue 22 ILE Chi-restraints excluded: chain P residue 28 CYS Chi-restraints excluded: chain P residue 35 ARG Chi-restraints excluded: chain P residue 51 VAL Chi-restraints excluded: chain P residue 63 ILE Chi-restraints excluded: chain P residue 67 THR Chi-restraints excluded: chain P residue 70 GLU Chi-restraints excluded: chain P residue 86 LYS Chi-restraints excluded: chain P residue 95 ARG Chi-restraints excluded: chain P residue 113 GLU Chi-restraints excluded: chain Q residue 2 ASN Chi-restraints excluded: chain Q residue 36 THR Chi-restraints excluded: chain Q residue 38 GLU Chi-restraints excluded: chain Q residue 78 THR Chi-restraints excluded: chain Q residue 80 ARG Chi-restraints excluded: chain Q residue 109 ARG Chi-restraints excluded: chain R residue 10 THR Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 42 SER Chi-restraints excluded: chain R residue 79 LEU Chi-restraints excluded: chain R residue 112 GLN Chi-restraints excluded: chain S residue 10 LYS Chi-restraints excluded: chain S residue 14 VAL Chi-restraints excluded: chain S residue 28 GLU Chi-restraints excluded: chain S residue 33 VAL Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 75 GLN Chi-restraints excluded: chain S residue 98 GLU Chi-restraints excluded: chain S residue 101 ASN Chi-restraints excluded: chain T residue 11 THR Chi-restraints excluded: chain T residue 14 THR Chi-restraints excluded: chain T residue 26 ILE Chi-restraints excluded: chain T residue 29 ILE Chi-restraints excluded: chain T residue 70 ASP Chi-restraints excluded: chain T residue 75 VAL Chi-restraints excluded: chain T residue 105 THR Chi-restraints excluded: chain T residue 106 SER Chi-restraints excluded: chain T residue 109 THR Chi-restraints excluded: chain U residue 3 LEU Chi-restraints excluded: chain U residue 16 SER Chi-restraints excluded: chain U residue 36 THR Chi-restraints excluded: chain U residue 42 VAL Chi-restraints excluded: chain U residue 55 ILE Chi-restraints excluded: chain U residue 56 LEU Chi-restraints excluded: chain U residue 75 ARG Chi-restraints excluded: chain U residue 84 GLU Chi-restraints excluded: chain V residue 2 PHE Chi-restraints excluded: chain V residue 5 LYS Chi-restraints excluded: chain V residue 7 ASP Chi-restraints excluded: chain V residue 9 VAL Chi-restraints excluded: chain V residue 13 THR Chi-restraints excluded: chain V residue 17 LYS Chi-restraints excluded: chain V residue 33 VAL Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain V residue 68 VAL Chi-restraints excluded: chain V residue 90 LYS Chi-restraints excluded: chain V residue 91 VAL Chi-restraints excluded: chain V residue 94 SER Chi-restraints excluded: chain V residue 99 GLU Chi-restraints excluded: chain X residue 18 SER Chi-restraints excluded: chain X residue 19 THR Chi-restraints excluded: chain X residue 20 SER Chi-restraints excluded: chain X residue 23 ARG Chi-restraints excluded: chain X residue 24 ASP Chi-restraints excluded: chain X residue 39 THR Chi-restraints excluded: chain X residue 40 VAL Chi-restraints excluded: chain X residue 58 VAL Chi-restraints excluded: chain X residue 67 THR Chi-restraints excluded: chain X residue 75 VAL Chi-restraints excluded: chain X residue 79 GLU Chi-restraints excluded: chain X residue 88 VAL Chi-restraints excluded: chain X residue 93 VAL Chi-restraints excluded: chain Y residue 12 THR Chi-restraints excluded: chain Y residue 22 MET Chi-restraints excluded: chain Y residue 24 SER Chi-restraints excluded: chain Y residue 28 THR Chi-restraints excluded: chain Y residue 35 LYS Chi-restraints excluded: chain Y residue 40 ILE Chi-restraints excluded: chain Z residue 2 LYS Chi-restraints excluded: chain Z residue 3 VAL Chi-restraints excluded: chain Z residue 10 THR Chi-restraints excluded: chain Z residue 18 GLU Chi-restraints excluded: chain Z residue 24 GLU Chi-restraints excluded: chain Z residue 37 LEU Chi-restraints excluded: chain 0 residue 30 LYS Chi-restraints excluded: chain 0 residue 35 VAL Chi-restraints excluded: chain 0 residue 54 VAL Chi-restraints excluded: chain 0 residue 59 VAL Chi-restraints excluded: chain 2 residue 3 VAL Chi-restraints excluded: chain 2 residue 8 THR Chi-restraints excluded: chain 2 residue 18 THR Chi-restraints excluded: chain 2 residue 23 THR Chi-restraints excluded: chain 2 residue 56 SER Chi-restraints excluded: chain 3 residue 24 ARG Chi-restraints excluded: chain 3 residue 38 ARG Chi-restraints excluded: chain 3 residue 44 LEU Chi-restraints excluded: chain 4 residue 1 MET Chi-restraints excluded: chain 4 residue 20 LYS Chi-restraints excluded: chain 4 residue 24 THR Chi-restraints excluded: chain 5 residue 14 VAL Chi-restraints excluded: chain 5 residue 17 THR Chi-restraints excluded: chain 5 residue 32 ARG Chi-restraints excluded: chain 5 residue 58 ILE Chi-restraints excluded: chain 5 residue 60 GLN Chi-restraints excluded: chain 6 residue 4 ARG Chi-restraints excluded: chain 6 residue 11 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 920 random chunks: chunk 548 optimal weight: 9.9990 chunk 354 optimal weight: 9.9990 chunk 529 optimal weight: 10.0000 chunk 267 optimal weight: 10.0000 chunk 174 optimal weight: 0.4980 chunk 171 optimal weight: 9.9990 chunk 563 optimal weight: 9.9990 chunk 604 optimal weight: 10.0000 chunk 438 optimal weight: 10.0000 chunk 82 optimal weight: 10.0000 chunk 696 optimal weight: 0.9980 overall best weight: 6.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 67 ASN ** g 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 77 HIS ** m 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 9 ASN o 38 GLN ** s 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 44 ASN O 61 GLN ** O 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 54 ASN X 87 GLN Z 48 GLN Z 60 GLN 0 17 GLN 3 20 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.1234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.110 145353 Z= 0.353 Angle : 0.791 10.844 217934 Z= 0.400 Chirality : 0.045 0.319 27945 Planarity : 0.007 0.087 11316 Dihedral : 23.023 179.739 73952 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.46 % Favored : 90.48 % Rotamer: Outliers : 10.97 % Allowed : 25.86 % Favored : 63.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.17 % Twisted Proline : 0.54 % Twisted General : 0.08 % 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: -1.96 (0.11), residues: 4970 helix: -0.12 (0.13), residues: 1466 sheet: -0.52 (0.16), residues: 1019 loop : -2.45 (0.11), residues: 2485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP d 9 HIS 0.007 0.002 HIS h 22 PHE 0.024 0.003 PHE V 2 TYR 0.024 0.002 TYR l 28 ARG 0.011 0.001 ARG j 31 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9940 Ramachandran restraints generated. 4970 Oldfield, 0 Emsley, 4970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9940 Ramachandran restraints generated. 4970 Oldfield, 0 Emsley, 4970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1123 residues out of total 4231 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 464 poor density : 659 time to evaluate : 5.627 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: c 200 TRP cc_start: 0.7978 (OUTLIER) cc_final: 0.7377 (m100) REVERT: d 114 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8484 (mt) REVERT: d 143 ARG cc_start: 0.7553 (OUTLIER) cc_final: 0.6399 (ttt-90) REVERT: f 3 GLN cc_start: 0.6150 (OUTLIER) cc_final: 0.5207 (mm110) REVERT: h 49 VAL cc_start: 0.8812 (OUTLIER) cc_final: 0.8384 (t) REVERT: i 113 ARG cc_start: 0.8515 (OUTLIER) cc_final: 0.8163 (ttt180) REVERT: j 4 GLN cc_start: 0.4642 (OUTLIER) cc_final: 0.4369 (tm-30) REVERT: j 85 ASP cc_start: 0.6018 (OUTLIER) cc_final: 0.5702 (m-30) REVERT: k 72 LYS cc_start: 0.6842 (OUTLIER) cc_final: 0.6555 (ttpp) REVERT: l 28 TYR cc_start: 0.4803 (OUTLIER) cc_final: 0.3650 (p90) REVERT: l 63 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.6767 (mtt90) REVERT: m 11 ARG cc_start: 0.4480 (OUTLIER) cc_final: 0.3872 (mmt180) REVERT: m 100 GLN cc_start: 0.8096 (OUTLIER) cc_final: 0.7663 (mp10) REVERT: m 103 LYS cc_start: 0.5016 (OUTLIER) cc_final: 0.2869 (mmtp) REVERT: m 109 ARG cc_start: 0.7976 (OUTLIER) cc_final: 0.7328 (tpt-90) REVERT: n 7 ILE cc_start: 0.8246 (OUTLIER) cc_final: 0.7810 (mm) REVERT: o 56 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8201 (tp) REVERT: o 84 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.8157 (ttp-170) REVERT: s 7 LYS cc_start: 0.5044 (OUTLIER) cc_final: 0.3688 (pttt) REVERT: s 37 ARG cc_start: 0.8125 (OUTLIER) cc_final: 0.7030 (ptp-170) REVERT: C 30 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7259 (tm-30) REVERT: C 175 ARG cc_start: 0.7808 (OUTLIER) cc_final: 0.7115 (ttp-110) REVERT: D 90 GLU cc_start: 0.6838 (OUTLIER) cc_final: 0.5879 (tm-30) REVERT: D 103 GLN cc_start: 0.7381 (pm20) cc_final: 0.6901 (pm20) REVERT: D 138 ARG cc_start: 0.8109 (OUTLIER) cc_final: 0.7706 (mtt180) REVERT: D 168 ARG cc_start: 0.8447 (OUTLIER) cc_final: 0.7994 (ptt180) REVERT: E 30 GLU cc_start: 0.7105 (OUTLIER) cc_final: 0.6344 (mp0) REVERT: E 45 ARG cc_start: 0.8887 (OUTLIER) cc_final: 0.7162 (mtt180) REVERT: E 66 ARG cc_start: 0.5637 (mtm110) cc_final: 0.5090 (mtt-85) REVERT: E 147 SER cc_start: 0.8155 (p) cc_final: 0.7920 (m) REVERT: E 190 ASN cc_start: 0.8600 (OUTLIER) cc_final: 0.8255 (t0) REVERT: F 8 TYR cc_start: 0.4268 (OUTLIER) cc_final: 0.3676 (m-10) REVERT: F 36 ILE cc_start: 0.8094 (OUTLIER) cc_final: 0.7688 (mp) REVERT: F 169 LEU cc_start: 0.6864 (OUTLIER) cc_final: 0.6598 (tp) REVERT: G 144 LEU cc_start: 0.8007 (OUTLIER) cc_final: 0.7509 (mp) REVERT: G 171 ARG cc_start: 0.7856 (OUTLIER) cc_final: 0.7301 (mmm160) REVERT: K 14 ARG cc_start: 0.8205 (OUTLIER) cc_final: 0.6726 (mtp180) REVERT: L 19 ILE cc_start: 0.8059 (OUTLIER) cc_final: 0.7685 (pt) REVERT: L 71 ARG cc_start: 0.7916 (OUTLIER) cc_final: 0.7656 (mpt-90) REVERT: M 16 ARG cc_start: 0.6956 (OUTLIER) cc_final: 0.6742 (mtt180) REVERT: M 39 LYS cc_start: 0.8725 (OUTLIER) cc_final: 0.8483 (mtpm) REVERT: M 79 LEU cc_start: 0.7380 (OUTLIER) cc_final: 0.6694 (mp) REVERT: M 103 LYS cc_start: 0.8273 (OUTLIER) cc_final: 0.8021 (pttm) REVERT: M 133 GLN cc_start: 0.7233 (tt0) cc_final: 0.6906 (tt0) REVERT: N 11 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.7901 (mpt180) REVERT: N 74 TYR cc_start: 0.5487 (OUTLIER) cc_final: 0.5270 (m-80) REVERT: N 130 LYS cc_start: 0.7850 (OUTLIER) cc_final: 0.7560 (mtmm) REVERT: O 19 ASP cc_start: 0.7562 (m-30) cc_final: 0.7213 (m-30) REVERT: O 108 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8516 (mp) REVERT: P 22 ILE cc_start: 0.8614 (OUTLIER) cc_final: 0.8096 (mp) REVERT: P 35 ARG cc_start: 0.8285 (OUTLIER) cc_final: 0.7152 (ttm170) REVERT: P 113 GLU cc_start: 0.6035 (OUTLIER) cc_final: 0.5798 (mt-10) REVERT: Q 6 GLN cc_start: 0.7403 (mt0) cc_final: 0.7133 (mt0) REVERT: Q 38 GLU cc_start: 0.6454 (OUTLIER) cc_final: 0.5870 (tp30) REVERT: R 56 ASP cc_start: 0.7426 (m-30) cc_final: 0.7168 (m-30) REVERT: S 96 MET cc_start: 0.7557 (mmm) cc_final: 0.7347 (tpp) REVERT: S 98 GLU cc_start: 0.7333 (OUTLIER) cc_final: 0.6992 (mt-10) REVERT: U 75 ARG cc_start: 0.8196 (OUTLIER) cc_final: 0.7589 (mtt90) REVERT: V 5 LYS cc_start: 0.7838 (OUTLIER) cc_final: 0.6959 (tttm) REVERT: V 17 LYS cc_start: 0.8262 (OUTLIER) cc_final: 0.8055 (ttmt) REVERT: X 23 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.7536 (ptt90) REVERT: Y 22 MET cc_start: 0.7627 (OUTLIER) cc_final: 0.7104 (mmp) REVERT: Y 35 LYS cc_start: 0.8166 (OUTLIER) cc_final: 0.7886 (ttmm) REVERT: Z 2 LYS cc_start: 0.7193 (OUTLIER) cc_final: 0.5501 (pptt) REVERT: 0 40 ASN cc_start: 0.7640 (m-40) cc_final: 0.7365 (m-40) REVERT: 0 58 GLU cc_start: 0.7095 (mm-30) cc_final: 0.6835 (tp30) REVERT: 3 24 ARG cc_start: 0.6869 (OUTLIER) cc_final: 0.6596 (ttm170) REVERT: 3 32 LYS cc_start: 0.7731 (mmtt) cc_final: 0.7391 (mtpp) REVERT: 4 24 THR cc_start: 0.8163 (OUTLIER) cc_final: 0.7954 (t) outliers start: 464 outliers final: 366 residues processed: 1006 average time/residue: 1.9041 time to fit residues: 2765.6482 Evaluate side-chains 1076 residues out of total 4231 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 424 poor density : 652 time to evaluate : 5.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 21 LYS Chi-restraints excluded: chain c residue 25 GLU Chi-restraints excluded: chain c residue 51 VAL Chi-restraints excluded: chain c residue 67 ILE Chi-restraints excluded: chain c residue 69 THR Chi-restraints excluded: chain c residue 75 VAL Chi-restraints excluded: chain c residue 98 VAL Chi-restraints excluded: chain c residue 100 ILE Chi-restraints excluded: chain c residue 103 VAL Chi-restraints excluded: chain c residue 153 SER Chi-restraints excluded: chain c residue 164 SER Chi-restraints excluded: chain c residue 168 SER Chi-restraints excluded: chain c residue 171 THR Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain c residue 200 TRP Chi-restraints excluded: chain d residue 14 ARG Chi-restraints excluded: chain d residue 22 THR Chi-restraints excluded: chain d residue 24 LYS Chi-restraints excluded: chain d residue 58 ARG Chi-restraints excluded: chain d residue 63 MET Chi-restraints excluded: chain d residue 71 LEU Chi-restraints excluded: chain d residue 114 LEU Chi-restraints excluded: chain d residue 120 ILE Chi-restraints excluded: chain d residue 139 VAL Chi-restraints excluded: chain d residue 140 ILE Chi-restraints excluded: chain d residue 143 ARG Chi-restraints excluded: chain d residue 150 SER Chi-restraints excluded: chain d residue 159 THR Chi-restraints excluded: chain d residue 186 LEU 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 39 VAL Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 52 LYS Chi-restraints excluded: chain e residue 76 MET Chi-restraints excluded: chain e residue 84 GLU Chi-restraints excluded: chain e residue 94 ILE Chi-restraints excluded: chain e residue 95 LEU Chi-restraints excluded: chain e residue 96 MET Chi-restraints excluded: chain e residue 100 VAL Chi-restraints excluded: chain e residue 105 VAL Chi-restraints excluded: chain e residue 111 VAL Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain e residue 125 SER Chi-restraints excluded: chain e residue 128 LEU Chi-restraints excluded: chain e residue 144 LEU Chi-restraints excluded: chain e residue 147 LEU Chi-restraints excluded: chain e residue 160 SER Chi-restraints excluded: chain e residue 164 ILE Chi-restraints excluded: chain f residue 3 GLN Chi-restraints excluded: chain f residue 4 ASP Chi-restraints excluded: chain f residue 5 THR Chi-restraints excluded: chain f residue 33 LEU Chi-restraints excluded: chain f residue 36 ASN Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 41 ILE Chi-restraints excluded: chain f residue 45 ASP Chi-restraints excluded: chain f residue 65 ILE Chi-restraints excluded: chain f residue 66 VAL Chi-restraints excluded: chain f residue 68 VAL Chi-restraints excluded: chain g residue 43 ILE Chi-restraints excluded: chain g residue 56 ASN Chi-restraints excluded: chain g residue 75 VAL Chi-restraints excluded: chain g residue 85 TYR Chi-restraints excluded: chain g residue 91 VAL Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain g residue 131 THR Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain h residue 2 VAL Chi-restraints excluded: chain h residue 24 THR Chi-restraints excluded: chain h residue 27 VAL Chi-restraints excluded: chain h residue 49 VAL Chi-restraints excluded: chain h residue 52 ILE Chi-restraints excluded: chain h residue 54 ASP Chi-restraints excluded: chain h residue 62 VAL Chi-restraints excluded: chain h residue 69 ASN Chi-restraints excluded: chain h residue 73 VAL Chi-restraints excluded: chain h residue 75 THR Chi-restraints excluded: chain h residue 89 VAL Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 99 ASN Chi-restraints excluded: chain h residue 126 GLU Chi-restraints excluded: chain h residue 131 VAL Chi-restraints excluded: chain i residue 16 VAL Chi-restraints excluded: chain i residue 29 THR Chi-restraints excluded: chain i residue 35 VAL Chi-restraints excluded: chain i residue 47 VAL Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain i residue 83 ILE Chi-restraints excluded: chain i residue 113 ARG Chi-restraints excluded: chain j residue 4 GLN Chi-restraints excluded: chain j residue 18 LEU Chi-restraints excluded: chain j residue 25 ILE Chi-restraints excluded: chain j residue 51 VAL Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain j residue 84 VAL Chi-restraints excluded: chain j residue 85 ASP Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 35 THR Chi-restraints excluded: chain k residue 37 THR Chi-restraints excluded: chain k residue 45 SER Chi-restraints excluded: chain k residue 46 SER Chi-restraints excluded: chain k residue 65 MET Chi-restraints excluded: chain k residue 72 LYS Chi-restraints excluded: chain k residue 81 THR Chi-restraints excluded: chain k residue 82 VAL Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain k residue 85 THR Chi-restraints excluded: chain k residue 86 VAL Chi-restraints excluded: chain k residue 107 VAL Chi-restraints excluded: chain l residue 8 VAL Chi-restraints excluded: chain l residue 14 SER Chi-restraints excluded: chain l residue 17 GLU Chi-restraints excluded: chain l residue 21 SER Chi-restraints excluded: chain l residue 25 ASN Chi-restraints excluded: chain l residue 28 TYR Chi-restraints excluded: chain l residue 54 THR Chi-restraints excluded: chain l residue 63 ARG Chi-restraints excluded: chain l residue 72 ASN Chi-restraints excluded: chain l residue 77 THR Chi-restraints excluded: chain l residue 92 VAL Chi-restraints excluded: chain l residue 107 ARG Chi-restraints excluded: chain l residue 111 VAL Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain l residue 121 ASN Chi-restraints excluded: chain l residue 122 ASP Chi-restraints excluded: chain m residue 11 ARG Chi-restraints excluded: chain m residue 14 ARG Chi-restraints excluded: chain m residue 15 VAL Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 28 THR Chi-restraints excluded: chain m residue 39 VAL Chi-restraints excluded: chain m residue 80 LEU Chi-restraints excluded: chain m residue 100 GLN Chi-restraints excluded: chain m residue 102 THR Chi-restraints excluded: chain m residue 103 LYS Chi-restraints excluded: chain m residue 109 ARG Chi-restraints excluded: chain n residue 7 ILE Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain n residue 42 ILE Chi-restraints excluded: chain o residue 22 THR Chi-restraints excluded: chain o residue 56 LEU Chi-restraints excluded: chain o residue 67 LEU Chi-restraints excluded: chain o residue 73 THR Chi-restraints excluded: chain o residue 75 ILE Chi-restraints excluded: chain o residue 84 ARG Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain p residue 32 ARG Chi-restraints excluded: chain p residue 36 THR Chi-restraints excluded: chain p residue 44 LYS Chi-restraints excluded: chain p residue 73 ILE Chi-restraints excluded: chain q residue 10 VAL Chi-restraints excluded: chain q residue 16 VAL Chi-restraints excluded: chain q residue 21 ASP Chi-restraints excluded: chain q residue 32 LYS Chi-restraints excluded: chain q residue 55 THR Chi-restraints excluded: chain q residue 80 GLU Chi-restraints excluded: chain q residue 81 VAL Chi-restraints excluded: chain r residue 20 ASN Chi-restraints excluded: chain r residue 22 ILE Chi-restraints excluded: chain r residue 34 LYS Chi-restraints excluded: chain r residue 48 VAL 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 11 VAL Chi-restraints excluded: chain s residue 14 HIS Chi-restraints excluded: chain s residue 26 GLU Chi-restraints excluded: chain s residue 27 LYS Chi-restraints excluded: chain s residue 37 ARG Chi-restraints excluded: chain s residue 39 THR Chi-restraints excluded: chain s residue 45 VAL Chi-restraints excluded: chain s residue 51 VAL Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain s residue 73 GLU Chi-restraints excluded: chain s residue 78 ARG Chi-restraints excluded: chain t residue 13 THR Chi-restraints excluded: chain t residue 39 VAL Chi-restraints excluded: chain t residue 49 LEU Chi-restraints excluded: chain t residue 59 MET Chi-restraints excluded: chain t residue 81 LEU Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 38 LYS Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 108 LYS Chi-restraints excluded: chain C residue 175 ARG Chi-restraints excluded: chain C residue 177 ASN Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 138 ARG Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 167 ASP Chi-restraints excluded: chain D residue 168 ARG Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 184 ASN Chi-restraints excluded: chain D residue 191 ASN Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain E residue 6 LEU Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 30 GLU Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 80 SER Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 105 VAL Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 190 ASN Chi-restraints excluded: chain E residue 195 THR Chi-restraints excluded: chain F residue 8 TYR Chi-restraints excluded: chain F residue 15 SER Chi-restraints excluded: chain F residue 23 SER Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 32 ASP Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 88 LYS Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 123 ASP Chi-restraints excluded: chain F residue 127 ASN Chi-restraints excluded: chain F residue 133 LYS Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain G residue 2 SER Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 24 ILE Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 101 ASN Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 144 LEU Chi-restraints excluded: chain G residue 165 VAL Chi-restraints excluded: chain G residue 171 ARG Chi-restraints excluded: chain K residue 2 ARG Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 14 ARG Chi-restraints excluded: chain K residue 15 LYS Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 58 ILE Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 114 THR Chi-restraints excluded: chain K residue 115 LEU Chi-restraints excluded: chain K residue 145 ASN Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 19 ILE Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 53 LYS Chi-restraints excluded: chain L residue 54 LYS Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 71 ARG Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain L residue 108 GLU Chi-restraints excluded: chain L residue 112 MET Chi-restraints excluded: chain M residue 16 ARG Chi-restraints excluded: chain M residue 36 LYS Chi-restraints excluded: chain M residue 39 LYS Chi-restraints excluded: chain M residue 42 SER Chi-restraints excluded: chain M residue 67 THR Chi-restraints excluded: chain M residue 79 LEU Chi-restraints excluded: chain M residue 81 THR Chi-restraints excluded: chain M residue 87 ASP Chi-restraints excluded: chain M residue 103 LYS Chi-restraints excluded: chain M residue 105 GLU Chi-restraints excluded: chain M residue 122 THR Chi-restraints excluded: chain M residue 131 SER Chi-restraints excluded: chain N residue 5 LYS Chi-restraints excluded: chain N residue 11 ARG Chi-restraints excluded: chain N residue 26 GLU Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 74 TYR Chi-restraints excluded: chain N residue 75 THR Chi-restraints excluded: chain N residue 85 LYS Chi-restraints excluded: chain N residue 122 SER Chi-restraints excluded: chain N residue 127 VAL Chi-restraints excluded: chain N residue 130 LYS Chi-restraints excluded: chain N residue 133 LYS Chi-restraints excluded: chain O residue 24 LEU Chi-restraints excluded: chain O residue 72 SER Chi-restraints excluded: chain O residue 108 LEU Chi-restraints excluded: chain O residue 121 VAL Chi-restraints excluded: chain O residue 124 GLU Chi-restraints excluded: chain P residue 2 ILE Chi-restraints excluded: chain P residue 6 ASP Chi-restraints excluded: chain P residue 11 ARG Chi-restraints excluded: chain P residue 13 LYS Chi-restraints excluded: chain P residue 18 VAL Chi-restraints excluded: chain P residue 22 ILE Chi-restraints excluded: chain P residue 28 CYS Chi-restraints excluded: chain P residue 35 ARG Chi-restraints excluded: chain P residue 51 VAL Chi-restraints excluded: chain P residue 57 SER Chi-restraints excluded: chain P residue 63 ILE Chi-restraints excluded: chain P residue 67 THR Chi-restraints excluded: chain P residue 86 LYS Chi-restraints excluded: chain P residue 95 ARG Chi-restraints excluded: chain P residue 113 GLU Chi-restraints excluded: chain Q residue 2 ASN Chi-restraints excluded: chain Q residue 36 THR Chi-restraints excluded: chain Q residue 38 GLU Chi-restraints excluded: chain Q residue 78 THR Chi-restraints excluded: chain Q residue 80 ARG Chi-restraints excluded: chain Q residue 109 ARG Chi-restraints excluded: chain R residue 10 THR Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 42 SER Chi-restraints excluded: chain R residue 79 LEU Chi-restraints excluded: chain S residue 10 LYS Chi-restraints excluded: chain S residue 14 VAL Chi-restraints excluded: chain S residue 28 GLU Chi-restraints excluded: chain S residue 33 VAL Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 75 GLN Chi-restraints excluded: chain S residue 98 GLU Chi-restraints excluded: chain S residue 101 ASN Chi-restraints excluded: chain T residue 11 THR Chi-restraints excluded: chain T residue 14 THR Chi-restraints excluded: chain T residue 26 ILE Chi-restraints excluded: chain T residue 29 ILE Chi-restraints excluded: chain T residue 70 ASP Chi-restraints excluded: chain T residue 75 VAL Chi-restraints excluded: chain T residue 105 THR Chi-restraints excluded: chain T residue 106 SER Chi-restraints excluded: chain T residue 109 THR Chi-restraints excluded: chain U residue 3 LEU Chi-restraints excluded: chain U residue 16 SER Chi-restraints excluded: chain U residue 36 THR Chi-restraints excluded: chain U residue 42 VAL Chi-restraints excluded: chain U residue 55 ILE Chi-restraints excluded: chain U residue 56 LEU Chi-restraints excluded: chain U residue 75 ARG Chi-restraints excluded: chain U residue 84 GLU Chi-restraints excluded: chain V residue 2 PHE Chi-restraints excluded: chain V residue 5 LYS Chi-restraints excluded: chain V residue 7 ASP Chi-restraints excluded: chain V residue 9 VAL Chi-restraints excluded: chain V residue 13 THR Chi-restraints excluded: chain V residue 17 LYS Chi-restraints excluded: chain V residue 33 VAL Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain V residue 68 VAL Chi-restraints excluded: chain V residue 90 LYS Chi-restraints excluded: chain V residue 91 VAL Chi-restraints excluded: chain V residue 94 SER Chi-restraints excluded: chain V residue 99 GLU Chi-restraints excluded: chain X residue 19 THR Chi-restraints excluded: chain X residue 20 SER Chi-restraints excluded: chain X residue 23 ARG Chi-restraints excluded: chain X residue 24 ASP Chi-restraints excluded: chain X residue 39 THR Chi-restraints excluded: chain X residue 40 VAL Chi-restraints excluded: chain X residue 58 VAL Chi-restraints excluded: chain X residue 67 THR Chi-restraints excluded: chain X residue 75 VAL Chi-restraints excluded: chain X residue 79 GLU Chi-restraints excluded: chain X residue 88 VAL Chi-restraints excluded: chain X residue 93 VAL Chi-restraints excluded: chain Y residue 12 THR Chi-restraints excluded: chain Y residue 22 MET Chi-restraints excluded: chain Y residue 24 SER Chi-restraints excluded: chain Y residue 28 THR Chi-restraints excluded: chain Y residue 35 LYS Chi-restraints excluded: chain Y residue 40 ILE Chi-restraints excluded: chain Z residue 2 LYS Chi-restraints excluded: chain Z residue 3 VAL Chi-restraints excluded: chain Z residue 10 THR Chi-restraints excluded: chain Z residue 18 GLU Chi-restraints excluded: chain Z residue 24 GLU Chi-restraints excluded: chain Z residue 37 LEU Chi-restraints excluded: chain Z residue 49 SER Chi-restraints excluded: chain 0 residue 30 LYS Chi-restraints excluded: chain 0 residue 35 VAL Chi-restraints excluded: chain 0 residue 54 VAL Chi-restraints excluded: chain 0 residue 59 VAL Chi-restraints excluded: chain 2 residue 3 VAL Chi-restraints excluded: chain 2 residue 8 THR Chi-restraints excluded: chain 2 residue 18 THR Chi-restraints excluded: chain 2 residue 23 THR Chi-restraints excluded: chain 2 residue 56 SER Chi-restraints excluded: chain 3 residue 24 ARG Chi-restraints excluded: chain 3 residue 38 ARG Chi-restraints excluded: chain 3 residue 44 LEU Chi-restraints excluded: chain 4 residue 1 MET Chi-restraints excluded: chain 4 residue 20 LYS Chi-restraints excluded: chain 4 residue 24 THR Chi-restraints excluded: chain 5 residue 14 VAL Chi-restraints excluded: chain 5 residue 17 THR Chi-restraints excluded: chain 5 residue 32 ARG Chi-restraints excluded: chain 5 residue 58 ILE Chi-restraints excluded: chain 5 residue 60 GLN Chi-restraints excluded: chain 6 residue 4 ARG Chi-restraints excluded: chain 6 residue 11 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 920 random chunks: chunk 806 optimal weight: 3.9990 chunk 849 optimal weight: 8.9990 chunk 775 optimal weight: 5.9990 chunk 826 optimal weight: 5.9990 chunk 497 optimal weight: 10.0000 chunk 359 optimal weight: 10.0000 chunk 648 optimal weight: 8.9990 chunk 253 optimal weight: 9.9990 chunk 746 optimal weight: 4.9990 chunk 781 optimal weight: 2.9990 chunk 823 optimal weight: 1.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 67 ASN ** g 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 77 HIS ** m 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 9 ASN o 38 GLN ** s 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 143 ASN ** F 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 44 ASN O 61 GLN ** O 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 54 ASN X 87 GLN Z 48 GLN Z 60 GLN 0 17 GLN 3 20 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 145353 Z= 0.243 Angle : 0.697 10.312 217934 Z= 0.362 Chirality : 0.041 0.395 27945 Planarity : 0.006 0.069 11316 Dihedral : 23.000 179.671 73951 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.34 % Favored : 90.60 % Rotamer: Outliers : 10.26 % Allowed : 26.54 % Favored : 63.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.17 % Twisted Proline : 0.54 % Twisted General : 0.08 % 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: -1.84 (0.11), residues: 4970 helix: 0.04 (0.14), residues: 1466 sheet: -0.48 (0.16), residues: 1020 loop : -2.40 (0.11), residues: 2484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP d 9 HIS 0.006 0.001 HIS T 107 PHE 0.022 0.002 PHE V 2 TYR 0.022 0.002 TYR l 28 ARG 0.005 0.001 ARG i 130 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9940 Ramachandran restraints generated. 4970 Oldfield, 0 Emsley, 4970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9940 Ramachandran restraints generated. 4970 Oldfield, 0 Emsley, 4970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1084 residues out of total 4231 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 434 poor density : 650 time to evaluate : 5.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 200 TRP cc_start: 0.7966 (OUTLIER) cc_final: 0.7365 (m100) REVERT: d 106 THR cc_start: 0.7518 (OUTLIER) cc_final: 0.7279 (m) REVERT: d 114 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8481 (mt) REVERT: d 143 ARG cc_start: 0.7524 (OUTLIER) cc_final: 0.6220 (ttt-90) REVERT: f 3 GLN cc_start: 0.6123 (OUTLIER) cc_final: 0.5163 (mm110) REVERT: h 49 VAL cc_start: 0.8808 (OUTLIER) cc_final: 0.8375 (t) REVERT: j 4 GLN cc_start: 0.4621 (OUTLIER) cc_final: 0.4351 (tm-30) REVERT: j 67 MET cc_start: 0.8014 (ttm) cc_final: 0.7644 (ttp) REVERT: j 85 ASP cc_start: 0.5973 (OUTLIER) cc_final: 0.5655 (m-30) REVERT: k 72 LYS cc_start: 0.6818 (OUTLIER) cc_final: 0.6578 (mtpp) REVERT: l 28 TYR cc_start: 0.4792 (OUTLIER) cc_final: 0.3774 (p90) REVERT: l 63 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.6711 (mtt90) REVERT: m 11 ARG cc_start: 0.4415 (OUTLIER) cc_final: 0.3787 (mmt180) REVERT: m 100 GLN cc_start: 0.8043 (OUTLIER) cc_final: 0.7630 (mp10) REVERT: m 103 LYS cc_start: 0.4971 (OUTLIER) cc_final: 0.2890 (mmtp) REVERT: m 109 ARG cc_start: 0.7951 (OUTLIER) cc_final: 0.7299 (tpt-90) REVERT: n 7 ILE cc_start: 0.8212 (OUTLIER) cc_final: 0.7812 (mm) REVERT: o 56 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8184 (tp) REVERT: o 84 ARG cc_start: 0.8499 (OUTLIER) cc_final: 0.8129 (ttp-170) REVERT: s 7 LYS cc_start: 0.4947 (OUTLIER) cc_final: 0.3644 (pttt) REVERT: s 37 ARG cc_start: 0.8119 (OUTLIER) cc_final: 0.7019 (ptp-170) REVERT: C 30 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7211 (tm-30) REVERT: C 38 LYS cc_start: 0.8076 (OUTLIER) cc_final: 0.7867 (tmtt) REVERT: C 175 ARG cc_start: 0.7789 (OUTLIER) cc_final: 0.7101 (ttp-110) REVERT: D 90 GLU cc_start: 0.6813 (OUTLIER) cc_final: 0.5875 (tm-30) REVERT: D 103 GLN cc_start: 0.7329 (pm20) cc_final: 0.6837 (pm20) REVERT: D 138 ARG cc_start: 0.8041 (OUTLIER) cc_final: 0.7623 (mtt180) REVERT: D 168 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.7920 (ptt180) REVERT: E 30 GLU cc_start: 0.7074 (OUTLIER) cc_final: 0.6338 (mp0) REVERT: E 45 ARG cc_start: 0.8861 (OUTLIER) cc_final: 0.7137 (mtt180) REVERT: E 66 ARG cc_start: 0.5626 (mtm110) cc_final: 0.5084 (mtt-85) REVERT: E 147 SER cc_start: 0.8147 (p) cc_final: 0.7918 (m) REVERT: E 190 ASN cc_start: 0.8592 (OUTLIER) cc_final: 0.8260 (t0) REVERT: F 8 TYR cc_start: 0.4253 (OUTLIER) cc_final: 0.3599 (m-10) REVERT: F 36 ILE cc_start: 0.8075 (OUTLIER) cc_final: 0.7672 (mp) REVERT: F 169 LEU cc_start: 0.7159 (OUTLIER) cc_final: 0.6859 (tp) REVERT: G 144 LEU cc_start: 0.8030 (OUTLIER) cc_final: 0.7530 (mp) REVERT: G 171 ARG cc_start: 0.7840 (OUTLIER) cc_final: 0.7314 (mmm160) REVERT: L 19 ILE cc_start: 0.8015 (OUTLIER) cc_final: 0.7656 (pt) REVERT: L 71 ARG cc_start: 0.7911 (OUTLIER) cc_final: 0.7644 (mpt-90) REVERT: M 16 ARG cc_start: 0.6888 (OUTLIER) cc_final: 0.6687 (mtt180) REVERT: M 39 LYS cc_start: 0.8720 (OUTLIER) cc_final: 0.8496 (mtpm) REVERT: M 133 GLN cc_start: 0.7211 (tt0) cc_final: 0.6878 (tt0) REVERT: N 11 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.7839 (mpt180) REVERT: N 74 TYR cc_start: 0.5461 (OUTLIER) cc_final: 0.5235 (m-80) REVERT: N 130 LYS cc_start: 0.7822 (OUTLIER) cc_final: 0.7529 (mtmm) REVERT: O 19 ASP cc_start: 0.7523 (m-30) cc_final: 0.7172 (m-30) REVERT: P 22 ILE cc_start: 0.8601 (OUTLIER) cc_final: 0.8084 (mp) REVERT: P 35 ARG cc_start: 0.8271 (OUTLIER) cc_final: 0.7087 (ttm170) REVERT: P 113 GLU cc_start: 0.6039 (OUTLIER) cc_final: 0.5801 (mt-10) REVERT: Q 6 GLN cc_start: 0.7374 (mt0) cc_final: 0.7110 (mt0) REVERT: Q 38 GLU cc_start: 0.6454 (OUTLIER) cc_final: 0.5871 (tp30) REVERT: R 56 ASP cc_start: 0.7375 (m-30) cc_final: 0.7117 (m-30) REVERT: S 96 MET cc_start: 0.7546 (mmm) cc_final: 0.7314 (tpp) REVERT: S 98 GLU cc_start: 0.7333 (OUTLIER) cc_final: 0.6989 (mt-10) REVERT: U 75 ARG cc_start: 0.8178 (OUTLIER) cc_final: 0.7542 (mtt90) REVERT: V 5 LYS cc_start: 0.7911 (OUTLIER) cc_final: 0.6902 (tptm) REVERT: V 17 LYS cc_start: 0.8210 (OUTLIER) cc_final: 0.8000 (ttmt) REVERT: X 23 ARG cc_start: 0.8415 (OUTLIER) cc_final: 0.7849 (mtm-85) REVERT: Y 22 MET cc_start: 0.7611 (OUTLIER) cc_final: 0.6969 (mmp) REVERT: Y 35 LYS cc_start: 0.8063 (OUTLIER) cc_final: 0.7795 (ttmm) REVERT: Z 2 LYS cc_start: 0.7170 (OUTLIER) cc_final: 0.5482 (pptt) REVERT: 0 40 ASN cc_start: 0.7600 (m-40) cc_final: 0.7320 (m-40) REVERT: 0 58 GLU cc_start: 0.7091 (mm-30) cc_final: 0.6831 (tp30) REVERT: 3 24 ARG cc_start: 0.6863 (OUTLIER) cc_final: 0.6588 (ttm170) REVERT: 3 32 LYS cc_start: 0.7726 (mmtt) cc_final: 0.7379 (mtpp) REVERT: 3 38 ARG cc_start: 0.7577 (OUTLIER) cc_final: 0.6598 (ttp80) REVERT: 4 24 THR cc_start: 0.8142 (OUTLIER) cc_final: 0.7937 (t) outliers start: 434 outliers final: 342 residues processed: 973 average time/residue: 1.9219 time to fit residues: 2693.5111 Evaluate side-chains 1047 residues out of total 4231 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 398 poor density : 649 time to evaluate : 5.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 21 LYS Chi-restraints excluded: chain c residue 25 GLU Chi-restraints excluded: chain c residue 51 VAL Chi-restraints excluded: chain c residue 67 ILE Chi-restraints excluded: chain c residue 69 THR Chi-restraints excluded: chain c residue 75 VAL Chi-restraints excluded: chain c residue 98 VAL Chi-restraints excluded: chain c residue 100 ILE Chi-restraints excluded: chain c residue 153 SER Chi-restraints excluded: chain c residue 164 SER Chi-restraints excluded: chain c residue 168 SER Chi-restraints excluded: chain c residue 171 THR Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain c residue 200 TRP Chi-restraints excluded: chain d residue 14 ARG Chi-restraints excluded: chain d residue 22 THR Chi-restraints excluded: chain d residue 24 LYS Chi-restraints excluded: chain d residue 58 ARG Chi-restraints excluded: chain d residue 63 MET Chi-restraints excluded: chain d residue 71 LEU Chi-restraints excluded: chain d residue 106 THR Chi-restraints excluded: chain d residue 114 LEU Chi-restraints excluded: chain d residue 120 ILE Chi-restraints excluded: chain d residue 139 VAL Chi-restraints excluded: chain d residue 140 ILE Chi-restraints excluded: chain d residue 143 ARG Chi-restraints excluded: chain d residue 150 SER Chi-restraints excluded: chain d residue 159 THR Chi-restraints excluded: chain d residue 186 LEU Chi-restraints excluded: chain d residue 192 GLU Chi-restraints excluded: chain e residue 9 LEU Chi-restraints excluded: chain e residue 21 VAL Chi-restraints excluded: chain e residue 22 THR Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 52 LYS Chi-restraints excluded: chain e residue 76 MET Chi-restraints excluded: chain e residue 84 GLU Chi-restraints excluded: chain e residue 95 LEU Chi-restraints excluded: chain e residue 96 MET Chi-restraints excluded: chain e residue 100 VAL Chi-restraints excluded: chain e residue 111 VAL Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain e residue 125 SER Chi-restraints excluded: chain e residue 128 LEU Chi-restraints excluded: chain e residue 144 LEU Chi-restraints excluded: chain e residue 147 LEU Chi-restraints excluded: chain e residue 160 SER Chi-restraints excluded: chain e residue 164 ILE Chi-restraints excluded: chain e residue 165 ILE Chi-restraints excluded: chain f residue 3 GLN Chi-restraints excluded: chain f residue 5 THR Chi-restraints excluded: chain f residue 36 ASN Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 41 ILE Chi-restraints excluded: chain f residue 45 ASP Chi-restraints excluded: chain f residue 65 ILE Chi-restraints excluded: chain f residue 66 VAL Chi-restraints excluded: chain f residue 68 VAL Chi-restraints excluded: chain g residue 43 ILE Chi-restraints excluded: chain g residue 56 ASN Chi-restraints excluded: chain g residue 72 VAL Chi-restraints excluded: chain g residue 75 VAL Chi-restraints excluded: chain g residue 85 TYR Chi-restraints excluded: chain g residue 91 VAL Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain g residue 131 THR Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain h residue 2 VAL Chi-restraints excluded: chain h residue 24 THR Chi-restraints excluded: chain h residue 27 VAL Chi-restraints excluded: chain h residue 49 VAL Chi-restraints excluded: chain h residue 52 ILE Chi-restraints excluded: chain h residue 54 ASP Chi-restraints excluded: chain h residue 62 VAL Chi-restraints excluded: chain h residue 69 ASN Chi-restraints excluded: chain h residue 73 VAL Chi-restraints excluded: chain h residue 75 THR Chi-restraints excluded: chain h residue 89 VAL Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 99 ASN Chi-restraints excluded: chain h residue 126 GLU Chi-restraints excluded: chain h residue 131 VAL Chi-restraints excluded: chain i residue 16 VAL Chi-restraints excluded: chain i residue 29 THR Chi-restraints excluded: chain i residue 35 VAL Chi-restraints excluded: chain i residue 47 VAL Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain i residue 83 ILE Chi-restraints excluded: chain j residue 4 GLN Chi-restraints excluded: chain j residue 18 LEU Chi-restraints excluded: chain j residue 25 ILE Chi-restraints excluded: chain j residue 51 VAL Chi-restraints excluded: chain j residue 84 VAL Chi-restraints excluded: chain j residue 85 ASP Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 35 THR Chi-restraints excluded: chain k residue 37 THR Chi-restraints excluded: chain k residue 45 SER Chi-restraints excluded: chain k residue 46 SER Chi-restraints excluded: chain k residue 65 MET Chi-restraints excluded: chain k residue 72 LYS Chi-restraints excluded: chain k residue 81 THR Chi-restraints excluded: chain k residue 82 VAL Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain k residue 85 THR Chi-restraints excluded: chain k residue 86 VAL Chi-restraints excluded: chain k residue 107 VAL Chi-restraints excluded: chain l residue 8 VAL Chi-restraints excluded: chain l residue 14 SER Chi-restraints excluded: chain l residue 17 GLU Chi-restraints excluded: chain l residue 21 SER Chi-restraints excluded: chain l residue 25 ASN Chi-restraints excluded: chain l residue 28 TYR Chi-restraints excluded: chain l residue 54 THR Chi-restraints excluded: chain l residue 63 ARG Chi-restraints excluded: chain l residue 72 ASN Chi-restraints excluded: chain l residue 77 THR Chi-restraints excluded: chain l residue 92 VAL Chi-restraints excluded: chain l residue 107 ARG Chi-restraints excluded: chain l residue 111 VAL Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain l residue 121 ASN Chi-restraints excluded: chain l residue 122 ASP Chi-restraints excluded: chain m residue 11 ARG Chi-restraints excluded: chain m residue 14 ARG Chi-restraints excluded: chain m residue 15 VAL Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 28 THR Chi-restraints excluded: chain m residue 100 GLN Chi-restraints excluded: chain m residue 102 THR Chi-restraints excluded: chain m residue 103 LYS Chi-restraints excluded: chain m residue 109 ARG Chi-restraints excluded: chain n residue 7 ILE Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain n residue 42 ILE Chi-restraints excluded: chain o residue 56 LEU Chi-restraints excluded: chain o residue 67 LEU Chi-restraints excluded: chain o residue 75 ILE Chi-restraints excluded: chain o residue 84 ARG Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain p residue 32 ARG Chi-restraints excluded: chain p residue 36 THR Chi-restraints excluded: chain q residue 10 VAL Chi-restraints excluded: chain q residue 16 VAL Chi-restraints excluded: chain q residue 21 ASP Chi-restraints excluded: chain q residue 32 LYS Chi-restraints excluded: chain q residue 55 THR Chi-restraints excluded: chain q residue 80 GLU Chi-restraints excluded: chain q residue 81 VAL Chi-restraints excluded: chain r residue 20 ASN Chi-restraints excluded: chain r residue 22 ILE Chi-restraints excluded: chain r residue 34 LYS Chi-restraints excluded: chain r residue 48 VAL 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 11 VAL Chi-restraints excluded: chain s residue 14 HIS Chi-restraints excluded: chain s residue 26 GLU Chi-restraints excluded: chain s residue 27 LYS Chi-restraints excluded: chain s residue 37 ARG Chi-restraints excluded: chain s residue 39 THR Chi-restraints excluded: chain s residue 45 VAL Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain s residue 73 GLU Chi-restraints excluded: chain s residue 78 ARG Chi-restraints excluded: chain t residue 39 VAL Chi-restraints excluded: chain t residue 49 LEU Chi-restraints excluded: chain t residue 81 LEU Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 38 LYS Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 108 LYS Chi-restraints excluded: chain C residue 175 ARG Chi-restraints excluded: chain C residue 177 ASN Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 138 ARG Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 167 ASP Chi-restraints excluded: chain D residue 168 ARG Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 184 ASN Chi-restraints excluded: chain D residue 191 ASN Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain E residue 6 LEU Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 30 GLU Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 80 SER Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 105 VAL Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 190 ASN Chi-restraints excluded: chain E residue 195 THR Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain F residue 8 TYR Chi-restraints excluded: chain F residue 15 SER Chi-restraints excluded: chain F residue 32 ASP Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 88 LYS Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 123 ASP Chi-restraints excluded: chain F residue 127 ASN Chi-restraints excluded: chain F residue 133 LYS Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain G residue 2 SER Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 101 ASN Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 144 LEU Chi-restraints excluded: chain G residue 165 VAL Chi-restraints excluded: chain G residue 171 ARG Chi-restraints excluded: chain K residue 2 ARG Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 14 ARG Chi-restraints excluded: chain K residue 15 LYS Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 58 ILE Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 114 THR Chi-restraints excluded: chain K residue 115 LEU Chi-restraints excluded: chain K residue 145 ASN Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 19 ILE Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 53 LYS Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 71 ARG Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain L residue 108 GLU Chi-restraints excluded: chain L residue 112 MET Chi-restraints excluded: chain M residue 16 ARG Chi-restraints excluded: chain M residue 36 LYS Chi-restraints excluded: chain M residue 39 LYS Chi-restraints excluded: chain M residue 42 SER Chi-restraints excluded: chain M residue 67 THR Chi-restraints excluded: chain M residue 81 THR Chi-restraints excluded: chain M residue 87 ASP Chi-restraints excluded: chain M residue 105 GLU Chi-restraints excluded: chain M residue 122 THR Chi-restraints excluded: chain M residue 131 SER Chi-restraints excluded: chain N residue 5 LYS Chi-restraints excluded: chain N residue 11 ARG Chi-restraints excluded: chain N residue 26 GLU Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 74 TYR Chi-restraints excluded: chain N residue 85 LYS Chi-restraints excluded: chain N residue 122 SER Chi-restraints excluded: chain N residue 127 VAL Chi-restraints excluded: chain N residue 130 LYS Chi-restraints excluded: chain N residue 133 LYS Chi-restraints excluded: chain O residue 24 LEU Chi-restraints excluded: chain O residue 72 SER Chi-restraints excluded: chain O residue 121 VAL Chi-restraints excluded: chain O residue 124 GLU Chi-restraints excluded: chain P residue 2 ILE Chi-restraints excluded: chain P residue 6 ASP Chi-restraints excluded: chain P residue 11 ARG Chi-restraints excluded: chain P residue 13 LYS Chi-restraints excluded: chain P residue 18 VAL Chi-restraints excluded: chain P residue 22 ILE Chi-restraints excluded: chain P residue 28 CYS Chi-restraints excluded: chain P residue 35 ARG Chi-restraints excluded: chain P residue 51 VAL Chi-restraints excluded: chain P residue 63 ILE Chi-restraints excluded: chain P residue 67 THR Chi-restraints excluded: chain P residue 86 LYS Chi-restraints excluded: chain P residue 95 ARG Chi-restraints excluded: chain P residue 104 VAL Chi-restraints excluded: chain P residue 113 GLU Chi-restraints excluded: chain Q residue 2 ASN Chi-restraints excluded: chain Q residue 36 THR Chi-restraints excluded: chain Q residue 38 GLU Chi-restraints excluded: chain Q residue 78 THR Chi-restraints excluded: chain Q residue 80 ARG Chi-restraints excluded: chain Q residue 109 ARG Chi-restraints excluded: chain R residue 10 THR Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 79 LEU Chi-restraints excluded: chain S residue 10 LYS Chi-restraints excluded: chain S residue 14 VAL Chi-restraints excluded: chain S residue 28 GLU Chi-restraints excluded: chain S residue 33 VAL Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 75 GLN Chi-restraints excluded: chain S residue 98 GLU Chi-restraints excluded: chain S residue 101 ASN Chi-restraints excluded: chain T residue 11 THR Chi-restraints excluded: chain T residue 14 THR Chi-restraints excluded: chain T residue 26 ILE Chi-restraints excluded: chain T residue 29 ILE Chi-restraints excluded: chain T residue 75 VAL Chi-restraints excluded: chain T residue 105 THR Chi-restraints excluded: chain T residue 106 SER Chi-restraints excluded: chain T residue 109 THR Chi-restraints excluded: chain U residue 3 LEU Chi-restraints excluded: chain U residue 16 SER Chi-restraints excluded: chain U residue 36 THR Chi-restraints excluded: chain U residue 42 VAL Chi-restraints excluded: chain U residue 55 ILE Chi-restraints excluded: chain U residue 56 LEU Chi-restraints excluded: chain U residue 75 ARG Chi-restraints excluded: chain U residue 84 GLU Chi-restraints excluded: chain V residue 5 LYS Chi-restraints excluded: chain V residue 7 ASP Chi-restraints excluded: chain V residue 9 VAL Chi-restraints excluded: chain V residue 13 THR Chi-restraints excluded: chain V residue 17 LYS Chi-restraints excluded: chain V residue 33 VAL Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain V residue 68 VAL Chi-restraints excluded: chain V residue 91 VAL Chi-restraints excluded: chain V residue 94 SER Chi-restraints excluded: chain V residue 99 GLU Chi-restraints excluded: chain X residue 19 THR Chi-restraints excluded: chain X residue 20 SER Chi-restraints excluded: chain X residue 23 ARG Chi-restraints excluded: chain X residue 24 ASP Chi-restraints excluded: chain X residue 39 THR Chi-restraints excluded: chain X residue 40 VAL Chi-restraints excluded: chain X residue 58 VAL Chi-restraints excluded: chain X residue 67 THR Chi-restraints excluded: chain X residue 75 VAL Chi-restraints excluded: chain X residue 79 GLU Chi-restraints excluded: chain X residue 88 VAL Chi-restraints excluded: chain X residue 93 VAL Chi-restraints excluded: chain Y residue 12 THR Chi-restraints excluded: chain Y residue 22 MET Chi-restraints excluded: chain Y residue 24 SER Chi-restraints excluded: chain Y residue 28 THR Chi-restraints excluded: chain Y residue 35 LYS Chi-restraints excluded: chain Y residue 40 ILE Chi-restraints excluded: chain Z residue 2 LYS Chi-restraints excluded: chain Z residue 3 VAL Chi-restraints excluded: chain Z residue 24 GLU Chi-restraints excluded: chain Z residue 37 LEU Chi-restraints excluded: chain 0 residue 30 LYS Chi-restraints excluded: chain 0 residue 35 VAL Chi-restraints excluded: chain 0 residue 54 VAL Chi-restraints excluded: chain 0 residue 59 VAL Chi-restraints excluded: chain 2 residue 3 VAL Chi-restraints excluded: chain 2 residue 8 THR Chi-restraints excluded: chain 2 residue 18 THR Chi-restraints excluded: chain 2 residue 23 THR Chi-restraints excluded: chain 2 residue 56 SER Chi-restraints excluded: chain 3 residue 24 ARG Chi-restraints excluded: chain 3 residue 38 ARG Chi-restraints excluded: chain 3 residue 44 LEU Chi-restraints excluded: chain 4 residue 1 MET Chi-restraints excluded: chain 4 residue 20 LYS Chi-restraints excluded: chain 4 residue 24 THR Chi-restraints excluded: chain 5 residue 14 VAL Chi-restraints excluded: chain 5 residue 17 THR Chi-restraints excluded: chain 5 residue 32 ARG Chi-restraints excluded: chain 5 residue 58 ILE Chi-restraints excluded: chain 5 residue 60 GLN Chi-restraints excluded: chain 5 residue 65 MET Chi-restraints excluded: chain 6 residue 4 ARG Chi-restraints excluded: chain 6 residue 11 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 920 random chunks: chunk 542 optimal weight: 9.9990 chunk 873 optimal weight: 8.9990 chunk 533 optimal weight: 10.0000 chunk 414 optimal weight: 10.0000 chunk 607 optimal weight: 10.0000 chunk 916 optimal weight: 10.0000 chunk 843 optimal weight: 1.9990 chunk 729 optimal weight: 30.0000 chunk 75 optimal weight: 10.0000 chunk 563 optimal weight: 9.9990 chunk 447 optimal weight: 10.0000 overall best weight: 8.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 67 ASN f 87 ASN ** g 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 77 HIS ** m 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 9 ASN o 38 GLN ** s 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 ASN ** F 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 44 ASN O 61 GLN ** O 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 87 GLN Z 48 GLN Z 60 GLN 0 17 GLN 3 20 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.1092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.131 145353 Z= 0.452 Angle : 0.899 12.000 217934 Z= 0.448 Chirality : 0.050 0.344 27945 Planarity : 0.007 0.086 11316 Dihedral : 23.119 179.307 73951 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.06 % Favored : 89.86 % Rotamer: Outliers : 10.00 % Allowed : 26.80 % Favored : 63.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.17 % Twisted Proline : 0.54 % Twisted General : 0.08 % 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: -2.07 (0.11), residues: 4970 helix: -0.24 (0.13), residues: 1464 sheet: -0.54 (0.16), residues: 1022 loop : -2.51 (0.11), residues: 2484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP d 9 HIS 0.008 0.002 HIS K 133 PHE 0.028 0.003 PHE V 2 TYR 0.027 0.003 TYR l 28 ARG 0.010 0.001 ARG C 52 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9940 Ramachandran restraints generated. 4970 Oldfield, 0 Emsley, 4970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9940 Ramachandran restraints generated. 4970 Oldfield, 0 Emsley, 4970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1069 residues out of total 4231 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 423 poor density : 646 time to evaluate : 5.679 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: c 200 TRP cc_start: 0.7987 (OUTLIER) cc_final: 0.7355 (m100) REVERT: d 106 THR cc_start: 0.7619 (OUTLIER) cc_final: 0.7393 (m) REVERT: d 114 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8526 (mt) REVERT: d 140 ILE cc_start: 0.7709 (OUTLIER) cc_final: 0.7235 (mp) REVERT: d 143 ARG cc_start: 0.7618 (OUTLIER) cc_final: 0.6509 (ttt-90) REVERT: f 3 GLN cc_start: 0.6184 (OUTLIER) cc_final: 0.5187 (mm110) REVERT: h 49 VAL cc_start: 0.8812 (OUTLIER) cc_final: 0.8401 (t) REVERT: j 4 GLN cc_start: 0.4687 (OUTLIER) cc_final: 0.4389 (tm-30) REVERT: j 67 MET cc_start: 0.8069 (ttm) cc_final: 0.7627 (ttp) REVERT: j 85 ASP cc_start: 0.6089 (OUTLIER) cc_final: 0.5717 (m-30) REVERT: l 28 TYR cc_start: 0.4827 (OUTLIER) cc_final: 0.3964 (p90) REVERT: l 63 ARG cc_start: 0.8499 (OUTLIER) cc_final: 0.6748 (mtt90) REVERT: m 11 ARG cc_start: 0.4561 (OUTLIER) cc_final: 0.3886 (mmt180) REVERT: m 100 GLN cc_start: 0.8125 (OUTLIER) cc_final: 0.7683 (mp10) REVERT: m 109 ARG cc_start: 0.8031 (OUTLIER) cc_final: 0.7380 (tpt-90) REVERT: n 7 ILE cc_start: 0.8261 (OUTLIER) cc_final: 0.7841 (mm) REVERT: o 56 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8162 (tp) REVERT: o 84 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.8184 (ttp-170) REVERT: s 7 LYS cc_start: 0.5169 (OUTLIER) cc_final: 0.3709 (pttt) REVERT: s 37 ARG cc_start: 0.8148 (OUTLIER) cc_final: 0.7051 (ptp-170) REVERT: C 30 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7318 (tm-30) REVERT: C 175 ARG cc_start: 0.7827 (OUTLIER) cc_final: 0.7133 (ttp-110) REVERT: D 90 GLU cc_start: 0.6975 (OUTLIER) cc_final: 0.5959 (tm-30) REVERT: D 103 GLN cc_start: 0.7504 (pm20) cc_final: 0.7184 (pm20) REVERT: D 138 ARG cc_start: 0.8112 (OUTLIER) cc_final: 0.7724 (mtt180) REVERT: D 168 ARG cc_start: 0.8445 (OUTLIER) cc_final: 0.8030 (ptt180) REVERT: D 170 THR cc_start: 0.8739 (OUTLIER) cc_final: 0.8489 (t) REVERT: E 30 GLU cc_start: 0.7141 (OUTLIER) cc_final: 0.6378 (mp0) REVERT: E 45 ARG cc_start: 0.8879 (OUTLIER) cc_final: 0.7181 (mtt180) REVERT: E 66 ARG cc_start: 0.5613 (mtm110) cc_final: 0.5044 (mtt-85) REVERT: E 147 SER cc_start: 0.8131 (p) cc_final: 0.7885 (m) REVERT: E 190 ASN cc_start: 0.8609 (OUTLIER) cc_final: 0.8276 (t0) REVERT: F 8 TYR cc_start: 0.4212 (OUTLIER) cc_final: 0.3532 (m-10) REVERT: F 36 ILE cc_start: 0.8111 (OUTLIER) cc_final: 0.7712 (mp) REVERT: F 169 LEU cc_start: 0.7021 (OUTLIER) cc_final: 0.6711 (tp) REVERT: G 144 LEU cc_start: 0.8040 (OUTLIER) cc_final: 0.7536 (mp) REVERT: G 171 ARG cc_start: 0.7867 (OUTLIER) cc_final: 0.7317 (mmm160) REVERT: K 14 ARG cc_start: 0.8163 (OUTLIER) cc_final: 0.6698 (mtp180) REVERT: L 19 ILE cc_start: 0.8062 (OUTLIER) cc_final: 0.7666 (pt) REVERT: L 71 ARG cc_start: 0.7925 (OUTLIER) cc_final: 0.7676 (mpt-90) REVERT: M 16 ARG cc_start: 0.7073 (OUTLIER) cc_final: 0.6855 (mtt180) REVERT: M 39 LYS cc_start: 0.8718 (OUTLIER) cc_final: 0.8431 (mtpm) REVERT: M 79 LEU cc_start: 0.7456 (OUTLIER) cc_final: 0.6787 (mp) REVERT: M 103 LYS cc_start: 0.8256 (OUTLIER) cc_final: 0.7992 (pttm) REVERT: M 133 GLN cc_start: 0.7276 (tt0) cc_final: 0.6885 (tt0) REVERT: N 11 ARG cc_start: 0.8600 (OUTLIER) cc_final: 0.7900 (mpt180) REVERT: N 26 GLU cc_start: 0.7312 (OUTLIER) cc_final: 0.6946 (mm-30) REVERT: O 19 ASP cc_start: 0.7557 (m-30) cc_final: 0.7200 (m-30) REVERT: O 108 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8497 (mp) REVERT: P 22 ILE cc_start: 0.8610 (OUTLIER) cc_final: 0.8094 (mp) REVERT: P 35 ARG cc_start: 0.8391 (OUTLIER) cc_final: 0.7280 (ttm170) REVERT: P 95 ARG cc_start: 0.7668 (OUTLIER) cc_final: 0.5674 (mtp180) REVERT: P 113 GLU cc_start: 0.6108 (OUTLIER) cc_final: 0.5880 (mt-10) REVERT: Q 38 GLU cc_start: 0.6485 (OUTLIER) cc_final: 0.5895 (tp30) REVERT: R 56 ASP cc_start: 0.7456 (m-30) cc_final: 0.7193 (m-30) REVERT: S 98 GLU cc_start: 0.7350 (OUTLIER) cc_final: 0.7001 (mt-10) REVERT: U 75 ARG cc_start: 0.8201 (OUTLIER) cc_final: 0.7605 (mtt90) REVERT: V 5 LYS cc_start: 0.7800 (OUTLIER) cc_final: 0.6957 (tttm) REVERT: X 23 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.7571 (ptt90) REVERT: Y 22 MET cc_start: 0.7626 (OUTLIER) cc_final: 0.6986 (mmp) REVERT: Y 35 LYS cc_start: 0.8167 (OUTLIER) cc_final: 0.7822 (ttmm) REVERT: Z 2 LYS cc_start: 0.7209 (OUTLIER) cc_final: 0.5491 (pptt) REVERT: 0 58 GLU cc_start: 0.7121 (mm-30) cc_final: 0.6864 (tp30) REVERT: 3 24 ARG cc_start: 0.6849 (OUTLIER) cc_final: 0.6575 (ttm170) REVERT: 3 32 LYS cc_start: 0.7667 (mmtt) cc_final: 0.7370 (mtpp) REVERT: 4 24 THR cc_start: 0.8188 (OUTLIER) cc_final: 0.7980 (t) outliers start: 423 outliers final: 336 residues processed: 967 average time/residue: 1.9474 time to fit residues: 2713.8629 Evaluate side-chains 1035 residues out of total 4231 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 393 poor density : 642 time to evaluate : 5.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 21 LYS Chi-restraints excluded: chain c residue 25 GLU Chi-restraints excluded: chain c residue 51 VAL Chi-restraints excluded: chain c residue 67 ILE Chi-restraints excluded: chain c residue 69 THR Chi-restraints excluded: chain c residue 75 VAL Chi-restraints excluded: chain c residue 98 VAL Chi-restraints excluded: chain c residue 100 ILE Chi-restraints excluded: chain c residue 153 SER Chi-restraints excluded: chain c residue 164 SER Chi-restraints excluded: chain c residue 168 SER Chi-restraints excluded: chain c residue 171 THR Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain c residue 200 TRP Chi-restraints excluded: chain d residue 14 ARG Chi-restraints excluded: chain d residue 22 THR Chi-restraints excluded: chain d residue 24 LYS Chi-restraints excluded: chain d residue 58 ARG Chi-restraints excluded: chain d residue 63 MET Chi-restraints excluded: chain d residue 71 LEU Chi-restraints excluded: chain d residue 106 THR Chi-restraints excluded: chain d residue 114 LEU Chi-restraints excluded: chain d residue 139 VAL Chi-restraints excluded: chain d residue 140 ILE Chi-restraints excluded: chain d residue 143 ARG Chi-restraints excluded: chain d residue 150 SER Chi-restraints excluded: chain d residue 159 THR Chi-restraints excluded: chain d residue 186 LEU 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 39 VAL Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 52 LYS Chi-restraints excluded: chain e residue 76 MET Chi-restraints excluded: chain e residue 84 GLU Chi-restraints excluded: chain e residue 94 ILE Chi-restraints excluded: chain e residue 95 LEU Chi-restraints excluded: chain e residue 96 MET Chi-restraints excluded: chain e residue 100 VAL Chi-restraints excluded: chain e residue 111 VAL Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain e residue 125 SER Chi-restraints excluded: chain e residue 128 LEU Chi-restraints excluded: chain e residue 144 LEU Chi-restraints excluded: chain e residue 147 LEU Chi-restraints excluded: chain e residue 160 SER Chi-restraints excluded: chain e residue 164 ILE Chi-restraints excluded: chain e residue 165 ILE Chi-restraints excluded: chain f residue 3 GLN Chi-restraints excluded: chain f residue 5 THR Chi-restraints excluded: chain f residue 36 ASN Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 41 ILE Chi-restraints excluded: chain f residue 45 ASP Chi-restraints excluded: chain f residue 65 ILE Chi-restraints excluded: chain f residue 66 VAL Chi-restraints excluded: chain f residue 68 VAL Chi-restraints excluded: chain g residue 43 ILE Chi-restraints excluded: chain g residue 56 ASN Chi-restraints excluded: chain g residue 75 VAL Chi-restraints excluded: chain g residue 85 TYR Chi-restraints excluded: chain g residue 91 VAL Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain g residue 131 THR Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain h residue 2 VAL Chi-restraints excluded: chain h residue 24 THR Chi-restraints excluded: chain h residue 27 VAL Chi-restraints excluded: chain h residue 49 VAL Chi-restraints excluded: chain h residue 52 ILE Chi-restraints excluded: chain h residue 54 ASP Chi-restraints excluded: chain h residue 62 VAL Chi-restraints excluded: chain h residue 69 ASN Chi-restraints excluded: chain h residue 73 VAL Chi-restraints excluded: chain h residue 75 THR Chi-restraints excluded: chain h residue 89 VAL Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 99 ASN Chi-restraints excluded: chain h residue 117 GLU Chi-restraints excluded: chain h residue 131 VAL Chi-restraints excluded: chain i residue 29 THR Chi-restraints excluded: chain i residue 35 VAL Chi-restraints excluded: chain i residue 47 VAL Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain i residue 83 ILE Chi-restraints excluded: chain j residue 4 GLN Chi-restraints excluded: chain j residue 18 LEU Chi-restraints excluded: chain j residue 25 ILE Chi-restraints excluded: chain j residue 51 VAL Chi-restraints excluded: chain j residue 84 VAL Chi-restraints excluded: chain j residue 85 ASP Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 35 THR Chi-restraints excluded: chain k residue 37 THR Chi-restraints excluded: chain k residue 45 SER Chi-restraints excluded: chain k residue 46 SER Chi-restraints excluded: chain k residue 65 MET Chi-restraints excluded: chain k residue 81 THR Chi-restraints excluded: chain k residue 82 VAL Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain k residue 85 THR Chi-restraints excluded: chain k residue 86 VAL Chi-restraints excluded: chain k residue 107 VAL Chi-restraints excluded: chain l residue 8 VAL Chi-restraints excluded: chain l residue 14 SER Chi-restraints excluded: chain l residue 17 GLU Chi-restraints excluded: chain l residue 21 SER Chi-restraints excluded: chain l residue 25 ASN Chi-restraints excluded: chain l residue 28 TYR Chi-restraints excluded: chain l residue 54 THR Chi-restraints excluded: chain l residue 63 ARG Chi-restraints excluded: chain l residue 72 ASN Chi-restraints excluded: chain l residue 77 THR Chi-restraints excluded: chain l residue 92 VAL Chi-restraints excluded: chain l residue 107 ARG Chi-restraints excluded: chain l residue 110 ILE Chi-restraints excluded: chain l residue 111 VAL Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain l residue 121 ASN Chi-restraints excluded: chain l residue 122 ASP Chi-restraints excluded: chain m residue 11 ARG Chi-restraints excluded: chain m residue 14 ARG Chi-restraints excluded: chain m residue 15 VAL Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 28 THR Chi-restraints excluded: chain m residue 39 VAL Chi-restraints excluded: chain m residue 80 LEU Chi-restraints excluded: chain m residue 100 GLN Chi-restraints excluded: chain m residue 102 THR Chi-restraints excluded: chain m residue 103 LYS Chi-restraints excluded: chain m residue 109 ARG Chi-restraints excluded: chain n residue 7 ILE Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain n residue 42 ILE Chi-restraints excluded: chain o residue 22 THR Chi-restraints excluded: chain o residue 56 LEU Chi-restraints excluded: chain o residue 67 LEU Chi-restraints excluded: chain o residue 75 ILE Chi-restraints excluded: chain o residue 84 ARG Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain p residue 32 ARG Chi-restraints excluded: chain p residue 36 THR Chi-restraints excluded: chain p residue 73 ILE Chi-restraints excluded: chain q residue 10 VAL Chi-restraints excluded: chain q residue 16 VAL Chi-restraints excluded: chain q residue 21 ASP Chi-restraints excluded: chain q residue 32 LYS Chi-restraints excluded: chain q residue 55 THR Chi-restraints excluded: chain q residue 80 GLU Chi-restraints excluded: chain q residue 81 VAL Chi-restraints excluded: chain r residue 20 ASN Chi-restraints excluded: chain r residue 22 ILE Chi-restraints excluded: chain r residue 32 LEU Chi-restraints excluded: chain r residue 48 VAL 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 11 VAL Chi-restraints excluded: chain s residue 14 HIS Chi-restraints excluded: chain s residue 26 GLU Chi-restraints excluded: chain s residue 27 LYS Chi-restraints excluded: chain s residue 37 ARG Chi-restraints excluded: chain s residue 39 THR Chi-restraints excluded: chain s residue 45 VAL Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain s residue 73 GLU Chi-restraints excluded: chain s residue 78 ARG Chi-restraints excluded: chain t residue 39 VAL Chi-restraints excluded: chain t residue 49 LEU Chi-restraints excluded: chain t residue 81 LEU Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 38 LYS Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 108 LYS Chi-restraints excluded: chain C residue 175 ARG Chi-restraints excluded: chain C residue 177 ASN Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 138 ARG Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 167 ASP Chi-restraints excluded: chain D residue 168 ARG Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 184 ASN Chi-restraints excluded: chain D residue 191 ASN Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain E residue 6 LEU Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 30 GLU Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 80 SER Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 105 VAL Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 190 ASN Chi-restraints excluded: chain E residue 195 THR Chi-restraints excluded: chain F residue 8 TYR Chi-restraints excluded: chain F residue 15 SER Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 88 LYS Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 123 ASP Chi-restraints excluded: chain F residue 127 ASN Chi-restraints excluded: chain F residue 133 LYS Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 101 ASN Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 144 LEU Chi-restraints excluded: chain G residue 165 VAL Chi-restraints excluded: chain G residue 171 ARG Chi-restraints excluded: chain K residue 2 ARG Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 14 ARG Chi-restraints excluded: chain K residue 15 LYS Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 58 ILE Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 114 THR Chi-restraints excluded: chain K residue 115 LEU Chi-restraints excluded: chain K residue 145 ASN Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 19 ILE Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 53 LYS Chi-restraints excluded: chain L residue 54 LYS Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 71 ARG Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain L residue 112 MET Chi-restraints excluded: chain M residue 16 ARG Chi-restraints excluded: chain M residue 36 LYS Chi-restraints excluded: chain M residue 39 LYS Chi-restraints excluded: chain M residue 42 SER Chi-restraints excluded: chain M residue 67 THR Chi-restraints excluded: chain M residue 79 LEU Chi-restraints excluded: chain M residue 81 THR Chi-restraints excluded: chain M residue 87 ASP Chi-restraints excluded: chain M residue 103 LYS Chi-restraints excluded: chain M residue 105 GLU Chi-restraints excluded: chain M residue 122 THR Chi-restraints excluded: chain M residue 131 SER Chi-restraints excluded: chain N residue 5 LYS Chi-restraints excluded: chain N residue 11 ARG Chi-restraints excluded: chain N residue 26 GLU Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 75 THR Chi-restraints excluded: chain N residue 85 LYS Chi-restraints excluded: chain N residue 122 SER 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 72 SER Chi-restraints excluded: chain O residue 108 LEU Chi-restraints excluded: chain O residue 121 VAL Chi-restraints excluded: chain O residue 124 GLU Chi-restraints excluded: chain P residue 2 ILE Chi-restraints excluded: chain P residue 6 ASP Chi-restraints excluded: chain P residue 11 ARG Chi-restraints excluded: chain P residue 13 LYS Chi-restraints excluded: chain P residue 18 VAL Chi-restraints excluded: chain P residue 22 ILE Chi-restraints excluded: chain P residue 28 CYS Chi-restraints excluded: chain P residue 35 ARG Chi-restraints excluded: chain P residue 51 VAL Chi-restraints excluded: chain P residue 63 ILE Chi-restraints excluded: chain P residue 67 THR Chi-restraints excluded: chain P residue 86 LYS Chi-restraints excluded: chain P residue 95 ARG Chi-restraints excluded: chain P residue 104 VAL Chi-restraints excluded: chain P residue 113 GLU Chi-restraints excluded: chain Q residue 2 ASN Chi-restraints excluded: chain Q residue 36 THR Chi-restraints excluded: chain Q residue 38 GLU Chi-restraints excluded: chain Q residue 78 THR Chi-restraints excluded: chain Q residue 80 ARG Chi-restraints excluded: chain Q residue 109 ARG Chi-restraints excluded: chain R residue 10 THR Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 79 LEU Chi-restraints excluded: chain R residue 112 GLN Chi-restraints excluded: chain S residue 10 LYS Chi-restraints excluded: chain S residue 14 VAL Chi-restraints excluded: chain S residue 28 GLU Chi-restraints excluded: chain S residue 33 VAL Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 75 GLN Chi-restraints excluded: chain S residue 98 GLU Chi-restraints excluded: chain S residue 101 ASN Chi-restraints excluded: chain T residue 11 THR Chi-restraints excluded: chain T residue 14 THR Chi-restraints excluded: chain T residue 26 ILE Chi-restraints excluded: chain T residue 29 ILE Chi-restraints excluded: chain T residue 75 VAL Chi-restraints excluded: chain T residue 105 THR Chi-restraints excluded: chain T residue 109 THR Chi-restraints excluded: chain U residue 3 LEU Chi-restraints excluded: chain U residue 16 SER Chi-restraints excluded: chain U residue 36 THR Chi-restraints excluded: chain U residue 42 VAL Chi-restraints excluded: chain U residue 55 ILE Chi-restraints excluded: chain U residue 56 LEU Chi-restraints excluded: chain U residue 75 ARG Chi-restraints excluded: chain U residue 84 GLU Chi-restraints excluded: chain V residue 5 LYS Chi-restraints excluded: chain V residue 9 VAL Chi-restraints excluded: chain V residue 13 THR Chi-restraints excluded: chain V residue 33 VAL Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain V residue 68 VAL Chi-restraints excluded: chain V residue 94 SER Chi-restraints excluded: chain V residue 99 GLU Chi-restraints excluded: chain X residue 19 THR Chi-restraints excluded: chain X residue 20 SER Chi-restraints excluded: chain X residue 23 ARG Chi-restraints excluded: chain X residue 24 ASP Chi-restraints excluded: chain X residue 39 THR Chi-restraints excluded: chain X residue 40 VAL Chi-restraints excluded: chain X residue 58 VAL Chi-restraints excluded: chain X residue 67 THR Chi-restraints excluded: chain X residue 75 VAL Chi-restraints excluded: chain X residue 79 GLU Chi-restraints excluded: chain X residue 88 VAL Chi-restraints excluded: chain X residue 93 VAL Chi-restraints excluded: chain Y residue 12 THR Chi-restraints excluded: chain Y residue 22 MET Chi-restraints excluded: chain Y residue 24 SER Chi-restraints excluded: chain Y residue 28 THR Chi-restraints excluded: chain Y residue 35 LYS Chi-restraints excluded: chain Y residue 40 ILE Chi-restraints excluded: chain Z residue 2 LYS Chi-restraints excluded: chain Z residue 3 VAL Chi-restraints excluded: chain Z residue 24 GLU Chi-restraints excluded: chain Z residue 37 LEU Chi-restraints excluded: chain 0 residue 30 LYS Chi-restraints excluded: chain 0 residue 35 VAL Chi-restraints excluded: chain 0 residue 54 VAL Chi-restraints excluded: chain 0 residue 59 VAL Chi-restraints excluded: chain 2 residue 3 VAL Chi-restraints excluded: chain 2 residue 8 THR Chi-restraints excluded: chain 2 residue 18 THR Chi-restraints excluded: chain 2 residue 23 THR Chi-restraints excluded: chain 2 residue 56 SER Chi-restraints excluded: chain 3 residue 24 ARG Chi-restraints excluded: chain 3 residue 38 ARG Chi-restraints excluded: chain 3 residue 44 LEU Chi-restraints excluded: chain 4 residue 1 MET Chi-restraints excluded: chain 4 residue 20 LYS Chi-restraints excluded: chain 4 residue 24 THR Chi-restraints excluded: chain 5 residue 14 VAL Chi-restraints excluded: chain 5 residue 17 THR Chi-restraints excluded: chain 5 residue 32 ARG Chi-restraints excluded: chain 5 residue 58 ILE Chi-restraints excluded: chain 5 residue 60 GLN Chi-restraints excluded: chain 6 residue 4 ARG Chi-restraints excluded: chain 6 residue 11 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 920 random chunks: chunk 579 optimal weight: 8.9990 chunk 777 optimal weight: 0.0770 chunk 223 optimal weight: 7.9990 chunk 672 optimal weight: 8.9990 chunk 107 optimal weight: 10.0000 chunk 202 optimal weight: 20.0000 chunk 731 optimal weight: 6.9990 chunk 305 optimal weight: 8.9990 chunk 750 optimal weight: 2.9990 chunk 92 optimal weight: 20.0000 chunk 134 optimal weight: 10.0000 overall best weight: 5.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 67 ASN ** g 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 77 HIS ** m 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 9 ASN o 38 GLN ** s 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 44 ASN O 61 GLN ** O 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 87 GLN ** Z 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 60 GLN 0 17 GLN 3 20 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.078643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.059779 restraints weight = 277616.622| |-----------------------------------------------------------------------------| r_work (start): 0.2790 rms_B_bonded: 0.64 r_work: 0.2659 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2575 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.2575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.1188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.100 145353 Z= 0.317 Angle : 0.773 11.080 217934 Z= 0.395 Chirality : 0.044 0.308 27945 Planarity : 0.006 0.112 11316 Dihedral : 23.080 179.275 73946 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.56 % Favored : 90.38 % Rotamer: Outliers : 9.64 % Allowed : 27.16 % Favored : 63.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.17 % Twisted Proline : 0.54 % Twisted General : 0.08 % 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: -1.99 (0.11), residues: 4970 helix: -0.14 (0.13), residues: 1467 sheet: -0.51 (0.16), residues: 1021 loop : -2.48 (0.11), residues: 2482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP d 9 HIS 0.007 0.002 HIS T 107 PHE 0.021 0.002 PHE E 139 TYR 0.027 0.002 TYR N 74 ARG 0.006 0.001 ARG R 50 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 40312.87 seconds wall clock time: 698 minutes 42.67 seconds (41922.67 seconds total)