Starting phenix.real_space_refine on Tue Feb 20 00:44:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wu9_21907/02_2024/6wu9_21907.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wu9_21907/02_2024/6wu9_21907.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/6wu9_21907/02_2024/6wu9_21907.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wu9_21907/02_2024/6wu9_21907.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wu9_21907/02_2024/6wu9_21907.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wu9_21907/02_2024/6wu9_21907.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= -0.000 sd= 0.009 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 3 6.06 5 P 2855 5.49 5 S 71 5.16 5 C 40511 2.51 5 N 15251 2.21 5 O 23604 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped 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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 82295 Number of models: 1 Model: "" Number of chains: 30 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: "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: "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 80472 SG CYS 2 30 183.480 140.306 86.693 1.00 11.93 S ATOM 80492 SG CYS 2 33 185.981 137.507 88.840 1.00 15.95 S ATOM 80570 SG CYS 2 43 182.310 138.566 90.028 1.00 7.68 S ATOM 80588 SG CYS 2 46 185.390 140.813 90.534 1.00 11.63 S ATOM 80745 SG CYS 3 9 71.872 42.693 136.022 1.00 17.23 S ATOM 80764 SG CYS 3 12 75.568 41.685 137.123 1.00 19.37 S ATOM 80977 SG CYS 3 36 74.555 40.855 133.529 1.00 12.53 S ATOM 82073 SG CYS 6 11 73.835 124.568 49.335 1.00 16.19 S ATOM 82098 SG CYS 6 14 77.324 122.889 50.457 1.00 14.26 S ATOM 82204 SG CYS 6 27 77.133 126.153 48.919 1.00 10.76 S Time building chain proxies: 35.28, per 1000 atoms: 0.43 Number of scatterers: 82295 At special positions: 0 Unit cell: (220.497, 209.527, 225.982, 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 3 29.99 S 71 16.00 P 2855 15.00 O 23604 8.00 N 15251 7.00 C 40511 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: 31.54 Conformation dependent library (CDL) restraints added in 3.3 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 " Number of angles added : 9 5294 Ramachandran restraints generated. 2647 Oldfield, 0 Emsley, 2647 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4930 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 40 sheets defined 28.4% alpha, 20.2% beta 928 base pairs and 1531 stacking pairs defined. Time for finding SS restraints: 30.71 Creating SS restraints... 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 '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=AA2, 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=AA3, 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=AA4, 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=AA5, 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=AA6, 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=AA7, 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=AA8, 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=AA9, 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=AB1, 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=AB2, 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=AB3, 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=AB4, first strand: chain 'M' and resid 110 through 111 Processing sheet with id=AB5, 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=AB6, 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=AB7, first strand: chain 'N' and resid 40 through 43 Processing sheet with id=AB8, 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=AB9, 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=AC1, first strand: chain 'P' and resid 34 through 35 Processing sheet with id=AC2, 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=AC3, 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=AC4, 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=AC5, first strand: chain 'S' and resid 71 through 76 Processing sheet with id=AC6, 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=AC7, first strand: chain 'T' and resid 87 through 92 Processing sheet with id=AC8, 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=AC9, first strand: chain 'U' and resid 62 through 64 Processing sheet with id=AD1, 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=AD2, first strand: chain 'V' and resid 40 through 42 Processing sheet with id=AD3, first strand: chain 'V' and resid 81 through 83 Processing sheet with id=AD4, 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=AD5, 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=AD6, 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=AD7, first strand: chain 'Y' and resid 33 through 39 Processing sheet with id=AD8, first strand: chain '0' and resid 34 through 38 Processing sheet with id=AD9, first strand: chain '2' and resid 27 through 29 Processing sheet with id=AE1, 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=AE2, 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=AE3, first strand: chain '5' and resid 14 through 16 Processing sheet with id=AE4, 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) 701 hydrogen bonds defined for protein. 1938 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2324 hydrogen bonds 3718 hydrogen bond angles 0 basepair planarities 928 basepair parallelities 1531 stacking parallelities Total time for adding SS restraints: 138.48 Time building geometry restraints manager: 34.35 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: 8114 1.31 - 1.44: 40568 1.44 - 1.57: 35402 1.57 - 1.70: 5702 1.70 - 1.83: 130 Bond restraints: 89916 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 89911 not shown) Histogram of bond angle deviations from ideal: 96.31 - 105.41: 14582 105.41 - 114.51: 59724 114.51 - 123.61: 47061 123.61 - 132.71: 13921 132.71 - 141.81: 266 Bond angle restraints: 135554 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=" 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=" C2' G A 992 " pdb=" C1' G A 992 " pdb=" N9 G A 992 " ideal model delta sigma weight residual 114.00 106.27 7.73 1.50e+00 4.44e-01 2.65e+01 angle pdb=" O6 G A 903 " pdb=" C6 G A 903 " pdb=" N1 G A 903 " ideal model delta sigma weight residual 119.90 105.42 14.48 3.00e+00 1.11e-01 2.33e+01 ... (remaining 135549 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.82: 50214 35.82 - 71.65: 6595 71.65 - 107.47: 652 107.47 - 143.30: 10 143.30 - 179.12: 13 Dihedral angle restraints: 57484 sinusoidal: 49824 harmonic: 7660 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 57481 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 14619 0.078 - 0.155: 2554 0.155 - 0.233: 270 0.233 - 0.311: 46 0.311 - 0.388: 11 Chirality restraints: 17500 Sorted by residual: 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 chirality pdb=" C1' G A2829 " pdb=" O4' G A2829 " pdb=" C2' G A2829 " pdb=" N9 G A2829 " both_signs ideal model delta sigma weight residual False 2.46 2.09 0.37 2.00e-01 2.50e+01 3.37e+00 ... (remaining 17497 not shown) Planarity restraints: 6513 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' A A 904 " 0.070 2.00e-02 2.50e+03 3.21e-02 2.84e+01 pdb=" N9 A A 904 " -0.075 2.00e-02 2.50e+03 pdb=" C8 A A 904 " -0.004 2.00e-02 2.50e+03 pdb=" N7 A A 904 " 0.001 2.00e-02 2.50e+03 pdb=" C5 A A 904 " 0.005 2.00e-02 2.50e+03 pdb=" C6 A A 904 " 0.017 2.00e-02 2.50e+03 pdb=" N6 A A 904 " 0.011 2.00e-02 2.50e+03 pdb=" N1 A A 904 " 0.004 2.00e-02 2.50e+03 pdb=" C2 A A 904 " -0.003 2.00e-02 2.50e+03 pdb=" N3 A A 904 " -0.011 2.00e-02 2.50e+03 pdb=" C4 A A 904 " -0.015 2.00e-02 2.50e+03 ... (remaining 6510 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 590 2.57 - 3.15: 55955 3.15 - 3.74: 147596 3.74 - 4.32: 224124 4.32 - 4.90: 294648 Nonbonded interactions: 722913 Sorted by model distance: nonbonded pdb=" OG SER V 94 " pdb=" O LYS V 95 " model vdw 1.989 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=" O6 G A1488 " pdb=" O6 G A1508 " model vdw 2.043 2.432 nonbonded pdb=" N ASP P 6 " pdb=" OD1 ASP P 6 " model vdw 2.090 2.520 ... (remaining 722908 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.210 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: 0.070 Extract box with map and model: 20.280 Check model and map are aligned: 0.950 Set scattering table: 0.580 Process input model: 304.230 Find NCS groups from input model: 1.300 Set up NCS constraints: 0.190 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:13.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 346.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 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 : 0.011 0.160 89916 Z= 0.638 Angle : 1.148 21.620 135554 Z= 0.561 Chirality : 0.060 0.388 17500 Planarity : 0.008 0.081 6513 Dihedral : 23.600 179.124 52554 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.34 % Allowed : 10.73 % Favored : 88.93 % Rotamer: Outliers : 16.81 % Allowed : 13.34 % Favored : 69.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 1.06 % Twisted General : 0.27 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.84 (0.13), residues: 2647 helix: -2.43 (0.15), residues: 671 sheet: -1.70 (0.20), residues: 549 loop : -3.03 (0.13), residues: 1427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.004 TRP E 83 HIS 0.010 0.003 HIS T 107 PHE 0.033 0.004 PHE V 2 TYR 0.022 0.004 TYR K 126 ARG 0.011 0.001 ARG 5 45 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5294 Ramachandran restraints generated. 2647 Oldfield, 0 Emsley, 2647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5294 Ramachandran restraints generated. 2647 Oldfield, 0 Emsley, 2647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 845 residues out of total 2249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 378 poor density : 467 time to evaluate : 3.321 Fit side-chains revert: symmetry clash REVERT: D 3 LYS cc_start: 0.8372 (mttt) cc_final: 0.8127 (mtpt) REVERT: D 49 ILE cc_start: 0.9006 (OUTLIER) cc_final: 0.8789 (mm) REVERT: D 90 GLU cc_start: 0.7040 (OUTLIER) cc_final: 0.5832 (tm-30) REVERT: E 45 ARG cc_start: 0.8860 (OUTLIER) cc_final: 0.7291 (mtt180) REVERT: E 78 ILE cc_start: 0.7964 (OUTLIER) cc_final: 0.7507 (mp) REVERT: E 190 ASN cc_start: 0.8590 (OUTLIER) cc_final: 0.8172 (t0) REVERT: G 44 ASN cc_start: 0.4643 (OUTLIER) cc_final: 0.4287 (t0) REVERT: G 171 ARG cc_start: 0.7845 (OUTLIER) cc_final: 0.7270 (mmm160) REVERT: K 14 ARG cc_start: 0.8150 (OUTLIER) cc_final: 0.6593 (mtt180) REVERT: K 26 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8515 (tp) REVERT: K 94 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.8349 (ttp-170) REVERT: L 18 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.7433 (tt0) REVERT: L 19 ILE cc_start: 0.8411 (OUTLIER) cc_final: 0.8085 (pt) REVERT: L 105 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7681 (mm-30) REVERT: L 110 ASN cc_start: 0.6707 (OUTLIER) cc_final: 0.6259 (m110) REVERT: L 112 MET cc_start: 0.7776 (mmm) cc_final: 0.7547 (mmm) REVERT: M 79 LEU cc_start: 0.7495 (OUTLIER) cc_final: 0.6741 (mp) REVERT: N 11 ARG cc_start: 0.8584 (OUTLIER) cc_final: 0.6369 (mmt90) REVERT: N 26 GLU cc_start: 0.7288 (OUTLIER) cc_final: 0.6666 (mm-30) REVERT: N 51 ARG cc_start: 0.7573 (OUTLIER) cc_final: 0.6408 (ttm110) REVERT: O 19 ASP cc_start: 0.7689 (m-30) cc_final: 0.7050 (m-30) REVERT: P 22 ILE cc_start: 0.8484 (OUTLIER) cc_final: 0.8087 (mp) REVERT: P 35 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.6674 (ttm170) REVERT: Q 44 GLU cc_start: 0.7215 (mt-10) cc_final: 0.6891 (tt0) REVERT: Q 109 ARG cc_start: 0.7965 (OUTLIER) cc_final: 0.7651 (mtm-85) REVERT: R 56 ASP cc_start: 0.7608 (m-30) cc_final: 0.7288 (m-30) REVERT: S 63 GLU cc_start: 0.7291 (mt-10) cc_final: 0.7089 (mt-10) REVERT: S 96 MET cc_start: 0.7528 (mmm) cc_final: 0.7214 (tpt) REVERT: S 101 ASN cc_start: 0.5678 (OUTLIER) cc_final: 0.5440 (t0) REVERT: U 30 ASP cc_start: 0.7676 (t70) cc_final: 0.7321 (t70) REVERT: U 75 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.7847 (mtt90) REVERT: U 89 ILE cc_start: 0.7376 (OUTLIER) cc_final: 0.7030 (mt) REVERT: V 5 LYS cc_start: 0.7958 (OUTLIER) cc_final: 0.7003 (tttm) REVERT: V 29 LYS cc_start: 0.7313 (OUTLIER) cc_final: 0.7060 (pttt) REVERT: X 23 ARG cc_start: 0.8547 (OUTLIER) cc_final: 0.7586 (ptt90) REVERT: Y 22 MET cc_start: 0.7885 (OUTLIER) cc_final: 0.7462 (mmp) REVERT: Y 37 ARG cc_start: 0.7183 (mtt90) cc_final: 0.6905 (mtt-85) REVERT: Z 15 LEU cc_start: 0.7551 (OUTLIER) cc_final: 0.7293 (mp) REVERT: Z 44 LYS cc_start: 0.8426 (tttt) cc_final: 0.8171 (ttmt) REVERT: 3 5 ILE cc_start: 0.7674 (OUTLIER) cc_final: 0.7305 (pt) REVERT: 5 57 ARG cc_start: 0.8630 (OUTLIER) cc_final: 0.6967 (ttp80) REVERT: 6 36 ARG cc_start: 0.8612 (OUTLIER) cc_final: 0.7864 (ptt90) outliers start: 378 outliers final: 192 residues processed: 744 average time/residue: 1.7327 time to fit residues: 1699.2420 Evaluate side-chains 560 residues out of total 2249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 224 poor density : 336 time to evaluate : 3.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 21 GLU 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 49 ILE 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 78 ILE Chi-restraints excluded: chain E residue 79 ARG 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 88 LYS Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 127 ASN Chi-restraints excluded: chain F residue 133 LYS 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 94 ARG 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 18 GLU 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 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 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 70 ASP 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 U residue 89 ILE 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 29 LYS Chi-restraints excluded: chain V residue 33 VAL Chi-restraints excluded: chain V residue 41 VAL 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 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 15 LYS Chi-restraints excluded: chain 6 residue 36 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 541 random chunks: chunk 456 optimal weight: 5.9990 chunk 410 optimal weight: 5.9990 chunk 227 optimal weight: 2.9990 chunk 140 optimal weight: 9.9990 chunk 276 optimal weight: 30.0000 chunk 219 optimal weight: 5.9990 chunk 424 optimal weight: 8.9990 chunk 164 optimal weight: 9.9990 chunk 257 optimal weight: 7.9990 chunk 315 optimal weight: 1.9990 chunk 491 optimal weight: 6.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 73 ASN K 59 ASN K 131 HIS M 38 GLN M 133 GLN N 44 ASN O 61 GLN P 12 GLN P 15 HIS P 20 ASN P 114 ASN Q 6 GLN Q 41 GLN ** R 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 86 GLN S 88 HIS T 4 GLN T 46 ASN T 66 ASN X 49 GLN X 59 ASN X 87 GLN Y 17 ASN Y 23 ASN Y 32 ASN Z 36 GLN 2 40 HIS 4 8 ASN 5 31 HIS Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.1147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 89916 Z= 0.243 Angle : 0.710 10.912 135554 Z= 0.369 Chirality : 0.042 0.306 17500 Planarity : 0.006 0.063 6513 Dihedral : 23.188 179.817 47602 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.12 % Favored : 91.84 % Rotamer: Outliers : 10.98 % Allowed : 21.34 % Favored : 67.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 1.06 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.68 (0.14), residues: 2647 helix: -0.93 (0.18), residues: 702 sheet: -1.14 (0.20), residues: 594 loop : -2.60 (0.14), residues: 1351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP E 83 HIS 0.008 0.001 HIS R 29 PHE 0.024 0.002 PHE V 2 TYR 0.013 0.002 TYR K 126 ARG 0.007 0.001 ARG Q 88 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5294 Ramachandran restraints generated. 2647 Oldfield, 0 Emsley, 2647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5294 Ramachandran restraints generated. 2647 Oldfield, 0 Emsley, 2647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 595 residues out of total 2249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 247 poor density : 348 time to evaluate : 3.355 Fit side-chains REVERT: D 49 ILE cc_start: 0.8911 (OUTLIER) cc_final: 0.8661 (mm) REVERT: D 90 GLU cc_start: 0.6922 (OUTLIER) cc_final: 0.5899 (tm-30) REVERT: D 138 ARG cc_start: 0.8144 (OUTLIER) cc_final: 0.7525 (mtt180) REVERT: D 168 ARG cc_start: 0.8291 (OUTLIER) cc_final: 0.7780 (ptt180) REVERT: E 45 ARG cc_start: 0.8838 (OUTLIER) cc_final: 0.7171 (mtt180) REVERT: E 78 ILE cc_start: 0.7830 (OUTLIER) cc_final: 0.7544 (mp) REVERT: E 190 ASN cc_start: 0.8502 (OUTLIER) cc_final: 0.8091 (t0) REVERT: F 51 ASP cc_start: 0.3688 (OUTLIER) cc_final: 0.3384 (m-30) REVERT: F 112 ARG cc_start: 0.4883 (OUTLIER) cc_final: 0.4421 (mpt-90) REVERT: F 138 PHE cc_start: 0.5366 (m-80) cc_final: 0.4859 (m-80) REVERT: G 84 GLN cc_start: 0.6595 (OUTLIER) cc_final: 0.6243 (mm-40) REVERT: G 171 ARG cc_start: 0.7726 (OUTLIER) cc_final: 0.7198 (mmm160) REVERT: K 14 ARG cc_start: 0.8105 (OUTLIER) cc_final: 0.6186 (mtt-85) REVERT: L 19 ILE cc_start: 0.8227 (OUTLIER) cc_final: 0.7959 (pt) REVERT: L 87 ILE cc_start: 0.8706 (OUTLIER) cc_final: 0.8479 (mp) REVERT: L 110 ASN cc_start: 0.6623 (OUTLIER) cc_final: 0.6097 (m-40) REVERT: M 73 ASP cc_start: 0.7823 (m-30) cc_final: 0.7571 (m-30) REVERT: M 133 GLN cc_start: 0.7224 (tt0) cc_final: 0.6715 (tt0) REVERT: O 19 ASP cc_start: 0.7692 (m-30) cc_final: 0.7126 (m-30) REVERT: P 22 ILE cc_start: 0.8497 (OUTLIER) cc_final: 0.8019 (mp) REVERT: R 56 ASP cc_start: 0.7539 (m-30) cc_final: 0.7270 (m-30) REVERT: S 63 GLU cc_start: 0.7335 (mt-10) cc_final: 0.7130 (mt-10) REVERT: S 96 MET cc_start: 0.7648 (mmm) cc_final: 0.7415 (tpp) REVERT: S 101 ASN cc_start: 0.5452 (OUTLIER) cc_final: 0.5251 (t0) REVERT: U 75 ARG cc_start: 0.8201 (OUTLIER) cc_final: 0.7608 (mtt90) REVERT: U 84 GLU cc_start: 0.5575 (OUTLIER) cc_final: 0.4730 (mp0) REVERT: U 88 GLU cc_start: 0.6921 (OUTLIER) cc_final: 0.6690 (mm-30) REVERT: V 5 LYS cc_start: 0.7967 (OUTLIER) cc_final: 0.7069 (tttm) REVERT: X 23 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.7532 (ptt90) REVERT: Z 2 LYS cc_start: 0.7016 (OUTLIER) cc_final: 0.5227 (pptt) REVERT: Z 52 ARG cc_start: 0.8682 (mtt180) cc_final: 0.8450 (mtt90) REVERT: 3 24 ARG cc_start: 0.6995 (OUTLIER) cc_final: 0.6713 (ttm170) REVERT: 3 32 LYS cc_start: 0.7712 (mmtt) cc_final: 0.7390 (mtpp) REVERT: 3 33 GLN cc_start: 0.8343 (mm-40) cc_final: 0.7987 (tp40) REVERT: 4 10 ARG cc_start: 0.8830 (OUTLIER) cc_final: 0.8578 (ttt-90) outliers start: 247 outliers final: 150 residues processed: 543 average time/residue: 1.6608 time to fit residues: 1205.1229 Evaluate side-chains 499 residues out of total 2249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 324 time to evaluate : 3.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 49 ILE 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 158 LYS 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 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 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 44 VAL Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 88 LYS Chi-restraints excluded: chain F residue 112 ARG Chi-restraints excluded: chain F residue 125 ARG Chi-restraints excluded: chain F residue 127 ASN Chi-restraints excluded: chain F residue 133 LYS Chi-restraints excluded: chain F residue 154 ILE Chi-restraints excluded: chain F residue 162 THR 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 84 GLN 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 G residue 173 GLU 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 114 THR Chi-restraints excluded: chain K residue 115 LEU Chi-restraints excluded: chain K residue 145 ASN 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 36 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 N residue 5 LYS Chi-restraints excluded: chain N residue 26 GLU Chi-restraints excluded: chain N residue 76 SER 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 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 22 ILE Chi-restraints excluded: chain P residue 28 CYS Chi-restraints excluded: chain P residue 31 LEU 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 89 LYS Chi-restraints excluded: chain P residue 95 ARG 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 109 ARG Chi-restraints excluded: chain R residue 10 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 59 GLU 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 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 U residue 88 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 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 40 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 24 SER Chi-restraints excluded: chain Z residue 2 LYS Chi-restraints excluded: chain Z residue 3 VAL Chi-restraints excluded: chain Z residue 37 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 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 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 17 THR Chi-restraints excluded: chain 5 residue 32 ARG Chi-restraints excluded: chain 5 residue 58 ILE Chi-restraints excluded: chain 6 residue 11 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 541 random chunks: chunk 273 optimal weight: 20.0000 chunk 152 optimal weight: 10.0000 chunk 408 optimal weight: 20.0000 chunk 334 optimal weight: 6.9990 chunk 135 optimal weight: 10.0000 chunk 492 optimal weight: 7.9990 chunk 531 optimal weight: 9.9990 chunk 438 optimal weight: 7.9990 chunk 488 optimal weight: 8.9990 chunk 167 optimal weight: 20.0000 chunk 394 optimal weight: 7.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 54 GLN N 44 ASN R 101 ASN S 83 HIS T 66 ASN Z 60 GLN 0 40 ASN 3 20 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.0981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.096 89916 Z= 0.380 Angle : 0.849 11.066 135554 Z= 0.430 Chirality : 0.048 0.334 17500 Planarity : 0.007 0.069 6513 Dihedral : 23.241 179.260 47422 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.60 % Favored : 90.33 % Rotamer: Outliers : 10.63 % Allowed : 23.25 % Favored : 66.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 1.06 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.15), residues: 2647 helix: -0.58 (0.18), residues: 702 sheet: -0.81 (0.21), residues: 575 loop : -2.48 (0.14), residues: 1370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.003 TRP E 83 HIS 0.008 0.002 HIS R 29 PHE 0.028 0.003 PHE V 2 TYR 0.017 0.003 TYR K 126 ARG 0.007 0.001 ARG 5 45 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5294 Ramachandran restraints generated. 2647 Oldfield, 0 Emsley, 2647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5294 Ramachandran restraints generated. 2647 Oldfield, 0 Emsley, 2647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 2249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 239 poor density : 320 time to evaluate : 4.161 Fit side-chains REVERT: D 90 GLU cc_start: 0.6882 (OUTLIER) cc_final: 0.5831 (tm-30) REVERT: D 138 ARG cc_start: 0.8217 (OUTLIER) cc_final: 0.7736 (mtt180) REVERT: D 168 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.7949 (ptt180) REVERT: E 10 ASP cc_start: 0.6680 (OUTLIER) cc_final: 0.6429 (p0) REVERT: E 45 ARG cc_start: 0.8850 (OUTLIER) cc_final: 0.7207 (mtt180) REVERT: E 78 ILE cc_start: 0.7995 (OUTLIER) cc_final: 0.7614 (mp) REVERT: E 190 ASN cc_start: 0.8499 (OUTLIER) cc_final: 0.8098 (t0) REVERT: F 51 ASP cc_start: 0.3504 (OUTLIER) cc_final: 0.3212 (m-30) REVERT: F 112 ARG cc_start: 0.4866 (OUTLIER) cc_final: 0.4407 (mpt-90) REVERT: F 138 PHE cc_start: 0.5319 (m-80) cc_final: 0.4812 (m-80) REVERT: G 144 LEU cc_start: 0.7800 (OUTLIER) cc_final: 0.7337 (mp) REVERT: G 171 ARG cc_start: 0.7760 (OUTLIER) cc_final: 0.7274 (mmm160) REVERT: G 173 GLU cc_start: 0.6030 (OUTLIER) cc_final: 0.5624 (tt0) REVERT: K 14 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.6169 (mtt-85) REVERT: L 19 ILE cc_start: 0.8326 (OUTLIER) cc_final: 0.8057 (pt) REVERT: L 87 ILE cc_start: 0.8756 (OUTLIER) cc_final: 0.8480 (mp) REVERT: L 110 ASN cc_start: 0.6721 (OUTLIER) cc_final: 0.6254 (m110) REVERT: M 73 ASP cc_start: 0.7908 (m-30) cc_final: 0.7631 (m-30) REVERT: M 79 LEU cc_start: 0.7444 (OUTLIER) cc_final: 0.6702 (mp) REVERT: M 133 GLN cc_start: 0.7322 (tt0) cc_final: 0.6774 (tt0) REVERT: O 19 ASP cc_start: 0.7756 (m-30) cc_final: 0.7222 (m-30) REVERT: O 108 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8460 (mp) REVERT: P 22 ILE cc_start: 0.8525 (OUTLIER) cc_final: 0.8055 (mp) REVERT: P 95 ARG cc_start: 0.7423 (OUTLIER) cc_final: 0.5464 (mtp180) REVERT: P 113 GLU cc_start: 0.5991 (OUTLIER) cc_final: 0.5715 (mt-10) REVERT: R 56 ASP cc_start: 0.7644 (m-30) cc_final: 0.7384 (m-30) REVERT: R 90 ILE cc_start: 0.8397 (mt) cc_final: 0.8133 (tt) REVERT: S 63 GLU cc_start: 0.7272 (mt-10) cc_final: 0.7068 (mt-10) REVERT: S 96 MET cc_start: 0.7631 (mmm) cc_final: 0.7353 (tpp) REVERT: S 101 ASN cc_start: 0.5534 (OUTLIER) cc_final: 0.5311 (OUTLIER) REVERT: U 75 ARG cc_start: 0.8311 (OUTLIER) cc_final: 0.7720 (mtt90) REVERT: V 5 LYS cc_start: 0.7939 (OUTLIER) cc_final: 0.7059 (tttm) REVERT: X 23 ARG cc_start: 0.8547 (OUTLIER) cc_final: 0.7497 (ptt90) REVERT: Z 2 LYS cc_start: 0.7127 (OUTLIER) cc_final: 0.5369 (pptt) REVERT: Z 58 ARG cc_start: 0.6965 (tpt90) cc_final: 0.6488 (tmt170) REVERT: 0 58 GLU cc_start: 0.6900 (mm-30) cc_final: 0.6677 (tp30) REVERT: 3 24 ARG cc_start: 0.6960 (OUTLIER) cc_final: 0.6688 (ttm170) REVERT: 3 32 LYS cc_start: 0.7783 (mmtt) cc_final: 0.7332 (mtpp) outliers start: 239 outliers final: 170 residues processed: 508 average time/residue: 1.6529 time to fit residues: 1123.5722 Evaluate side-chains 505 residues out of total 2249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 309 time to evaluate : 3.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 138 ARG 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 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 199 LEU Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain E residue 6 LEU Chi-restraints excluded: chain E residue 10 ASP 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 79 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 E residue 195 THR 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 44 VAL Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 88 LYS Chi-restraints excluded: chain F residue 112 ARG Chi-restraints excluded: chain F residue 125 ARG Chi-restraints excluded: chain F residue 127 ASN Chi-restraints excluded: chain F residue 133 LYS Chi-restraints excluded: chain F residue 154 ILE Chi-restraints excluded: chain F residue 162 THR 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 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 133 VAL Chi-restraints excluded: chain G residue 144 LEU Chi-restraints excluded: chain G residue 171 ARG Chi-restraints excluded: chain G residue 173 GLU 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 114 THR Chi-restraints excluded: chain K residue 115 LEU Chi-restraints excluded: chain K residue 145 ASN 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 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 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 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 133 LYS Chi-restraints excluded: chain O residue 24 LEU Chi-restraints excluded: chain O residue 49 THR 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 31 LEU Chi-restraints excluded: chain P residue 51 VAL Chi-restraints excluded: chain P residue 63 ILE Chi-restraints excluded: chain P residue 70 GLU Chi-restraints excluded: chain P residue 86 LYS Chi-restraints excluded: chain P residue 89 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 109 ARG Chi-restraints excluded: chain R residue 10 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 12 VAL 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 59 GLU Chi-restraints excluded: chain S residue 61 THR Chi-restraints excluded: chain S residue 67 LYS 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 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 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 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 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 24 SER Chi-restraints excluded: chain Y residue 28 THR Chi-restraints excluded: chain Z residue 2 LYS 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 541 random chunks: chunk 486 optimal weight: 0.8980 chunk 370 optimal weight: 9.9990 chunk 255 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 chunk 234 optimal weight: 20.0000 chunk 330 optimal weight: 7.9990 chunk 493 optimal weight: 8.9990 chunk 522 optimal weight: 1.9990 chunk 258 optimal weight: 10.0000 chunk 468 optimal weight: 0.6980 chunk 140 optimal weight: 10.0000 overall best weight: 4.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 103 GLN F 37 ASN ** F 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 44 ASN O 61 GLN R 101 ASN T 66 ASN X 87 GLN Z 60 GLN 0 40 ASN 3 20 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.1181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 89916 Z= 0.216 Angle : 0.699 11.503 135554 Z= 0.367 Chirality : 0.041 0.307 17500 Planarity : 0.006 0.065 6513 Dihedral : 23.170 179.182 47409 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.54 % Favored : 91.42 % Rotamer: Outliers : 10.49 % Allowed : 23.65 % Favored : 65.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 1.06 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.15), residues: 2647 helix: -0.24 (0.19), residues: 706 sheet: -0.75 (0.21), residues: 595 loop : -2.36 (0.15), residues: 1346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP E 83 HIS 0.006 0.001 HIS R 29 PHE 0.025 0.002 PHE V 2 TYR 0.013 0.002 TYR F 128 ARG 0.007 0.001 ARG P 16 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5294 Ramachandran restraints generated. 2647 Oldfield, 0 Emsley, 2647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5294 Ramachandran restraints generated. 2647 Oldfield, 0 Emsley, 2647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 2249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 236 poor density : 317 time to evaluate : 3.325 Fit side-chains REVERT: D 90 GLU cc_start: 0.6955 (OUTLIER) cc_final: 0.5937 (tm-30) REVERT: D 138 ARG cc_start: 0.8096 (OUTLIER) cc_final: 0.7579 (mtt180) REVERT: D 168 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.7747 (ptt180) REVERT: E 10 ASP cc_start: 0.6414 (OUTLIER) cc_final: 0.6181 (p0) REVERT: E 45 ARG cc_start: 0.8820 (OUTLIER) cc_final: 0.7131 (mtt180) REVERT: E 78 ILE cc_start: 0.7939 (OUTLIER) cc_final: 0.7617 (mp) REVERT: E 190 ASN cc_start: 0.8479 (OUTLIER) cc_final: 0.8067 (t0) REVERT: F 51 ASP cc_start: 0.3469 (OUTLIER) cc_final: 0.3178 (m-30) REVERT: F 112 ARG cc_start: 0.4912 (OUTLIER) cc_final: 0.4461 (mpt-90) REVERT: F 138 PHE cc_start: 0.5282 (m-80) cc_final: 0.4795 (m-80) REVERT: F 172 GLN cc_start: 0.6089 (OUTLIER) cc_final: 0.5816 (mm110) REVERT: G 144 LEU cc_start: 0.7775 (OUTLIER) cc_final: 0.7322 (mp) REVERT: G 171 ARG cc_start: 0.7731 (OUTLIER) cc_final: 0.7276 (mmm160) REVERT: G 173 GLU cc_start: 0.5946 (OUTLIER) cc_final: 0.5537 (tt0) REVERT: K 14 ARG cc_start: 0.8117 (OUTLIER) cc_final: 0.6187 (mtt-85) REVERT: L 19 ILE cc_start: 0.8208 (OUTLIER) cc_final: 0.8001 (pt) REVERT: L 87 ILE cc_start: 0.8699 (OUTLIER) cc_final: 0.8435 (mp) REVERT: L 105 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7477 (mm-30) REVERT: L 110 ASN cc_start: 0.6637 (OUTLIER) cc_final: 0.6127 (m-40) REVERT: M 73 ASP cc_start: 0.7898 (m-30) cc_final: 0.7611 (m-30) REVERT: M 79 LEU cc_start: 0.7350 (OUTLIER) cc_final: 0.6618 (mp) REVERT: M 97 LYS cc_start: 0.7346 (OUTLIER) cc_final: 0.7146 (ttpt) REVERT: M 133 GLN cc_start: 0.7311 (tt0) cc_final: 0.6742 (tt0) REVERT: N 1 MET cc_start: 0.5853 (mmt) cc_final: 0.5318 (mtt) REVERT: O 8 ARG cc_start: 0.8122 (OUTLIER) cc_final: 0.7888 (mmt180) REVERT: O 19 ASP cc_start: 0.7695 (m-30) cc_final: 0.7308 (m-30) REVERT: O 108 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8406 (mp) REVERT: P 22 ILE cc_start: 0.8517 (OUTLIER) cc_final: 0.8028 (mp) REVERT: P 35 ARG cc_start: 0.8045 (OUTLIER) cc_final: 0.6995 (ttm170) REVERT: P 113 GLU cc_start: 0.5959 (OUTLIER) cc_final: 0.5658 (mt-10) REVERT: Q 109 ARG cc_start: 0.8072 (OUTLIER) cc_final: 0.7779 (mtm-85) REVERT: R 56 ASP cc_start: 0.7585 (m-30) cc_final: 0.7346 (m-30) REVERT: R 90 ILE cc_start: 0.8377 (mt) cc_final: 0.8137 (tt) REVERT: S 63 GLU cc_start: 0.7298 (mt-10) cc_final: 0.7089 (mt-10) REVERT: S 96 MET cc_start: 0.7584 (mmm) cc_final: 0.7308 (tpt) REVERT: U 75 ARG cc_start: 0.8236 (OUTLIER) cc_final: 0.7613 (mtt90) REVERT: U 89 ILE cc_start: 0.7222 (OUTLIER) cc_final: 0.6989 (mt) REVERT: V 5 LYS cc_start: 0.7960 (OUTLIER) cc_final: 0.6985 (tptm) REVERT: X 23 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.7428 (ptt90) REVERT: Y 35 LYS cc_start: 0.7660 (ttmt) cc_final: 0.7412 (ttmm) REVERT: Z 2 LYS cc_start: 0.7039 (OUTLIER) cc_final: 0.5366 (pptt) REVERT: Z 58 ARG cc_start: 0.6880 (tpt90) cc_final: 0.6579 (tmt170) REVERT: 0 30 LYS cc_start: 0.8001 (OUTLIER) cc_final: 0.7765 (mtmp) REVERT: 0 58 GLU cc_start: 0.6887 (mm-30) cc_final: 0.6669 (tp30) REVERT: 3 24 ARG cc_start: 0.6871 (OUTLIER) cc_final: 0.6638 (ttm170) REVERT: 3 32 LYS cc_start: 0.7777 (mmtt) cc_final: 0.7328 (mtpp) outliers start: 236 outliers final: 165 residues processed: 499 average time/residue: 1.6745 time to fit residues: 1117.0688 Evaluate side-chains 507 residues out of total 2249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 309 time to evaluate : 3.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 71 LYS 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 158 LYS 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 199 LEU Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain E residue 6 LEU Chi-restraints excluded: chain E residue 10 ASP 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 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 E residue 195 THR 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 88 LYS Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 112 ARG Chi-restraints excluded: chain F residue 125 ARG Chi-restraints excluded: chain F residue 127 ASN Chi-restraints excluded: chain F residue 133 LYS Chi-restraints excluded: chain F residue 154 ILE Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 172 GLN 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 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 144 LEU Chi-restraints excluded: chain G residue 171 ARG Chi-restraints excluded: chain G residue 173 GLU 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 114 THR Chi-restraints excluded: chain K residue 115 LEU Chi-restraints excluded: chain K residue 145 ASN 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 36 LYS 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 97 LYS 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 75 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 133 LYS Chi-restraints excluded: chain O residue 8 ARG 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 70 GLU Chi-restraints excluded: chain P residue 86 LYS Chi-restraints excluded: chain P residue 89 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 109 ARG Chi-restraints excluded: chain R residue 10 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 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 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 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 U residue 89 ILE 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 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 24 SER Chi-restraints excluded: chain Y residue 28 THR Chi-restraints excluded: chain Z residue 2 LYS Chi-restraints excluded: chain Z residue 3 VAL Chi-restraints excluded: chain Z residue 14 MET 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 541 random chunks: chunk 435 optimal weight: 1.9990 chunk 296 optimal weight: 0.0000 chunk 7 optimal weight: 20.0000 chunk 389 optimal weight: 5.9990 chunk 215 optimal weight: 30.0000 chunk 446 optimal weight: 6.9990 chunk 361 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 267 optimal weight: 10.0000 chunk 469 optimal weight: 4.9990 chunk 131 optimal weight: 10.0000 overall best weight: 3.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 103 GLN E 158 ASN ** F 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 84 GLN M 17 ASN N 44 ASN O 61 GLN T 66 ASN X 87 GLN Z 60 GLN 0 40 ASN 3 20 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 89916 Z= 0.201 Angle : 0.652 10.616 135554 Z= 0.343 Chirality : 0.040 0.290 17500 Planarity : 0.005 0.062 6513 Dihedral : 23.033 179.959 47403 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.42 % Favored : 91.54 % Rotamer: Outliers : 10.14 % Allowed : 24.10 % Favored : 65.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 1.06 % Twisted General : 0.12 % 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: -1.79 (0.15), residues: 2647 helix: 0.09 (0.19), residues: 709 sheet: -0.52 (0.21), residues: 583 loop : -2.27 (0.15), residues: 1355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP E 83 HIS 0.005 0.001 HIS R 29 PHE 0.020 0.002 PHE V 2 TYR 0.017 0.002 TYR F 128 ARG 0.005 0.001 ARG P 16 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5294 Ramachandran restraints generated. 2647 Oldfield, 0 Emsley, 2647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5294 Ramachandran restraints generated. 2647 Oldfield, 0 Emsley, 2647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 2249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 228 poor density : 326 time to evaluate : 3.313 Fit side-chains REVERT: D 90 GLU cc_start: 0.6957 (OUTLIER) cc_final: 0.6034 (tm-30) REVERT: D 138 ARG cc_start: 0.8007 (OUTLIER) cc_final: 0.7497 (mtt180) REVERT: D 168 ARG cc_start: 0.8241 (OUTLIER) cc_final: 0.7726 (ptt180) REVERT: E 10 ASP cc_start: 0.6225 (OUTLIER) cc_final: 0.5981 (p0) REVERT: E 45 ARG cc_start: 0.8853 (OUTLIER) cc_final: 0.7166 (mtt180) REVERT: E 78 ILE cc_start: 0.8179 (OUTLIER) cc_final: 0.7766 (mp) REVERT: E 190 ASN cc_start: 0.8470 (OUTLIER) cc_final: 0.8048 (t0) REVERT: F 51 ASP cc_start: 0.3459 (OUTLIER) cc_final: 0.3208 (m-30) REVERT: F 138 PHE cc_start: 0.5402 (m-80) cc_final: 0.4930 (m-80) REVERT: F 169 LEU cc_start: 0.7298 (OUTLIER) cc_final: 0.7089 (tm) REVERT: F 172 GLN cc_start: 0.6016 (OUTLIER) cc_final: 0.5762 (mm110) REVERT: G 144 LEU cc_start: 0.7766 (OUTLIER) cc_final: 0.7376 (mp) REVERT: G 171 ARG cc_start: 0.7819 (OUTLIER) cc_final: 0.7341 (mmm160) REVERT: G 173 GLU cc_start: 0.5877 (OUTLIER) cc_final: 0.5458 (tt0) REVERT: L 19 ILE cc_start: 0.8205 (OUTLIER) cc_final: 0.7999 (pt) REVERT: L 110 ASN cc_start: 0.6636 (OUTLIER) cc_final: 0.6113 (m-40) REVERT: M 73 ASP cc_start: 0.7943 (m-30) cc_final: 0.7682 (m-30) REVERT: M 133 GLN cc_start: 0.7379 (tt0) cc_final: 0.6777 (tt0) REVERT: N 59 LYS cc_start: 0.5640 (OUTLIER) cc_final: 0.5141 (mttp) REVERT: O 8 ARG cc_start: 0.8113 (OUTLIER) cc_final: 0.7877 (mmt180) REVERT: O 19 ASP cc_start: 0.7677 (m-30) cc_final: 0.7294 (m-30) REVERT: P 22 ILE cc_start: 0.8538 (OUTLIER) cc_final: 0.8014 (mp) REVERT: P 35 ARG cc_start: 0.8039 (OUTLIER) cc_final: 0.7002 (ttm170) REVERT: P 113 GLU cc_start: 0.5884 (OUTLIER) cc_final: 0.5634 (mt-10) REVERT: Q 109 ARG cc_start: 0.8049 (OUTLIER) cc_final: 0.7794 (mtm-85) REVERT: R 56 ASP cc_start: 0.7500 (m-30) cc_final: 0.7259 (m-30) REVERT: R 90 ILE cc_start: 0.8419 (OUTLIER) cc_final: 0.8179 (tt) REVERT: S 63 GLU cc_start: 0.7321 (mt-10) cc_final: 0.7108 (mt-10) REVERT: S 96 MET cc_start: 0.7579 (mmm) cc_final: 0.7325 (tpp) REVERT: U 75 ARG cc_start: 0.8196 (OUTLIER) cc_final: 0.7584 (mtt90) REVERT: U 89 ILE cc_start: 0.7241 (OUTLIER) cc_final: 0.7000 (mt) REVERT: V 5 LYS cc_start: 0.7913 (OUTLIER) cc_final: 0.7001 (tptm) REVERT: Y 35 LYS cc_start: 0.7821 (ttmt) cc_final: 0.7566 (ttmm) REVERT: Z 2 LYS cc_start: 0.6995 (OUTLIER) cc_final: 0.5316 (pptt) REVERT: 0 58 GLU cc_start: 0.6909 (mm-30) cc_final: 0.6682 (tp30) REVERT: 3 24 ARG cc_start: 0.6891 (OUTLIER) cc_final: 0.6680 (ttm170) REVERT: 3 32 LYS cc_start: 0.7715 (mmtt) cc_final: 0.7286 (mtpp) REVERT: 3 38 ARG cc_start: 0.7608 (OUTLIER) cc_final: 0.6632 (ttp80) outliers start: 228 outliers final: 158 residues processed: 506 average time/residue: 1.6841 time to fit residues: 1136.2174 Evaluate side-chains 497 residues out of total 2249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 311 time to evaluate : 3.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 71 LYS 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 10 ASP 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 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 E residue 195 THR 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 44 VAL Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 88 LYS Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 112 ARG Chi-restraints excluded: chain F residue 125 ARG Chi-restraints excluded: chain F residue 127 ASN Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 172 GLN Chi-restraints excluded: chain G residue 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 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 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 G residue 173 GLU 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 114 THR Chi-restraints excluded: chain K residue 115 LEU Chi-restraints excluded: chain K residue 145 ASN 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 110 ASN Chi-restraints excluded: chain M residue 36 LYS 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 59 LYS Chi-restraints excluded: chain N residue 75 THR 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 133 LYS Chi-restraints excluded: chain O residue 8 ARG Chi-restraints excluded: chain O residue 24 LEU Chi-restraints excluded: chain O residue 84 SER 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 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 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 109 ARG Chi-restraints excluded: chain R residue 10 THR 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 59 GLU Chi-restraints excluded: chain S residue 61 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 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 U residue 89 ILE 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 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 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 88 VAL Chi-restraints excluded: chain X residue 93 VAL Chi-restraints excluded: chain Y residue 12 THR Chi-restraints excluded: chain Y residue 24 SER 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 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 38 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 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: 541 random chunks: chunk 175 optimal weight: 10.0000 chunk 470 optimal weight: 0.9990 chunk 103 optimal weight: 10.0000 chunk 307 optimal weight: 5.9990 chunk 129 optimal weight: 10.0000 chunk 523 optimal weight: 20.0000 chunk 434 optimal weight: 5.9990 chunk 242 optimal weight: 10.0000 chunk 43 optimal weight: 10.0000 chunk 173 optimal weight: 10.0000 chunk 274 optimal weight: 20.0000 overall best weight: 6.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 37 ASN ** F 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 84 GLN N 44 ASN X 87 GLN Z 60 GLN 0 40 ASN 3 20 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.1223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 89916 Z= 0.316 Angle : 0.768 10.545 135554 Z= 0.394 Chirality : 0.044 0.308 17500 Planarity : 0.006 0.064 6513 Dihedral : 23.092 179.700 47363 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.26 % Favored : 90.71 % Rotamer: Outliers : 9.96 % Allowed : 24.46 % Favored : 65.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 1.06 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.15), residues: 2647 helix: -0.01 (0.19), residues: 705 sheet: -0.49 (0.21), residues: 578 loop : -2.27 (0.15), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP E 83 HIS 0.007 0.002 HIS R 29 PHE 0.024 0.002 PHE V 2 TYR 0.015 0.002 TYR F 128 ARG 0.008 0.001 ARG M 16 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5294 Ramachandran restraints generated. 2647 Oldfield, 0 Emsley, 2647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5294 Ramachandran restraints generated. 2647 Oldfield, 0 Emsley, 2647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 2249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 224 poor density : 312 time to evaluate : 3.297 Fit side-chains REVERT: D 90 GLU cc_start: 0.6888 (OUTLIER) cc_final: 0.5880 (tm-30) REVERT: D 138 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.7699 (mtt180) REVERT: D 168 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.7949 (ptt180) REVERT: E 10 ASP cc_start: 0.6449 (OUTLIER) cc_final: 0.6205 (p0) REVERT: E 45 ARG cc_start: 0.8859 (OUTLIER) cc_final: 0.7215 (mtt180) REVERT: E 78 ILE cc_start: 0.8137 (OUTLIER) cc_final: 0.7717 (mp) REVERT: E 190 ASN cc_start: 0.8472 (OUTLIER) cc_final: 0.8054 (t0) REVERT: F 51 ASP cc_start: 0.3448 (OUTLIER) cc_final: 0.3201 (m-30) REVERT: F 138 PHE cc_start: 0.5450 (m-80) cc_final: 0.4945 (m-80) REVERT: F 169 LEU cc_start: 0.7225 (OUTLIER) cc_final: 0.7019 (tm) REVERT: F 172 GLN cc_start: 0.6114 (OUTLIER) cc_final: 0.5896 (mm-40) REVERT: G 144 LEU cc_start: 0.7779 (OUTLIER) cc_final: 0.7332 (mp) REVERT: G 171 ARG cc_start: 0.7710 (OUTLIER) cc_final: 0.7224 (mmm160) REVERT: G 173 GLU cc_start: 0.5983 (OUTLIER) cc_final: 0.5572 (tt0) REVERT: L 19 ILE cc_start: 0.8251 (OUTLIER) cc_final: 0.8010 (pt) REVERT: L 110 ASN cc_start: 0.6701 (OUTLIER) cc_final: 0.6211 (m-40) REVERT: M 73 ASP cc_start: 0.7892 (m-30) cc_final: 0.7622 (m-30) REVERT: M 133 GLN cc_start: 0.7331 (tt0) cc_final: 0.6792 (tt0) REVERT: O 8 ARG cc_start: 0.8122 (OUTLIER) cc_final: 0.7884 (mmt180) REVERT: O 19 ASP cc_start: 0.7722 (m-30) cc_final: 0.7349 (m-30) REVERT: P 22 ILE cc_start: 0.8541 (OUTLIER) cc_final: 0.8036 (mp) REVERT: P 35 ARG cc_start: 0.8109 (OUTLIER) cc_final: 0.7005 (ttm170) REVERT: P 113 GLU cc_start: 0.5957 (OUTLIER) cc_final: 0.5712 (mt-10) REVERT: Q 109 ARG cc_start: 0.8079 (OUTLIER) cc_final: 0.7787 (mtm-85) REVERT: R 56 ASP cc_start: 0.7554 (m-30) cc_final: 0.7304 (m-30) REVERT: R 90 ILE cc_start: 0.8451 (OUTLIER) cc_final: 0.8161 (tt) REVERT: S 96 MET cc_start: 0.7583 (mmm) cc_final: 0.7345 (tpp) REVERT: U 75 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.7646 (mtt90) REVERT: U 89 ILE cc_start: 0.7205 (OUTLIER) cc_final: 0.6970 (mt) REVERT: V 5 LYS cc_start: 0.7916 (OUTLIER) cc_final: 0.7096 (tttm) REVERT: V 58 GLU cc_start: 0.7240 (OUTLIER) cc_final: 0.6815 (mt-10) REVERT: X 23 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.7491 (ptt90) REVERT: Y 35 LYS cc_start: 0.7870 (ttmt) cc_final: 0.7645 (ttmm) REVERT: Z 2 LYS cc_start: 0.7059 (OUTLIER) cc_final: 0.5377 (pptt) REVERT: 0 58 GLU cc_start: 0.6933 (mm-30) cc_final: 0.6707 (tp30) REVERT: 3 24 ARG cc_start: 0.6922 (OUTLIER) cc_final: 0.6692 (ttm170) REVERT: 3 32 LYS cc_start: 0.7725 (mmtt) cc_final: 0.7292 (mtpp) REVERT: 3 38 ARG cc_start: 0.7640 (OUTLIER) cc_final: 0.6683 (ttp80) REVERT: 4 10 ARG cc_start: 0.9030 (OUTLIER) cc_final: 0.8731 (ttt180) outliers start: 224 outliers final: 170 residues processed: 490 average time/residue: 1.6771 time to fit residues: 1099.6414 Evaluate side-chains 507 residues out of total 2249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 307 time to evaluate : 3.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 71 LYS 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 10 ASP 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 190 ASN Chi-restraints excluded: chain E residue 195 THR 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 44 VAL Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 88 LYS Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 112 ARG Chi-restraints excluded: chain F residue 123 ASP Chi-restraints excluded: chain F residue 125 ARG Chi-restraints excluded: chain F residue 127 ASN Chi-restraints excluded: chain F residue 143 TYR Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 172 GLN Chi-restraints excluded: chain G residue 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 92 VAL Chi-restraints excluded: chain G residue 98 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 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 G residue 173 GLU 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 114 THR Chi-restraints excluded: chain K residue 115 LEU Chi-restraints excluded: chain K residue 145 ASN 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 110 ASN Chi-restraints excluded: chain M residue 36 LYS 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 75 THR 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 133 LYS Chi-restraints excluded: chain O residue 8 ARG Chi-restraints excluded: chain O residue 24 LEU 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 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 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 109 ARG Chi-restraints excluded: chain R residue 10 THR Chi-restraints excluded: chain R residue 30 THR 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 61 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 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 U residue 89 ILE 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 33 VAL Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain V residue 58 GLU 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 24 SER 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 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 38 ARG 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 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: 541 random chunks: chunk 504 optimal weight: 7.9990 chunk 59 optimal weight: 10.0000 chunk 298 optimal weight: 1.9990 chunk 382 optimal weight: 3.9990 chunk 296 optimal weight: 0.5980 chunk 440 optimal weight: 0.0020 chunk 292 optimal weight: 2.9990 chunk 521 optimal weight: 10.0000 chunk 326 optimal weight: 10.0000 chunk 317 optimal weight: 10.0000 chunk 240 optimal weight: 10.0000 overall best weight: 1.9194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 49 ASN G 19 GLN N 44 ASN O 61 GLN ** R 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 66 ASN X 87 GLN Z 60 GLN 0 40 ASN 2 41 HIS 3 20 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 89916 Z= 0.132 Angle : 0.561 9.781 135554 Z= 0.298 Chirality : 0.035 0.271 17500 Planarity : 0.005 0.055 6513 Dihedral : 22.830 178.565 47362 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.33 % Favored : 92.63 % Rotamer: Outliers : 7.60 % Allowed : 26.68 % Favored : 65.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 1.06 % 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: -1.39 (0.16), residues: 2647 helix: 0.52 (0.20), residues: 703 sheet: -0.28 (0.21), residues: 582 loop : -2.07 (0.15), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 61 HIS 0.006 0.001 HIS R 29 PHE 0.016 0.001 PHE V 2 TYR 0.012 0.001 TYR F 128 ARG 0.005 0.000 ARG Z 58 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5294 Ramachandran restraints generated. 2647 Oldfield, 0 Emsley, 2647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5294 Ramachandran restraints generated. 2647 Oldfield, 0 Emsley, 2647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 2249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 343 time to evaluate : 3.289 Fit side-chains REVERT: D 90 GLU cc_start: 0.6653 (OUTLIER) cc_final: 0.5880 (tm-30) REVERT: D 103 GLN cc_start: 0.7376 (pm20) cc_final: 0.6852 (pm20) REVERT: D 138 ARG cc_start: 0.7946 (OUTLIER) cc_final: 0.7414 (mtt180) REVERT: D 170 THR cc_start: 0.8639 (OUTLIER) cc_final: 0.8336 (t) REVERT: E 45 ARG cc_start: 0.8860 (OUTLIER) cc_final: 0.7221 (mtt180) REVERT: E 66 ARG cc_start: 0.5461 (mtm110) cc_final: 0.5222 (mtm180) REVERT: E 78 ILE cc_start: 0.8096 (OUTLIER) cc_final: 0.7689 (mp) REVERT: F 38 MET cc_start: 0.6061 (mtp) cc_final: 0.5831 (mtp) REVERT: F 175 MET cc_start: 0.3836 (tpp) cc_final: 0.3558 (tpp) REVERT: F 177 PHE cc_start: 0.4968 (m-10) cc_final: 0.4622 (m-80) REVERT: G 171 ARG cc_start: 0.7801 (OUTLIER) cc_final: 0.7306 (mmm160) REVERT: G 173 GLU cc_start: 0.5943 (OUTLIER) cc_final: 0.5506 (tt0) REVERT: M 73 ASP cc_start: 0.7856 (m-30) cc_final: 0.7604 (m-30) REVERT: M 133 GLN cc_start: 0.7360 (tt0) cc_final: 0.6746 (tt0) REVERT: N 59 LYS cc_start: 0.5612 (OUTLIER) cc_final: 0.5053 (mttp) REVERT: N 137 MET cc_start: 0.2845 (mmm) cc_final: 0.1587 (tmm) REVERT: O 8 ARG cc_start: 0.8078 (OUTLIER) cc_final: 0.7844 (mmt180) REVERT: O 19 ASP cc_start: 0.7672 (m-30) cc_final: 0.7289 (m-30) REVERT: O 91 ASN cc_start: 0.7667 (m-40) cc_final: 0.7196 (m110) REVERT: P 35 ARG cc_start: 0.7938 (OUTLIER) cc_final: 0.6971 (ttm170) REVERT: Q 38 GLU cc_start: 0.6649 (OUTLIER) cc_final: 0.6424 (mm-30) REVERT: Q 109 ARG cc_start: 0.8067 (OUTLIER) cc_final: 0.7867 (mtm-85) REVERT: R 56 ASP cc_start: 0.7436 (m-30) cc_final: 0.7191 (m-30) REVERT: R 80 MET cc_start: 0.8186 (mmp) cc_final: 0.7808 (mmm) REVERT: S 75 GLN cc_start: 0.8222 (OUTLIER) cc_final: 0.7860 (mt0) REVERT: U 65 MET cc_start: 0.4645 (OUTLIER) cc_final: 0.3737 (mmm) REVERT: U 75 ARG cc_start: 0.8108 (OUTLIER) cc_final: 0.7481 (mtt90) REVERT: U 89 ILE cc_start: 0.7294 (OUTLIER) cc_final: 0.7051 (mt) REVERT: X 23 ARG cc_start: 0.8449 (OUTLIER) cc_final: 0.7445 (ptt90) REVERT: Y 35 LYS cc_start: 0.7899 (ttmt) cc_final: 0.7667 (ttmm) REVERT: Z 2 LYS cc_start: 0.6944 (OUTLIER) cc_final: 0.5309 (pptt) REVERT: Z 23 GLU cc_start: 0.6617 (OUTLIER) cc_final: 0.6373 (mm-30) REVERT: 0 40 ASN cc_start: 0.7303 (m-40) cc_final: 0.6733 (m110) REVERT: 0 58 GLU cc_start: 0.6933 (mm-30) cc_final: 0.6718 (tp30) REVERT: 3 24 ARG cc_start: 0.6942 (OUTLIER) cc_final: 0.6660 (ttm170) REVERT: 3 32 LYS cc_start: 0.7662 (mmtt) cc_final: 0.7259 (mtpp) REVERT: 3 38 ARG cc_start: 0.7645 (OUTLIER) cc_final: 0.6651 (ttp80) outliers start: 171 outliers final: 106 residues processed: 470 average time/residue: 1.7075 time to fit residues: 1067.5318 Evaluate side-chains 457 residues out of total 2249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 330 time to evaluate : 3.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 58 GLU 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 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 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 176 VAL Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain F residue 32 ASP Chi-restraints excluded: chain F residue 88 LYS Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 112 ARG Chi-restraints excluded: chain F residue 125 ARG Chi-restraints excluded: chain F residue 127 ASN Chi-restraints excluded: chain F residue 158 THR 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 101 ASN Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 171 ARG Chi-restraints excluded: chain G residue 173 GLU 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 46 THR Chi-restraints excluded: chain K residue 58 ILE Chi-restraints excluded: chain K residue 63 VAL 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 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 M residue 36 LYS Chi-restraints excluded: chain M residue 81 THR 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 59 LYS Chi-restraints excluded: chain N residue 122 SER Chi-restraints excluded: chain N residue 127 VAL Chi-restraints excluded: chain O residue 8 ARG Chi-restraints excluded: chain O residue 84 SER 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 13 LYS Chi-restraints excluded: chain P residue 28 CYS Chi-restraints excluded: chain P residue 35 ARG 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 109 ARG Chi-restraints excluded: chain R residue 10 THR Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain S residue 10 LYS Chi-restraints excluded: chain S residue 14 VAL Chi-restraints excluded: chain S residue 33 VAL Chi-restraints excluded: chain S residue 59 GLU 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 105 THR Chi-restraints excluded: chain T residue 109 THR 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 65 MET Chi-restraints excluded: chain U residue 75 ARG Chi-restraints excluded: chain U residue 84 GLU Chi-restraints excluded: chain U residue 89 ILE 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 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 99 GLU Chi-restraints excluded: chain X residue 19 THR Chi-restraints excluded: chain X residue 23 ARG 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 24 SER Chi-restraints excluded: chain Y residue 28 THR 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 23 GLU Chi-restraints excluded: chain Z residue 37 LEU Chi-restraints excluded: chain 0 residue 35 VAL Chi-restraints excluded: chain 0 residue 54 VAL Chi-restraints excluded: chain 2 residue 3 VAL Chi-restraints excluded: chain 2 residue 8 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 32 ARG Chi-restraints excluded: chain 5 residue 58 ILE Chi-restraints excluded: chain 6 residue 11 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 541 random chunks: chunk 322 optimal weight: 6.9990 chunk 208 optimal weight: 10.0000 chunk 311 optimal weight: 0.4980 chunk 157 optimal weight: 10.0000 chunk 102 optimal weight: 10.0000 chunk 101 optimal weight: 10.0000 chunk 331 optimal weight: 0.4980 chunk 355 optimal weight: 6.9990 chunk 257 optimal weight: 10.0000 chunk 48 optimal weight: 10.0000 chunk 409 optimal weight: 5.9990 overall best weight: 4.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 37 ASN N 44 ASN O 61 GLN S 86 GLN T 66 ASN Z 60 GLN 3 20 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 89916 Z= 0.218 Angle : 0.643 10.006 135554 Z= 0.335 Chirality : 0.039 0.268 17500 Planarity : 0.005 0.058 6513 Dihedral : 22.856 179.838 47306 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.27 % Favored : 91.69 % Rotamer: Outliers : 7.03 % Allowed : 27.39 % Favored : 65.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 1.06 % Twisted General : 0.12 % 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: -1.41 (0.16), residues: 2647 helix: 0.46 (0.20), residues: 704 sheet: -0.28 (0.21), residues: 583 loop : -2.07 (0.15), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP E 83 HIS 0.006 0.001 HIS R 29 PHE 0.018 0.002 PHE V 2 TYR 0.015 0.002 TYR G 94 ARG 0.006 0.001 ARG Z 58 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5294 Ramachandran restraints generated. 2647 Oldfield, 0 Emsley, 2647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5294 Ramachandran restraints generated. 2647 Oldfield, 0 Emsley, 2647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 2249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 325 time to evaluate : 3.300 Fit side-chains REVERT: D 90 GLU cc_start: 0.6807 (OUTLIER) cc_final: 0.5967 (tm-30) REVERT: D 103 GLN cc_start: 0.7406 (pm20) cc_final: 0.6860 (pm20) REVERT: D 138 ARG cc_start: 0.8065 (OUTLIER) cc_final: 0.7552 (mtt180) REVERT: D 168 ARG cc_start: 0.8312 (OUTLIER) cc_final: 0.7715 (ptt180) REVERT: D 170 THR cc_start: 0.8772 (OUTLIER) cc_final: 0.8502 (t) REVERT: E 45 ARG cc_start: 0.8857 (OUTLIER) cc_final: 0.7218 (mtt180) REVERT: E 66 ARG cc_start: 0.5432 (mtm110) cc_final: 0.5232 (mtm180) REVERT: E 78 ILE cc_start: 0.8108 (OUTLIER) cc_final: 0.7744 (mm) REVERT: F 175 MET cc_start: 0.3889 (tpp) cc_final: 0.3632 (tpp) REVERT: F 177 PHE cc_start: 0.4968 (m-10) cc_final: 0.4617 (m-80) REVERT: G 144 LEU cc_start: 0.7762 (OUTLIER) cc_final: 0.7461 (mp) REVERT: G 171 ARG cc_start: 0.7796 (OUTLIER) cc_final: 0.7300 (mmm160) REVERT: G 173 GLU cc_start: 0.5890 (OUTLIER) cc_final: 0.5456 (tt0) REVERT: M 73 ASP cc_start: 0.7895 (m-30) cc_final: 0.7644 (m-30) REVERT: M 133 GLN cc_start: 0.7351 (tt0) cc_final: 0.6768 (tt0) REVERT: N 59 LYS cc_start: 0.5511 (OUTLIER) cc_final: 0.5036 (mttp) REVERT: N 137 MET cc_start: 0.2797 (mmm) cc_final: 0.1543 (tmm) REVERT: O 8 ARG cc_start: 0.8105 (OUTLIER) cc_final: 0.7874 (mmt180) REVERT: O 19 ASP cc_start: 0.7687 (m-30) cc_final: 0.7312 (m-30) REVERT: P 35 ARG cc_start: 0.8027 (OUTLIER) cc_final: 0.7005 (ttm170) REVERT: Q 38 GLU cc_start: 0.6523 (OUTLIER) cc_final: 0.6277 (mm-30) REVERT: R 56 ASP cc_start: 0.7474 (m-30) cc_final: 0.7225 (m-30) REVERT: R 80 MET cc_start: 0.8136 (mmp) cc_final: 0.7744 (mmm) REVERT: U 65 MET cc_start: 0.4747 (OUTLIER) cc_final: 0.3551 (mmm) REVERT: U 75 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.7586 (mtt90) REVERT: U 89 ILE cc_start: 0.7290 (OUTLIER) cc_final: 0.7063 (mt) REVERT: X 23 ARG cc_start: 0.8342 (OUTLIER) cc_final: 0.7376 (ptt90) REVERT: Y 35 LYS cc_start: 0.7888 (ttmt) cc_final: 0.7382 (ttmm) REVERT: 0 40 ASN cc_start: 0.7360 (m-40) cc_final: 0.6789 (m110) REVERT: 0 58 GLU cc_start: 0.6949 (mm-30) cc_final: 0.6746 (tp30) REVERT: 3 38 ARG cc_start: 0.7687 (OUTLIER) cc_final: 0.6747 (ttp80) REVERT: 6 4 ARG cc_start: 0.8707 (OUTLIER) cc_final: 0.8154 (ptp-170) outliers start: 158 outliers final: 118 residues processed: 452 average time/residue: 1.7274 time to fit residues: 1032.7224 Evaluate side-chains 455 residues out of total 2249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 318 time to evaluate : 3.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 58 GLU 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 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 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 152 VAL Chi-restraints excluded: chain E residue 176 VAL 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 88 LYS Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 112 ARG Chi-restraints excluded: chain F residue 123 ASP Chi-restraints excluded: chain F residue 125 ARG Chi-restraints excluded: chain F residue 127 ASN 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 98 VAL Chi-restraints excluded: chain G residue 101 ASN Chi-restraints excluded: chain G residue 107 VAL 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 G residue 173 GLU 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 46 THR Chi-restraints excluded: chain K residue 58 ILE Chi-restraints excluded: chain K residue 63 VAL 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 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 M residue 36 LYS Chi-restraints excluded: chain M residue 81 THR 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 59 LYS Chi-restraints excluded: chain N residue 122 SER Chi-restraints excluded: chain N residue 127 VAL Chi-restraints excluded: chain O residue 8 ARG 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 28 CYS Chi-restraints excluded: chain P residue 35 ARG Chi-restraints excluded: chain P residue 63 ILE Chi-restraints excluded: chain P residue 70 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 109 ARG Chi-restraints excluded: chain R residue 10 THR Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain S residue 10 LYS Chi-restraints excluded: chain S residue 14 VAL Chi-restraints excluded: chain S residue 33 VAL Chi-restraints excluded: chain S residue 59 GLU 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 105 THR Chi-restraints excluded: chain T residue 106 SER Chi-restraints excluded: chain T residue 109 THR 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 65 MET Chi-restraints excluded: chain U residue 75 ARG Chi-restraints excluded: chain U residue 84 GLU Chi-restraints excluded: chain U residue 89 ILE 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 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 99 GLU Chi-restraints excluded: chain X residue 19 THR Chi-restraints excluded: chain X residue 23 ARG 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 24 SER Chi-restraints excluded: chain Z residue 3 VAL Chi-restraints excluded: chain Z residue 37 LEU Chi-restraints excluded: chain 0 residue 35 VAL Chi-restraints excluded: chain 0 residue 54 VAL Chi-restraints excluded: chain 2 residue 3 VAL Chi-restraints excluded: chain 2 residue 8 THR Chi-restraints excluded: chain 2 residue 23 THR Chi-restraints excluded: chain 2 residue 56 SER Chi-restraints excluded: chain 3 residue 38 ARG Chi-restraints excluded: chain 3 residue 44 LEU Chi-restraints excluded: chain 4 residue 20 LYS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 541 random chunks: chunk 474 optimal weight: 10.0000 chunk 499 optimal weight: 6.9990 chunk 455 optimal weight: 5.9990 chunk 485 optimal weight: 7.9990 chunk 292 optimal weight: 3.9990 chunk 211 optimal weight: 10.0000 chunk 381 optimal weight: 4.9990 chunk 149 optimal weight: 20.0000 chunk 439 optimal weight: 9.9990 chunk 459 optimal weight: 4.9990 chunk 484 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 61 GLN Z 60 GLN 3 20 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 89916 Z= 0.258 Angle : 0.695 10.006 135554 Z= 0.360 Chirality : 0.041 0.280 17500 Planarity : 0.006 0.060 6513 Dihedral : 22.924 179.975 47305 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.27 % Favored : 91.69 % Rotamer: Outliers : 7.16 % Allowed : 27.52 % Favored : 65.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 1.06 % Twisted General : 0.12 % 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: -1.49 (0.15), residues: 2647 helix: 0.35 (0.19), residues: 697 sheet: -0.27 (0.21), residues: 579 loop : -2.10 (0.15), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP E 83 HIS 0.006 0.001 HIS R 29 PHE 0.018 0.002 PHE V 2 TYR 0.015 0.002 TYR G 94 ARG 0.007 0.001 ARG M 16 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5294 Ramachandran restraints generated. 2647 Oldfield, 0 Emsley, 2647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5294 Ramachandran restraints generated. 2647 Oldfield, 0 Emsley, 2647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 2249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 318 time to evaluate : 3.915 Fit side-chains REVERT: D 90 GLU cc_start: 0.6854 (OUTLIER) cc_final: 0.5937 (tm-30) REVERT: D 138 ARG cc_start: 0.8122 (OUTLIER) cc_final: 0.7622 (mtt180) REVERT: D 168 ARG cc_start: 0.8327 (OUTLIER) cc_final: 0.7749 (ptt180) REVERT: E 45 ARG cc_start: 0.8865 (OUTLIER) cc_final: 0.7222 (mtt180) REVERT: E 66 ARG cc_start: 0.5460 (mtm110) cc_final: 0.5130 (mtm180) REVERT: E 78 ILE cc_start: 0.8093 (OUTLIER) cc_final: 0.7739 (mm) REVERT: F 175 MET cc_start: 0.3847 (tpp) cc_final: 0.3591 (tpp) REVERT: F 177 PHE cc_start: 0.4965 (m-10) cc_final: 0.4608 (m-80) REVERT: G 144 LEU cc_start: 0.7759 (OUTLIER) cc_final: 0.7485 (mp) REVERT: G 171 ARG cc_start: 0.7724 (OUTLIER) cc_final: 0.7215 (mmm160) REVERT: G 173 GLU cc_start: 0.5947 (OUTLIER) cc_final: 0.5529 (tt0) REVERT: M 73 ASP cc_start: 0.7851 (m-30) cc_final: 0.7608 (m-30) REVERT: M 133 GLN cc_start: 0.7376 (tt0) cc_final: 0.6812 (tt0) REVERT: N 54 MET cc_start: 0.8307 (OUTLIER) cc_final: 0.7563 (mtm) REVERT: N 59 LYS cc_start: 0.5552 (OUTLIER) cc_final: 0.5067 (mttp) REVERT: O 8 ARG cc_start: 0.8124 (OUTLIER) cc_final: 0.7891 (mmt180) REVERT: O 19 ASP cc_start: 0.7719 (m-30) cc_final: 0.7345 (m-30) REVERT: P 35 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.7066 (ttm170) REVERT: R 56 ASP cc_start: 0.7498 (m-30) cc_final: 0.7251 (m-30) REVERT: R 80 MET cc_start: 0.8153 (mmp) cc_final: 0.7771 (mmm) REVERT: U 65 MET cc_start: 0.4949 (OUTLIER) cc_final: 0.3812 (mmm) REVERT: U 75 ARG cc_start: 0.8259 (OUTLIER) cc_final: 0.7630 (mtt90) REVERT: U 89 ILE cc_start: 0.7283 (OUTLIER) cc_final: 0.7060 (mt) REVERT: X 23 ARG cc_start: 0.8350 (OUTLIER) cc_final: 0.7339 (ptt90) REVERT: Y 35 LYS cc_start: 0.7886 (ttmt) cc_final: 0.7393 (ttmm) REVERT: Z 23 GLU cc_start: 0.6696 (OUTLIER) cc_final: 0.6443 (mm-30) REVERT: 0 58 GLU cc_start: 0.6960 (mm-30) cc_final: 0.6717 (tp30) REVERT: 3 32 LYS cc_start: 0.7720 (mmtt) cc_final: 0.7271 (mtpp) REVERT: 3 38 ARG cc_start: 0.7688 (OUTLIER) cc_final: 0.6758 (ttp80) REVERT: 6 4 ARG cc_start: 0.8712 (OUTLIER) cc_final: 0.8159 (ptp-170) outliers start: 161 outliers final: 128 residues processed: 447 average time/residue: 1.7396 time to fit residues: 1030.4458 Evaluate side-chains 463 residues out of total 2249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 316 time to evaluate : 3.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 59 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 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 184 ASN Chi-restraints excluded: chain D residue 191 ASN Chi-restraints excluded: chain D residue 201 THR 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 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 88 LYS Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 112 ARG Chi-restraints excluded: chain F residue 123 ASP Chi-restraints excluded: chain F residue 125 ARG Chi-restraints excluded: chain F residue 127 ASN Chi-restraints excluded: chain F residue 158 THR 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 98 VAL Chi-restraints excluded: chain G residue 101 ASN Chi-restraints excluded: chain G residue 107 VAL 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 G residue 173 GLU 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 114 THR Chi-restraints excluded: chain K residue 115 LEU Chi-restraints excluded: chain K residue 145 ASN 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 M residue 36 LYS 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 54 MET Chi-restraints excluded: chain N residue 59 LYS Chi-restraints excluded: chain N residue 75 THR Chi-restraints excluded: chain N residue 122 SER Chi-restraints excluded: chain N residue 127 VAL Chi-restraints excluded: chain O residue 8 ARG Chi-restraints excluded: chain O residue 84 SER 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 13 LYS Chi-restraints excluded: chain P residue 28 CYS Chi-restraints excluded: chain P residue 35 ARG Chi-restraints excluded: chain P residue 63 ILE Chi-restraints excluded: chain P residue 70 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 109 ARG Chi-restraints excluded: chain R residue 10 THR Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain S residue 10 LYS Chi-restraints excluded: chain S residue 14 VAL Chi-restraints excluded: chain S residue 33 VAL Chi-restraints excluded: chain S residue 59 GLU 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 70 ASP 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 36 THR Chi-restraints excluded: chain U residue 55 ILE Chi-restraints excluded: chain U residue 56 LEU Chi-restraints excluded: chain U residue 65 MET Chi-restraints excluded: chain U residue 75 ARG Chi-restraints excluded: chain U residue 84 GLU Chi-restraints excluded: chain U residue 89 ILE 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 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 99 GLU Chi-restraints excluded: chain X residue 19 THR Chi-restraints excluded: chain X residue 23 ARG 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 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 23 GLU Chi-restraints excluded: chain Z residue 37 LEU Chi-restraints excluded: chain 0 residue 35 VAL Chi-restraints excluded: chain 0 residue 54 VAL Chi-restraints excluded: chain 2 residue 3 VAL Chi-restraints excluded: chain 2 residue 8 THR Chi-restraints excluded: chain 2 residue 23 THR Chi-restraints excluded: chain 2 residue 56 SER Chi-restraints excluded: chain 3 residue 38 ARG Chi-restraints excluded: chain 3 residue 44 LEU 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 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: 541 random chunks: chunk 319 optimal weight: 1.9990 chunk 513 optimal weight: 2.9990 chunk 313 optimal weight: 0.0470 chunk 243 optimal weight: 10.0000 chunk 357 optimal weight: 7.9990 chunk 538 optimal weight: 0.9990 chunk 496 optimal weight: 9.9990 chunk 429 optimal weight: 6.9990 chunk 44 optimal weight: 10.0000 chunk 331 optimal weight: 0.0010 chunk 263 optimal weight: 20.0000 overall best weight: 1.2090 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 37 ASN ** N 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 61 GLN Z 60 GLN 3 20 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 89916 Z= 0.126 Angle : 0.603 9.791 135554 Z= 0.318 Chirality : 0.036 0.289 17500 Planarity : 0.005 0.122 6513 Dihedral : 22.894 179.830 47304 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.67 % Favored : 92.29 % Rotamer: Outliers : 6.00 % Allowed : 28.37 % Favored : 65.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 1.06 % Twisted General : 0.12 % 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: -1.30 (0.16), residues: 2647 helix: 0.61 (0.20), residues: 698 sheet: -0.22 (0.21), residues: 582 loop : -2.01 (0.15), residues: 1367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 61 HIS 0.007 0.001 HIS R 29 PHE 0.013 0.001 PHE V 2 TYR 0.037 0.001 TYR F 128 ARG 0.019 0.001 ARG P 16 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5294 Ramachandran restraints generated. 2647 Oldfield, 0 Emsley, 2647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5294 Ramachandran restraints generated. 2647 Oldfield, 0 Emsley, 2647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 2249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 325 time to evaluate : 3.345 Fit side-chains REVERT: D 90 GLU cc_start: 0.6754 (OUTLIER) cc_final: 0.5904 (tm-30) REVERT: D 103 GLN cc_start: 0.7315 (pm20) cc_final: 0.6733 (pm20) REVERT: D 138 ARG cc_start: 0.7969 (OUTLIER) cc_final: 0.7432 (mtt180) REVERT: E 45 ARG cc_start: 0.8813 (OUTLIER) cc_final: 0.7144 (mtt180) REVERT: E 66 ARG cc_start: 0.5333 (mtm110) cc_final: 0.5110 (mtm180) REVERT: E 78 ILE cc_start: 0.8034 (OUTLIER) cc_final: 0.7672 (mm) REVERT: G 171 ARG cc_start: 0.7744 (OUTLIER) cc_final: 0.7257 (mmm160) REVERT: G 173 GLU cc_start: 0.5874 (OUTLIER) cc_final: 0.5459 (tt0) REVERT: M 73 ASP cc_start: 0.7853 (m-30) cc_final: 0.7611 (m-30) REVERT: M 133 GLN cc_start: 0.7388 (tt0) cc_final: 0.6793 (tt0) REVERT: N 54 MET cc_start: 0.8248 (OUTLIER) cc_final: 0.7522 (mtm) REVERT: N 59 LYS cc_start: 0.5440 (OUTLIER) cc_final: 0.4973 (mttp) REVERT: N 137 MET cc_start: 0.2863 (mmm) cc_final: 0.1544 (tmm) REVERT: O 8 ARG cc_start: 0.8099 (OUTLIER) cc_final: 0.7879 (mmt180) REVERT: O 19 ASP cc_start: 0.7685 (m-30) cc_final: 0.7293 (m-30) REVERT: P 35 ARG cc_start: 0.7998 (OUTLIER) cc_final: 0.6946 (ttm170) REVERT: Q 38 GLU cc_start: 0.6506 (OUTLIER) cc_final: 0.6286 (mm-30) REVERT: R 56 ASP cc_start: 0.7450 (m-30) cc_final: 0.7211 (m-30) REVERT: R 80 MET cc_start: 0.8100 (mmp) cc_final: 0.7822 (mmm) REVERT: U 75 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.7570 (mtt90) REVERT: U 89 ILE cc_start: 0.7285 (OUTLIER) cc_final: 0.7077 (mt) REVERT: Y 35 LYS cc_start: 0.7862 (ttmt) cc_final: 0.7365 (ttmm) REVERT: 0 40 ASN cc_start: 0.7348 (m-40) cc_final: 0.6781 (m110) REVERT: 0 58 GLU cc_start: 0.6940 (mm-30) cc_final: 0.6736 (tp30) REVERT: 3 32 LYS cc_start: 0.7733 (mmtt) cc_final: 0.7315 (mtpp) REVERT: 6 4 ARG cc_start: 0.8704 (OUTLIER) cc_final: 0.8123 (ptp-170) outliers start: 135 outliers final: 107 residues processed: 437 average time/residue: 1.7543 time to fit residues: 1017.4133 Evaluate side-chains 430 residues out of total 2249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 309 time to evaluate : 3.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 59 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 184 ASN Chi-restraints excluded: chain D residue 191 ASN Chi-restraints excluded: chain D residue 201 THR 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 176 VAL 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 88 LYS Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 112 ARG Chi-restraints excluded: chain F residue 123 ASP Chi-restraints excluded: chain F residue 125 ARG Chi-restraints excluded: chain F residue 127 ASN 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 101 ASN Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 171 ARG Chi-restraints excluded: chain G residue 173 GLU 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 46 THR Chi-restraints excluded: chain K residue 58 ILE Chi-restraints excluded: chain K residue 63 VAL 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 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 M residue 36 LYS Chi-restraints excluded: chain M residue 67 THR Chi-restraints excluded: chain M residue 81 THR 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 54 MET Chi-restraints excluded: chain N residue 59 LYS Chi-restraints excluded: chain N residue 127 VAL Chi-restraints excluded: chain O residue 8 ARG 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 28 CYS Chi-restraints excluded: chain P residue 35 ARG Chi-restraints excluded: chain P residue 70 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 109 ARG Chi-restraints excluded: chain R residue 10 THR Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain S residue 10 LYS Chi-restraints excluded: chain S residue 14 VAL Chi-restraints excluded: chain S residue 33 VAL Chi-restraints excluded: chain S residue 59 GLU 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 106 SER Chi-restraints excluded: chain T residue 109 THR 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 U residue 89 ILE 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 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 99 GLU Chi-restraints excluded: chain X residue 19 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 Y residue 24 SER Chi-restraints excluded: chain Z residue 3 VAL Chi-restraints excluded: chain Z residue 37 LEU Chi-restraints excluded: chain 0 residue 35 VAL Chi-restraints excluded: chain 0 residue 54 VAL Chi-restraints excluded: chain 2 residue 3 VAL Chi-restraints excluded: chain 2 residue 8 THR Chi-restraints excluded: chain 2 residue 23 THR Chi-restraints excluded: chain 2 residue 56 SER Chi-restraints excluded: chain 4 residue 20 LYS Chi-restraints excluded: chain 4 residue 24 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 541 random chunks: chunk 340 optimal weight: 6.9990 chunk 457 optimal weight: 9.9990 chunk 131 optimal weight: 10.0000 chunk 395 optimal weight: 10.0000 chunk 63 optimal weight: 10.0000 chunk 119 optimal weight: 10.0000 chunk 429 optimal weight: 5.9990 chunk 179 optimal weight: 20.0000 chunk 441 optimal weight: 4.9990 chunk 54 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 overall best weight: 7.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 37 ASN N 44 ASN O 61 GLN R 101 ASN ** S 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 48 GLN Z 60 GLN 3 20 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.091883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.078894 restraints weight = 127918.801| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 0.60 r_work: 0.2704 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2654 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.095 89916 Z= 0.360 Angle : 0.807 10.759 135554 Z= 0.409 Chirality : 0.046 0.318 17500 Planarity : 0.007 0.063 6513 Dihedral : 23.003 179.561 47302 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.88 % Favored : 91.08 % Rotamer: Outliers : 6.31 % Allowed : 28.32 % Favored : 65.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 1.06 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.15), residues: 2647 helix: 0.20 (0.19), residues: 698 sheet: -0.27 (0.21), residues: 576 loop : -2.16 (0.15), residues: 1373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP N 41 HIS 0.006 0.002 HIS R 29 PHE 0.021 0.003 PHE D 119 TYR 0.016 0.002 TYR K 126 ARG 0.009 0.001 ARG P 16 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17952.82 seconds wall clock time: 316 minutes 48.11 seconds (19008.11 seconds total)