Starting phenix.real_space_refine on Fri Feb 23 02:27:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ob9_12795/02_2024/7ob9_12795.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ob9_12795/02_2024/7ob9_12795.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ob9_12795/02_2024/7ob9_12795.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ob9_12795/02_2024/7ob9_12795.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ob9_12795/02_2024/7ob9_12795.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ob9_12795/02_2024/7ob9_12795.pdb" } resolution = 2.7 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= 0.003 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: 7 Type Number sf(0) Gaussians Zn 6 6.06 5 P 69 5.49 5 Mg 1 5.21 5 S 237 5.16 5 C 22831 2.51 5 N 6335 2.21 5 O 6866 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 10": "NH1" <-> "NH2" Residue "A ARG 37": "NH1" <-> "NH2" Residue "A ARG 114": "NH1" <-> "NH2" Residue "A ARG 140": "NH1" <-> "NH2" Residue "A ARG 212": "NH1" <-> "NH2" Residue "A ARG 262": "NH1" <-> "NH2" Residue "A ARG 291": "NH1" <-> "NH2" Residue "A ARG 314": "NH1" <-> "NH2" Residue "A ARG 393": "NH1" <-> "NH2" Residue "A ARG 418": "NH1" <-> "NH2" Residue "A ARG 504": "NH1" <-> "NH2" Residue "A ARG 565": "NH1" <-> "NH2" Residue "A ARG 644": "NH1" <-> "NH2" Residue "A ARG 650": "NH1" <-> "NH2" Residue "A ARG 659": "NH1" <-> "NH2" Residue "A ARG 667": "NH1" <-> "NH2" Residue "A ARG 722": "NH1" <-> "NH2" Residue "A ARG 740": "NH1" <-> "NH2" Residue "A TYR 754": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 793": "NH1" <-> "NH2" Residue "A ARG 814": "NH1" <-> "NH2" Residue "A ARG 828": "NH1" <-> "NH2" Residue "A ARG 843": "NH1" <-> "NH2" Residue "A ARG 856": "NH1" <-> "NH2" Residue "A ARG 887": "NH1" <-> "NH2" Residue "A ARG 1070": "NH1" <-> "NH2" Residue "A ARG 1085": "NH1" <-> "NH2" Residue "A ARG 1110": "NH1" <-> "NH2" Residue "A ARG 1113": "NH1" <-> "NH2" Residue "A ARG 1132": "NH1" <-> "NH2" Residue "A ARG 1133": "NH1" <-> "NH2" Residue "A ARG 1151": "NH1" <-> "NH2" Residue "A ARG 1191": "NH1" <-> "NH2" Residue "A ARG 1236": "NH1" <-> "NH2" Residue "A ARG 1277": "NH1" <-> "NH2" Residue "A ARG 1287": "NH1" <-> "NH2" Residue "A TYR 1327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1334": "NH1" <-> "NH2" Residue "A ARG 1340": "NH1" <-> "NH2" Residue "A ARG 1345": "NH1" <-> "NH2" Residue "A ARG 1506": "NH1" <-> "NH2" Residue "A PHE 1538": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1599": "NH1" <-> "NH2" Residue "A ARG 1663": "NH1" <-> "NH2" Residue "A ARG 1694": "NH1" <-> "NH2" Residue "A ARG 1707": "NH1" <-> "NH2" Residue "B ARG 8": "NH1" <-> "NH2" Residue "B ARG 40": "NH1" <-> "NH2" Residue "B ARG 72": "NH1" <-> "NH2" Residue "B ARG 107": "NH1" <-> "NH2" Residue "B ARG 149": "NH1" <-> "NH2" Residue "B ARG 187": "NH1" <-> "NH2" Residue "B ARG 279": "NH1" <-> "NH2" Residue "B ARG 440": "NH1" <-> "NH2" Residue "B ARG 482": "NH1" <-> "NH2" Residue "B ARG 488": "NH1" <-> "NH2" Residue "B ARG 548": "NH1" <-> "NH2" Residue "B ARG 585": "NH1" <-> "NH2" Residue "B ARG 588": "NH1" <-> "NH2" Residue "B PHE 662": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 723": "NH1" <-> "NH2" Residue "B ARG 978": "NH1" <-> "NH2" Residue "B ARG 1018": "NH1" <-> "NH2" Residue "B ARG 1029": "NH1" <-> "NH2" Residue "B ARG 1057": "NH1" <-> "NH2" Residue "B ARG 1064": "NH1" <-> "NH2" Residue "B ARG 1092": "NH1" <-> "NH2" Residue "B ARG 1094": "NH1" <-> "NH2" Residue "B ARG 1103": "NH1" <-> "NH2" Residue "B ARG 1117": "NH1" <-> "NH2" Residue "C ARG 120": "NH1" <-> "NH2" Residue "C TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 303": "NH1" <-> "NH2" Residue "E ARG 52": "NH1" <-> "NH2" Residue "F TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 81": "NH1" <-> "NH2" Residue "G TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 40": "NH1" <-> "NH2" Residue "I ARG 48": "NH1" <-> "NH2" Residue "K ARG 37": "NH1" <-> "NH2" Residue "K ARG 87": "NH1" <-> "NH2" Residue "K ARG 98": "NH1" <-> "NH2" Residue "L ARG 31": "NH1" <-> "NH2" Residue "N ARG 59": "NH1" <-> "NH2" Residue "N ARG 77": "NH1" <-> "NH2" Residue "N ARG 79": "NH1" <-> "NH2" Residue "N ARG 81": "NH1" <-> "NH2" Residue "N ARG 116": "NH1" <-> "NH2" Residue "N ARG 146": "NH1" <-> "NH2" Residue "N ARG 148": "NH1" <-> "NH2" Residue "N PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 53": "NH1" <-> "NH2" Residue "M ARG 55": "NH1" <-> "NH2" Residue "M ARG 149": "NH1" <-> "NH2" Residue "M ARG 270": "NH1" <-> "NH2" Residue "M ARG 275": "NH1" <-> "NH2" Residue "M ARG 325": "NH1" <-> "NH2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 36345 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 12222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1535, 12222 Classifications: {'peptide': 1535} Link IDs: {'PCIS': 4, 'PTRANS': 74, 'TRANS': 1456} Chain breaks: 3 Chain: "B" Number of atoms: 8957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1129, 8957 Classifications: {'peptide': 1129} Link IDs: {'PTRANS': 65, 'TRANS': 1063} Chain breaks: 1 Chain: "C" Number of atoms: 2458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2458 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 16, 'TRANS': 290} Chain: "E" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1720 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain: "F" Number of atoms: 636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 636 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "G" Number of atoms: 1369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1369 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "H" Number of atoms: 1197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1197 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 4, 'TRANS': 144} Chain: "I" Number of atoms: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 414 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "J" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 533 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "K" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 856 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "L" Number of atoms: 397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 397 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "N" Number of atoms: 1083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1083 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 25, 'TRANS': 123} Chain: "M" Number of atoms: 3062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3062 Classifications: {'peptide': 388} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 15, 'TRANS': 372} Chain breaks: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "R" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 449 Classifications: {'RNA': 21} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 11, 'rna3p_pyr': 9} Link IDs: {'rna2p': 1, 'rna3p': 19} Chain breaks: 1 Chain: "S" Number of atoms: 390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 390 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain breaks: 1 Chain: "T" Number of atoms: 595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 595 Classifications: {'DNA': 29} Link IDs: {'rna3p': 28} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" 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 470 SG CYS A 64 51.807 90.120 85.583 1.00 83.08 S ATOM 489 SG CYS A 67 51.664 87.348 88.128 1.00 83.94 S ATOM 544 SG CYS A 74 55.124 88.195 87.284 1.00 74.57 S ATOM 782 SG CYS A 104 64.222 68.398 41.498 1.00 82.18 S ATOM 804 SG CYS A 107 62.082 65.165 42.539 1.00 90.12 S ATOM 1588 SG CYS A 205 65.262 64.745 40.943 1.00101.60 S ATOM 1611 SG CYS A 208 63.470 66.639 38.332 1.00106.02 S ATOM 20714 SG CYS B1070 51.924 70.236 83.596 1.00 69.09 S ATOM 20736 SG CYS B1073 53.446 70.829 80.358 1.00 69.61 S ATOM 20888 SG CYS B1098 50.618 72.875 81.496 1.00 75.51 S ATOM 20909 SG CYS B1101 48.488 69.962 81.475 1.00 85.55 S ATOM 28638 SG CYS I 20 112.394 103.292 20.032 1.00 78.44 S ATOM 28658 SG CYS I 23 109.948 106.237 22.174 1.00 81.36 S ATOM 28758 SG CYS I 38 108.369 103.202 20.843 1.00 91.55 S ATOM 28783 SG CYS I 41 109.906 105.624 18.585 1.00 90.76 S ATOM 29028 SG CYS J 7 115.705 108.139 118.400 1.00 33.58 S ATOM 29052 SG CYS J 10 116.815 106.825 122.283 1.00 32.88 S ATOM 29316 SG CYS J 44 118.670 105.765 119.253 1.00 35.23 S ATOM 29322 SG CYS J 45 119.129 109.147 120.888 1.00 37.14 S ATOM 30429 SG CYS L 19 89.701 135.771 96.181 1.00 57.33 S ATOM 30448 SG CYS L 22 90.559 139.287 97.451 1.00 62.84 S ATOM 30565 SG CYS L 36 86.975 138.742 96.859 1.00 59.26 S ATOM 30591 SG CYS L 39 90.064 138.660 93.895 1.00 61.06 S Time building chain proxies: 18.16, per 1000 atoms: 0.50 Number of scatterers: 36345 At special positions: 0 Unit cell: (172.62, 155.358, 162.756, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 6 29.99 S 237 16.00 P 69 15.00 Mg 1 11.99 O 6866 8.00 N 6335 7.00 C 22831 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: 12.60 Conformation dependent library (CDL) restraints added in 6.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1801 " pdb="ZN ZN A1801 " - pdb=" NE2 HIS A 77 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 74 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 67 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 64 " pdb=" ZN A1802 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 107 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 104 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 205 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 208 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1098 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1070 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1101 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1073 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 38 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 20 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 23 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 41 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 39 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 22 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 19 " Number of angles added : 33 8722 Ramachandran restraints generated. 4361 Oldfield, 0 Emsley, 4361 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8246 Finding SS restraints... Secondary structure from input PDB file: 152 helices and 45 sheets defined 36.1% alpha, 17.8% beta 25 base pairs and 45 stacking pairs defined. Time for finding SS restraints: 11.55 Creating SS restraints... Processing helix chain 'A' and resid 21 through 29 Processing helix chain 'A' and resid 92 through 102 Processing helix chain 'A' and resid 113 through 129 removed outlier: 3.629A pdb=" N ILE A 117 " --> pdb=" O PRO A 113 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N VAL A 129 " --> pdb=" O ARG A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 149 removed outlier: 4.111A pdb=" N GLU A 137 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU A 139 " --> pdb=" O VAL A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 172 Processing helix chain 'A' and resid 181 through 199 Processing helix chain 'A' and resid 257 through 280 removed outlier: 3.744A pdb=" N GLU A 263 " --> pdb=" O THR A 259 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N PHE A 274 " --> pdb=" O LYS A 270 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N PHE A 275 " --> pdb=" O ASN A 271 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N TYR A 278 " --> pdb=" O PHE A 274 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU A 279 " --> pdb=" O PHE A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 296 removed outlier: 3.600A pdb=" N VAL A 296 " --> pdb=" O ASN A 293 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 293 through 296' Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 322 through 346 removed outlier: 3.817A pdb=" N ASP A 334 " --> pdb=" O ALA A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 403 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 427 through 432 Processing helix chain 'A' and resid 460 through 464 Processing helix chain 'A' and resid 476 through 487 Processing helix chain 'A' and resid 511 through 522 removed outlier: 4.104A pdb=" N ARG A 515 " --> pdb=" O ASP A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 559 No H-bonds generated for 'chain 'A' and resid 557 through 559' Processing helix chain 'A' and resid 581 through 586 Processing helix chain 'A' and resid 601 through 611 Processing helix chain 'A' and resid 613 through 617 Processing helix chain 'A' and resid 631 through 642 removed outlier: 3.572A pdb=" N MET A 635 " --> pdb=" O ILE A 631 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL A 636 " --> pdb=" O GLN A 632 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA A 639 " --> pdb=" O MET A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 661 Processing helix chain 'A' and resid 684 through 694 Processing helix chain 'A' and resid 712 through 716 removed outlier: 3.586A pdb=" N TRP A 716 " --> pdb=" O GLY A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 732 Processing helix chain 'A' and resid 760 through 769 Processing helix chain 'A' and resid 770 through 792 removed outlier: 3.836A pdb=" N SER A 774 " --> pdb=" O GLY A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 805 through 820 Processing helix chain 'A' and resid 823 through 832 removed outlier: 3.845A pdb=" N VAL A 827 " --> pdb=" O GLY A 823 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA A 830 " --> pdb=" O ALA A 826 " (cutoff:3.500A) Processing helix chain 'A' and resid 838 through 850 removed outlier: 3.572A pdb=" N ARG A 843 " --> pdb=" O TYR A 839 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 881 removed outlier: 4.022A pdb=" N HIS A 871 " --> pdb=" O GLU A 867 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N TYR A 872 " --> pdb=" O GLU A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 892 through 900 Processing helix chain 'A' and resid 905 through 914 removed outlier: 3.510A pdb=" N THR A 909 " --> pdb=" O SER A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 944 through 949 removed outlier: 3.783A pdb=" N GLY A 949 " --> pdb=" O ARG A 946 " (cutoff:3.500A) Processing helix chain 'A' and resid 960 through 997 removed outlier: 4.304A pdb=" N THR A 982 " --> pdb=" O THR A 978 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N SER A 983 " --> pdb=" O ALA A 979 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ARG A 984 " --> pdb=" O VAL A 980 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N TYR A 987 " --> pdb=" O SER A 983 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU A 988 " --> pdb=" O ARG A 984 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN A 989 " --> pdb=" O SER A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 1018 through 1022 removed outlier: 3.633A pdb=" N ASP A1022 " --> pdb=" O TYR A1019 " (cutoff:3.500A) Processing helix chain 'A' and resid 1025 through 1029 Processing helix chain 'A' and resid 1036 through 1042 Processing helix chain 'A' and resid 1043 through 1049 Processing helix chain 'A' and resid 1062 through 1079 Processing helix chain 'A' and resid 1087 through 1095 Processing helix chain 'A' and resid 1097 through 1102 Processing helix chain 'A' and resid 1114 through 1126 Processing helix chain 'A' and resid 1131 through 1138 removed outlier: 3.695A pdb=" N TYR A1135 " --> pdb=" O SER A1131 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1150 Processing helix chain 'A' and resid 1160 through 1181 removed outlier: 3.846A pdb=" N ALA A1176 " --> pdb=" O GLN A1172 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLN A1177 " --> pdb=" O GLU A1173 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR A1178 " --> pdb=" O TRP A1174 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLU A1179 " --> pdb=" O ALA A1175 " (cutoff:3.500A) Processing helix chain 'A' and resid 1188 through 1203 removed outlier: 3.525A pdb=" N LEU A1192 " --> pdb=" O SER A1188 " (cutoff:3.500A) Processing helix chain 'A' and resid 1210 through 1221 Processing helix chain 'A' and resid 1222 through 1226 Processing helix chain 'A' and resid 1243 through 1253 removed outlier: 3.882A pdb=" N ARG A1247 " --> pdb=" O LEU A1243 " (cutoff:3.500A) Processing helix chain 'A' and resid 1271 through 1286 removed outlier: 4.358A pdb=" N LYS A1279 " --> pdb=" O LEU A1275 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N SER A1280 " --> pdb=" O LYS A1276 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR A1286 " --> pdb=" O LYS A1282 " (cutoff:3.500A) Processing helix chain 'A' and resid 1289 through 1293 removed outlier: 3.948A pdb=" N VAL A1293 " --> pdb=" O CYS A1289 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1289 through 1293' Processing helix chain 'A' and resid 1323 through 1327 Processing helix chain 'A' and resid 1334 through 1345 Processing helix chain 'A' and resid 1345 through 1359 Processing helix chain 'A' and resid 1500 through 1507 Processing helix chain 'A' and resid 1539 through 1551 Processing helix chain 'A' and resid 1584 through 1588 Processing helix chain 'A' and resid 1596 through 1600 removed outlier: 3.621A pdb=" N LEU A1600 " --> pdb=" O LEU A1597 " (cutoff:3.500A) Processing helix chain 'A' and resid 1604 through 1612 Processing helix chain 'A' and resid 1613 through 1630 removed outlier: 3.537A pdb=" N ALA A1617 " --> pdb=" O GLY A1613 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ARG A1619 " --> pdb=" O GLU A1615 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS A1626 " --> pdb=" O GLU A1622 " (cutoff:3.500A) Processing helix chain 'A' and resid 1637 through 1649 removed outlier: 3.773A pdb=" N LEU A1641 " --> pdb=" O ASP A1637 " (cutoff:3.500A) Processing helix chain 'A' and resid 1661 through 1665 removed outlier: 3.765A pdb=" N SER A1664 " --> pdb=" O GLY A1661 " (cutoff:3.500A) Processing helix chain 'A' and resid 1667 through 1675 removed outlier: 3.647A pdb=" N GLU A1675 " --> pdb=" O GLN A1671 " (cutoff:3.500A) Processing helix chain 'A' and resid 1676 through 1688 Processing helix chain 'A' and resid 1695 through 1702 removed outlier: 3.554A pdb=" N LEU A1700 " --> pdb=" O PRO A1696 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL A1702 " --> pdb=" O ALA A1698 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 37 removed outlier: 3.573A pdb=" N GLN B 36 " --> pdb=" O LYS B 32 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU B 37 " --> pdb=" O ALA B 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 32 through 37' Processing helix chain 'B' and resid 39 through 61 removed outlier: 4.311A pdb=" N GLY B 53 " --> pdb=" O ALA B 49 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LEU B 54 " --> pdb=" O VAL B 50 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLY B 55 " --> pdb=" O HIS B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 106 removed outlier: 3.589A pdb=" N CYS B 103 " --> pdb=" O TYR B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 159 Processing helix chain 'B' and resid 196 through 201 removed outlier: 3.580A pdb=" N ARG B 201 " --> pdb=" O TRP B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 257 removed outlier: 3.874A pdb=" N VAL B 257 " --> pdb=" O LEU B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 269 Processing helix chain 'B' and resid 275 through 292 removed outlier: 3.935A pdb=" N VAL B 289 " --> pdb=" O MET B 285 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N MET B 290 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU B 292 " --> pdb=" O ILE B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 308 Processing helix chain 'B' and resid 319 through 331 removed outlier: 3.651A pdb=" N LEU B 327 " --> pdb=" O ALA B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 358 Processing helix chain 'B' and resid 368 through 370 No H-bonds generated for 'chain 'B' and resid 368 through 370' Processing helix chain 'B' and resid 376 through 406 Processing helix chain 'B' and resid 427 through 437 removed outlier: 4.138A pdb=" N LEU B 433 " --> pdb=" O PRO B 429 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N PHE B 434 " --> pdb=" O PHE B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 466 Processing helix chain 'B' and resid 467 through 469 No H-bonds generated for 'chain 'B' and resid 467 through 469' Processing helix chain 'B' and resid 476 through 481 removed outlier: 4.302A pdb=" N LYS B 480 " --> pdb=" O ALA B 476 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N MET B 481 " --> pdb=" O ASP B 477 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 476 through 481' Processing helix chain 'B' and resid 490 through 494 Processing helix chain 'B' and resid 529 through 537 Processing helix chain 'B' and resid 549 through 551 No H-bonds generated for 'chain 'B' and resid 549 through 551' Processing helix chain 'B' and resid 570 through 585 Processing helix chain 'B' and resid 636 through 640 removed outlier: 4.097A pdb=" N ILE B 640 " --> pdb=" O THR B 636 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 636 through 640' Processing helix chain 'B' and resid 670 through 674 removed outlier: 3.815A pdb=" N ILE B 674 " --> pdb=" O ALA B 671 " (cutoff:3.500A) Processing helix chain 'B' and resid 676 through 680 removed outlier: 3.547A pdb=" N ASN B 680 " --> pdb=" O SER B 677 " (cutoff:3.500A) Processing helix chain 'B' and resid 681 through 692 removed outlier: 3.581A pdb=" N GLN B 688 " --> pdb=" O ARG B 684 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN B 690 " --> pdb=" O MET B 686 " (cutoff:3.500A) Processing helix chain 'B' and resid 725 through 730 Processing helix chain 'B' and resid 731 through 735 Processing helix chain 'B' and resid 761 through 766 Processing helix chain 'B' and resid 916 through 920 Processing helix chain 'B' and resid 926 through 942 Processing helix chain 'B' and resid 957 through 969 Processing helix chain 'B' and resid 1005 through 1009 Processing helix chain 'B' and resid 1038 through 1047 Processing helix chain 'B' and resid 1050 through 1060 removed outlier: 3.745A pdb=" N LEU B1054 " --> pdb=" O THR B1050 " (cutoff:3.500A) Processing helix chain 'B' and resid 1113 through 1125 Processing helix chain 'C' and resid 41 through 49 Processing helix chain 'C' and resid 69 through 83 Processing helix chain 'C' and resid 102 through 112 removed outlier: 3.522A pdb=" N HIS C 108 " --> pdb=" O GLU C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 122 Processing helix chain 'C' and resid 158 through 162 Processing helix chain 'C' and resid 169 through 171 No H-bonds generated for 'chain 'C' and resid 169 through 171' Processing helix chain 'C' and resid 180 through 185 Processing helix chain 'C' and resid 222 through 226 Processing helix chain 'C' and resid 247 through 256 removed outlier: 3.701A pdb=" N GLU C 251 " --> pdb=" O GLY C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 281 removed outlier: 3.624A pdb=" N LEU C 280 " --> pdb=" O ASN C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 289 Processing helix chain 'C' and resid 292 through 295 removed outlier: 4.012A pdb=" N LYS C 295 " --> pdb=" O LYS C 292 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 292 through 295' Processing helix chain 'C' and resid 317 through 344 removed outlier: 3.772A pdb=" N LEU C 329 " --> pdb=" O ALA C 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 24 removed outlier: 3.634A pdb=" N ILE E 17 " --> pdb=" O ILE E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 34 Processing helix chain 'E' and resid 36 through 44 Processing helix chain 'E' and resid 83 through 97 removed outlier: 3.681A pdb=" N ILE E 87 " --> pdb=" O GLY E 83 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL E 89 " --> pdb=" O LYS E 85 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU E 96 " --> pdb=" O GLN E 92 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU E 97 " --> pdb=" O ARG E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 121 Processing helix chain 'E' and resid 133 through 136 removed outlier: 3.502A pdb=" N LEU E 136 " --> pdb=" O GLN E 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 133 through 136' Processing helix chain 'E' and resid 138 through 142 Processing helix chain 'E' and resid 152 through 163 Processing helix chain 'E' and resid 177 through 184 Processing helix chain 'F' and resid 58 through 75 removed outlier: 3.599A pdb=" N ALA F 63 " --> pdb=" O LYS F 59 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG F 64 " --> pdb=" O TYR F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 99 Processing helix chain 'F' and resid 121 through 123 No H-bonds generated for 'chain 'F' and resid 121 through 123' Processing helix chain 'G' and resid 34 through 41 removed outlier: 3.806A pdb=" N LEU G 40 " --> pdb=" O ALA G 36 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL G 41 " --> pdb=" O ALA G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 60 through 64 removed outlier: 3.730A pdb=" N LEU G 64 " --> pdb=" O PRO G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 66 through 79 Processing helix chain 'H' and resid 84 through 88 Processing helix chain 'I' and resid 48 through 53 removed outlier: 3.702A pdb=" N GLY I 52 " --> pdb=" O ASP I 49 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS I 53 " --> pdb=" O PHE I 50 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 16 No H-bonds generated for 'chain 'J' and resid 14 through 16' Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 30 through 37 Processing helix chain 'J' and resid 42 through 51 removed outlier: 3.592A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 54 through 60 removed outlier: 4.426A pdb=" N LYS J 58 " --> pdb=" O ASP J 54 " (cutoff:3.500A) Processing helix chain 'K' and resid 48 through 60 Processing helix chain 'K' and resid 93 through 129 removed outlier: 3.689A pdb=" N ASN K 129 " --> pdb=" O LYS K 125 " (cutoff:3.500A) Processing helix chain 'M' and resid 132 through 139 removed outlier: 3.540A pdb=" N MET M 135 " --> pdb=" O ARG M 132 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ILE M 139 " --> pdb=" O ASP M 136 " (cutoff:3.500A) Processing helix chain 'M' and resid 145 through 152 Processing helix chain 'M' and resid 153 through 158 Processing helix chain 'M' and resid 162 through 177 removed outlier: 3.862A pdb=" N ALA M 171 " --> pdb=" O ALA M 167 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASP M 177 " --> pdb=" O GLU M 173 " (cutoff:3.500A) Processing helix chain 'M' and resid 180 through 186 Processing helix chain 'M' and resid 187 through 189 No H-bonds generated for 'chain 'M' and resid 187 through 189' Processing helix chain 'M' and resid 221 through 227 Processing helix chain 'M' and resid 228 through 230 No H-bonds generated for 'chain 'M' and resid 228 through 230' Processing helix chain 'M' and resid 253 through 262 removed outlier: 5.360A pdb=" N ALA M 259 " --> pdb=" O PHE M 255 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N LEU M 260 " --> pdb=" O VAL M 256 " (cutoff:3.500A) Processing helix chain 'M' and resid 276 through 289 removed outlier: 3.621A pdb=" N LEU M 280 " --> pdb=" O CYS M 276 " (cutoff:3.500A) Processing helix chain 'M' and resid 303 through 314 Processing helix chain 'M' and resid 329 through 348 removed outlier: 3.636A pdb=" N HIS M 346 " --> pdb=" O ILE M 342 " (cutoff:3.500A) Processing helix chain 'M' and resid 353 through 361 removed outlier: 3.873A pdb=" N LEU M 357 " --> pdb=" O ASP M 353 " (cutoff:3.500A) Processing helix chain 'M' and resid 364 through 375 removed outlier: 3.650A pdb=" N MET M 368 " --> pdb=" O SER M 364 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1690 through 1691 removed outlier: 4.030A pdb=" N ARG A 11 " --> pdb=" O VAL B1135 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ASP B1133 " --> pdb=" O GLN A 13 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE A 15 " --> pdb=" O LYS B1131 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LYS B1131 " --> pdb=" O ILE A 15 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N PHE A 17 " --> pdb=" O LYS B1129 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LYS B1129 " --> pdb=" O PHE A 17 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 31 through 32 removed outlier: 6.632A pdb=" N LYS A 31 " --> pdb=" O HIS A 80 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N GLU A 82 " --> pdb=" O LYS A 31 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ASP A 300 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 11.120A pdb=" N LEU A 85 " --> pdb=" O PHE A 298 " (cutoff:3.500A) removed outlier: 9.983A pdb=" N PHE A 298 " --> pdb=" O LEU A 85 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 215 through 218 removed outlier: 4.493A pdb=" N LEU A 223 " --> pdb=" O LEU A 256 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 435 through 437 removed outlier: 3.949A pdb=" N ILE B1035 " --> pdb=" O VAL A 437 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 1011 through 1013 removed outlier: 5.954A pdb=" N ILE A 456 " --> pdb=" O ARG A 567 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LEU A 569 " --> pdb=" O ILE A 456 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N ILE A 458 " --> pdb=" O LEU A 569 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 467 through 471 removed outlier: 4.047A pdb=" N MET A 496 " --> pdb=" O CYS A 539 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N HIS A 541 " --> pdb=" O ALA A 494 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ALA A 494 " --> pdb=" O HIS A 541 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 647 through 648 Processing sheet with id=AA8, first strand: chain 'A' and resid 675 through 677 removed outlier: 6.182A pdb=" N VAL H 91 " --> pdb=" O LEU A 676 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N VAL H 96 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N SER H 117 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU H 121 " --> pdb=" O TYR H 118 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N GLU H 31 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N VAL H 12 " --> pdb=" O GLU H 31 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 705 through 707 removed outlier: 6.200A pdb=" N ILE A 738 " --> pdb=" O LEU A 745 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1000 through 1001 removed outlier: 6.708A pdb=" N VAL A1007 " --> pdb=" O VAL A1015 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1559 through 1566 removed outlier: 3.698A pdb=" N ARG A1561 " --> pdb=" O GLU A1581 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ASN A1565 " --> pdb=" O VAL A1577 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N VAL A1577 " --> pdb=" O ASN A1565 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1514 through 1517 removed outlier: 3.963A pdb=" N ASP A1514 " --> pdb=" O THR A1528 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL A1527 " --> pdb=" O LEU A1317 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ARG A1318 " --> pdb=" O ILE A1297 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ILE A1297 " --> pdb=" O ARG A1318 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N GLN A1320 " --> pdb=" O GLN A1295 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1302 through 1304 Processing sheet with id=AB5, first strand: chain 'F' and resid 117 through 119 removed outlier: 4.866A pdb=" N LEU A1715 " --> pdb=" O ILE G 105 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE G 105 " --> pdb=" O LEU A1715 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N PHE G 123 " --> pdb=" O PRO G 90 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ILE G 96 " --> pdb=" O GLU G 117 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N GLU G 117 " --> pdb=" O ILE G 96 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N VAL G 98 " --> pdb=" O ASN G 115 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N ASN G 115 " --> pdb=" O VAL G 98 " (cutoff:3.500A) removed outlier: 9.437A pdb=" N GLY G 100 " --> pdb=" O HIS G 113 " (cutoff:3.500A) removed outlier: 10.560A pdb=" N HIS G 113 " --> pdb=" O GLY G 100 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 64 through 67 removed outlier: 6.481A pdb=" N ASP B 117 " --> pdb=" O LEU B 78 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N ALA B 80 " --> pdb=" O THR B 115 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N THR B 115 " --> pdb=" O ALA B 80 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ILE B 82 " --> pdb=" O LYS B 113 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N LYS B 113 " --> pdb=" O ILE B 82 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N LEU B 114 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLY B 128 " --> pdb=" O TRP B 120 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N VAL B 122 " --> pdb=" O SER B 126 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N SER B 126 " --> pdb=" O VAL B 122 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 170 through 172 Processing sheet with id=AB8, first strand: chain 'B' and resid 372 through 375 removed outlier: 3.505A pdb=" N LEU B 182 " --> pdb=" O LEU B 375 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N MET B 181 " --> pdb=" O HIS B 473 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 191 through 194 removed outlier: 5.487A pdb=" N TYR B 228 " --> pdb=" O THR B 206 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N TYR B 208 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N LEU B 226 " --> pdb=" O TYR B 208 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N VAL B 210 " --> pdb=" O MET B 224 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N MET B 224 " --> pdb=" O VAL B 210 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N MET B 212 " --> pdb=" O VAL B 222 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N VAL B 222 " --> pdb=" O MET B 212 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N ASN B 223 " --> pdb=" O ILE B 239 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE B 239 " --> pdb=" O ASN B 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 519 through 520 Processing sheet with id=AC2, first strand: chain 'B' and resid 519 through 520 Processing sheet with id=AC3, first strand: chain 'B' and resid 540 through 541 removed outlier: 5.422A pdb=" N MET B 562 " --> pdb=" O LEU B 558 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU B 558 " --> pdb=" O MET B 562 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLY B 564 " --> pdb=" O VAL B 556 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N LEU B 610 " --> pdb=" O CYS B 553 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N LEU B 612 " --> pdb=" O PRO B 555 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N LEU B 557 " --> pdb=" O LEU B 612 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 712 through 714 removed outlier: 7.621A pdb=" N CYS B 866 " --> pdb=" O VAL B 854 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N VAL B 854 " --> pdb=" O CYS B 866 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N CYS B 868 " --> pdb=" O ILE B 852 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ILE B 852 " --> pdb=" O CYS B 868 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N THR B 870 " --> pdb=" O ASP B 850 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 712 through 714 removed outlier: 7.621A pdb=" N CYS B 866 " --> pdb=" O VAL B 854 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N VAL B 854 " --> pdb=" O CYS B 866 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N CYS B 868 " --> pdb=" O ILE B 852 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ILE B 852 " --> pdb=" O CYS B 868 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N THR B 870 " --> pdb=" O ASP B 850 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N ILE B 852 " --> pdb=" O LYS L 46 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 722 through 723 Processing sheet with id=AC7, first strand: chain 'B' and resid 739 through 741 removed outlier: 7.291A pdb=" N MET B 757 " --> pdb=" O SER B 894 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU B 896 " --> pdb=" O MET B 757 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N VAL B 759 " --> pdb=" O LEU B 896 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE B 758 " --> pdb=" O LEU B 914 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ALA B 744 " --> pdb=" O PHE B 915 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 792 through 794 Processing sheet with id=AC9, first strand: chain 'B' and resid 976 through 977 Processing sheet with id=AD1, first strand: chain 'B' and resid 1065 through 1070 Processing sheet with id=AD2, first strand: chain 'B' and resid 1079 through 1081 Processing sheet with id=AD3, first strand: chain 'C' and resid 50 through 57 removed outlier: 6.676A pdb=" N GLU C 62 " --> pdb=" O VAL C 54 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N MET C 56 " --> pdb=" O SER C 60 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N SER C 60 " --> pdb=" O MET C 56 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N SER C 309 " --> pdb=" O ALA C 231 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ALA C 231 " --> pdb=" O SER C 309 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N GLU C 311 " --> pdb=" O ALA C 229 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 50 through 57 removed outlier: 6.676A pdb=" N GLU C 62 " --> pdb=" O VAL C 54 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N MET C 56 " --> pdb=" O SER C 60 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N SER C 60 " --> pdb=" O MET C 56 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA C 300 " --> pdb=" O ASP C 238 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N LEU C 236 " --> pdb=" O VAL C 302 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 173 through 175 removed outlier: 6.482A pdb=" N GLU C 207 " --> pdb=" O ASN C 97 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASN C 97 " --> pdb=" O GLU C 207 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ASP C 209 " --> pdb=" O TYR C 95 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS C 91 " --> pdb=" O HIS C 213 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N VAL C 215 " --> pdb=" O VAL C 89 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N VAL C 89 " --> pdb=" O VAL C 215 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N GLY C 217 " --> pdb=" O MET C 87 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N MET C 87 " --> pdb=" O GLY C 217 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 115 through 116 removed outlier: 3.791A pdb=" N ARG C 191 " --> pdb=" O HIS C 116 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 147 through 148 Processing sheet with id=AD8, first strand: chain 'C' and resid 167 through 168 Processing sheet with id=AD9, first strand: chain 'C' and resid 262 through 266 Processing sheet with id=AE1, first strand: chain 'E' and resid 60 through 63 Processing sheet with id=AE2, first strand: chain 'E' and resid 101 through 106 removed outlier: 3.597A pdb=" N GLU E 128 " --> pdb=" O ALA E 102 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 147 through 150 removed outlier: 3.535A pdb=" N GLU E 147 " --> pdb=" O ILE E 194 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N ILE E 173 " --> pdb=" O GLN E 210 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 151 through 155 removed outlier: 6.536A pdb=" N GLY G 144 " --> pdb=" O ASN G 136 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 35 through 37 Processing sheet with id=AE6, first strand: chain 'K' and resid 27 through 31 removed outlier: 7.890A pdb=" N LYS K 79 " --> pdb=" O THR K 72 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N THR K 72 " --> pdb=" O LYS K 79 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ASN K 81 " --> pdb=" O TYR K 70 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N TYR K 70 " --> pdb=" O ASN K 81 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ARG K 83 " --> pdb=" O CYS K 68 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N CYS K 68 " --> pdb=" O ARG K 83 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N GLN K 85 " --> pdb=" O GLU K 66 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'N' and resid 24 through 26 removed outlier: 4.651A pdb=" N ASN M 72 " --> pdb=" O ASN M 108 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N ASN M 108 " --> pdb=" O ASN M 72 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLN M 98 " --> pdb=" O ASN M 93 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N HIS M 87 " --> pdb=" O ALA M 104 " (cutoff:3.500A) removed outlier: 10.121A pdb=" N GLY N 113 " --> pdb=" O THR N 40 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N LEU N 42 " --> pdb=" O GLY N 113 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N LEU N 115 " --> pdb=" O LEU N 42 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N LEU N 44 " --> pdb=" O LEU N 115 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N ILE N 117 " --> pdb=" O LEU N 44 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N GLN N 46 " --> pdb=" O ILE N 117 " (cutoff:3.500A) removed outlier: 8.709A pdb=" N GLU N 119 " --> pdb=" O GLN N 46 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLY N 65 " --> pdb=" O SER N 84 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'N' and resid 60 through 62 removed outlier: 7.590A pdb=" N MET M 99 " --> pdb=" O SER M 8 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ARG M 10 " --> pdb=" O MET M 99 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N VAL M 101 " --> pdb=" O ARG M 10 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N GLN M 12 " --> pdb=" O VAL M 101 " (cutoff:3.500A) removed outlier: 8.547A pdb=" N ASP M 103 " --> pdb=" O GLN M 12 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N VAL M 24 " --> pdb=" O LEU N 95 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'M' and resid 316 through 320 1339 hydrogen bonds defined for protein. 3696 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 61 hydrogen bonds 122 hydrogen bond angles 0 basepair planarities 25 basepair parallelities 45 stacking parallelities Total time for adding SS restraints: 16.50 Time building geometry restraints manager: 13.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 8379 1.33 - 1.45: 8162 1.45 - 1.57: 20200 1.57 - 1.69: 133 1.69 - 1.82: 367 Bond restraints: 37241 Sorted by residual: bond pdb=" C PRO N 22 " pdb=" N PRO N 23 " ideal model delta sigma weight residual 1.332 1.394 -0.062 8.90e-03 1.26e+04 4.82e+01 bond pdb=" N VAL B1135 " pdb=" CA VAL B1135 " ideal model delta sigma weight residual 1.458 1.543 -0.085 1.90e-02 2.77e+03 2.00e+01 bond pdb=" CG LEU A 25 " pdb=" CD2 LEU A 25 " ideal model delta sigma weight residual 1.521 1.394 0.127 3.30e-02 9.18e+02 1.49e+01 bond pdb=" CB VAL B 566 " pdb=" CG2 VAL B 566 " ideal model delta sigma weight residual 1.521 1.403 0.118 3.30e-02 9.18e+02 1.27e+01 bond pdb=" C PHE B 920 " pdb=" N PRO B 921 " ideal model delta sigma weight residual 1.336 1.377 -0.041 1.20e-02 6.94e+03 1.18e+01 ... (remaining 37236 not shown) Histogram of bond angle deviations from ideal: 94.84 - 102.78: 381 102.78 - 110.72: 12297 110.72 - 118.66: 17313 118.66 - 126.60: 19974 126.60 - 134.54: 685 Bond angle restraints: 50650 Sorted by residual: angle pdb=" N ARG B 309 " pdb=" CA ARG B 309 " pdb=" C ARG B 309 " ideal model delta sigma weight residual 114.62 106.30 8.32 1.14e+00 7.69e-01 5.33e+01 angle pdb=" C ASP C 195 " pdb=" N ASP C 196 " pdb=" CA ASP C 196 " ideal model delta sigma weight residual 121.54 133.86 -12.32 1.91e+00 2.74e-01 4.16e+01 angle pdb=" C GLU G 159 " pdb=" N GLN G 160 " pdb=" CA GLN G 160 " ideal model delta sigma weight residual 121.54 131.40 -9.86 1.91e+00 2.74e-01 2.66e+01 angle pdb=" N PRO A 961 " pdb=" CA PRO A 961 " pdb=" C PRO A 961 " ideal model delta sigma weight residual 110.70 116.68 -5.98 1.22e+00 6.72e-01 2.40e+01 angle pdb=" C ALA H 109 " pdb=" N THR H 110 " pdb=" CA THR H 110 " ideal model delta sigma weight residual 122.61 130.14 -7.53 1.56e+00 4.11e-01 2.33e+01 ... (remaining 50645 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.59: 20835 16.59 - 33.17: 1232 33.17 - 49.75: 398 49.75 - 66.34: 100 66.34 - 82.92: 31 Dihedral angle restraints: 22596 sinusoidal: 9819 harmonic: 12777 Sorted by residual: dihedral pdb=" CA GLU A 422 " pdb=" C GLU A 422 " pdb=" N LYS A 423 " pdb=" CA LYS A 423 " ideal model delta harmonic sigma weight residual 180.00 124.54 55.46 0 5.00e+00 4.00e-02 1.23e+02 dihedral pdb=" CA LYS A 423 " pdb=" C LYS A 423 " pdb=" N LYS A 424 " pdb=" CA LYS A 424 " ideal model delta harmonic sigma weight residual 180.00 144.70 35.30 0 5.00e+00 4.00e-02 4.99e+01 dihedral pdb=" CA THR G 168 " pdb=" C THR G 168 " pdb=" N MET G 169 " pdb=" CA MET G 169 " ideal model delta harmonic sigma weight residual -180.00 -146.13 -33.87 0 5.00e+00 4.00e-02 4.59e+01 ... (remaining 22593 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 4167 0.070 - 0.139: 1276 0.139 - 0.209: 166 0.209 - 0.279: 19 0.279 - 0.348: 7 Chirality restraints: 5635 Sorted by residual: chirality pdb=" CB ILE A 561 " pdb=" CA ILE A 561 " pdb=" CG1 ILE A 561 " pdb=" CG2 ILE A 561 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.35 2.00e-01 2.50e+01 3.04e+00 chirality pdb=" CB VAL B 620 " pdb=" CA VAL B 620 " pdb=" CG1 VAL B 620 " pdb=" CG2 VAL B 620 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.91e+00 chirality pdb=" CA MET A 881 " pdb=" N MET A 881 " pdb=" C MET A 881 " pdb=" CB MET A 881 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.82e+00 ... (remaining 5632 not shown) Planarity restraints: 6320 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY N 154 " 0.031 2.00e-02 2.50e+03 6.13e-02 3.75e+01 pdb=" C GLY N 154 " -0.106 2.00e-02 2.50e+03 pdb=" O GLY N 154 " 0.040 2.00e-02 2.50e+03 pdb=" N ASN N 155 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B1134 " -0.024 2.00e-02 2.50e+03 4.70e-02 2.21e+01 pdb=" C VAL B1134 " 0.081 2.00e-02 2.50e+03 pdb=" O VAL B1134 " -0.030 2.00e-02 2.50e+03 pdb=" N VAL B1135 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 999 " -0.028 2.00e-02 2.50e+03 2.78e-02 1.55e+01 pdb=" CG TYR B 999 " 0.069 2.00e-02 2.50e+03 pdb=" CD1 TYR B 999 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TYR B 999 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR B 999 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR B 999 " -0.006 2.00e-02 2.50e+03 pdb=" CZ TYR B 999 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 999 " -0.002 2.00e-02 2.50e+03 ... (remaining 6317 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 346 2.61 - 3.18: 29683 3.18 - 3.76: 56552 3.76 - 4.33: 81104 4.33 - 4.90: 133462 Nonbonded interactions: 301147 Sorted by model distance: nonbonded pdb=" O3' G R 19 " pdb="MG MG A1803 " model vdw 2.041 2.170 nonbonded pdb=" OD1 ASP A 588 " pdb="MG MG A1803 " model vdw 2.044 2.170 nonbonded pdb=" OD1 ASP A 590 " pdb="MG MG A1803 " model vdw 2.110 2.170 nonbonded pdb=" OG SER B 856 " pdb=" O ILE L 34 " model vdw 2.226 2.440 nonbonded pdb=" OD2 ASP B 810 " pdb=" OH TYR L 17 " model vdw 2.244 2.440 ... (remaining 301142 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: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 6.680 Check model and map are aligned: 0.510 Set scattering table: 0.290 Process input model: 103.270 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.120 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: 0.010 Load rotamer database and sin/cos tables:12.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 125.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 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 : 0.013 0.129 37241 Z= 0.836 Angle : 1.112 14.188 50650 Z= 0.593 Chirality : 0.065 0.348 5635 Planarity : 0.008 0.064 6320 Dihedral : 12.879 82.925 14350 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.48 % Favored : 94.47 % Rotamer: Outliers : 0.55 % Allowed : 4.50 % Favored : 94.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -3.33 (0.10), residues: 4361 helix: -2.58 (0.10), residues: 1366 sheet: -1.95 (0.18), residues: 658 loop : -2.02 (0.11), residues: 2337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.004 TRP A 846 HIS 0.033 0.003 HIS A 652 PHE 0.052 0.004 PHE C 283 TYR 0.069 0.004 TYR B 999 ARG 0.026 0.002 ARG F 51 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8722 Ramachandran restraints generated. 4361 Oldfield, 0 Emsley, 4361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8722 Ramachandran restraints generated. 4361 Oldfield, 0 Emsley, 4361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 603 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 582 time to evaluate : 4.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1096 ILE cc_start: 0.8106 (mm) cc_final: 0.7550 (mp) REVERT: A 1304 CYS cc_start: 0.8217 (t) cc_final: 0.7895 (t) REVERT: G 111 HIS cc_start: 0.8879 (m-70) cc_final: 0.8603 (m90) REVERT: H 55 LYS cc_start: 0.8997 (ttmt) cc_final: 0.8769 (ttmm) REVERT: H 133 HIS cc_start: 0.7957 (m-70) cc_final: 0.7749 (m-70) REVERT: I 21 SER cc_start: 0.8733 (p) cc_final: 0.8343 (t) REVERT: N 68 ILE cc_start: 0.9234 (mp) cc_final: 0.8842 (mp) REVERT: M 327 LEU cc_start: 0.8014 (mp) cc_final: 0.7728 (mm) REVERT: M 371 ILE cc_start: 0.8283 (mm) cc_final: 0.8022 (pp) outliers start: 21 outliers final: 7 residues processed: 599 average time/residue: 1.7657 time to fit residues: 1240.7679 Evaluate side-chains 379 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 372 time to evaluate : 4.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 391 TRP Chi-restraints excluded: chain A residue 1190 ASP Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 867 VAL Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain L residue 32 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 367 optimal weight: 2.9990 chunk 329 optimal weight: 20.0000 chunk 182 optimal weight: 5.9990 chunk 112 optimal weight: 1.9990 chunk 222 optimal weight: 2.9990 chunk 176 optimal weight: 4.9990 chunk 340 optimal weight: 6.9990 chunk 131 optimal weight: 5.9990 chunk 207 optimal weight: 2.9990 chunk 253 optimal weight: 0.9980 chunk 395 optimal weight: 30.0000 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN ** A 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 118 HIS A 264 HIS A 595 ASN A 859 ASN A 877 ASN A 895 GLN A 995 HIS A1054 HIS A1094 GLN A1109 ASN A1217 GLN A1309 GLN A1537 ASN B 30 GLN B 227 HIS B 266 GLN B 580 HIS B 889 GLN ** B 916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1060 ASN E 107 GLN K 38 HIS ** K 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 78 HIS M 34 GLN M 82 ASN M 108 ASN M 152 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 37241 Z= 0.250 Angle : 0.661 10.371 50650 Z= 0.345 Chirality : 0.044 0.159 5635 Planarity : 0.006 0.055 6320 Dihedral : 12.393 83.788 5643 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.49 % Favored : 95.48 % Rotamer: Outliers : 2.42 % Allowed : 10.87 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.12), residues: 4361 helix: -0.72 (0.13), residues: 1379 sheet: -1.55 (0.18), residues: 681 loop : -1.54 (0.12), residues: 2301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 846 HIS 0.012 0.001 HIS A1054 PHE 0.046 0.002 PHE B 308 TYR 0.026 0.002 TYR A 20 ARG 0.011 0.001 ARG N 77 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8722 Ramachandran restraints generated. 4361 Oldfield, 0 Emsley, 4361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8722 Ramachandran restraints generated. 4361 Oldfield, 0 Emsley, 4361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 400 time to evaluate : 4.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 LYS cc_start: 0.8960 (OUTLIER) cc_final: 0.8589 (mmmt) REVERT: A 314 ARG cc_start: 0.7098 (ttp-110) cc_final: 0.6741 (mtm-85) REVERT: A 1101 LYS cc_start: 0.7827 (pptt) cc_final: 0.7487 (ttpt) REVERT: A 1123 MET cc_start: 0.8485 (mtm) cc_final: 0.8258 (mpt) REVERT: A 1304 CYS cc_start: 0.8142 (t) cc_final: 0.7720 (t) REVERT: B 417 MET cc_start: 0.7603 (mmt) cc_final: 0.7286 (mmm) REVERT: H 133 HIS cc_start: 0.7953 (m-70) cc_final: 0.7738 (m-70) REVERT: I 21 SER cc_start: 0.8525 (p) cc_final: 0.8114 (t) REVERT: I 53 LYS cc_start: 0.7941 (OUTLIER) cc_final: 0.7588 (tmmm) REVERT: J 31 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.8010 (mt-10) REVERT: N 67 GLN cc_start: 0.7962 (tm-30) cc_final: 0.7613 (tm-30) REVERT: M 109 MET cc_start: 0.7660 (mmm) cc_final: 0.7272 (mmm) REVERT: M 327 LEU cc_start: 0.7881 (mp) cc_final: 0.7546 (mm) REVERT: M 371 ILE cc_start: 0.8172 (mm) cc_final: 0.7963 (pp) REVERT: M 375 MET cc_start: 0.6658 (tmt) cc_final: 0.5688 (tmt) outliers start: 93 outliers final: 22 residues processed: 448 average time/residue: 1.6086 time to fit residues: 862.5353 Evaluate side-chains 377 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 352 time to evaluate : 4.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 1052 HIS Chi-restraints excluded: chain A residue 1190 ASP Chi-restraints excluded: chain A residue 1263 MET Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 576 ASP Chi-restraints excluded: chain B residue 649 ASP Chi-restraints excluded: chain B residue 867 VAL Chi-restraints excluded: chain C residue 256 CYS Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain I residue 53 LYS Chi-restraints excluded: chain J residue 31 GLU Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 117 SER Chi-restraints excluded: chain N residue 69 VAL Chi-restraints excluded: chain N residue 82 VAL Chi-restraints excluded: chain M residue 205 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 219 optimal weight: 7.9990 chunk 122 optimal weight: 9.9990 chunk 328 optimal weight: 50.0000 chunk 268 optimal weight: 4.9990 chunk 108 optimal weight: 6.9990 chunk 395 optimal weight: 0.9990 chunk 427 optimal weight: 8.9990 chunk 352 optimal weight: 10.0000 chunk 392 optimal weight: 30.0000 chunk 134 optimal weight: 10.0000 chunk 317 optimal weight: 2.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 HIS A 201 ASN A 327 ASN A 859 ASN A 908 ASN A 967 HIS A1054 HIS B 639 GLN ** B 916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 55 HIS G 109 GLN G 111 HIS G 113 HIS ** K 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 124 GLN N 123 GLN M 108 ASN M 152 ASN M 358 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 37241 Z= 0.376 Angle : 0.642 7.611 50650 Z= 0.334 Chirality : 0.045 0.181 5635 Planarity : 0.005 0.049 6320 Dihedral : 12.181 84.060 5639 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.49 % Favored : 95.48 % Rotamer: Outliers : 2.99 % Allowed : 12.06 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.12), residues: 4361 helix: 0.12 (0.14), residues: 1399 sheet: -1.28 (0.19), residues: 679 loop : -1.23 (0.12), residues: 2283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 317 HIS 0.012 0.001 HIS A1054 PHE 0.018 0.002 PHE C 336 TYR 0.028 0.002 TYR A 388 ARG 0.008 0.001 ARG H 140 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8722 Ramachandran restraints generated. 4361 Oldfield, 0 Emsley, 4361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8722 Ramachandran restraints generated. 4361 Oldfield, 0 Emsley, 4361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 364 time to evaluate : 4.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 LYS cc_start: 0.8991 (OUTLIER) cc_final: 0.8673 (mmmt) REVERT: A 521 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.8114 (mp10) REVERT: A 862 ASP cc_start: 0.7880 (OUTLIER) cc_final: 0.7664 (t70) REVERT: A 1101 LYS cc_start: 0.7893 (pptt) cc_final: 0.7468 (ttpt) REVERT: B 337 LYS cc_start: 0.8281 (OUTLIER) cc_final: 0.7985 (ptmt) REVERT: B 411 MET cc_start: 0.4748 (pmt) cc_final: 0.3805 (ptp) REVERT: B 562 MET cc_start: 0.8715 (OUTLIER) cc_final: 0.8182 (ttt) REVERT: B 723 ARG cc_start: 0.8881 (OUTLIER) cc_final: 0.8432 (pmt100) REVERT: B 1082 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.7196 (pm20) REVERT: E 87 ILE cc_start: 0.9140 (OUTLIER) cc_final: 0.8895 (pt) REVERT: G 117 GLU cc_start: 0.6835 (mm-30) cc_final: 0.6285 (mp0) REVERT: G 173 MET cc_start: 0.4149 (OUTLIER) cc_final: 0.3797 (ptp) REVERT: H 81 ARG cc_start: 0.7275 (OUTLIER) cc_final: 0.6807 (ptm160) REVERT: I 17 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8672 (tt) REVERT: I 21 SER cc_start: 0.8685 (p) cc_final: 0.8253 (t) REVERT: I 53 LYS cc_start: 0.7921 (OUTLIER) cc_final: 0.7684 (tmmm) REVERT: N 67 GLN cc_start: 0.8096 (tm-30) cc_final: 0.7541 (tm-30) REVERT: M 109 MET cc_start: 0.7843 (mmm) cc_final: 0.7260 (mmm) REVERT: M 134 LYS cc_start: 0.5181 (OUTLIER) cc_final: 0.4919 (mmtm) REVERT: M 327 LEU cc_start: 0.7914 (mp) cc_final: 0.7586 (mm) outliers start: 115 outliers final: 35 residues processed: 433 average time/residue: 1.5647 time to fit residues: 810.2966 Evaluate side-chains 379 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 331 time to evaluate : 4.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 410 MET Chi-restraints excluded: chain A residue 512 MET Chi-restraints excluded: chain A residue 521 GLN Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 662 THR Chi-restraints excluded: chain A residue 862 ASP Chi-restraints excluded: chain A residue 1052 HIS Chi-restraints excluded: chain A residue 1190 ASP Chi-restraints excluded: chain A residue 1213 LEU Chi-restraints excluded: chain B residue 337 LYS Chi-restraints excluded: chain B residue 562 MET Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 649 ASP Chi-restraints excluded: chain B residue 723 ARG Chi-restraints excluded: chain B residue 867 VAL Chi-restraints excluded: chain B residue 1082 GLU Chi-restraints excluded: chain C residue 256 CYS Chi-restraints excluded: chain E residue 87 ILE Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 173 MET Chi-restraints excluded: chain H residue 18 GLU Chi-restraints excluded: chain H residue 81 ARG Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain I residue 17 LEU Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 53 LYS Chi-restraints excluded: chain I residue 64 LEU Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain K residue 117 SER Chi-restraints excluded: chain L residue 32 ASP Chi-restraints excluded: chain N residue 69 VAL Chi-restraints excluded: chain N residue 93 THR Chi-restraints excluded: chain N residue 118 LEU Chi-restraints excluded: chain N residue 133 ILE Chi-restraints excluded: chain N residue 158 VAL Chi-restraints excluded: chain M residue 134 LYS Chi-restraints excluded: chain M residue 205 ASP Chi-restraints excluded: chain M residue 220 LEU Chi-restraints excluded: chain M residue 311 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 390 optimal weight: 8.9990 chunk 297 optimal weight: 9.9990 chunk 205 optimal weight: 6.9990 chunk 43 optimal weight: 8.9990 chunk 188 optimal weight: 6.9990 chunk 265 optimal weight: 4.9990 chunk 397 optimal weight: 30.0000 chunk 420 optimal weight: 7.9990 chunk 207 optimal weight: 9.9990 chunk 376 optimal weight: 9.9990 chunk 113 optimal weight: 1.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1054 HIS A1217 GLN B 30 GLN ** B 916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 GLN E 107 GLN ** K 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 17 ASN M 87 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.079 37241 Z= 0.431 Angle : 0.654 8.367 50650 Z= 0.339 Chirality : 0.046 0.188 5635 Planarity : 0.005 0.054 6320 Dihedral : 12.141 84.198 5638 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.79 % Favored : 95.18 % Rotamer: Outliers : 3.20 % Allowed : 13.18 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.84 (0.12), residues: 4361 helix: 0.53 (0.14), residues: 1397 sheet: -1.13 (0.19), residues: 677 loop : -1.02 (0.13), residues: 2287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 317 HIS 0.011 0.001 HIS A1054 PHE 0.021 0.002 PHE B 246 TYR 0.031 0.002 TYR A 388 ARG 0.007 0.001 ARG H 140 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8722 Ramachandran restraints generated. 4361 Oldfield, 0 Emsley, 4361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8722 Ramachandran restraints generated. 4361 Oldfield, 0 Emsley, 4361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 348 time to evaluate : 3.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 LYS cc_start: 0.8993 (OUTLIER) cc_final: 0.8717 (mmmt) REVERT: A 272 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.7201 (mm-30) REVERT: A 521 GLN cc_start: 0.8513 (OUTLIER) cc_final: 0.8096 (mp10) REVERT: A 627 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8430 (pt) REVERT: A 862 ASP cc_start: 0.7927 (OUTLIER) cc_final: 0.7719 (t70) REVERT: A 1101 LYS cc_start: 0.7943 (pptt) cc_final: 0.7583 (ttpt) REVERT: B 158 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.7437 (mp0) REVERT: B 231 ASN cc_start: 0.9016 (OUTLIER) cc_final: 0.8571 (p0) REVERT: B 337 LYS cc_start: 0.8277 (OUTLIER) cc_final: 0.7970 (ptmt) REVERT: B 411 MET cc_start: 0.4732 (pmt) cc_final: 0.3783 (ptp) REVERT: B 700 LEU cc_start: 0.9407 (OUTLIER) cc_final: 0.9166 (pp) REVERT: B 1082 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.7226 (pm20) REVERT: F 75 MET cc_start: 0.8377 (OUTLIER) cc_final: 0.7887 (mmm) REVERT: G 101 GLU cc_start: 0.6522 (OUTLIER) cc_final: 0.5290 (tm-30) REVERT: G 117 GLU cc_start: 0.6995 (mm-30) cc_final: 0.6457 (mp0) REVERT: G 173 MET cc_start: 0.4074 (OUTLIER) cc_final: 0.3676 (pmm) REVERT: H 81 ARG cc_start: 0.7366 (OUTLIER) cc_final: 0.6819 (ptm160) REVERT: H 133 HIS cc_start: 0.7951 (m-70) cc_final: 0.7750 (m-70) REVERT: I 17 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8646 (tt) REVERT: I 21 SER cc_start: 0.8828 (p) cc_final: 0.8420 (t) REVERT: I 53 LYS cc_start: 0.8000 (OUTLIER) cc_final: 0.7715 (tmmm) REVERT: J 28 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7711 (mp0) REVERT: K 60 MET cc_start: 0.8585 (mmm) cc_final: 0.8378 (mmp) REVERT: N 41 GLU cc_start: 0.7616 (pm20) cc_final: 0.7274 (pp20) REVERT: N 67 GLN cc_start: 0.8240 (tm-30) cc_final: 0.7626 (tm-30) REVERT: N 93 THR cc_start: 0.8847 (OUTLIER) cc_final: 0.8638 (p) REVERT: M 109 MET cc_start: 0.7933 (mmm) cc_final: 0.7134 (mmm) REVERT: M 134 LYS cc_start: 0.5166 (OUTLIER) cc_final: 0.4944 (mmtm) REVERT: M 320 ASN cc_start: 0.6092 (OUTLIER) cc_final: 0.5467 (t0) REVERT: M 327 LEU cc_start: 0.7951 (mp) cc_final: 0.7630 (mm) REVERT: M 377 LEU cc_start: 0.4611 (OUTLIER) cc_final: 0.4365 (OUTLIER) outliers start: 123 outliers final: 45 residues processed: 429 average time/residue: 1.5960 time to fit residues: 816.9073 Evaluate side-chains 401 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 336 time to evaluate : 3.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 410 MET Chi-restraints excluded: chain A residue 512 MET Chi-restraints excluded: chain A residue 521 GLN Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain A residue 662 THR Chi-restraints excluded: chain A residue 862 ASP Chi-restraints excluded: chain A residue 1052 HIS Chi-restraints excluded: chain A residue 1111 ASN Chi-restraints excluded: chain A residue 1190 ASP Chi-restraints excluded: chain A residue 1213 LEU Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1324 HIS Chi-restraints excluded: chain A residue 1563 LEU Chi-restraints excluded: chain A residue 1618 LEU Chi-restraints excluded: chain B residue 158 GLU Chi-restraints excluded: chain B residue 231 ASN Chi-restraints excluded: chain B residue 313 ASN Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 337 LYS Chi-restraints excluded: chain B residue 481 MET Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 649 ASP Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 705 ASP Chi-restraints excluded: chain B residue 723 ARG Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 867 VAL Chi-restraints excluded: chain B residue 1082 GLU Chi-restraints excluded: chain C residue 256 CYS Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 87 ILE Chi-restraints excluded: chain F residue 75 MET Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain G residue 101 GLU Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 173 MET Chi-restraints excluded: chain H residue 18 GLU Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 81 ARG Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain I residue 17 LEU Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 53 LYS Chi-restraints excluded: chain J residue 28 GLU Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain K residue 117 SER Chi-restraints excluded: chain N residue 59 ARG Chi-restraints excluded: chain N residue 93 THR Chi-restraints excluded: chain N residue 118 LEU Chi-restraints excluded: chain M residue 134 LYS Chi-restraints excluded: chain M residue 205 ASP Chi-restraints excluded: chain M residue 213 VAL Chi-restraints excluded: chain M residue 220 LEU Chi-restraints excluded: chain M residue 311 LEU Chi-restraints excluded: chain M residue 320 ASN Chi-restraints excluded: chain M residue 377 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 350 optimal weight: 7.9990 chunk 238 optimal weight: 4.9990 chunk 6 optimal weight: 7.9990 chunk 313 optimal weight: 7.9990 chunk 173 optimal weight: 0.9990 chunk 358 optimal weight: 1.9990 chunk 290 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 214 optimal weight: 0.9980 chunk 377 optimal weight: 5.9990 chunk 106 optimal weight: 20.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 ASN A 581 ASN A1054 HIS B 30 GLN ** B 916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 167 GLN ** K 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 17 ASN N 60 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 37241 Z= 0.214 Angle : 0.583 10.271 50650 Z= 0.299 Chirality : 0.042 0.184 5635 Planarity : 0.004 0.054 6320 Dihedral : 11.996 84.017 5638 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.81 % Allowed : 13.93 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.54 (0.13), residues: 4361 helix: 0.84 (0.14), residues: 1406 sheet: -1.02 (0.19), residues: 687 loop : -0.87 (0.13), residues: 2268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 317 HIS 0.011 0.001 HIS A1054 PHE 0.018 0.001 PHE C 336 TYR 0.028 0.001 TYR A 388 ARG 0.012 0.000 ARG N 77 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8722 Ramachandran restraints generated. 4361 Oldfield, 0 Emsley, 4361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8722 Ramachandran restraints generated. 4361 Oldfield, 0 Emsley, 4361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 351 time to evaluate : 4.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 LYS cc_start: 0.8962 (OUTLIER) cc_final: 0.8697 (mmmt) REVERT: A 521 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.8069 (mp10) REVERT: A 862 ASP cc_start: 0.7894 (OUTLIER) cc_final: 0.7678 (t70) REVERT: A 1101 LYS cc_start: 0.7889 (pptt) cc_final: 0.7539 (tmmt) REVERT: A 1123 MET cc_start: 0.8477 (mtm) cc_final: 0.8194 (mtt) REVERT: A 1358 ASN cc_start: 0.8288 (OUTLIER) cc_final: 0.8075 (t0) REVERT: B 158 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.7476 (mp0) REVERT: B 212 MET cc_start: 0.8599 (OUTLIER) cc_final: 0.7793 (tpt) REVERT: B 216 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.7782 (ttt-90) REVERT: B 231 ASN cc_start: 0.8939 (OUTLIER) cc_final: 0.8491 (p0) REVERT: B 337 LYS cc_start: 0.8201 (OUTLIER) cc_final: 0.7924 (ptmt) REVERT: B 411 MET cc_start: 0.4675 (pmt) cc_final: 0.4151 (ptp) REVERT: B 417 MET cc_start: 0.7399 (mmt) cc_final: 0.7092 (mmm) REVERT: B 700 LEU cc_start: 0.9348 (OUTLIER) cc_final: 0.9109 (pp) REVERT: B 723 ARG cc_start: 0.8851 (OUTLIER) cc_final: 0.8263 (pmt100) REVERT: B 1082 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7258 (pm20) REVERT: E 87 ILE cc_start: 0.9048 (OUTLIER) cc_final: 0.8847 (pt) REVERT: G 117 GLU cc_start: 0.6977 (mm-30) cc_final: 0.6441 (mp0) REVERT: H 81 ARG cc_start: 0.7343 (OUTLIER) cc_final: 0.6763 (ptm160) REVERT: H 133 HIS cc_start: 0.7895 (m-70) cc_final: 0.7645 (m-70) REVERT: I 17 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8644 (tt) REVERT: I 21 SER cc_start: 0.8780 (p) cc_final: 0.8376 (t) REVERT: I 53 LYS cc_start: 0.8018 (OUTLIER) cc_final: 0.7772 (tmmm) REVERT: J 31 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.8025 (mp0) REVERT: K 31 GLN cc_start: 0.7898 (OUTLIER) cc_final: 0.7069 (mm-40) REVERT: N 41 GLU cc_start: 0.7176 (pm20) cc_final: 0.6583 (pm20) REVERT: N 67 GLN cc_start: 0.8328 (tm-30) cc_final: 0.7665 (tm-30) REVERT: N 93 THR cc_start: 0.8888 (OUTLIER) cc_final: 0.8673 (p) REVERT: M 51 ASN cc_start: 0.7253 (OUTLIER) cc_final: 0.6899 (p0) REVERT: M 109 MET cc_start: 0.7841 (mmm) cc_final: 0.7073 (mmm) REVERT: M 134 LYS cc_start: 0.5127 (OUTLIER) cc_final: 0.4904 (mmtm) REVERT: M 327 LEU cc_start: 0.7979 (mp) cc_final: 0.7679 (mm) outliers start: 108 outliers final: 32 residues processed: 412 average time/residue: 1.5980 time to fit residues: 787.4591 Evaluate side-chains 386 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 333 time to evaluate : 3.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 478 GLN Chi-restraints excluded: chain A residue 512 MET Chi-restraints excluded: chain A residue 521 GLN Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 862 ASP Chi-restraints excluded: chain A residue 1052 HIS Chi-restraints excluded: chain A residue 1111 ASN Chi-restraints excluded: chain A residue 1190 ASP Chi-restraints excluded: chain A residue 1213 LEU Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1358 ASN Chi-restraints excluded: chain A residue 1563 LEU Chi-restraints excluded: chain A residue 1672 MET Chi-restraints excluded: chain B residue 158 GLU Chi-restraints excluded: chain B residue 212 MET Chi-restraints excluded: chain B residue 216 ARG Chi-restraints excluded: chain B residue 231 ASN Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 337 LYS Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 705 ASP Chi-restraints excluded: chain B residue 723 ARG Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 867 VAL Chi-restraints excluded: chain B residue 1082 GLU Chi-restraints excluded: chain C residue 256 CYS Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 87 ILE Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 173 MET Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 81 ARG Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain I residue 17 LEU Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 53 LYS Chi-restraints excluded: chain J residue 31 GLU Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain K residue 31 GLN Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 117 SER Chi-restraints excluded: chain L residue 26 ASN Chi-restraints excluded: chain N residue 93 THR Chi-restraints excluded: chain N residue 131 GLN Chi-restraints excluded: chain M residue 51 ASN Chi-restraints excluded: chain M residue 134 LYS Chi-restraints excluded: chain M residue 205 ASP Chi-restraints excluded: chain M residue 220 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 141 optimal weight: 0.0000 chunk 378 optimal weight: 3.9990 chunk 83 optimal weight: 8.9990 chunk 246 optimal weight: 7.9990 chunk 103 optimal weight: 20.0000 chunk 420 optimal weight: 50.0000 chunk 349 optimal weight: 20.0000 chunk 194 optimal weight: 0.0980 chunk 34 optimal weight: 2.9990 chunk 139 optimal weight: 5.9990 chunk 220 optimal weight: 4.9990 overall best weight: 2.4190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 ASN A1054 HIS B 889 GLN ** B 916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 17 ASN M 34 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 37241 Z= 0.226 Angle : 0.577 12.688 50650 Z= 0.295 Chirality : 0.042 0.196 5635 Planarity : 0.004 0.051 6320 Dihedral : 11.908 84.040 5638 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.39 % Allowed : 15.02 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.31 (0.13), residues: 4361 helix: 1.04 (0.14), residues: 1404 sheet: -0.90 (0.19), residues: 686 loop : -0.73 (0.13), residues: 2271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 317 HIS 0.012 0.001 HIS A1054 PHE 0.017 0.001 PHE C 336 TYR 0.016 0.001 TYR A 450 ARG 0.009 0.000 ARG L 31 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8722 Ramachandran restraints generated. 4361 Oldfield, 0 Emsley, 4361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8722 Ramachandran restraints generated. 4361 Oldfield, 0 Emsley, 4361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 346 time to evaluate : 4.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8440 (mm) REVERT: A 209 LYS cc_start: 0.8947 (OUTLIER) cc_final: 0.8695 (mmmt) REVERT: A 345 MET cc_start: 0.7855 (tpp) cc_final: 0.7451 (mtt) REVERT: A 521 GLN cc_start: 0.8491 (OUTLIER) cc_final: 0.8086 (mp10) REVERT: A 862 ASP cc_start: 0.7902 (OUTLIER) cc_final: 0.7679 (t70) REVERT: A 1101 LYS cc_start: 0.7908 (pptt) cc_final: 0.7561 (tmmt) REVERT: A 1123 MET cc_start: 0.8481 (mtm) cc_final: 0.8167 (mtt) REVERT: B 158 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.7496 (mp0) REVERT: B 212 MET cc_start: 0.8576 (OUTLIER) cc_final: 0.7213 (tpt) REVERT: B 216 ARG cc_start: 0.8044 (OUTLIER) cc_final: 0.7774 (ttt-90) REVERT: B 231 ASN cc_start: 0.8938 (OUTLIER) cc_final: 0.8461 (p0) REVERT: B 337 LYS cc_start: 0.8205 (OUTLIER) cc_final: 0.7928 (ptmt) REVERT: B 411 MET cc_start: 0.4697 (pmt) cc_final: 0.4160 (ptp) REVERT: B 417 MET cc_start: 0.7380 (mmt) cc_final: 0.7077 (mmm) REVERT: B 700 LEU cc_start: 0.9351 (OUTLIER) cc_final: 0.9111 (pp) REVERT: B 723 ARG cc_start: 0.8850 (OUTLIER) cc_final: 0.8140 (pmt100) REVERT: E 87 ILE cc_start: 0.9112 (OUTLIER) cc_final: 0.8873 (pt) REVERT: G 117 GLU cc_start: 0.6997 (mm-30) cc_final: 0.6463 (mp0) REVERT: G 173 MET cc_start: 0.3755 (OUTLIER) cc_final: 0.3193 (tpt) REVERT: H 81 ARG cc_start: 0.7329 (OUTLIER) cc_final: 0.6799 (ptm160) REVERT: H 133 HIS cc_start: 0.7906 (m-70) cc_final: 0.7645 (m-70) REVERT: I 17 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8655 (tt) REVERT: I 21 SER cc_start: 0.8794 (p) cc_final: 0.8397 (t) REVERT: I 53 LYS cc_start: 0.8066 (OUTLIER) cc_final: 0.7800 (tmmm) REVERT: J 31 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.8030 (mp0) REVERT: K 31 GLN cc_start: 0.7894 (OUTLIER) cc_final: 0.7072 (mm-40) REVERT: N 67 GLN cc_start: 0.8351 (tm-30) cc_final: 0.7635 (tm-30) REVERT: M 5 VAL cc_start: 0.3910 (OUTLIER) cc_final: 0.3706 (m) REVERT: M 51 ASN cc_start: 0.7224 (OUTLIER) cc_final: 0.6960 (t0) REVERT: M 109 MET cc_start: 0.7851 (mmm) cc_final: 0.7061 (mmm) REVERT: M 134 LYS cc_start: 0.5086 (OUTLIER) cc_final: 0.4870 (mmtm) REVERT: M 198 LEU cc_start: 0.5178 (OUTLIER) cc_final: 0.4968 (pt) REVERT: M 320 ASN cc_start: 0.6103 (OUTLIER) cc_final: 0.5427 (t0) REVERT: M 327 LEU cc_start: 0.7957 (mp) cc_final: 0.7661 (mm) outliers start: 92 outliers final: 37 residues processed: 409 average time/residue: 1.6189 time to fit residues: 791.2003 Evaluate side-chains 382 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 322 time to evaluate : 4.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 512 MET Chi-restraints excluded: chain A residue 521 GLN Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 862 ASP Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1052 HIS Chi-restraints excluded: chain A residue 1111 ASN Chi-restraints excluded: chain A residue 1190 ASP Chi-restraints excluded: chain A residue 1213 LEU Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1563 LEU Chi-restraints excluded: chain A residue 1618 LEU Chi-restraints excluded: chain B residue 158 GLU Chi-restraints excluded: chain B residue 212 MET Chi-restraints excluded: chain B residue 216 ARG Chi-restraints excluded: chain B residue 231 ASN Chi-restraints excluded: chain B residue 313 ASN Chi-restraints excluded: chain B residue 337 LYS Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 705 ASP Chi-restraints excluded: chain B residue 723 ARG Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 867 VAL Chi-restraints excluded: chain C residue 256 CYS Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 87 ILE Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 121 ASP Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 173 MET Chi-restraints excluded: chain H residue 18 GLU Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 81 ARG Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain I residue 17 LEU Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 53 LYS Chi-restraints excluded: chain J residue 31 GLU Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain K residue 31 GLN Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 117 SER Chi-restraints excluded: chain N residue 118 LEU Chi-restraints excluded: chain N residue 131 GLN Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 51 ASN Chi-restraints excluded: chain M residue 134 LYS Chi-restraints excluded: chain M residue 198 LEU Chi-restraints excluded: chain M residue 213 VAL Chi-restraints excluded: chain M residue 220 LEU Chi-restraints excluded: chain M residue 320 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 405 optimal weight: 8.9990 chunk 47 optimal weight: 6.9990 chunk 239 optimal weight: 10.0000 chunk 307 optimal weight: 6.9990 chunk 238 optimal weight: 3.9990 chunk 354 optimal weight: 2.9990 chunk 235 optimal weight: 8.9990 chunk 419 optimal weight: 50.0000 chunk 262 optimal weight: 4.9990 chunk 255 optimal weight: 9.9990 chunk 193 optimal weight: 8.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A1054 HIS B 30 GLN ** B 916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 17 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 37241 Z= 0.393 Angle : 0.648 13.756 50650 Z= 0.330 Chirality : 0.045 0.200 5635 Planarity : 0.005 0.060 6320 Dihedral : 11.963 83.205 5638 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 2.70 % Allowed : 14.82 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.24 (0.13), residues: 4361 helix: 1.07 (0.14), residues: 1402 sheet: -0.83 (0.19), residues: 689 loop : -0.67 (0.13), residues: 2270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 317 HIS 0.014 0.001 HIS A1054 PHE 0.024 0.002 PHE B 434 TYR 0.022 0.002 TYR E 125 ARG 0.013 0.001 ARG N 77 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8722 Ramachandran restraints generated. 4361 Oldfield, 0 Emsley, 4361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8722 Ramachandran restraints generated. 4361 Oldfield, 0 Emsley, 4361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 333 time to evaluate : 3.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8643 (mm) REVERT: A 209 LYS cc_start: 0.8964 (OUTLIER) cc_final: 0.8702 (mmmt) REVERT: A 345 MET cc_start: 0.7936 (tpp) cc_final: 0.7576 (mtt) REVERT: A 521 GLN cc_start: 0.8473 (OUTLIER) cc_final: 0.8034 (mp10) REVERT: A 627 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8378 (pt) REVERT: A 862 ASP cc_start: 0.7936 (OUTLIER) cc_final: 0.7708 (t70) REVERT: A 1101 LYS cc_start: 0.7955 (pptt) cc_final: 0.7620 (ttpt) REVERT: A 1123 MET cc_start: 0.8490 (mtm) cc_final: 0.8175 (mtt) REVERT: B 158 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7495 (mp0) REVERT: B 216 ARG cc_start: 0.8158 (OUTLIER) cc_final: 0.7850 (ttt-90) REVERT: B 231 ASN cc_start: 0.8992 (OUTLIER) cc_final: 0.8526 (p0) REVERT: B 337 LYS cc_start: 0.8276 (OUTLIER) cc_final: 0.7982 (ptmt) REVERT: B 411 MET cc_start: 0.4662 (pmt) cc_final: 0.4155 (ptp) REVERT: B 417 MET cc_start: 0.7436 (mmt) cc_final: 0.7137 (mmm) REVERT: B 700 LEU cc_start: 0.9383 (OUTLIER) cc_final: 0.9139 (pp) REVERT: G 101 GLU cc_start: 0.6600 (OUTLIER) cc_final: 0.5452 (tm-30) REVERT: G 117 GLU cc_start: 0.7056 (mm-30) cc_final: 0.6488 (mp0) REVERT: G 173 MET cc_start: 0.3653 (OUTLIER) cc_final: 0.3273 (tpt) REVERT: H 81 ARG cc_start: 0.7307 (OUTLIER) cc_final: 0.6760 (ptm160) REVERT: I 17 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8655 (tt) REVERT: I 21 SER cc_start: 0.8958 (p) cc_final: 0.8558 (t) REVERT: I 53 LYS cc_start: 0.8097 (OUTLIER) cc_final: 0.7819 (tmmm) REVERT: J 28 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7688 (mp0) REVERT: J 31 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.8046 (mp0) REVERT: K 31 GLN cc_start: 0.7909 (OUTLIER) cc_final: 0.7610 (mt0) REVERT: N 41 GLU cc_start: 0.7148 (OUTLIER) cc_final: 0.6372 (pp20) REVERT: M 134 LYS cc_start: 0.5062 (OUTLIER) cc_final: 0.4838 (mmtm) REVERT: M 198 LEU cc_start: 0.5176 (OUTLIER) cc_final: 0.4958 (pt) REVERT: M 320 ASN cc_start: 0.6125 (OUTLIER) cc_final: 0.5647 (t0) REVERT: M 327 LEU cc_start: 0.7955 (mp) cc_final: 0.7677 (mm) outliers start: 104 outliers final: 44 residues processed: 409 average time/residue: 1.6235 time to fit residues: 800.9628 Evaluate side-chains 387 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 321 time to evaluate : 4.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 512 MET Chi-restraints excluded: chain A residue 521 GLN Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain A residue 862 ASP Chi-restraints excluded: chain A residue 1052 HIS Chi-restraints excluded: chain A residue 1111 ASN Chi-restraints excluded: chain A residue 1190 ASP Chi-restraints excluded: chain A residue 1213 LEU Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1563 LEU Chi-restraints excluded: chain A residue 1618 LEU Chi-restraints excluded: chain B residue 158 GLU Chi-restraints excluded: chain B residue 212 MET Chi-restraints excluded: chain B residue 216 ARG Chi-restraints excluded: chain B residue 231 ASN Chi-restraints excluded: chain B residue 337 LYS Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 705 ASP Chi-restraints excluded: chain B residue 723 ARG Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 867 VAL Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 256 CYS Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 87 ILE Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 121 ASP Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 101 GLU Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 173 MET Chi-restraints excluded: chain H residue 18 GLU Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 81 ARG Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain I residue 17 LEU Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 53 LYS Chi-restraints excluded: chain J residue 28 GLU Chi-restraints excluded: chain J residue 31 GLU Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain K residue 31 GLN Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 117 SER Chi-restraints excluded: chain N residue 18 PHE Chi-restraints excluded: chain N residue 41 GLU Chi-restraints excluded: chain N residue 45 ILE Chi-restraints excluded: chain N residue 118 LEU Chi-restraints excluded: chain N residue 131 GLN Chi-restraints excluded: chain M residue 134 LYS Chi-restraints excluded: chain M residue 198 LEU Chi-restraints excluded: chain M residue 205 ASP Chi-restraints excluded: chain M residue 213 VAL Chi-restraints excluded: chain M residue 320 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 259 optimal weight: 10.0000 chunk 167 optimal weight: 1.9990 chunk 250 optimal weight: 7.9990 chunk 126 optimal weight: 9.9990 chunk 82 optimal weight: 9.9990 chunk 81 optimal weight: 0.9990 chunk 266 optimal weight: 6.9990 chunk 285 optimal weight: 5.9990 chunk 207 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 329 optimal weight: 7.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 859 ASN A1054 HIS B 30 GLN ** B 916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 17 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 37241 Z= 0.237 Angle : 0.600 13.458 50650 Z= 0.304 Chirality : 0.043 0.191 5635 Planarity : 0.004 0.049 6320 Dihedral : 11.892 82.278 5638 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.98 % Allowed : 15.86 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.10 (0.13), residues: 4361 helix: 1.18 (0.14), residues: 1409 sheet: -0.74 (0.19), residues: 685 loop : -0.60 (0.13), residues: 2267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 317 HIS 0.013 0.001 HIS A1054 PHE 0.018 0.001 PHE C 336 TYR 0.016 0.001 TYR A 450 ARG 0.010 0.000 ARG N 77 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8722 Ramachandran restraints generated. 4361 Oldfield, 0 Emsley, 4361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8722 Ramachandran restraints generated. 4361 Oldfield, 0 Emsley, 4361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 330 time to evaluate : 4.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 LYS cc_start: 0.8946 (OUTLIER) cc_final: 0.8709 (mmmt) REVERT: A 345 MET cc_start: 0.7884 (tpp) cc_final: 0.7562 (mtt) REVERT: A 521 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.7987 (mp10) REVERT: A 862 ASP cc_start: 0.7886 (OUTLIER) cc_final: 0.7667 (t70) REVERT: A 1052 HIS cc_start: 0.6870 (OUTLIER) cc_final: 0.6459 (m-70) REVERT: A 1101 LYS cc_start: 0.7944 (pptt) cc_final: 0.7612 (tmmt) REVERT: A 1123 MET cc_start: 0.8467 (mtm) cc_final: 0.8135 (mtt) REVERT: B 216 ARG cc_start: 0.8071 (OUTLIER) cc_final: 0.7780 (ttt-90) REVERT: B 231 ASN cc_start: 0.8950 (OUTLIER) cc_final: 0.8475 (p0) REVERT: B 337 LYS cc_start: 0.8212 (OUTLIER) cc_final: 0.7933 (ptmt) REVERT: B 411 MET cc_start: 0.4573 (pmt) cc_final: 0.4068 (ptp) REVERT: B 417 MET cc_start: 0.7378 (mmt) cc_final: 0.7075 (mmm) REVERT: B 700 LEU cc_start: 0.9342 (OUTLIER) cc_final: 0.9101 (pp) REVERT: B 723 ARG cc_start: 0.8848 (OUTLIER) cc_final: 0.8270 (pmt100) REVERT: E 87 ILE cc_start: 0.9105 (OUTLIER) cc_final: 0.8864 (pt) REVERT: G 78 GLU cc_start: 0.7575 (tp30) cc_final: 0.7311 (tp30) REVERT: G 101 GLU cc_start: 0.6538 (OUTLIER) cc_final: 0.5410 (tm-30) REVERT: G 117 GLU cc_start: 0.7054 (mm-30) cc_final: 0.6459 (mp0) REVERT: G 126 GLU cc_start: 0.5518 (tt0) cc_final: 0.4908 (tm-30) REVERT: G 173 MET cc_start: 0.3614 (OUTLIER) cc_final: 0.3265 (tpt) REVERT: H 81 ARG cc_start: 0.7318 (OUTLIER) cc_final: 0.6860 (ptm160) REVERT: I 17 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8666 (tt) REVERT: I 21 SER cc_start: 0.8915 (p) cc_final: 0.8519 (t) REVERT: I 53 LYS cc_start: 0.8101 (OUTLIER) cc_final: 0.7849 (tmmm) REVERT: J 31 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.8032 (mp0) REVERT: K 31 GLN cc_start: 0.7912 (OUTLIER) cc_final: 0.7641 (mt0) REVERT: K 102 GLU cc_start: 0.7739 (mt-10) cc_final: 0.7444 (mt-10) REVERT: M 109 MET cc_start: 0.8417 (mmm) cc_final: 0.8179 (mmm) REVERT: M 134 LYS cc_start: 0.5021 (OUTLIER) cc_final: 0.4820 (mmtm) REVERT: M 198 LEU cc_start: 0.5126 (OUTLIER) cc_final: 0.4918 (pt) REVERT: M 320 ASN cc_start: 0.6117 (OUTLIER) cc_final: 0.5600 (t0) REVERT: M 327 LEU cc_start: 0.7947 (mp) cc_final: 0.7648 (mm) outliers start: 76 outliers final: 35 residues processed: 384 average time/residue: 1.6918 time to fit residues: 786.4244 Evaluate side-chains 373 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 318 time to evaluate : 4.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 512 MET Chi-restraints excluded: chain A residue 521 GLN Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 862 ASP Chi-restraints excluded: chain A residue 1052 HIS Chi-restraints excluded: chain A residue 1111 ASN Chi-restraints excluded: chain A residue 1190 ASP Chi-restraints excluded: chain A residue 1213 LEU Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1563 LEU Chi-restraints excluded: chain A residue 1618 LEU Chi-restraints excluded: chain B residue 216 ARG Chi-restraints excluded: chain B residue 231 ASN Chi-restraints excluded: chain B residue 337 LYS Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 705 ASP Chi-restraints excluded: chain B residue 723 ARG Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 867 VAL Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 256 CYS Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 87 ILE Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 121 ASP Chi-restraints excluded: chain G residue 101 GLU Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 173 MET Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 81 ARG Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain I residue 17 LEU Chi-restraints excluded: chain I residue 53 LYS Chi-restraints excluded: chain J residue 31 GLU Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain K residue 31 GLN Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 117 SER Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain N residue 131 GLN Chi-restraints excluded: chain M residue 134 LYS Chi-restraints excluded: chain M residue 198 LEU Chi-restraints excluded: chain M residue 205 ASP Chi-restraints excluded: chain M residue 213 VAL Chi-restraints excluded: chain M residue 311 LEU Chi-restraints excluded: chain M residue 320 ASN Chi-restraints excluded: chain M residue 399 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 381 optimal weight: 10.0000 chunk 401 optimal weight: 20.0000 chunk 366 optimal weight: 10.0000 chunk 390 optimal weight: 6.9990 chunk 235 optimal weight: 8.9990 chunk 170 optimal weight: 5.9990 chunk 306 optimal weight: 9.9990 chunk 119 optimal weight: 9.9990 chunk 353 optimal weight: 0.0370 chunk 369 optimal weight: 0.7980 chunk 389 optimal weight: 5.9990 overall best weight: 3.9664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 431 HIS A 859 ASN A1054 HIS ** A1509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 GLN ** B 916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 63 GLN ** K 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 17 ASN M 358 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 37241 Z= 0.320 Angle : 0.636 12.697 50650 Z= 0.321 Chirality : 0.044 0.194 5635 Planarity : 0.004 0.072 6320 Dihedral : 11.880 81.516 5638 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.13 % Allowed : 16.06 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.06 (0.13), residues: 4361 helix: 1.20 (0.14), residues: 1416 sheet: -0.68 (0.19), residues: 689 loop : -0.58 (0.13), residues: 2256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 317 HIS 0.014 0.001 HIS A1054 PHE 0.032 0.001 PHE B 308 TYR 0.024 0.002 TYR E 125 ARG 0.013 0.000 ARG N 77 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8722 Ramachandran restraints generated. 4361 Oldfield, 0 Emsley, 4361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8722 Ramachandran restraints generated. 4361 Oldfield, 0 Emsley, 4361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 316 time to evaluate : 3.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 MET cc_start: 0.9131 (mmt) cc_final: 0.8801 (mmt) REVERT: A 209 LYS cc_start: 0.8953 (OUTLIER) cc_final: 0.8713 (mmmt) REVERT: A 345 MET cc_start: 0.7814 (OUTLIER) cc_final: 0.7555 (mtt) REVERT: A 521 GLN cc_start: 0.8436 (OUTLIER) cc_final: 0.7999 (mp10) REVERT: A 862 ASP cc_start: 0.7906 (OUTLIER) cc_final: 0.7684 (t70) REVERT: A 1052 HIS cc_start: 0.6844 (OUTLIER) cc_final: 0.6427 (m-70) REVERT: A 1101 LYS cc_start: 0.7946 (pptt) cc_final: 0.7644 (ttpt) REVERT: A 1123 MET cc_start: 0.8469 (mtm) cc_final: 0.8123 (mtt) REVERT: B 212 MET cc_start: 0.8670 (OUTLIER) cc_final: 0.7386 (tpt) REVERT: B 216 ARG cc_start: 0.8131 (OUTLIER) cc_final: 0.7838 (ttt-90) REVERT: B 231 ASN cc_start: 0.8961 (OUTLIER) cc_final: 0.8499 (p0) REVERT: B 337 LYS cc_start: 0.8256 (OUTLIER) cc_final: 0.7972 (ptmt) REVERT: B 411 MET cc_start: 0.4511 (pmt) cc_final: 0.4016 (ptp) REVERT: B 417 MET cc_start: 0.7378 (mmt) cc_final: 0.7070 (mmm) REVERT: B 700 LEU cc_start: 0.9373 (OUTLIER) cc_final: 0.9125 (pp) REVERT: B 723 ARG cc_start: 0.8876 (OUTLIER) cc_final: 0.8307 (pmt100) REVERT: G 101 GLU cc_start: 0.6536 (OUTLIER) cc_final: 0.5396 (tm-30) REVERT: H 81 ARG cc_start: 0.7317 (OUTLIER) cc_final: 0.6937 (ptm160) REVERT: I 18 ASP cc_start: 0.7773 (t0) cc_final: 0.7481 (t0) REVERT: I 21 SER cc_start: 0.8971 (p) cc_final: 0.8560 (t) REVERT: I 53 LYS cc_start: 0.8100 (OUTLIER) cc_final: 0.7842 (tmmm) REVERT: J 28 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7722 (mp0) REVERT: J 31 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.8044 (mp0) REVERT: J 58 LYS cc_start: 0.9018 (OUTLIER) cc_final: 0.8804 (mttt) REVERT: K 31 GLN cc_start: 0.7922 (OUTLIER) cc_final: 0.7638 (mt0) REVERT: K 102 GLU cc_start: 0.7743 (mt-10) cc_final: 0.7441 (mt-10) REVERT: M 109 MET cc_start: 0.8478 (mmm) cc_final: 0.8236 (mmm) REVERT: M 134 LYS cc_start: 0.5016 (OUTLIER) cc_final: 0.4814 (mmtm) REVERT: M 198 LEU cc_start: 0.5053 (OUTLIER) cc_final: 0.4852 (pt) REVERT: M 320 ASN cc_start: 0.6125 (OUTLIER) cc_final: 0.5624 (t0) REVERT: M 327 LEU cc_start: 0.7963 (mp) cc_final: 0.7668 (mm) outliers start: 82 outliers final: 42 residues processed: 375 average time/residue: 1.5308 time to fit residues: 688.6435 Evaluate side-chains 374 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 311 time to evaluate : 3.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 512 MET Chi-restraints excluded: chain A residue 521 GLN Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 862 ASP Chi-restraints excluded: chain A residue 1052 HIS Chi-restraints excluded: chain A residue 1111 ASN Chi-restraints excluded: chain A residue 1190 ASP Chi-restraints excluded: chain A residue 1213 LEU Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1563 LEU Chi-restraints excluded: chain A residue 1618 LEU Chi-restraints excluded: chain B residue 212 MET Chi-restraints excluded: chain B residue 216 ARG Chi-restraints excluded: chain B residue 231 ASN Chi-restraints excluded: chain B residue 337 LYS Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 705 ASP Chi-restraints excluded: chain B residue 723 ARG Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 867 VAL Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 256 CYS Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 87 ILE Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 121 ASP Chi-restraints excluded: chain G residue 101 GLU Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 173 MET Chi-restraints excluded: chain H residue 18 GLU Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 81 ARG Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 53 LYS Chi-restraints excluded: chain J residue 28 GLU Chi-restraints excluded: chain J residue 31 GLU Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain J residue 58 LYS Chi-restraints excluded: chain K residue 31 GLN Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 117 SER Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain N residue 45 ILE Chi-restraints excluded: chain N residue 131 GLN Chi-restraints excluded: chain M residue 134 LYS Chi-restraints excluded: chain M residue 198 LEU Chi-restraints excluded: chain M residue 205 ASP Chi-restraints excluded: chain M residue 213 VAL Chi-restraints excluded: chain M residue 311 LEU Chi-restraints excluded: chain M residue 320 ASN Chi-restraints excluded: chain M residue 399 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 256 optimal weight: 2.9990 chunk 413 optimal weight: 7.9990 chunk 252 optimal weight: 5.9990 chunk 195 optimal weight: 6.9990 chunk 287 optimal weight: 2.9990 chunk 433 optimal weight: 30.0000 chunk 398 optimal weight: 10.0000 chunk 345 optimal weight: 4.9990 chunk 35 optimal weight: 8.9990 chunk 266 optimal weight: 5.9990 chunk 211 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: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1054 HIS ** A1509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 GLN ** B 916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 63 GLN K 85 GLN N 17 ASN ** M 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 37241 Z= 0.359 Angle : 0.653 12.301 50650 Z= 0.330 Chirality : 0.044 0.264 5635 Planarity : 0.004 0.061 6320 Dihedral : 11.899 80.105 5638 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.85 % Allowed : 16.48 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.05 (0.13), residues: 4361 helix: 1.19 (0.14), residues: 1411 sheet: -0.65 (0.19), residues: 689 loop : -0.56 (0.13), residues: 2261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 317 HIS 0.015 0.001 HIS A1054 PHE 0.021 0.001 PHE B 434 TYR 0.021 0.002 TYR A 450 ARG 0.014 0.000 ARG N 77 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8722 Ramachandran restraints generated. 4361 Oldfield, 0 Emsley, 4361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8722 Ramachandran restraints generated. 4361 Oldfield, 0 Emsley, 4361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 319 time to evaluate : 3.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 345 MET cc_start: 0.7865 (OUTLIER) cc_final: 0.7593 (mtt) REVERT: A 862 ASP cc_start: 0.7935 (OUTLIER) cc_final: 0.7703 (t70) REVERT: A 1101 LYS cc_start: 0.7992 (pptt) cc_final: 0.7727 (ttpt) REVERT: A 1123 MET cc_start: 0.8474 (mtm) cc_final: 0.8133 (mtt) REVERT: B 216 ARG cc_start: 0.8144 (OUTLIER) cc_final: 0.7847 (ttt-90) REVERT: B 231 ASN cc_start: 0.8978 (OUTLIER) cc_final: 0.8518 (p0) REVERT: B 337 LYS cc_start: 0.8259 (OUTLIER) cc_final: 0.7981 (ptmt) REVERT: B 411 MET cc_start: 0.4526 (pmt) cc_final: 0.4024 (ptp) REVERT: B 417 MET cc_start: 0.7368 (mmt) cc_final: 0.7064 (mmm) REVERT: B 700 LEU cc_start: 0.9369 (OUTLIER) cc_final: 0.9129 (pp) REVERT: B 723 ARG cc_start: 0.8897 (OUTLIER) cc_final: 0.8419 (pmt100) REVERT: G 101 GLU cc_start: 0.6580 (OUTLIER) cc_final: 0.5470 (tm-30) REVERT: H 81 ARG cc_start: 0.7302 (OUTLIER) cc_final: 0.6917 (ptm160) REVERT: I 21 SER cc_start: 0.9011 (p) cc_final: 0.8602 (t) REVERT: I 53 LYS cc_start: 0.8095 (OUTLIER) cc_final: 0.7839 (tmmm) REVERT: J 28 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7737 (mp0) REVERT: J 58 LYS cc_start: 0.9021 (OUTLIER) cc_final: 0.8811 (mttt) REVERT: K 31 GLN cc_start: 0.7940 (OUTLIER) cc_final: 0.7638 (mt0) REVERT: K 102 GLU cc_start: 0.7762 (mt-10) cc_final: 0.7449 (mt-10) REVERT: M 109 MET cc_start: 0.8473 (mmm) cc_final: 0.8233 (mmm) REVERT: M 198 LEU cc_start: 0.5098 (OUTLIER) cc_final: 0.4882 (pt) REVERT: M 320 ASN cc_start: 0.6090 (OUTLIER) cc_final: 0.5606 (t0) REVERT: M 327 LEU cc_start: 0.7967 (mp) cc_final: 0.7686 (mm) outliers start: 71 outliers final: 40 residues processed: 372 average time/residue: 1.6430 time to fit residues: 731.5276 Evaluate side-chains 364 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 309 time to evaluate : 4.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 512 MET Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 862 ASP Chi-restraints excluded: chain A residue 1052 HIS Chi-restraints excluded: chain A residue 1111 ASN Chi-restraints excluded: chain A residue 1190 ASP Chi-restraints excluded: chain A residue 1213 LEU Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1563 LEU Chi-restraints excluded: chain A residue 1618 LEU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 216 ARG Chi-restraints excluded: chain B residue 231 ASN Chi-restraints excluded: chain B residue 337 LYS Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 705 ASP Chi-restraints excluded: chain B residue 723 ARG Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 867 VAL Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 256 CYS Chi-restraints excluded: chain E residue 87 ILE Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 121 ASP Chi-restraints excluded: chain G residue 101 GLU Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 173 MET Chi-restraints excluded: chain H residue 18 GLU Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 81 ARG Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 53 LYS Chi-restraints excluded: chain J residue 28 GLU Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain J residue 58 LYS Chi-restraints excluded: chain K residue 31 GLN Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 117 SER Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain N residue 45 ILE Chi-restraints excluded: chain N residue 131 GLN Chi-restraints excluded: chain M residue 198 LEU Chi-restraints excluded: chain M residue 205 ASP Chi-restraints excluded: chain M residue 311 LEU Chi-restraints excluded: chain M residue 320 ASN Chi-restraints excluded: chain M residue 399 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 274 optimal weight: 6.9990 chunk 367 optimal weight: 1.9990 chunk 105 optimal weight: 20.0000 chunk 318 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 95 optimal weight: 0.9980 chunk 345 optimal weight: 6.9990 chunk 144 optimal weight: 5.9990 chunk 354 optimal weight: 0.5980 chunk 43 optimal weight: 6.9990 chunk 63 optimal weight: 0.8980 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1054 HIS A1509 HIS B 30 GLN B 547 HIS ** B 916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 17 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.107371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.066360 restraints weight = 72326.131| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 2.75 r_work: 0.2796 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.2659 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 moved from start: 0.3235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 37241 Z= 0.207 Angle : 0.613 12.213 50650 Z= 0.309 Chirality : 0.042 0.194 5635 Planarity : 0.004 0.077 6320 Dihedral : 11.819 78.999 5638 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.64 % Allowed : 16.95 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.08 (0.13), residues: 4361 helix: 1.32 (0.14), residues: 1407 sheet: -0.61 (0.19), residues: 688 loop : -0.49 (0.13), residues: 2266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 317 HIS 0.014 0.001 HIS A1054 PHE 0.046 0.001 PHE B 308 TYR 0.022 0.001 TYR E 125 ARG 0.019 0.000 ARG N 77 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13737.01 seconds wall clock time: 244 minutes 16.95 seconds (14656.95 seconds total)