Starting phenix.real_space_refine on Sun Feb 18 18:45:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wyy_32898/02_2024/7wyy_32898_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wyy_32898/02_2024/7wyy_32898.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wyy_32898/02_2024/7wyy_32898.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wyy_32898/02_2024/7wyy_32898.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wyy_32898/02_2024/7wyy_32898_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wyy_32898/02_2024/7wyy_32898_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 26 5.49 5 Mg 6 5.21 5 S 118 5.16 5 C 14674 2.51 5 N 3518 2.21 5 O 4314 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 923": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 923": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 22656 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 7687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 993, 7687 Classifications: {'peptide': 993} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 43, 'TRANS': 949} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PHD:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2399 Classifications: {'peptide': 294} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 278} Chain: "G" Number of atoms: 311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 311 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "C" Number of atoms: 7687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 993, 7687 Classifications: {'peptide': 993} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 43, 'TRANS': 949} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PHD:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 2399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2399 Classifications: {'peptide': 294} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 278} Chain: "E" Number of atoms: 311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 311 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "F" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "H" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "I" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 60 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "L" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "M" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 60 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 447 Unusual residues: {' MG': 3, '7Q2': 1, 'CLR': 1, 'PCW': 9} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 96 Planarities with less than four sites: {'PCW:plan-2': 3, 'PCW:plan-4': 3} Unresolved non-hydrogen planarities: 24 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'CLR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 190 Unusual residues: {'CLR': 1, 'PCW': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 447 Unusual residues: {' MG': 3, '7Q2': 1, 'CLR': 1, 'PCW': 9} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 96 Planarities with less than four sites: {'PCW:plan-2': 3, 'PCW:plan-4': 3} Unresolved non-hydrogen planarities: 24 Chain: "D" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'CLR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 190 Unusual residues: {'CLR': 1, 'PCW': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Time building chain proxies: 12.38, per 1000 atoms: 0.55 Number of scatterers: 22656 At special positions: 0 Unit cell: (216.276, 180.768, 103.296, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 118 16.00 P 26 15.00 Mg 6 11.99 O 4314 8.00 N 3518 7.00 C 14674 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS B 127 " - pdb=" SG CYS B 150 " distance=2.04 Simple disulfide: pdb=" SG CYS B 160 " - pdb=" SG CYS B 176 " distance=2.03 Simple disulfide: pdb=" SG CYS B 215 " - pdb=" SG CYS B 278 " distance=2.03 Simple disulfide: pdb=" SG CYS D 127 " - pdb=" SG CYS D 150 " distance=2.04 Simple disulfide: pdb=" SG CYS D 160 " - pdb=" SG CYS D 176 " distance=2.03 Simple disulfide: pdb=" SG CYS D 215 " - pdb=" SG CYS D 278 " distance=2.03 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 Links applied ALPHA1-3 " BMA F 3 " - " MAN F 4 " " BMA H 3 " - " MAN H 4 " " BMA I 3 " - " MAN I 4 " " BMA K 3 " - " MAN K 4 " " BMA L 3 " - " MAN L 4 " " BMA M 3 " - " MAN M 4 " ALPHA1-6 " BMA F 3 " - " MAN F 5 " " BMA H 3 " - " MAN H 6 " " BMA K 3 " - " MAN K 5 " " BMA L 3 " - " MAN L 6 " BETA1-2 " MAN H 4 " - " NAG H 5 " " MAN L 4 " - " NAG L 5 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " BETA1-6 " NAG F 1 " - " FUC F 6 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG I 1 " - " FUC I 5 " " NAG K 1 " - " FUC K 6 " " NAG M 1 " - " FUC M 5 " NAG-ASN " NAG F 1 " - " ASN B 114 " " NAG H 1 " - " ASN B 159 " " NAG I 1 " - " ASN B 194 " " NAG J 1 " - " ASN B 267 " " NAG K 1 " - " ASN D 114 " " NAG L 1 " - " ASN D 159 " " NAG M 1 " - " ASN D 194 " " NAG N 1 " - " ASN D 267 " Time building additional restraints: 9.08 Conformation dependent library (CDL) restraints added in 4.2 seconds 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4912 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 108 helices and 16 sheets defined 43.9% alpha, 10.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.76 Creating SS restraints... Processing helix chain 'A' and resid 34 through 37 No H-bonds generated for 'chain 'A' and resid 34 through 37' Processing helix chain 'A' and resid 48 through 55 Processing helix chain 'A' and resid 65 through 75 Processing helix chain 'A' and resid 88 through 96 Processing helix chain 'A' and resid 100 through 121 Processing helix chain 'A' and resid 128 through 161 removed outlier: 4.485A pdb=" N PHE A 161 " --> pdb=" O ILE A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 184 No H-bonds generated for 'chain 'A' and resid 182 through 184' Processing helix chain 'A' and resid 262 through 264 No H-bonds generated for 'chain 'A' and resid 262 through 264' Processing helix chain 'A' and resid 266 through 275 Processing helix chain 'A' and resid 283 through 312 Processing helix chain 'A' and resid 317 through 330 removed outlier: 3.684A pdb=" N ILE A 322 " --> pdb=" O LEU A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 354 removed outlier: 3.665A pdb=" N THR A 347 " --> pdb=" O CYS A 343 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA A 348 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS A 349 " --> pdb=" O THR A 345 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG A 350 " --> pdb=" O LEU A 346 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS A 354 " --> pdb=" O ARG A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 364 No H-bonds generated for 'chain 'A' and resid 362 through 364' Processing helix chain 'A' and resid 366 through 369 No H-bonds generated for 'chain 'A' and resid 366 through 369' Processing helix chain 'A' and resid 416 through 427 Processing helix chain 'A' and resid 451 through 463 Processing helix chain 'A' and resid 467 through 472 Processing helix chain 'A' and resid 511 through 517 removed outlier: 3.517A pdb=" N ARG A 517 " --> pdb=" O ARG A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 547 Processing helix chain 'A' and resid 599 through 608 Processing helix chain 'A' and resid 621 through 631 removed outlier: 3.933A pdb=" N ALA A 626 " --> pdb=" O ILE A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 648 Processing helix chain 'A' and resid 657 through 659 No H-bonds generated for 'chain 'A' and resid 657 through 659' Processing helix chain 'A' and resid 667 through 672 removed outlier: 4.174A pdb=" N ASP A 672 " --> pdb=" O SER A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 675 through 684 Processing helix chain 'A' and resid 695 through 706 Processing helix chain 'A' and resid 719 through 727 Proline residue: A 723 - end of helix removed outlier: 4.138A pdb=" N LYS A 726 " --> pdb=" O PRO A 723 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LYS A 727 " --> pdb=" O ALA A 724 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 745 Processing helix chain 'A' and resid 756 through 786 removed outlier: 3.839A pdb=" N GLY A 765 " --> pdb=" O VAL A 762 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ILE A 768 " --> pdb=" O GLY A 765 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASN A 771 " --> pdb=" O ILE A 768 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N SER A 782 " --> pdb=" O THR A 779 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE A 784 " --> pdb=" O THR A 781 " (cutoff:3.500A) Proline residue: A 785 - end of helix Processing helix chain 'A' and resid 788 through 796 Processing helix chain 'A' and resid 804 through 811 Processing helix chain 'A' and resid 814 through 824 Proline residue: A 818 - end of helix removed outlier: 4.323A pdb=" N ALA A 823 " --> pdb=" O ALA A 819 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N TYR A 824 " --> pdb=" O ILE A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 847 through 853 removed outlier: 3.635A pdb=" N MET A 852 " --> pdb=" O ARG A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 875 Processing helix chain 'A' and resid 880 through 883 No H-bonds generated for 'chain 'A' and resid 880 through 883' Processing helix chain 'A' and resid 887 through 891 Processing helix chain 'A' and resid 908 through 938 removed outlier: 3.515A pdb=" N VAL A 914 " --> pdb=" O GLN A 910 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ALA A 932 " --> pdb=" O VAL A 928 " (cutoff:3.500A) Processing helix chain 'A' and resid 944 through 947 No H-bonds generated for 'chain 'A' and resid 944 through 947' Processing helix chain 'A' and resid 952 through 970 removed outlier: 3.598A pdb=" N ALA A 965 " --> pdb=" O GLU A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 974 through 977 No H-bonds generated for 'chain 'A' and resid 974 through 977' Processing helix chain 'A' and resid 987 through 989 No H-bonds generated for 'chain 'A' and resid 987 through 989' Processing helix chain 'A' and resid 992 through 1011 removed outlier: 3.513A pdb=" N PHE A1007 " --> pdb=" O GLU A1003 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE A1008 " --> pdb=" O MET A1004 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE A1009 " --> pdb=" O ARG A1005 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ARG A1010 " --> pdb=" O ARG A1006 " (cutoff:3.500A) Processing helix chain 'A' and resid 1016 through 1021 Processing helix chain 'B' and resid 15 through 17 No H-bonds generated for 'chain 'B' and resid 15 through 17' Processing helix chain 'B' and resid 30 through 61 removed outlier: 4.339A pdb=" N PHE B 34 " --> pdb=" O GLY B 30 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS B 35 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU B 58 " --> pdb=" O THR B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 98 No H-bonds generated for 'chain 'B' and resid 96 through 98' Processing helix chain 'B' and resid 100 through 112 removed outlier: 3.580A pdb=" N SER B 105 " --> pdb=" O SER B 101 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N LEU B 112 " --> pdb=" O LYS B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 203 No H-bonds generated for 'chain 'B' and resid 201 through 203' Processing helix chain 'B' and resid 221 through 225 Processing helix chain 'B' and resid 234 through 236 No H-bonds generated for 'chain 'B' and resid 234 through 236' Processing helix chain 'B' and resid 242 through 244 No H-bonds generated for 'chain 'B' and resid 242 through 244' Processing helix chain 'B' and resid 249 through 253 Processing helix chain 'G' and resid 10 through 12 No H-bonds generated for 'chain 'G' and resid 10 through 12' Processing helix chain 'G' and resid 16 through 39 Processing helix chain 'C' and resid 34 through 37 No H-bonds generated for 'chain 'C' and resid 34 through 37' Processing helix chain 'C' and resid 48 through 55 Processing helix chain 'C' and resid 65 through 75 Processing helix chain 'C' and resid 88 through 96 Processing helix chain 'C' and resid 100 through 121 Processing helix chain 'C' and resid 128 through 161 removed outlier: 4.485A pdb=" N PHE C 161 " --> pdb=" O ILE C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 184 No H-bonds generated for 'chain 'C' and resid 182 through 184' Processing helix chain 'C' and resid 262 through 264 No H-bonds generated for 'chain 'C' and resid 262 through 264' Processing helix chain 'C' and resid 266 through 275 Processing helix chain 'C' and resid 283 through 312 Processing helix chain 'C' and resid 317 through 330 removed outlier: 3.684A pdb=" N ILE C 322 " --> pdb=" O LEU C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 354 removed outlier: 3.665A pdb=" N THR C 347 " --> pdb=" O CYS C 343 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA C 348 " --> pdb=" O LEU C 344 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS C 349 " --> pdb=" O THR C 345 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG C 350 " --> pdb=" O LEU C 346 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS C 354 " --> pdb=" O ARG C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 364 No H-bonds generated for 'chain 'C' and resid 362 through 364' Processing helix chain 'C' and resid 366 through 369 No H-bonds generated for 'chain 'C' and resid 366 through 369' Processing helix chain 'C' and resid 416 through 427 Processing helix chain 'C' and resid 451 through 463 Processing helix chain 'C' and resid 467 through 472 Processing helix chain 'C' and resid 511 through 517 removed outlier: 3.516A pdb=" N ARG C 517 " --> pdb=" O ARG C 513 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 547 Processing helix chain 'C' and resid 599 through 608 Processing helix chain 'C' and resid 621 through 631 removed outlier: 3.932A pdb=" N ALA C 626 " --> pdb=" O ILE C 622 " (cutoff:3.500A) Processing helix chain 'C' and resid 641 through 648 Processing helix chain 'C' and resid 657 through 659 No H-bonds generated for 'chain 'C' and resid 657 through 659' Processing helix chain 'C' and resid 667 through 672 removed outlier: 4.173A pdb=" N ASP C 672 " --> pdb=" O SER C 668 " (cutoff:3.500A) Processing helix chain 'C' and resid 675 through 684 Processing helix chain 'C' and resid 695 through 706 Processing helix chain 'C' and resid 719 through 727 Proline residue: C 723 - end of helix removed outlier: 4.138A pdb=" N LYS C 726 " --> pdb=" O PRO C 723 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LYS C 727 " --> pdb=" O ALA C 724 " (cutoff:3.500A) Processing helix chain 'C' and resid 740 through 745 Processing helix chain 'C' and resid 756 through 786 removed outlier: 3.840A pdb=" N GLY C 765 " --> pdb=" O VAL C 762 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ILE C 768 " --> pdb=" O GLY C 765 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASN C 771 " --> pdb=" O ILE C 768 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N SER C 782 " --> pdb=" O THR C 779 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE C 784 " --> pdb=" O THR C 781 " (cutoff:3.500A) Proline residue: C 785 - end of helix Processing helix chain 'C' and resid 788 through 796 Processing helix chain 'C' and resid 804 through 811 Processing helix chain 'C' and resid 814 through 824 Proline residue: C 818 - end of helix removed outlier: 4.323A pdb=" N ALA C 823 " --> pdb=" O ALA C 819 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N TYR C 824 " --> pdb=" O ILE C 820 " (cutoff:3.500A) Processing helix chain 'C' and resid 847 through 853 removed outlier: 3.634A pdb=" N MET C 852 " --> pdb=" O ARG C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 857 through 875 Processing helix chain 'C' and resid 880 through 883 No H-bonds generated for 'chain 'C' and resid 880 through 883' Processing helix chain 'C' and resid 887 through 891 Processing helix chain 'C' and resid 908 through 938 removed outlier: 3.515A pdb=" N VAL C 914 " --> pdb=" O GLN C 910 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ALA C 932 " --> pdb=" O VAL C 928 " (cutoff:3.500A) Processing helix chain 'C' and resid 944 through 947 No H-bonds generated for 'chain 'C' and resid 944 through 947' Processing helix chain 'C' and resid 952 through 970 removed outlier: 3.597A pdb=" N ALA C 965 " --> pdb=" O GLU C 961 " (cutoff:3.500A) Processing helix chain 'C' and resid 974 through 977 No H-bonds generated for 'chain 'C' and resid 974 through 977' Processing helix chain 'C' and resid 987 through 989 No H-bonds generated for 'chain 'C' and resid 987 through 989' Processing helix chain 'C' and resid 992 through 1011 removed outlier: 3.514A pdb=" N PHE C1007 " --> pdb=" O GLU C1003 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE C1008 " --> pdb=" O MET C1004 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE C1009 " --> pdb=" O ARG C1005 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ARG C1010 " --> pdb=" O ARG C1006 " (cutoff:3.500A) Processing helix chain 'C' and resid 1016 through 1021 Processing helix chain 'D' and resid 15 through 17 No H-bonds generated for 'chain 'D' and resid 15 through 17' Processing helix chain 'D' and resid 30 through 61 removed outlier: 4.338A pdb=" N PHE D 34 " --> pdb=" O GLY D 30 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS D 35 " --> pdb=" O SER D 31 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU D 58 " --> pdb=" O THR D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 98 No H-bonds generated for 'chain 'D' and resid 96 through 98' Processing helix chain 'D' and resid 100 through 112 removed outlier: 3.580A pdb=" N SER D 105 " --> pdb=" O SER D 101 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LEU D 112 " --> pdb=" O LYS D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 203 No H-bonds generated for 'chain 'D' and resid 201 through 203' Processing helix chain 'D' and resid 221 through 225 Processing helix chain 'D' and resid 234 through 236 No H-bonds generated for 'chain 'D' and resid 234 through 236' Processing helix chain 'D' and resid 242 through 244 No H-bonds generated for 'chain 'D' and resid 242 through 244' Processing helix chain 'D' and resid 249 through 253 Processing helix chain 'E' and resid 10 through 12 No H-bonds generated for 'chain 'E' and resid 10 through 12' Processing helix chain 'E' and resid 16 through 39 Processing sheet with id= A, first strand: chain 'A' and resid 176 through 181 removed outlier: 11.695A pdb=" N GLN A 168 " --> pdb=" O LYS A 194 " (cutoff:3.500A) removed outlier: 9.248A pdb=" N LYS A 194 " --> pdb=" O GLN A 168 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N LEU A 170 " --> pdb=" O GLU A 192 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU A 190 " --> pdb=" O ILE A 172 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N THR A 253 " --> pdb=" O HIS A 209 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N SER A 207 " --> pdb=" O ARG A 255 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 356 through 358 removed outlier: 6.703A pdb=" N THR A 372 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N THR A 715 " --> pdb=" O THR A 372 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N CYS A 374 " --> pdb=" O THR A 715 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LYS A 612 " --> pdb=" O ILE A 373 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N SER A 375 " --> pdb=" O LYS A 612 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ILE A 614 " --> pdb=" O SER A 375 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N ILE A 688 " --> pdb=" O VAL A 613 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 390 through 392 Processing sheet with id= D, first strand: chain 'A' and resid 526 through 529 removed outlier: 7.290A pdb=" N LEU A 583 " --> pdb=" O SER A 519 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N ILE A 521 " --> pdb=" O LEU A 583 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N PHE A 585 " --> pdb=" O ILE A 521 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LEU A 523 " --> pdb=" O PHE A 585 " (cutoff:3.500A) removed outlier: 11.234A pdb=" N GLY A 587 " --> pdb=" O LEU A 523 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N PHE A 555 " --> pdb=" O VAL A 586 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N LEU A 588 " --> pdb=" O LEU A 553 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LEU A 553 " --> pdb=" O LEU A 588 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ALA A 590 " --> pdb=" O ARG A 551 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ARG A 551 " --> pdb=" O ALA A 590 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N TYR A 503 " --> pdb=" O LEU A 560 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU A 490 " --> pdb=" O ILE A 480 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N GLU A 494 " --> pdb=" O LYS A 476 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LYS A 476 " --> pdb=" O GLU A 494 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 202 through 205 removed outlier: 6.396A pdb=" N ARG A 204 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N VAL A 258 " --> pdb=" O ARG A 204 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 78 through 80 removed outlier: 3.669A pdb=" N THR B 266 " --> pdb=" O SER B 228 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 88 through 91 removed outlier: 7.918A pdb=" N ILE B 89 " --> pdb=" O GLU B 298 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N LYS B 300 " --> pdb=" O ILE B 89 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N PHE B 91 " --> pdb=" O LYS B 300 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N GLU B 302 " --> pdb=" O PHE B 91 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 210 through 212 Processing sheet with id= I, first strand: chain 'C' and resid 176 through 181 removed outlier: 11.695A pdb=" N GLN C 168 " --> pdb=" O LYS C 194 " (cutoff:3.500A) removed outlier: 9.248A pdb=" N LYS C 194 " --> pdb=" O GLN C 168 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N LEU C 170 " --> pdb=" O GLU C 192 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU C 190 " --> pdb=" O ILE C 172 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR C 253 " --> pdb=" O HIS C 209 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N SER C 207 " --> pdb=" O ARG C 255 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 356 through 358 removed outlier: 6.702A pdb=" N THR C 372 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N THR C 715 " --> pdb=" O THR C 372 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N CYS C 374 " --> pdb=" O THR C 715 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LYS C 612 " --> pdb=" O ILE C 373 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N SER C 375 " --> pdb=" O LYS C 612 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ILE C 614 " --> pdb=" O SER C 375 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N ILE C 688 " --> pdb=" O VAL C 613 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 390 through 392 Processing sheet with id= L, first strand: chain 'C' and resid 526 through 529 removed outlier: 7.290A pdb=" N LEU C 583 " --> pdb=" O SER C 519 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N ILE C 521 " --> pdb=" O LEU C 583 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N PHE C 585 " --> pdb=" O ILE C 521 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LEU C 523 " --> pdb=" O PHE C 585 " (cutoff:3.500A) removed outlier: 11.233A pdb=" N GLY C 587 " --> pdb=" O LEU C 523 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N PHE C 555 " --> pdb=" O VAL C 586 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N LEU C 588 " --> pdb=" O LEU C 553 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LEU C 553 " --> pdb=" O LEU C 588 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ALA C 590 " --> pdb=" O ARG C 551 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ARG C 551 " --> pdb=" O ALA C 590 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N TYR C 503 " --> pdb=" O LEU C 560 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU C 490 " --> pdb=" O ILE C 480 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N GLU C 494 " --> pdb=" O LYS C 476 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LYS C 476 " --> pdb=" O GLU C 494 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 202 through 205 removed outlier: 6.397A pdb=" N ARG C 204 " --> pdb=" O VAL C 258 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N VAL C 258 " --> pdb=" O ARG C 204 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 78 through 80 removed outlier: 3.669A pdb=" N THR D 266 " --> pdb=" O SER D 228 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 88 through 91 removed outlier: 7.918A pdb=" N ILE D 89 " --> pdb=" O GLU D 298 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N LYS D 300 " --> pdb=" O ILE D 89 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N PHE D 91 " --> pdb=" O LYS D 300 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N GLU D 302 " --> pdb=" O PHE D 91 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 210 through 212 842 hydrogen bonds defined for protein. 2334 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.06 Time building geometry restraints manager: 9.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 6847 1.35 - 1.47: 5211 1.47 - 1.59: 10792 1.59 - 1.71: 60 1.71 - 1.83: 172 Bond restraints: 23082 Sorted by residual: bond pdb=" OD1 PHD A 376 " pdb=" P PHD A 376 " ideal model delta sigma weight residual 1.816 1.508 0.308 2.00e-02 2.50e+03 2.37e+02 bond pdb=" OD1 PHD C 376 " pdb=" P PHD C 376 " ideal model delta sigma weight residual 1.816 1.509 0.307 2.00e-02 2.50e+03 2.36e+02 bond pdb=" C39 PCW G1304 " pdb=" C40 PCW G1304 " ideal model delta sigma weight residual 1.333 1.546 -0.213 2.00e-02 2.50e+03 1.13e+02 bond pdb=" C39 PCW E1304 " pdb=" C40 PCW E1304 " ideal model delta sigma weight residual 1.333 1.545 -0.212 2.00e-02 2.50e+03 1.13e+02 bond pdb=" C19 PCW C1109 " pdb=" C20 PCW C1109 " ideal model delta sigma weight residual 1.333 1.541 -0.208 2.00e-02 2.50e+03 1.08e+02 ... (remaining 23077 not shown) Histogram of bond angle deviations from ideal: 98.44 - 105.57: 643 105.57 - 112.70: 12224 112.70 - 119.84: 8387 119.84 - 126.97: 9685 126.97 - 134.10: 209 Bond angle restraints: 31148 Sorted by residual: angle pdb=" N LEU D 157 " pdb=" CA LEU D 157 " pdb=" C LEU D 157 " ideal model delta sigma weight residual 108.67 98.44 10.23 1.55e+00 4.16e-01 4.36e+01 angle pdb=" N LEU B 157 " pdb=" CA LEU B 157 " pdb=" C LEU B 157 " ideal model delta sigma weight residual 108.67 98.45 10.22 1.55e+00 4.16e-01 4.34e+01 angle pdb=" N SER D 32 " pdb=" CA SER D 32 " pdb=" C SER D 32 " ideal model delta sigma weight residual 111.14 116.99 -5.85 1.08e+00 8.57e-01 2.94e+01 angle pdb=" N THR C 57 " pdb=" CA THR C 57 " pdb=" C THR C 57 " ideal model delta sigma weight residual 108.46 116.64 -8.18 1.51e+00 4.39e-01 2.93e+01 angle pdb=" N SER B 32 " pdb=" CA SER B 32 " pdb=" C SER B 32 " ideal model delta sigma weight residual 111.14 116.99 -5.85 1.08e+00 8.57e-01 2.93e+01 ... (remaining 31143 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.90: 14167 35.90 - 71.80: 771 71.80 - 107.70: 84 107.70 - 143.61: 40 143.61 - 179.51: 2 Dihedral angle restraints: 15064 sinusoidal: 7408 harmonic: 7656 Sorted by residual: dihedral pdb=" C33 PCW E1303 " pdb=" C31 PCW E1303 " pdb=" C32 PCW E1303 " pdb=" O2 PCW E1303 " ideal model delta sinusoidal sigma weight residual -168.17 11.34 -179.51 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C33 PCW G1303 " pdb=" C31 PCW G1303 " pdb=" C32 PCW G1303 " pdb=" O2 PCW G1303 " ideal model delta sinusoidal sigma weight residual -168.17 11.21 -179.38 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C33 PCW A1112 " pdb=" C31 PCW A1112 " pdb=" C32 PCW A1112 " pdb=" O2 PCW A1112 " ideal model delta sinusoidal sigma weight residual -168.17 -29.89 -138.28 1 3.00e+01 1.11e-03 1.86e+01 ... (remaining 15061 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 2871 0.079 - 0.158: 549 0.158 - 0.237: 61 0.237 - 0.316: 23 0.316 - 0.395: 20 Chirality restraints: 3524 Sorted by residual: chirality pdb=" C1 FUC I 5 " pdb=" O6 NAG I 1 " pdb=" C2 FUC I 5 " pdb=" O5 FUC I 5 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-02 2.50e+03 7.54e+01 chirality pdb=" C1 FUC M 5 " pdb=" O6 NAG M 1 " pdb=" C2 FUC M 5 " pdb=" O5 FUC M 5 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-02 2.50e+03 7.45e+01 chirality pdb=" C1 FUC F 6 " pdb=" O6 NAG F 1 " pdb=" C2 FUC F 6 " pdb=" O5 FUC F 6 " both_signs ideal model delta sigma weight residual False -2.40 -2.34 -0.06 2.00e-02 2.50e+03 9.70e+00 ... (remaining 3521 not shown) Planarity restraints: 3818 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER D 122 " 0.093 5.00e-02 4.00e+02 1.46e-01 3.39e+01 pdb=" N PRO D 123 " -0.252 5.00e-02 4.00e+02 pdb=" CA PRO D 123 " 0.079 5.00e-02 4.00e+02 pdb=" CD PRO D 123 " 0.079 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 122 " -0.093 5.00e-02 4.00e+02 1.45e-01 3.38e+01 pdb=" N PRO B 123 " 0.252 5.00e-02 4.00e+02 pdb=" CA PRO B 123 " -0.079 5.00e-02 4.00e+02 pdb=" CD PRO B 123 " -0.079 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 124 " 0.065 5.00e-02 4.00e+02 9.81e-02 1.54e+01 pdb=" N PRO A 125 " -0.170 5.00e-02 4.00e+02 pdb=" CA PRO A 125 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO A 125 " 0.052 5.00e-02 4.00e+02 ... (remaining 3815 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 108 2.47 - 3.08: 15084 3.08 - 3.68: 30828 3.68 - 4.29: 48295 4.29 - 4.90: 78282 Nonbonded interactions: 172597 Sorted by model distance: nonbonded pdb=" OP3 PHD C 376 " pdb="MG MG C1101 " model vdw 1.860 2.170 nonbonded pdb=" OP3 PHD A 376 " pdb="MG MG A1101 " model vdw 1.860 2.170 nonbonded pdb=" OD2 ASP A 811 " pdb="MG MG A1103 " model vdw 1.969 2.170 nonbonded pdb=" OD2 ASP C 811 " pdb="MG MG C1103 " model vdw 1.970 2.170 nonbonded pdb="MG MG C1101 " pdb=" O HOH C1202 " model vdw 1.991 2.170 ... (remaining 172592 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'G' } ncs_group { reference = (chain 'F' and resid 1 through 4) selection = (chain 'H' and resid 1 through 4) selection = (chain 'K' and resid 1 through 4) selection = (chain 'L' and resid 1 through 4) } ncs_group { reference = chain 'I' selection = chain 'M' } ncs_group { reference = chain 'J' selection = chain 'N' } 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 group one per residue 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: 0.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.340 Check model and map are aligned: 0.350 Set scattering table: 0.210 Process input model: 61.650 Find NCS groups from input model: 1.160 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 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 : 0.012 0.308 23082 Z= 0.668 Angle : 1.470 12.010 31148 Z= 0.755 Chirality : 0.069 0.395 3524 Planarity : 0.009 0.146 3810 Dihedral : 20.042 179.507 10134 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.61 % Allowed : 8.69 % Favored : 90.71 % Rotamer: Outliers : 10.61 % Allowed : 8.97 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -3.53 (0.14), residues: 2636 helix: -1.87 (0.13), residues: 1186 sheet: -2.42 (0.29), residues: 250 loop : -2.77 (0.15), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP D 33 HIS 0.010 0.002 HIS C 493 PHE 0.031 0.003 PHE B 297 TYR 0.038 0.002 TYR B 206 ARG 0.014 0.001 ARG C 596 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 794 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 240 poor density : 554 time to evaluate : 2.833 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 65 ASN cc_start: 0.5782 (OUTLIER) cc_final: 0.5022 (m-40) REVERT: A 71 ILE cc_start: 0.7036 (mt) cc_final: 0.6592 (mm) REVERT: A 127 ASN cc_start: 0.6881 (OUTLIER) cc_final: 0.6048 (p0) REVERT: A 158 MET cc_start: 0.8251 (OUTLIER) cc_final: 0.7828 (tpp) REVERT: A 351 MET cc_start: 0.8038 (OUTLIER) cc_final: 0.7569 (mtm) REVERT: A 488 TYR cc_start: 0.7031 (OUTLIER) cc_final: 0.6287 (p90) REVERT: A 504 LEU cc_start: 0.6747 (tp) cc_final: 0.6304 (pp) REVERT: A 721 ASP cc_start: 0.8784 (m-30) cc_final: 0.8156 (m-30) REVERT: A 810 ILE cc_start: 0.8826 (OUTLIER) cc_final: 0.8540 (mt) REVERT: A 852 MET cc_start: 0.7519 (mmm) cc_final: 0.7283 (mmp) REVERT: B 242 LEU cc_start: 0.9225 (OUTLIER) cc_final: 0.8666 (mt) REVERT: G 13 THR cc_start: 0.8081 (OUTLIER) cc_final: 0.7875 (p) REVERT: C 65 ASN cc_start: 0.5457 (OUTLIER) cc_final: 0.4671 (m-40) REVERT: C 71 ILE cc_start: 0.7226 (mt) cc_final: 0.6725 (mm) REVERT: C 158 MET cc_start: 0.8264 (OUTLIER) cc_final: 0.7837 (tpp) REVERT: C 351 MET cc_start: 0.7992 (OUTLIER) cc_final: 0.7595 (mtp) REVERT: C 488 TYR cc_start: 0.6966 (OUTLIER) cc_final: 0.6313 (p90) REVERT: C 504 LEU cc_start: 0.6590 (tp) cc_final: 0.6264 (pp) REVERT: C 708 GLN cc_start: 0.7738 (OUTLIER) cc_final: 0.7344 (mt0) REVERT: C 721 ASP cc_start: 0.8742 (m-30) cc_final: 0.8115 (m-30) REVERT: C 815 ASP cc_start: 0.7498 (OUTLIER) cc_final: 0.6902 (t0) REVERT: C 852 MET cc_start: 0.7304 (mmm) cc_final: 0.7074 (mmp) REVERT: D 106 MET cc_start: 0.8179 (mmm) cc_final: 0.7908 (mtt) REVERT: D 287 TYR cc_start: 0.8108 (OUTLIER) cc_final: 0.7782 (m-80) outliers start: 240 outliers final: 44 residues processed: 722 average time/residue: 0.4084 time to fit residues: 430.0946 Evaluate side-chains 292 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 233 time to evaluate : 2.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 343 CYS Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 488 TYR Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 571 PHE Chi-restraints excluded: chain A residue 810 ILE Chi-restraints excluded: chain A residue 846 ASN Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 872 ILE Chi-restraints excluded: chain A residue 894 TRP Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 156 TRP Chi-restraints excluded: chain B residue 160 CYS Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 343 CYS Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 351 MET Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 488 TYR Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 571 PHE Chi-restraints excluded: chain C residue 708 GLN Chi-restraints excluded: chain C residue 815 ASP Chi-restraints excluded: chain C residue 846 ASN Chi-restraints excluded: chain C residue 847 GLU Chi-restraints excluded: chain C residue 872 ILE Chi-restraints excluded: chain C residue 894 TRP Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 64 ASP Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 156 TRP Chi-restraints excluded: chain D residue 160 CYS Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain D residue 287 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 222 optimal weight: 3.9990 chunk 200 optimal weight: 1.9990 chunk 111 optimal weight: 0.0270 chunk 68 optimal weight: 1.9990 chunk 134 optimal weight: 9.9990 chunk 106 optimal weight: 9.9990 chunk 206 optimal weight: 0.7980 chunk 80 optimal weight: 6.9990 chunk 125 optimal weight: 6.9990 chunk 154 optimal weight: 9.9990 chunk 239 optimal weight: 10.0000 overall best weight: 1.7644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 HIS A 209 HIS A 474 ASN A 486 ASN A 620 HIS A 683 HIS A 744 GLN A 826 GLN A 904 GLN A1019 GLN B 56 GLN B 203 GLN B 258 GLN B 270 GLN C 52 HIS C 474 ASN C 486 ASN C 566 ASN C 620 HIS C 683 HIS C 744 GLN C 754 ASN C 826 GLN C 904 GLN ** C1019 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 56 GLN D 146 GLN D 258 GLN D 270 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 23082 Z= 0.235 Angle : 0.698 9.761 31148 Z= 0.343 Chirality : 0.046 0.422 3524 Planarity : 0.006 0.072 3810 Dihedral : 16.890 174.317 5286 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 5.53 % Allowed : 15.21 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.64 (0.15), residues: 2636 helix: -0.09 (0.15), residues: 1188 sheet: -1.68 (0.28), residues: 264 loop : -1.97 (0.16), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 392 HIS 0.011 0.002 HIS A 493 PHE 0.015 0.002 PHE B 25 TYR 0.017 0.001 TYR B 40 ARG 0.005 0.001 ARG C 430 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 255 time to evaluate : 2.586 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 71 ILE cc_start: 0.6987 (mt) cc_final: 0.6635 (mm) REVERT: A 308 ILE cc_start: 0.8911 (OUTLIER) cc_final: 0.8561 (mp) REVERT: A 351 MET cc_start: 0.8072 (mmm) cc_final: 0.7718 (mtp) REVERT: A 721 ASP cc_start: 0.8810 (m-30) cc_final: 0.8219 (m-30) REVERT: A 975 ASP cc_start: 0.8112 (OUTLIER) cc_final: 0.7856 (p0) REVERT: B 20 SER cc_start: 0.5713 (OUTLIER) cc_final: 0.4926 (p) REVERT: B 107 HIS cc_start: 0.8188 (OUTLIER) cc_final: 0.7844 (m-70) REVERT: G 13 THR cc_start: 0.8327 (m) cc_final: 0.8105 (p) REVERT: C 64 THR cc_start: 0.5651 (OUTLIER) cc_final: 0.5234 (p) REVERT: C 71 ILE cc_start: 0.7109 (mt) cc_final: 0.6727 (mm) REVERT: C 287 GLU cc_start: 0.7088 (mm-30) cc_final: 0.6854 (mm-30) REVERT: C 351 MET cc_start: 0.8136 (mmm) cc_final: 0.7896 (mtp) REVERT: C 721 ASP cc_start: 0.8806 (m-30) cc_final: 0.8166 (m-30) REVERT: D 20 SER cc_start: 0.6058 (OUTLIER) cc_final: 0.5269 (p) REVERT: D 142 ASP cc_start: 0.5652 (t0) cc_final: 0.5278 (t0) outliers start: 125 outliers final: 78 residues processed: 352 average time/residue: 0.3068 time to fit residues: 176.7143 Evaluate side-chains 268 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 184 time to evaluate : 2.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 45 LYS Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 145 CYS Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 362 GLU Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 571 PHE Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 760 THR Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 846 ASN Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 866 PHE Chi-restraints excluded: chain A residue 871 VAL Chi-restraints excluded: chain A residue 872 ILE Chi-restraints excluded: chain A residue 894 TRP Chi-restraints excluded: chain A residue 935 ILE Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 975 ASP Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 107 HIS Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 160 CYS Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain C residue 41 MET Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 145 CYS Chi-restraints excluded: chain C residue 248 ASN Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 362 GLU Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 470 MET Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 571 PHE Chi-restraints excluded: chain C residue 577 ASN Chi-restraints excluded: chain C residue 641 ILE Chi-restraints excluded: chain C residue 741 VAL Chi-restraints excluded: chain C residue 760 THR Chi-restraints excluded: chain C residue 846 ASN Chi-restraints excluded: chain C residue 847 GLU Chi-restraints excluded: chain C residue 866 PHE Chi-restraints excluded: chain C residue 871 VAL Chi-restraints excluded: chain C residue 894 TRP Chi-restraints excluded: chain C residue 935 ILE Chi-restraints excluded: chain C residue 943 SER Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 64 ASP Chi-restraints excluded: chain D residue 71 ASP Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 160 CYS Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 37 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 133 optimal weight: 10.0000 chunk 74 optimal weight: 0.9990 chunk 199 optimal weight: 1.9990 chunk 163 optimal weight: 5.9990 chunk 66 optimal weight: 0.8980 chunk 240 optimal weight: 6.9990 chunk 259 optimal weight: 8.9990 chunk 213 optimal weight: 1.9990 chunk 238 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 192 optimal weight: 8.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 557 HIS A 654 GLN A 826 GLN B 243 GLN C1019 GLN D 243 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.3842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 23082 Z= 0.196 Angle : 0.597 9.000 31148 Z= 0.290 Chirality : 0.044 0.401 3524 Planarity : 0.005 0.062 3810 Dihedral : 15.283 168.572 5231 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 4.02 % Allowed : 17.42 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.69 (0.16), residues: 2636 helix: 0.64 (0.15), residues: 1182 sheet: -1.35 (0.29), residues: 256 loop : -1.35 (0.17), residues: 1198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 392 HIS 0.008 0.001 HIS A 493 PHE 0.022 0.001 PHE C 411 TYR 0.025 0.001 TYR C 488 ARG 0.007 0.000 ARG C 979 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 218 time to evaluate : 2.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 MET cc_start: 0.7896 (tpp) cc_final: 0.7199 (tpt) REVERT: A 351 MET cc_start: 0.8077 (OUTLIER) cc_final: 0.7750 (mtp) REVERT: A 470 MET cc_start: 0.8445 (OUTLIER) cc_final: 0.7690 (mpp) REVERT: A 514 ILE cc_start: 0.8905 (mm) cc_final: 0.8701 (mm) REVERT: A 589 MET cc_start: 0.7069 (tpp) cc_final: 0.6812 (ttm) REVERT: A 721 ASP cc_start: 0.8853 (m-30) cc_final: 0.8364 (m-30) REVERT: A 975 ASP cc_start: 0.8394 (OUTLIER) cc_final: 0.8115 (p0) REVERT: B 20 SER cc_start: 0.5819 (OUTLIER) cc_final: 0.5094 (p) REVERT: B 94 SER cc_start: 0.8791 (OUTLIER) cc_final: 0.8452 (p) REVERT: B 111 ASP cc_start: 0.7757 (OUTLIER) cc_final: 0.6807 (t70) REVERT: B 142 ASP cc_start: 0.5926 (t0) cc_final: 0.5557 (t0) REVERT: G 13 THR cc_start: 0.8458 (m) cc_final: 0.8216 (p) REVERT: C 48 LEU cc_start: 0.6903 (tp) cc_final: 0.6614 (tp) REVERT: C 64 THR cc_start: 0.5648 (OUTLIER) cc_final: 0.5283 (p) REVERT: C 158 MET cc_start: 0.7911 (tpp) cc_final: 0.7310 (tpt) REVERT: C 351 MET cc_start: 0.8160 (OUTLIER) cc_final: 0.7916 (mtp) REVERT: C 470 MET cc_start: 0.8405 (OUTLIER) cc_final: 0.7344 (mpp) REVERT: C 507 MET cc_start: 0.8521 (tpp) cc_final: 0.8192 (tpp) REVERT: C 721 ASP cc_start: 0.8832 (m-30) cc_final: 0.8151 (m-30) REVERT: D 20 SER cc_start: 0.6071 (OUTLIER) cc_final: 0.5353 (p) REVERT: D 111 ASP cc_start: 0.7646 (OUTLIER) cc_final: 0.6809 (t70) REVERT: D 142 ASP cc_start: 0.5994 (t0) cc_final: 0.5584 (t0) outliers start: 91 outliers final: 65 residues processed: 289 average time/residue: 0.3271 time to fit residues: 156.9585 Evaluate side-chains 268 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 192 time to evaluate : 2.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 145 CYS Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 470 MET Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 659 ASP Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 846 ASN Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 866 PHE Chi-restraints excluded: chain A residue 871 VAL Chi-restraints excluded: chain A residue 872 ILE Chi-restraints excluded: chain A residue 894 TRP Chi-restraints excluded: chain A residue 935 ILE Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 975 ASP Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain C residue 41 MET Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 127 ASN Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 145 CYS Chi-restraints excluded: chain C residue 248 ASN Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 351 MET Chi-restraints excluded: chain C residue 470 MET Chi-restraints excluded: chain C residue 480 ILE Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 577 ASN Chi-restraints excluded: chain C residue 641 ILE Chi-restraints excluded: chain C residue 741 VAL Chi-restraints excluded: chain C residue 846 ASN Chi-restraints excluded: chain C residue 847 GLU Chi-restraints excluded: chain C residue 866 PHE Chi-restraints excluded: chain C residue 871 VAL Chi-restraints excluded: chain C residue 894 TRP Chi-restraints excluded: chain C residue 935 ILE Chi-restraints excluded: chain C residue 943 SER Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 71 ASP Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 37 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 237 optimal weight: 9.9990 chunk 180 optimal weight: 9.9990 chunk 124 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 114 optimal weight: 9.9990 chunk 161 optimal weight: 2.9990 chunk 241 optimal weight: 7.9990 chunk 255 optimal weight: 8.9990 chunk 125 optimal weight: 7.9990 chunk 228 optimal weight: 0.7980 chunk 68 optimal weight: 3.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 826 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.4811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 23082 Z= 0.325 Angle : 0.674 9.451 31148 Z= 0.326 Chirality : 0.047 0.441 3524 Planarity : 0.005 0.049 3810 Dihedral : 14.510 153.296 5216 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 5.31 % Allowed : 17.33 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 (0.16), residues: 2636 helix: 0.67 (0.15), residues: 1168 sheet: -0.95 (0.31), residues: 250 loop : -1.21 (0.16), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 890 HIS 0.006 0.001 HIS C 493 PHE 0.038 0.002 PHE A 578 TYR 0.025 0.002 TYR C 488 ARG 0.007 0.001 ARG A 473 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 185 time to evaluate : 2.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 PHE cc_start: 0.8100 (OUTLIER) cc_final: 0.7617 (m-80) REVERT: A 351 MET cc_start: 0.8142 (OUTLIER) cc_final: 0.7804 (mtp) REVERT: A 470 MET cc_start: 0.8344 (OUTLIER) cc_final: 0.7408 (mpp) REVERT: A 719 VAL cc_start: 0.8691 (OUTLIER) cc_final: 0.8277 (t) REVERT: A 975 ASP cc_start: 0.8633 (OUTLIER) cc_final: 0.8384 (p0) REVERT: B 20 SER cc_start: 0.6355 (OUTLIER) cc_final: 0.5370 (p) REVERT: B 111 ASP cc_start: 0.7907 (OUTLIER) cc_final: 0.6951 (t70) REVERT: B 142 ASP cc_start: 0.6145 (t0) cc_final: 0.5687 (t0) REVERT: B 203 GLN cc_start: 0.7928 (OUTLIER) cc_final: 0.7458 (mt0) REVERT: B 287 TYR cc_start: 0.8337 (OUTLIER) cc_final: 0.7889 (m-80) REVERT: G 13 THR cc_start: 0.8807 (m) cc_final: 0.8580 (p) REVERT: C 48 LEU cc_start: 0.6905 (tp) cc_final: 0.6441 (tp) REVERT: C 64 THR cc_start: 0.5845 (OUTLIER) cc_final: 0.5522 (p) REVERT: C 351 MET cc_start: 0.8217 (OUTLIER) cc_final: 0.7811 (mtp) REVERT: C 470 MET cc_start: 0.8447 (OUTLIER) cc_final: 0.7167 (mpp) REVERT: C 719 VAL cc_start: 0.8681 (OUTLIER) cc_final: 0.8249 (t) REVERT: C 721 ASP cc_start: 0.8844 (m-30) cc_final: 0.8539 (m-30) REVERT: C 975 ASP cc_start: 0.8525 (OUTLIER) cc_final: 0.8291 (p0) REVERT: D 20 SER cc_start: 0.6377 (OUTLIER) cc_final: 0.5501 (p) REVERT: D 111 ASP cc_start: 0.7849 (OUTLIER) cc_final: 0.6947 (t70) REVERT: D 142 ASP cc_start: 0.6277 (t0) cc_final: 0.5606 (t0) outliers start: 120 outliers final: 76 residues processed: 281 average time/residue: 0.2966 time to fit residues: 139.5471 Evaluate side-chains 248 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 156 time to evaluate : 2.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 145 CYS Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 470 MET Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 659 ASP Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 753 ASP Chi-restraints excluded: chain A residue 760 THR Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 846 ASN Chi-restraints excluded: chain A residue 866 PHE Chi-restraints excluded: chain A residue 871 VAL Chi-restraints excluded: chain A residue 872 ILE Chi-restraints excluded: chain A residue 881 MET Chi-restraints excluded: chain A residue 894 TRP Chi-restraints excluded: chain A residue 935 ILE Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 975 ASP Chi-restraints excluded: chain A residue 986 SER Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1002 ASP Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 156 TRP Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 287 TYR Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain C residue 41 MET Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 127 ASN Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 145 CYS Chi-restraints excluded: chain C residue 248 ASN Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 351 MET Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 470 MET Chi-restraints excluded: chain C residue 480 ILE Chi-restraints excluded: chain C residue 577 ASN Chi-restraints excluded: chain C residue 641 ILE Chi-restraints excluded: chain C residue 659 ASP Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 741 VAL Chi-restraints excluded: chain C residue 760 THR Chi-restraints excluded: chain C residue 784 ILE Chi-restraints excluded: chain C residue 846 ASN Chi-restraints excluded: chain C residue 866 PHE Chi-restraints excluded: chain C residue 871 VAL Chi-restraints excluded: chain C residue 872 ILE Chi-restraints excluded: chain C residue 894 TRP Chi-restraints excluded: chain C residue 935 ILE Chi-restraints excluded: chain C residue 943 SER Chi-restraints excluded: chain C residue 975 ASP Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 71 ASP Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 156 TRP Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 37 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 212 optimal weight: 6.9990 chunk 144 optimal weight: 1.9990 chunk 3 optimal weight: 7.9990 chunk 190 optimal weight: 1.9990 chunk 105 optimal weight: 6.9990 chunk 217 optimal weight: 3.9990 chunk 176 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 130 optimal weight: 0.9980 chunk 229 optimal weight: 0.8980 chunk 64 optimal weight: 10.0000 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 182 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.5014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 23082 Z= 0.184 Angle : 0.560 8.893 31148 Z= 0.268 Chirality : 0.044 0.450 3524 Planarity : 0.004 0.045 3810 Dihedral : 13.729 149.500 5207 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 4.16 % Allowed : 19.14 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.16 (0.16), residues: 2636 helix: 1.02 (0.16), residues: 1174 sheet: -0.78 (0.30), residues: 260 loop : -1.06 (0.17), residues: 1202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 988 HIS 0.005 0.001 HIS C 493 PHE 0.024 0.001 PHE C 967 TYR 0.024 0.001 TYR A 488 ARG 0.004 0.000 ARG C 430 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 184 time to evaluate : 2.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 THR cc_start: 0.6020 (OUTLIER) cc_final: 0.5662 (p) REVERT: A 158 MET cc_start: 0.7798 (tpp) cc_final: 0.7349 (tpt) REVERT: A 351 MET cc_start: 0.8170 (mmm) cc_final: 0.7900 (mtp) REVERT: A 391 MET cc_start: 0.7194 (mtm) cc_final: 0.6912 (mtm) REVERT: A 470 MET cc_start: 0.8177 (OUTLIER) cc_final: 0.7219 (mpp) REVERT: A 897 ASP cc_start: 0.8030 (OUTLIER) cc_final: 0.7816 (p0) REVERT: B 111 ASP cc_start: 0.7774 (OUTLIER) cc_final: 0.6802 (t70) REVERT: B 142 ASP cc_start: 0.6048 (t0) cc_final: 0.5308 (t0) REVERT: B 203 GLN cc_start: 0.8172 (OUTLIER) cc_final: 0.7549 (mt0) REVERT: B 287 TYR cc_start: 0.8292 (OUTLIER) cc_final: 0.7792 (m-80) REVERT: G 13 THR cc_start: 0.8751 (m) cc_final: 0.8518 (p) REVERT: C 48 LEU cc_start: 0.6911 (tp) cc_final: 0.6532 (tp) REVERT: C 158 MET cc_start: 0.7833 (tpp) cc_final: 0.7368 (tpt) REVERT: C 351 MET cc_start: 0.8250 (mmm) cc_final: 0.7918 (mtp) REVERT: C 453 GLU cc_start: 0.7312 (OUTLIER) cc_final: 0.6963 (mm-30) REVERT: C 470 MET cc_start: 0.8464 (OUTLIER) cc_final: 0.7257 (mpp) REVERT: C 507 MET cc_start: 0.8540 (tpp) cc_final: 0.8138 (tpp) REVERT: C 721 ASP cc_start: 0.8831 (m-30) cc_final: 0.8530 (m-30) REVERT: D 20 SER cc_start: 0.6537 (OUTLIER) cc_final: 0.5880 (p) REVERT: D 111 ASP cc_start: 0.7780 (OUTLIER) cc_final: 0.6866 (t70) REVERT: D 142 ASP cc_start: 0.6214 (t0) cc_final: 0.5517 (t0) outliers start: 94 outliers final: 58 residues processed: 260 average time/residue: 0.3019 time to fit residues: 132.6721 Evaluate side-chains 224 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 156 time to evaluate : 2.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 470 MET Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 782 SER Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 846 ASN Chi-restraints excluded: chain A residue 866 PHE Chi-restraints excluded: chain A residue 871 VAL Chi-restraints excluded: chain A residue 872 ILE Chi-restraints excluded: chain A residue 881 MET Chi-restraints excluded: chain A residue 894 TRP Chi-restraints excluded: chain A residue 897 ASP Chi-restraints excluded: chain A residue 935 ILE Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 1002 ASP Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 156 TRP Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 287 TYR Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain C residue 127 ASN Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 248 ASN Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 453 GLU Chi-restraints excluded: chain C residue 470 MET Chi-restraints excluded: chain C residue 480 ILE Chi-restraints excluded: chain C residue 641 ILE Chi-restraints excluded: chain C residue 741 VAL Chi-restraints excluded: chain C residue 758 ILE Chi-restraints excluded: chain C residue 782 SER Chi-restraints excluded: chain C residue 846 ASN Chi-restraints excluded: chain C residue 866 PHE Chi-restraints excluded: chain C residue 871 VAL Chi-restraints excluded: chain C residue 872 ILE Chi-restraints excluded: chain C residue 894 TRP Chi-restraints excluded: chain C residue 935 ILE Chi-restraints excluded: chain C residue 943 SER Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 71 ASP Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 35 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 85 optimal weight: 0.6980 chunk 229 optimal weight: 3.9990 chunk 50 optimal weight: 10.0000 chunk 149 optimal weight: 8.9990 chunk 62 optimal weight: 0.5980 chunk 255 optimal weight: 4.9990 chunk 212 optimal weight: 4.9990 chunk 118 optimal weight: 0.8980 chunk 21 optimal weight: 9.9990 chunk 84 optimal weight: 0.9980 chunk 134 optimal weight: 10.0000 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 666 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.5233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23082 Z= 0.175 Angle : 0.543 8.958 31148 Z= 0.259 Chirality : 0.043 0.454 3524 Planarity : 0.004 0.044 3810 Dihedral : 13.085 142.834 5203 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.71 % Allowed : 19.81 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.03 (0.16), residues: 2636 helix: 1.19 (0.16), residues: 1174 sheet: -0.60 (0.30), residues: 260 loop : -1.00 (0.17), residues: 1202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 988 HIS 0.002 0.001 HIS C 493 PHE 0.023 0.001 PHE C 967 TYR 0.017 0.001 TYR C 488 ARG 0.006 0.000 ARG C 979 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 180 time to evaluate : 2.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 THR cc_start: 0.6171 (OUTLIER) cc_final: 0.5873 (p) REVERT: A 158 MET cc_start: 0.7813 (tpp) cc_final: 0.7241 (tpt) REVERT: A 351 MET cc_start: 0.8152 (mmm) cc_final: 0.7884 (mtp) REVERT: A 470 MET cc_start: 0.8152 (OUTLIER) cc_final: 0.7138 (mpp) REVERT: B 111 ASP cc_start: 0.7738 (OUTLIER) cc_final: 0.6817 (t70) REVERT: B 142 ASP cc_start: 0.5964 (t0) cc_final: 0.5507 (t0) REVERT: B 287 TYR cc_start: 0.8303 (OUTLIER) cc_final: 0.7729 (m-80) REVERT: G 13 THR cc_start: 0.8655 (m) cc_final: 0.8430 (p) REVERT: C 48 LEU cc_start: 0.6876 (tp) cc_final: 0.6511 (tp) REVERT: C 70 GLU cc_start: 0.7582 (tp30) cc_final: 0.6890 (mt-10) REVERT: C 158 MET cc_start: 0.7873 (tpp) cc_final: 0.7264 (tpt) REVERT: C 351 MET cc_start: 0.8217 (mmm) cc_final: 0.7870 (mtp) REVERT: C 453 GLU cc_start: 0.7397 (OUTLIER) cc_final: 0.7060 (mm-30) REVERT: C 470 MET cc_start: 0.8240 (OUTLIER) cc_final: 0.7149 (mpp) REVERT: C 507 MET cc_start: 0.8525 (tpp) cc_final: 0.8127 (tpp) REVERT: C 897 ASP cc_start: 0.8068 (OUTLIER) cc_final: 0.7845 (p0) REVERT: D 142 ASP cc_start: 0.6313 (t0) cc_final: 0.5660 (t0) REVERT: D 234 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8209 (tm) REVERT: D 283 GLU cc_start: 0.7262 (OUTLIER) cc_final: 0.6994 (mt-10) outliers start: 84 outliers final: 57 residues processed: 248 average time/residue: 0.3069 time to fit residues: 127.3921 Evaluate side-chains 225 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 159 time to evaluate : 2.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 470 MET Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 659 ASP Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 782 SER Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 846 ASN Chi-restraints excluded: chain A residue 866 PHE Chi-restraints excluded: chain A residue 871 VAL Chi-restraints excluded: chain A residue 872 ILE Chi-restraints excluded: chain A residue 894 TRP Chi-restraints excluded: chain A residue 935 ILE Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 1002 ASP Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain B residue 287 TYR Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain C residue 127 ASN Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 248 ASN Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 453 GLU Chi-restraints excluded: chain C residue 470 MET Chi-restraints excluded: chain C residue 480 ILE Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain C residue 641 ILE Chi-restraints excluded: chain C residue 741 VAL Chi-restraints excluded: chain C residue 758 ILE Chi-restraints excluded: chain C residue 782 SER Chi-restraints excluded: chain C residue 846 ASN Chi-restraints excluded: chain C residue 866 PHE Chi-restraints excluded: chain C residue 871 VAL Chi-restraints excluded: chain C residue 872 ILE Chi-restraints excluded: chain C residue 894 TRP Chi-restraints excluded: chain C residue 897 ASP Chi-restraints excluded: chain C residue 935 ILE Chi-restraints excluded: chain C residue 943 SER Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 71 ASP Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 35 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 246 optimal weight: 7.9990 chunk 28 optimal weight: 0.6980 chunk 145 optimal weight: 7.9990 chunk 186 optimal weight: 0.7980 chunk 144 optimal weight: 2.9990 chunk 215 optimal weight: 0.7980 chunk 142 optimal weight: 4.9990 chunk 254 optimal weight: 7.9990 chunk 159 optimal weight: 3.9990 chunk 155 optimal weight: 9.9990 chunk 117 optimal weight: 9.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 683 HIS C 683 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.5439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 23082 Z= 0.196 Angle : 0.560 9.462 31148 Z= 0.267 Chirality : 0.043 0.452 3524 Planarity : 0.004 0.042 3810 Dihedral : 12.704 139.317 5198 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 4.07 % Allowed : 19.67 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.11 (0.16), residues: 2636 helix: 1.24 (0.16), residues: 1174 sheet: -0.54 (0.33), residues: 236 loop : -0.94 (0.16), residues: 1226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP A 392 HIS 0.017 0.001 HIS A 683 PHE 0.024 0.002 PHE C 555 TYR 0.025 0.001 TYR C 488 ARG 0.004 0.000 ARG C 979 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 177 time to evaluate : 2.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.7394 (mm) cc_final: 0.6932 (tp) REVERT: A 158 MET cc_start: 0.7895 (tpp) cc_final: 0.7275 (tpt) REVERT: A 351 MET cc_start: 0.8153 (OUTLIER) cc_final: 0.7730 (mtp) REVERT: A 470 MET cc_start: 0.8063 (OUTLIER) cc_final: 0.7131 (mpp) REVERT: B 16 PHE cc_start: 0.7319 (t80) cc_final: 0.7034 (t80) REVERT: B 142 ASP cc_start: 0.6194 (t0) cc_final: 0.5653 (t0) REVERT: B 287 TYR cc_start: 0.8308 (OUTLIER) cc_final: 0.7754 (m-80) REVERT: G 4 GLU cc_start: 0.4502 (pm20) cc_final: 0.4177 (tm-30) REVERT: C 48 LEU cc_start: 0.6922 (tp) cc_final: 0.6688 (tp) REVERT: C 158 MET cc_start: 0.7873 (tpp) cc_final: 0.7261 (tpt) REVERT: C 203 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8047 (pp) REVERT: C 351 MET cc_start: 0.8219 (mmm) cc_final: 0.7841 (mtp) REVERT: C 453 GLU cc_start: 0.7449 (OUTLIER) cc_final: 0.7130 (mm-30) REVERT: C 470 MET cc_start: 0.8275 (OUTLIER) cc_final: 0.7261 (mpp) REVERT: C 897 ASP cc_start: 0.8125 (OUTLIER) cc_final: 0.7767 (p0) REVERT: D 111 ASP cc_start: 0.7773 (OUTLIER) cc_final: 0.6880 (t70) REVERT: D 142 ASP cc_start: 0.6376 (t0) cc_final: 0.5736 (t0) REVERT: D 234 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8222 (tm) REVERT: D 283 GLU cc_start: 0.7206 (OUTLIER) cc_final: 0.6943 (mt-10) outliers start: 92 outliers final: 67 residues processed: 249 average time/residue: 0.2998 time to fit residues: 125.2341 Evaluate side-chains 236 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 159 time to evaluate : 2.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 145 CYS Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 470 MET Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 659 ASP Chi-restraints excluded: chain A residue 683 HIS Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 753 ASP Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 782 SER Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 846 ASN Chi-restraints excluded: chain A residue 866 PHE Chi-restraints excluded: chain A residue 871 VAL Chi-restraints excluded: chain A residue 872 ILE Chi-restraints excluded: chain A residue 894 TRP Chi-restraints excluded: chain A residue 935 ILE Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 1002 ASP Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 156 TRP Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 287 TYR Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 127 ASN Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 145 CYS Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 248 ASN Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 453 GLU Chi-restraints excluded: chain C residue 470 MET Chi-restraints excluded: chain C residue 480 ILE Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain C residue 641 ILE Chi-restraints excluded: chain C residue 683 HIS Chi-restraints excluded: chain C residue 741 VAL Chi-restraints excluded: chain C residue 758 ILE Chi-restraints excluded: chain C residue 782 SER Chi-restraints excluded: chain C residue 846 ASN Chi-restraints excluded: chain C residue 871 VAL Chi-restraints excluded: chain C residue 872 ILE Chi-restraints excluded: chain C residue 881 MET Chi-restraints excluded: chain C residue 894 TRP Chi-restraints excluded: chain C residue 897 ASP Chi-restraints excluded: chain C residue 935 ILE Chi-restraints excluded: chain C residue 943 SER Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 71 ASP Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain E residue 33 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 157 optimal weight: 5.9990 chunk 101 optimal weight: 0.6980 chunk 151 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 49 optimal weight: 8.9990 chunk 161 optimal weight: 6.9990 chunk 173 optimal weight: 8.9990 chunk 125 optimal weight: 8.9990 chunk 23 optimal weight: 6.9990 chunk 200 optimal weight: 0.8980 chunk 231 optimal weight: 9.9990 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 434 GLN ** A 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 683 HIS C 683 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.5622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 23082 Z= 0.294 Angle : 0.601 9.884 31148 Z= 0.289 Chirality : 0.044 0.439 3524 Planarity : 0.004 0.041 3810 Dihedral : 12.673 140.324 5197 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.76 % Allowed : 20.42 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.04 (0.16), residues: 2636 helix: 1.06 (0.16), residues: 1178 sheet: -0.66 (0.31), residues: 256 loop : -0.96 (0.16), residues: 1202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP C 392 HIS 0.034 0.002 HIS A 683 PHE 0.025 0.002 PHE A 967 TYR 0.026 0.002 TYR C 488 ARG 0.003 0.000 ARG C 979 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 163 time to evaluate : 2.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 MET cc_start: 0.7977 (tpp) cc_final: 0.7611 (tpp) REVERT: A 351 MET cc_start: 0.8097 (OUTLIER) cc_final: 0.7701 (mtp) REVERT: A 470 MET cc_start: 0.7991 (OUTLIER) cc_final: 0.7123 (mpp) REVERT: B 142 ASP cc_start: 0.6279 (t0) cc_final: 0.5695 (t0) REVERT: B 203 GLN cc_start: 0.8553 (OUTLIER) cc_final: 0.8203 (mp10) REVERT: B 234 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8330 (tm) REVERT: B 287 TYR cc_start: 0.8354 (OUTLIER) cc_final: 0.7782 (m-80) REVERT: G 4 GLU cc_start: 0.4428 (pm20) cc_final: 0.4216 (tm-30) REVERT: C 158 MET cc_start: 0.7963 (tpp) cc_final: 0.7591 (tpp) REVERT: C 351 MET cc_start: 0.8181 (mmm) cc_final: 0.7784 (mtp) REVERT: C 470 MET cc_start: 0.8300 (OUTLIER) cc_final: 0.7329 (mpp) REVERT: C 897 ASP cc_start: 0.8189 (OUTLIER) cc_final: 0.7859 (p0) REVERT: D 18 TRP cc_start: 0.7676 (t-100) cc_final: 0.7395 (t60) REVERT: D 111 ASP cc_start: 0.7855 (OUTLIER) cc_final: 0.6982 (t70) REVERT: D 142 ASP cc_start: 0.6429 (t0) cc_final: 0.5782 (t0) REVERT: D 234 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8268 (tm) REVERT: D 283 GLU cc_start: 0.7223 (OUTLIER) cc_final: 0.6965 (mt-10) outliers start: 85 outliers final: 65 residues processed: 234 average time/residue: 0.2963 time to fit residues: 114.7801 Evaluate side-chains 234 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 159 time to evaluate : 2.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 145 CYS Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 470 MET Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 659 ASP Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 753 ASP Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 782 SER Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 846 ASN Chi-restraints excluded: chain A residue 871 VAL Chi-restraints excluded: chain A residue 872 ILE Chi-restraints excluded: chain A residue 894 TRP Chi-restraints excluded: chain A residue 935 ILE Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 1002 ASP Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 156 TRP Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 287 TYR Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 127 ASN Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 145 CYS Chi-restraints excluded: chain C residue 248 ASN Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 470 MET Chi-restraints excluded: chain C residue 480 ILE Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain C residue 641 ILE Chi-restraints excluded: chain C residue 741 VAL Chi-restraints excluded: chain C residue 758 ILE Chi-restraints excluded: chain C residue 760 THR Chi-restraints excluded: chain C residue 782 SER Chi-restraints excluded: chain C residue 846 ASN Chi-restraints excluded: chain C residue 871 VAL Chi-restraints excluded: chain C residue 872 ILE Chi-restraints excluded: chain C residue 881 MET Chi-restraints excluded: chain C residue 894 TRP Chi-restraints excluded: chain C residue 897 ASP Chi-restraints excluded: chain C residue 935 ILE Chi-restraints excluded: chain C residue 943 SER Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 71 ASP Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 35 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 243 optimal weight: 3.9990 chunk 222 optimal weight: 0.9990 chunk 237 optimal weight: 5.9990 chunk 142 optimal weight: 0.9980 chunk 103 optimal weight: 0.7980 chunk 186 optimal weight: 0.6980 chunk 72 optimal weight: 3.9990 chunk 214 optimal weight: 3.9990 chunk 224 optimal weight: 3.9990 chunk 236 optimal weight: 5.9990 chunk 155 optimal weight: 7.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 683 HIS C 683 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.5730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23082 Z= 0.174 Angle : 0.544 10.066 31148 Z= 0.259 Chirality : 0.042 0.430 3524 Planarity : 0.004 0.042 3810 Dihedral : 12.193 131.147 5197 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.58 % Allowed : 20.78 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.14 (0.16), residues: 2636 helix: 1.26 (0.16), residues: 1178 sheet: -0.65 (0.33), residues: 232 loop : -0.89 (0.16), residues: 1226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP C 392 HIS 0.014 0.001 HIS A 683 PHE 0.028 0.001 PHE A 967 TYR 0.031 0.001 TYR C 488 ARG 0.004 0.000 ARG C 979 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 172 time to evaluate : 2.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 MET cc_start: 0.7954 (tpp) cc_final: 0.7631 (tpp) REVERT: A 351 MET cc_start: 0.8083 (OUTLIER) cc_final: 0.7710 (mtp) REVERT: A 470 MET cc_start: 0.7970 (OUTLIER) cc_final: 0.7119 (mpp) REVERT: B 142 ASP cc_start: 0.6257 (t0) cc_final: 0.5635 (t0) REVERT: B 234 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8288 (tm) REVERT: B 287 TYR cc_start: 0.8314 (OUTLIER) cc_final: 0.7669 (m-80) REVERT: C 158 MET cc_start: 0.7938 (tpp) cc_final: 0.7435 (tpt) REVERT: C 287 GLU cc_start: 0.7028 (mm-30) cc_final: 0.6771 (mm-30) REVERT: C 351 MET cc_start: 0.8212 (mmm) cc_final: 0.7767 (mtp) REVERT: C 453 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.7148 (mm-30) REVERT: C 470 MET cc_start: 0.8291 (OUTLIER) cc_final: 0.7323 (mpp) REVERT: C 897 ASP cc_start: 0.8234 (OUTLIER) cc_final: 0.7912 (p0) REVERT: D 18 TRP cc_start: 0.7623 (t-100) cc_final: 0.7386 (t60) REVERT: D 142 ASP cc_start: 0.6464 (t0) cc_final: 0.5782 (t0) REVERT: D 234 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8228 (tm) REVERT: D 283 GLU cc_start: 0.7188 (OUTLIER) cc_final: 0.6931 (mt-10) outliers start: 81 outliers final: 60 residues processed: 240 average time/residue: 0.2950 time to fit residues: 117.2313 Evaluate side-chains 234 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 165 time to evaluate : 2.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 470 MET Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 659 ASP Chi-restraints excluded: chain A residue 683 HIS Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 753 ASP Chi-restraints excluded: chain A residue 782 SER Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 846 ASN Chi-restraints excluded: chain A residue 866 PHE Chi-restraints excluded: chain A residue 871 VAL Chi-restraints excluded: chain A residue 872 ILE Chi-restraints excluded: chain A residue 894 TRP Chi-restraints excluded: chain A residue 935 ILE Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 1002 ASP Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 156 TRP Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 287 TYR Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 36 ILE Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 127 ASN Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 145 CYS Chi-restraints excluded: chain C residue 248 ASN Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 453 GLU Chi-restraints excluded: chain C residue 470 MET Chi-restraints excluded: chain C residue 480 ILE Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain C residue 641 ILE Chi-restraints excluded: chain C residue 683 HIS Chi-restraints excluded: chain C residue 741 VAL Chi-restraints excluded: chain C residue 782 SER Chi-restraints excluded: chain C residue 846 ASN Chi-restraints excluded: chain C residue 871 VAL Chi-restraints excluded: chain C residue 872 ILE Chi-restraints excluded: chain C residue 894 TRP Chi-restraints excluded: chain C residue 897 ASP Chi-restraints excluded: chain C residue 935 ILE Chi-restraints excluded: chain C residue 943 SER Chi-restraints excluded: chain C residue 998 ILE Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 71 ASP Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain E residue 33 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 250 optimal weight: 0.0020 chunk 153 optimal weight: 8.9990 chunk 118 optimal weight: 9.9990 chunk 174 optimal weight: 10.0000 chunk 263 optimal weight: 10.0000 chunk 242 optimal weight: 5.9990 chunk 209 optimal weight: 2.9990 chunk 21 optimal weight: 10.0000 chunk 161 optimal weight: 1.9990 chunk 128 optimal weight: 0.9990 chunk 166 optimal weight: 8.9990 overall best weight: 2.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 557 HIS A 683 HIS C 683 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.5819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 23082 Z= 0.232 Angle : 0.576 10.263 31148 Z= 0.277 Chirality : 0.043 0.421 3524 Planarity : 0.004 0.042 3810 Dihedral : 12.066 130.197 5194 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.40 % Allowed : 20.73 % Favored : 75.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 (0.16), residues: 2636 helix: 1.19 (0.16), residues: 1176 sheet: -0.72 (0.33), residues: 232 loop : -0.87 (0.16), residues: 1228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C 392 HIS 0.025 0.002 HIS C 683 PHE 0.028 0.002 PHE A 967 TYR 0.020 0.001 TYR A 684 ARG 0.005 0.000 ARG C 204 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 166 time to evaluate : 2.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 MET cc_start: 0.8000 (tpp) cc_final: 0.7715 (tpp) REVERT: A 351 MET cc_start: 0.8094 (OUTLIER) cc_final: 0.7647 (mtp) REVERT: A 470 MET cc_start: 0.7981 (OUTLIER) cc_final: 0.7143 (mpp) REVERT: B 142 ASP cc_start: 0.6316 (t0) cc_final: 0.5689 (t0) REVERT: B 234 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8300 (tm) REVERT: B 287 TYR cc_start: 0.8331 (OUTLIER) cc_final: 0.7684 (m-80) REVERT: C 158 MET cc_start: 0.7943 (tpp) cc_final: 0.7720 (tpp) REVERT: C 287 GLU cc_start: 0.7110 (mm-30) cc_final: 0.6779 (mm-30) REVERT: C 351 MET cc_start: 0.8176 (mmm) cc_final: 0.7638 (mtp) REVERT: C 470 MET cc_start: 0.8302 (OUTLIER) cc_final: 0.7349 (mpp) REVERT: C 719 VAL cc_start: 0.8605 (OUTLIER) cc_final: 0.8185 (t) REVERT: C 897 ASP cc_start: 0.8259 (OUTLIER) cc_final: 0.7951 (p0) REVERT: D 142 ASP cc_start: 0.6494 (t0) cc_final: 0.5792 (t0) REVERT: D 234 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8269 (tm) REVERT: D 283 GLU cc_start: 0.7223 (OUTLIER) cc_final: 0.6952 (mt-10) outliers start: 77 outliers final: 66 residues processed: 231 average time/residue: 0.3024 time to fit residues: 117.1168 Evaluate side-chains 237 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 162 time to evaluate : 2.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 470 MET Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 659 ASP Chi-restraints excluded: chain A residue 683 HIS Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 753 ASP Chi-restraints excluded: chain A residue 760 THR Chi-restraints excluded: chain A residue 782 SER Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 846 ASN Chi-restraints excluded: chain A residue 866 PHE Chi-restraints excluded: chain A residue 871 VAL Chi-restraints excluded: chain A residue 872 ILE Chi-restraints excluded: chain A residue 894 TRP Chi-restraints excluded: chain A residue 935 ILE Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 1002 ASP Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 156 TRP Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 287 TYR Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 36 ILE Chi-restraints excluded: chain C residue 41 MET Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 127 ASN Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 145 CYS Chi-restraints excluded: chain C residue 248 ASN Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 470 MET Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain C residue 641 ILE Chi-restraints excluded: chain C residue 683 HIS Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 741 VAL Chi-restraints excluded: chain C residue 758 ILE Chi-restraints excluded: chain C residue 782 SER Chi-restraints excluded: chain C residue 846 ASN Chi-restraints excluded: chain C residue 871 VAL Chi-restraints excluded: chain C residue 872 ILE Chi-restraints excluded: chain C residue 894 TRP Chi-restraints excluded: chain C residue 897 ASP Chi-restraints excluded: chain C residue 935 ILE Chi-restraints excluded: chain C residue 943 SER Chi-restraints excluded: chain C residue 998 ILE Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 71 ASP Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 36 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 223 optimal weight: 5.9990 chunk 64 optimal weight: 8.9990 chunk 193 optimal weight: 7.9990 chunk 30 optimal weight: 6.9990 chunk 58 optimal weight: 6.9990 chunk 209 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 215 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 38 optimal weight: 8.9990 chunk 184 optimal weight: 7.9990 overall best weight: 2.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 683 HIS C 683 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.121440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.091631 restraints weight = 43174.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.091317 restraints weight = 42070.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.093025 restraints weight = 34907.421| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.5903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23082 Z= 0.224 Angle : 0.569 10.358 31148 Z= 0.274 Chirality : 0.043 0.412 3524 Planarity : 0.004 0.044 3810 Dihedral : 11.946 127.975 5194 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.76 % Allowed : 20.29 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 (0.16), residues: 2636 helix: 1.18 (0.16), residues: 1176 sheet: -0.73 (0.33), residues: 232 loop : -0.85 (0.16), residues: 1228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C 392 HIS 0.028 0.002 HIS C 683 PHE 0.029 0.002 PHE A 967 TYR 0.030 0.001 TYR A 488 ARG 0.005 0.000 ARG C 204 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4033.51 seconds wall clock time: 74 minutes 49.17 seconds (4489.17 seconds total)