Starting phenix.real_space_refine on Sun Feb 18 19:32:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wyx_32897/02_2024/7wyx_32897_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wyx_32897/02_2024/7wyx_32897.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wyx_32897/02_2024/7wyx_32897.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wyx_32897/02_2024/7wyx_32897.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wyx_32897/02_2024/7wyx_32897_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wyx_32897/02_2024/7wyx_32897_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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: 7 Type Number sf(0) Gaussians P 32 5.49 5 Mg 2 5.21 5 S 118 5.16 5 Na 2 4.78 5 C 14694 2.51 5 N 3528 2.21 5 O 4338 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: 22714 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: 477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 477 Unusual residues: {' MG': 1, ' NA': 1, '7Q2': 1, 'ATP': 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: 477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 477 Unusual residues: {' MG': 1, ' NA': 1, '7Q2': 1, 'ATP': 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: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 13.05, per 1000 atoms: 0.57 Number of scatterers: 22714 At special positions: 0 Unit cell: (216.276, 181.844, 104.372, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 118 16.00 P 32 15.00 Mg 2 11.99 Na 2 11.00 O 4338 8.00 N 3528 7.00 C 14694 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=2.03 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=2.03 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: 10.37 Conformation dependent library (CDL) restraints added in 3.9 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: 106 helices and 16 sheets defined 43.5% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.52 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: 4.474A 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: 3.659A pdb=" N ILE A 322 " --> pdb=" O LEU A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 353 removed outlier: 3.598A pdb=" N THR A 347 " --> pdb=" O CYS A 343 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG A 350 " --> pdb=" O LEU A 346 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N MET A 351 " --> pdb=" O THR A 347 " (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: 3.533A 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: 3.827A 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: 4.164A 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: 4.144A pdb=" N LYS A 726 " --> pdb=" O PRO A 723 " (cutoff:3.500A) removed outlier: 3.872A 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: 3.720A pdb=" N ARG A 766 " --> pdb=" O VAL A 762 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE A 769 " --> pdb=" O GLY A 765 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N SER A 782 " --> pdb=" O TYR A 778 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ASN A 783 " --> pdb=" O THR A 779 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ILE A 784 " --> pdb=" O LEU A 780 " (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: 4.288A pdb=" N ALA A 823 " --> pdb=" O ALA A 819 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N TYR A 824 " --> pdb=" O ILE A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 847 through 853 removed outlier: 3.655A 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: 4.035A 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: 3.595A 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: 3.527A pdb=" N PHE A1007 " --> pdb=" O GLU A1003 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE A1008 " --> pdb=" O MET A1004 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE A1009 " --> pdb=" O ARG A1005 " (cutoff:3.500A) removed outlier: 4.458A 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 30 through 61 removed outlier: 3.787A pdb=" N PHE B 34 " --> pdb=" O GLY B 30 " (cutoff:3.500A) removed outlier: 3.799A 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: 3.558A pdb=" N SER B 105 " --> pdb=" O SER B 101 " (cutoff:3.500A) removed outlier: 4.278A 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 252 No H-bonds generated for 'chain 'B' and resid 249 through 252' 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: 4.473A 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: 3.659A pdb=" N ILE C 322 " --> pdb=" O LEU C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 353 removed outlier: 3.599A pdb=" N THR C 347 " --> pdb=" O CYS C 343 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG C 350 " --> pdb=" O LEU C 346 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N MET C 351 " --> pdb=" O THR C 347 " (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: 3.532A 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: 3.827A 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: 4.165A 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: 4.143A pdb=" N LYS C 726 " --> pdb=" O PRO C 723 " (cutoff:3.500A) removed outlier: 3.873A 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: 3.721A pdb=" N ARG C 766 " --> pdb=" O VAL C 762 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE C 769 " --> pdb=" O GLY C 765 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N SER C 782 " --> pdb=" O TYR C 778 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ASN C 783 " --> pdb=" O THR C 779 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ILE C 784 " --> pdb=" O LEU C 780 " (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: 4.287A pdb=" N ALA C 823 " --> pdb=" O ALA C 819 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N TYR C 824 " --> pdb=" O ILE C 820 " (cutoff:3.500A) Processing helix chain 'C' and resid 847 through 853 removed outlier: 3.654A 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: 4.035A 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: 3.595A 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: 3.525A pdb=" N PHE C1007 " --> pdb=" O GLU C1003 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE C1008 " --> pdb=" O MET C1004 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE C1009 " --> pdb=" O ARG C1005 " (cutoff:3.500A) removed outlier: 4.458A 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 30 through 61 removed outlier: 3.787A pdb=" N PHE D 34 " --> pdb=" O GLY D 30 " (cutoff:3.500A) removed outlier: 3.799A 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: 3.558A pdb=" N SER D 105 " --> pdb=" O SER D 101 " (cutoff:3.500A) removed outlier: 4.278A 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 252 No H-bonds generated for 'chain 'D' and resid 249 through 252' 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: 11.758A pdb=" N GLN A 168 " --> pdb=" O LYS A 194 " (cutoff:3.500A) removed outlier: 9.270A pdb=" N LYS A 194 " --> pdb=" O GLN A 168 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N LEU A 170 " --> pdb=" O GLU A 192 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LEU A 190 " --> pdb=" O ILE A 172 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR A 253 " --> pdb=" O HIS A 209 " (cutoff:3.500A) removed outlier: 3.901A 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: 6.716A pdb=" N THR A 372 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N THR A 715 " --> pdb=" O THR A 372 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N CYS A 374 " --> pdb=" O THR A 715 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N LYS A 612 " --> pdb=" O ILE A 373 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N SER A 375 " --> pdb=" O LYS A 612 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ILE A 614 " --> pdb=" O SER A 375 " (cutoff:3.500A) removed outlier: 4.746A 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: 7.285A pdb=" N LEU A 583 " --> pdb=" O SER A 519 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N ILE A 521 " --> pdb=" O LEU A 583 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N PHE A 585 " --> pdb=" O ILE A 521 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LEU A 523 " --> pdb=" O PHE A 585 " (cutoff:3.500A) removed outlier: 11.277A pdb=" N GLY A 587 " --> pdb=" O LEU A 523 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N PHE A 555 " --> pdb=" O VAL A 586 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N LEU A 588 " --> pdb=" O LEU A 553 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N LEU A 553 " --> pdb=" O LEU A 588 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ALA A 590 " --> pdb=" O ARG A 551 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ARG A 551 " --> pdb=" O ALA A 590 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TYR A 503 " --> pdb=" O LEU A 560 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU A 490 " --> pdb=" O ILE A 480 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N GLU A 494 " --> pdb=" O LYS A 476 " (cutoff:3.500A) removed outlier: 6.495A 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: 6.382A pdb=" N ARG A 204 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 5.844A 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 Processing sheet with id= G, first strand: chain 'B' and resid 88 through 92 removed outlier: 7.942A pdb=" N ILE B 89 " --> pdb=" O GLU B 298 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N LYS B 300 " --> pdb=" O ILE B 89 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N PHE B 91 " --> pdb=" O LYS B 300 " (cutoff:3.500A) removed outlier: 6.746A 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: 11.759A pdb=" N GLN C 168 " --> pdb=" O LYS C 194 " (cutoff:3.500A) removed outlier: 9.271A pdb=" N LYS C 194 " --> pdb=" O GLN C 168 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N LEU C 170 " --> pdb=" O GLU C 192 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LEU C 190 " --> pdb=" O ILE C 172 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR C 253 " --> pdb=" O HIS C 209 " (cutoff:3.500A) removed outlier: 3.900A 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: 6.716A pdb=" N THR C 372 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N THR C 715 " --> pdb=" O THR C 372 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N CYS C 374 " --> pdb=" O THR C 715 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N LYS C 612 " --> pdb=" O ILE C 373 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N SER C 375 " --> pdb=" O LYS C 612 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ILE C 614 " --> pdb=" O SER C 375 " (cutoff:3.500A) removed outlier: 4.746A 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: 7.285A pdb=" N LEU C 583 " --> pdb=" O SER C 519 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N ILE C 521 " --> pdb=" O LEU C 583 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N PHE C 585 " --> pdb=" O ILE C 521 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU C 523 " --> pdb=" O PHE C 585 " (cutoff:3.500A) removed outlier: 11.278A pdb=" N GLY C 587 " --> pdb=" O LEU C 523 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N PHE C 555 " --> pdb=" O VAL C 586 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N LEU C 588 " --> pdb=" O LEU C 553 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LEU C 553 " --> pdb=" O LEU C 588 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ALA C 590 " --> pdb=" O ARG C 551 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ARG C 551 " --> pdb=" O ALA C 590 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TYR C 503 " --> pdb=" O LEU C 560 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU C 490 " --> pdb=" O ILE C 480 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N GLU C 494 " --> pdb=" O LYS C 476 " (cutoff:3.500A) removed outlier: 6.495A 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: 6.382A pdb=" N ARG C 204 " --> pdb=" O VAL C 258 " (cutoff:3.500A) removed outlier: 5.846A 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 Processing sheet with id= O, first strand: chain 'D' and resid 88 through 92 removed outlier: 7.942A pdb=" N ILE D 89 " --> pdb=" O GLU D 298 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N LYS D 300 " --> pdb=" O ILE D 89 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N PHE D 91 " --> pdb=" O LYS D 300 " (cutoff:3.500A) removed outlier: 6.746A 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 212 846 hydrogen bonds defined for protein. 2472 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: 7.87 Time building geometry restraints manager: 10.95 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: 6867 1.35 - 1.47: 5216 1.47 - 1.59: 10823 1.59 - 1.70: 70 1.70 - 1.82: 172 Bond restraints: 23148 Sorted by residual: bond pdb=" OD1 PHD C 376 " pdb=" P PHD C 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 A 376 " pdb=" P PHD A 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 1.542 -0.209 2.00e-02 2.50e+03 1.09e+02 bond pdb=" C39 PCW E1304 " pdb=" C40 PCW E1304 " ideal model delta sigma weight residual 1.333 1.542 -0.209 2.00e-02 2.50e+03 1.09e+02 bond pdb=" C19 PCW A1109 " pdb=" C20 PCW A1109 " ideal model delta sigma weight residual 1.333 1.539 -0.206 2.00e-02 2.50e+03 1.06e+02 ... (remaining 23143 not shown) Histogram of bond angle deviations from ideal: 98.68 - 106.88: 903 106.88 - 115.07: 14328 115.07 - 123.26: 14908 123.26 - 131.45: 1071 131.45 - 139.65: 42 Bond angle restraints: 31252 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 108.67 100.99 7.68 1.55e+00 4.16e-01 2.45e+01 angle pdb=" N LEU B 157 " pdb=" CA LEU B 157 " pdb=" C LEU B 157 " ideal model delta sigma weight residual 108.67 101.00 7.67 1.55e+00 4.16e-01 2.45e+01 angle pdb=" N GLY A 855 " pdb=" CA GLY A 855 " pdb=" C GLY A 855 " ideal model delta sigma weight residual 113.18 124.49 -11.31 2.37e+00 1.78e-01 2.28e+01 angle pdb=" N LYS D 158 " pdb=" CA LYS D 158 " pdb=" C LYS D 158 " ideal model delta sigma weight residual 110.80 120.96 -10.16 2.13e+00 2.20e-01 2.28e+01 angle pdb=" N GLY C 855 " pdb=" CA GLY C 855 " pdb=" C GLY C 855 " ideal model delta sigma weight residual 113.18 124.46 -11.28 2.37e+00 1.78e-01 2.26e+01 ... (remaining 31247 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.90: 14206 35.90 - 71.81: 800 71.81 - 107.71: 84 107.71 - 143.61: 40 143.61 - 179.51: 2 Dihedral angle restraints: 15132 sinusoidal: 7476 harmonic: 7656 Sorted by residual: 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 11.34 -179.51 1 3.00e+01 1.11e-03 2.13e+01 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 11.29 -179.46 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 -29.70 -138.47 1 3.00e+01 1.11e-03 1.87e+01 ... (remaining 15129 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 2967 0.078 - 0.157: 455 0.157 - 0.235: 62 0.235 - 0.314: 30 0.314 - 0.392: 18 Chirality restraints: 3532 Sorted by residual: 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 -2.25 -0.15 2.00e-02 2.50e+03 5.38e+01 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 -2.25 -0.15 2.00e-02 2.50e+03 5.37e+01 chirality pdb=" C1 FUC K 6 " pdb=" O6 NAG K 1 " pdb=" C2 FUC K 6 " pdb=" O5 FUC K 6 " both_signs ideal model delta sigma weight residual False -2.40 -2.33 -0.07 2.00e-02 2.50e+03 1.13e+01 ... (remaining 3529 not shown) Planarity restraints: 3820 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 122 " -0.088 5.00e-02 4.00e+02 1.38e-01 3.05e+01 pdb=" N PRO B 123 " 0.239 5.00e-02 4.00e+02 pdb=" CA PRO B 123 " -0.076 5.00e-02 4.00e+02 pdb=" CD PRO B 123 " -0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 122 " 0.088 5.00e-02 4.00e+02 1.38e-01 3.05e+01 pdb=" N PRO D 123 " -0.239 5.00e-02 4.00e+02 pdb=" CA PRO D 123 " 0.076 5.00e-02 4.00e+02 pdb=" CD PRO D 123 " 0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 124 " 0.063 5.00e-02 4.00e+02 9.58e-02 1.47e+01 pdb=" N PRO A 125 " -0.166 5.00e-02 4.00e+02 pdb=" CA PRO A 125 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO A 125 " 0.052 5.00e-02 4.00e+02 ... (remaining 3817 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 102 2.49 - 3.10: 15911 3.10 - 3.70: 31286 3.70 - 4.30: 48282 4.30 - 4.90: 78019 Nonbonded interactions: 173600 Sorted by model distance: nonbonded pdb=" OP3 PHD C 376 " pdb="MG MG C1101 " model vdw 1.893 2.170 nonbonded pdb=" OP3 PHD A 376 " pdb="MG MG A1101 " model vdw 1.893 2.170 nonbonded pdb="MG MG A1101 " pdb=" O HOH A1202 " model vdw 1.973 2.170 nonbonded pdb="MG MG C1101 " pdb=" O HOH C1202 " model vdw 1.976 2.170 nonbonded pdb=" O THR A 378 " pdb="MG MG A1101 " model vdw 2.007 2.170 ... (remaining 173595 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.710 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.480 Check model and map are aligned: 0.370 Set scattering table: 0.240 Process input model: 62.570 Find NCS groups from input model: 1.250 Set up NCS constraints: 0.210 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: 0.000 Load rotamer database and sin/cos tables:3.170 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.308 23148 Z= 0.668 Angle : 1.353 11.630 31252 Z= 0.651 Chirality : 0.066 0.392 3532 Planarity : 0.009 0.138 3812 Dihedral : 20.164 179.514 10202 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.68 % Allowed : 8.35 % Favored : 90.97 % Rotamer: Outliers : 10.43 % Allowed : 8.58 % Favored : 80.99 % 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: -3.31 (0.14), residues: 2636 helix: -1.58 (0.13), residues: 1190 sheet: -2.36 (0.28), residues: 260 loop : -2.77 (0.16), residues: 1186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 894 HIS 0.009 0.002 HIS C 493 PHE 0.024 0.002 PHE D 297 TYR 0.030 0.002 TYR B 40 ARG 0.011 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 682 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 236 poor density : 446 time to evaluate : 2.333 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: 0.5629 (OUTLIER) cc_final: 0.5246 (m-40) REVERT: A 127 ASN cc_start: 0.6712 (OUTLIER) cc_final: 0.6026 (m110) REVERT: A 248 ASN cc_start: 0.7413 (OUTLIER) cc_final: 0.7114 (p0) REVERT: A 267 MET cc_start: 0.8414 (ppp) cc_final: 0.7749 (ttt) REVERT: A 308 ILE cc_start: 0.8619 (mp) cc_final: 0.8368 (mm) REVERT: A 350 ARG cc_start: 0.7553 (OUTLIER) cc_final: 0.7236 (mtt180) REVERT: A 460 ILE cc_start: 0.8305 (mm) cc_final: 0.8000 (mt) REVERT: A 484 SER cc_start: 0.7136 (OUTLIER) cc_final: 0.6635 (p) REVERT: A 708 GLN cc_start: 0.8040 (OUTLIER) cc_final: 0.7253 (mm-40) REVERT: A 846 ASN cc_start: 0.8021 (OUTLIER) cc_final: 0.7504 (p0) REVERT: A 1007 PHE cc_start: 0.8024 (OUTLIER) cc_final: 0.7780 (t80) REVERT: B 26 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8472 (mt) REVERT: B 32 SER cc_start: 0.8101 (OUTLIER) cc_final: 0.7755 (t) REVERT: B 73 VAL cc_start: 0.7355 (OUTLIER) cc_final: 0.7150 (m) REVERT: B 154 ARG cc_start: 0.8255 (OUTLIER) cc_final: 0.8045 (ttt180) REVERT: B 156 TRP cc_start: 0.8775 (OUTLIER) cc_final: 0.8309 (m-10) REVERT: C 65 ASN cc_start: 0.5754 (OUTLIER) cc_final: 0.5400 (m-40) REVERT: C 127 ASN cc_start: 0.6682 (OUTLIER) cc_final: 0.5956 (m110) REVERT: C 267 MET cc_start: 0.8412 (ppp) cc_final: 0.7797 (ttt) REVERT: C 308 ILE cc_start: 0.8593 (mp) cc_final: 0.8333 (mm) REVERT: C 350 ARG cc_start: 0.7597 (OUTLIER) cc_final: 0.7332 (mtt180) REVERT: C 460 ILE cc_start: 0.8405 (mm) cc_final: 0.8092 (mt) REVERT: C 484 SER cc_start: 0.7419 (OUTLIER) cc_final: 0.6897 (p) REVERT: C 708 GLN cc_start: 0.8003 (OUTLIER) cc_final: 0.7204 (mm-40) REVERT: C 949 MET cc_start: 0.8357 (mmm) cc_final: 0.8101 (mtp) REVERT: C 1007 PHE cc_start: 0.7968 (OUTLIER) cc_final: 0.7707 (t80) REVERT: D 26 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8508 (mt) REVERT: D 32 SER cc_start: 0.8223 (OUTLIER) cc_final: 0.7859 (t) REVERT: D 73 VAL cc_start: 0.7467 (OUTLIER) cc_final: 0.7202 (p) outliers start: 236 outliers final: 50 residues processed: 621 average time/residue: 0.4040 time to fit residues: 364.1203 Evaluate side-chains 282 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 210 time to evaluate : 2.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 240 ARG Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 343 CYS Chi-restraints excluded: chain A residue 350 ARG Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 445 ARG Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 488 TYR Chi-restraints excluded: chain A residue 493 HIS Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 571 PHE Chi-restraints excluded: chain A residue 692 ARG Chi-restraints excluded: chain A residue 708 GLN Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 846 ASN Chi-restraints excluded: chain A residue 894 TRP Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 975 ASP Chi-restraints excluded: chain A residue 1007 PHE Chi-restraints excluded: chain A residue 1011 ARG Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 32 SER 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 154 ARG Chi-restraints excluded: chain B residue 156 TRP Chi-restraints excluded: chain B residue 160 CYS Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 127 ASN Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 240 ARG Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 343 CYS Chi-restraints excluded: chain C residue 350 ARG Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 415 SER Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 445 ARG Chi-restraints excluded: chain C residue 484 SER Chi-restraints excluded: chain C residue 488 TYR Chi-restraints excluded: chain C residue 493 HIS Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 571 PHE Chi-restraints excluded: chain C residue 692 ARG Chi-restraints excluded: chain C residue 708 GLN Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 846 ASN Chi-restraints excluded: chain C residue 894 TRP Chi-restraints excluded: chain C residue 943 SER Chi-restraints excluded: chain C residue 975 ASP Chi-restraints excluded: chain C residue 1007 PHE Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 107 HIS Chi-restraints excluded: chain D residue 160 CYS Chi-restraints excluded: chain D residue 203 GLN Chi-restraints excluded: chain D residue 269 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 222 optimal weight: 0.9990 chunk 200 optimal weight: 5.9990 chunk 111 optimal weight: 0.0870 chunk 68 optimal weight: 5.9990 chunk 134 optimal weight: 9.9990 chunk 106 optimal weight: 6.9990 chunk 206 optimal weight: 0.8980 chunk 80 optimal weight: 7.9990 chunk 125 optimal weight: 5.9990 chunk 154 optimal weight: 0.9980 chunk 239 optimal weight: 0.0980 overall best weight: 0.6160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 225 GLN A 474 ASN A 620 HIS A 683 HIS A 904 GLN B 56 GLN B 203 GLN B 258 GLN B 271 ASN ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 225 GLN C 474 ASN C 566 ASN C 620 HIS C 904 GLN D 56 GLN D 203 GLN D 258 GLN D 271 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 23148 Z= 0.171 Angle : 0.618 9.322 31252 Z= 0.300 Chirality : 0.044 0.421 3532 Planarity : 0.005 0.072 3812 Dihedral : 17.610 179.057 5392 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.63 % Allowed : 13.44 % Favored : 82.94 % 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: -1.58 (0.15), residues: 2636 helix: 0.08 (0.15), residues: 1200 sheet: -2.02 (0.26), residues: 270 loop : -1.99 (0.16), residues: 1166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 392 HIS 0.005 0.001 HIS A 493 PHE 0.020 0.002 PHE A 585 TYR 0.015 0.001 TYR B 40 ARG 0.005 0.000 ARG A 517 *********************** 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 324 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 242 time to evaluate : 2.738 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 100 PHE cc_start: 0.7448 (OUTLIER) cc_final: 0.6843 (m-80) REVERT: A 127 ASN cc_start: 0.6633 (OUTLIER) cc_final: 0.6040 (m110) REVERT: A 267 MET cc_start: 0.8339 (ppp) cc_final: 0.7717 (ttt) REVERT: A 351 MET cc_start: 0.7700 (mmm) cc_final: 0.7170 (mtt) REVERT: A 470 MET cc_start: 0.8362 (mmm) cc_final: 0.7925 (mpp) REVERT: A 488 TYR cc_start: 0.7418 (OUTLIER) cc_final: 0.7102 (p90) REVERT: A 680 ASP cc_start: 0.7174 (m-30) cc_final: 0.6827 (m-30) REVERT: A 833 LYS cc_start: 0.8549 (mptt) cc_final: 0.8246 (mptt) REVERT: A 1006 ARG cc_start: 0.7565 (mtm180) cc_final: 0.7314 (mtm180) REVERT: A 1007 PHE cc_start: 0.8042 (OUTLIER) cc_final: 0.7761 (t80) REVERT: B 32 SER cc_start: 0.8140 (OUTLIER) cc_final: 0.7765 (t) REVERT: B 73 VAL cc_start: 0.7359 (OUTLIER) cc_final: 0.7123 (p) REVERT: B 156 TRP cc_start: 0.8752 (OUTLIER) cc_final: 0.7796 (m-10) REVERT: C 127 ASN cc_start: 0.6605 (OUTLIER) cc_final: 0.6058 (m110) REVERT: C 267 MET cc_start: 0.8279 (ppp) cc_final: 0.7643 (ttt) REVERT: C 460 ILE cc_start: 0.8353 (mm) cc_final: 0.8051 (mt) REVERT: C 585 PHE cc_start: 0.7544 (t80) cc_final: 0.7123 (t80) REVERT: C 1007 PHE cc_start: 0.8058 (OUTLIER) cc_final: 0.7747 (t80) REVERT: D 26 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8596 (mt) REVERT: D 32 SER cc_start: 0.8355 (OUTLIER) cc_final: 0.7919 (t) REVERT: D 255 LYS cc_start: 0.8407 (mttt) cc_final: 0.8080 (mmtm) outliers start: 82 outliers final: 47 residues processed: 312 average time/residue: 0.3767 time to fit residues: 177.9479 Evaluate side-chains 235 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 177 time to evaluate : 2.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LYS Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 464 CYS Chi-restraints excluded: chain A residue 488 TYR Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 656 ASN Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 846 ASN Chi-restraints excluded: chain A residue 894 TRP Chi-restraints excluded: chain A residue 1007 PHE Chi-restraints excluded: chain A residue 1011 ARG Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 156 TRP Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 160 CYS Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain C residue 91 LYS Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 127 ASN Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 415 SER Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 464 CYS Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 656 ASN Chi-restraints excluded: chain C residue 678 LEU Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 846 ASN Chi-restraints excluded: chain C residue 894 TRP Chi-restraints excluded: chain C residue 1007 PHE Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 29 THR 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 130 THR Chi-restraints excluded: chain D residue 159 ASN Chi-restraints excluded: chain D residue 160 CYS Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 203 GLN Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain E residue 11 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 133 optimal weight: 9.9990 chunk 74 optimal weight: 3.9990 chunk 199 optimal weight: 7.9990 chunk 163 optimal weight: 6.9990 chunk 66 optimal weight: 10.0000 chunk 240 optimal weight: 3.9990 chunk 259 optimal weight: 5.9990 chunk 213 optimal weight: 0.5980 chunk 238 optimal weight: 7.9990 chunk 81 optimal weight: 5.9990 chunk 192 optimal weight: 10.0000 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 GLN B 284 ASN ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 243 GLN D 284 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.3906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 23148 Z= 0.395 Angle : 0.724 14.287 31252 Z= 0.354 Chirality : 0.049 0.426 3532 Planarity : 0.005 0.050 3812 Dihedral : 16.146 167.380 5303 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 4.42 % Allowed : 13.22 % Favored : 82.36 % 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: -0.79 (0.16), residues: 2636 helix: 0.53 (0.15), residues: 1194 sheet: -1.19 (0.31), residues: 246 loop : -1.45 (0.16), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP A 392 HIS 0.004 0.001 HIS A 52 PHE 0.022 0.003 PHE A 793 TYR 0.031 0.003 TYR A 684 ARG 0.008 0.001 ARG A 517 *********************** 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 288 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 188 time to evaluate : 2.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ASP cc_start: 0.7174 (t0) cc_final: 0.6340 (m-30) REVERT: A 100 PHE cc_start: 0.7859 (OUTLIER) cc_final: 0.7382 (m-80) REVERT: A 470 MET cc_start: 0.8366 (mmm) cc_final: 0.7746 (mpp) REVERT: A 678 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.8141 (tt) REVERT: B 55 ILE cc_start: 0.8245 (OUTLIER) cc_final: 0.7657 (tp) REVERT: B 73 VAL cc_start: 0.8071 (OUTLIER) cc_final: 0.7682 (p) REVERT: B 110 MET cc_start: 0.8516 (mmt) cc_final: 0.8268 (mmt) REVERT: B 156 TRP cc_start: 0.8884 (OUTLIER) cc_final: 0.7823 (m-10) REVERT: C 58 ASP cc_start: 0.7037 (t0) cc_final: 0.6479 (m-30) REVERT: C 100 PHE cc_start: 0.7889 (OUTLIER) cc_final: 0.7393 (m-80) REVERT: D 26 LEU cc_start: 0.9331 (OUTLIER) cc_final: 0.9090 (mt) REVERT: D 55 ILE cc_start: 0.8206 (OUTLIER) cc_final: 0.7633 (tp) outliers start: 100 outliers final: 58 residues processed: 273 average time/residue: 0.3628 time to fit residues: 154.1768 Evaluate side-chains 229 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 163 time to evaluate : 2.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain A residue 639 GLU Chi-restraints excluded: chain A residue 656 ASN Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 737 SER Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 846 ASN Chi-restraints excluded: chain A residue 894 TRP Chi-restraints excluded: chain A residue 986 SER Chi-restraints excluded: chain A residue 1011 ARG Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 156 TRP Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain C residue 197 ASP Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 601 ASP Chi-restraints excluded: chain C residue 656 ASN Chi-restraints excluded: chain C residue 675 THR Chi-restraints excluded: chain C residue 737 SER Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 846 ASN Chi-restraints excluded: chain C residue 894 TRP Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 64 ASP Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 203 GLN Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain D residue 284 ASN Chi-restraints excluded: chain E residue 35 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 237 optimal weight: 2.9990 chunk 180 optimal weight: 10.0000 chunk 124 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 114 optimal weight: 5.9990 chunk 161 optimal weight: 0.8980 chunk 241 optimal weight: 7.9990 chunk 255 optimal weight: 2.9990 chunk 125 optimal weight: 5.9990 chunk 228 optimal weight: 0.7980 chunk 68 optimal weight: 9.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 HIS ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.4115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23148 Z= 0.179 Angle : 0.552 9.034 31252 Z= 0.265 Chirality : 0.044 0.425 3532 Planarity : 0.004 0.055 3812 Dihedral : 15.199 164.829 5287 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.30 % Allowed : 15.83 % Favored : 81.87 % 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: 1.17 (0.15), residues: 1186 sheet: -0.94 (0.32), residues: 266 loop : -1.23 (0.17), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 392 HIS 0.003 0.001 HIS C 52 PHE 0.022 0.002 PHE A 585 TYR 0.026 0.001 TYR A 684 ARG 0.011 0.000 ARG C 61 *********************** 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 222 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 170 time to evaluate : 2.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 PHE cc_start: 0.7563 (OUTLIER) cc_final: 0.7276 (m-80) REVERT: A 351 MET cc_start: 0.8078 (mmm) cc_final: 0.7700 (mtp) REVERT: A 473 ARG cc_start: 0.7390 (ttp-170) cc_final: 0.7099 (tpt90) REVERT: A 678 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.8152 (tt) REVERT: B 37 PHE cc_start: 0.8082 (t80) cc_final: 0.7801 (t80) REVERT: B 73 VAL cc_start: 0.7975 (OUTLIER) cc_final: 0.7731 (p) REVERT: C 58 ASP cc_start: 0.7259 (t0) cc_final: 0.6702 (m-30) REVERT: C 100 PHE cc_start: 0.7586 (OUTLIER) cc_final: 0.7271 (m-80) REVERT: C 351 MET cc_start: 0.7980 (mmm) cc_final: 0.7649 (mtp) REVERT: C 391 MET cc_start: 0.8027 (mtm) cc_final: 0.7811 (mtt) REVERT: C 392 TRP cc_start: 0.7449 (t60) cc_final: 0.6784 (t60) REVERT: C 473 ARG cc_start: 0.7556 (ttm170) cc_final: 0.7209 (tpt90) REVERT: C 578 PHE cc_start: 0.6123 (OUTLIER) cc_final: 0.5859 (m-10) REVERT: C 832 MET cc_start: 0.9034 (mmm) cc_final: 0.8816 (mmp) REVERT: D 26 LEU cc_start: 0.9306 (OUTLIER) cc_final: 0.9084 (mt) REVERT: D 37 PHE cc_start: 0.8100 (t80) cc_final: 0.7811 (t80) REVERT: D 224 GLU cc_start: 0.7546 (mm-30) cc_final: 0.7123 (mp0) REVERT: D 255 LYS cc_start: 0.8365 (mttt) cc_final: 0.8011 (mmtm) outliers start: 52 outliers final: 41 residues processed: 213 average time/residue: 0.3470 time to fit residues: 116.0979 Evaluate side-chains 206 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 159 time to evaluate : 2.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain A residue 656 ASN Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 737 SER Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 846 ASN Chi-restraints excluded: chain A residue 894 TRP Chi-restraints excluded: chain A residue 1011 ARG Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 180 LYS Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 127 ASN Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 578 PHE Chi-restraints excluded: chain C residue 601 ASP Chi-restraints excluded: chain C residue 639 GLU Chi-restraints excluded: chain C residue 656 ASN Chi-restraints excluded: chain C residue 675 THR Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 846 ASN Chi-restraints excluded: chain C residue 894 TRP Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 64 ASP Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 180 LYS Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 203 GLN Chi-restraints excluded: chain D residue 210 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 212 optimal weight: 0.9990 chunk 144 optimal weight: 3.9990 chunk 3 optimal weight: 0.0970 chunk 190 optimal weight: 7.9990 chunk 105 optimal weight: 3.9990 chunk 217 optimal weight: 3.9990 chunk 176 optimal weight: 30.0000 chunk 0 optimal weight: 10.0000 chunk 130 optimal weight: 7.9990 chunk 229 optimal weight: 1.9990 chunk 64 optimal weight: 6.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.4486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 23148 Z= 0.234 Angle : 0.552 8.303 31252 Z= 0.265 Chirality : 0.044 0.440 3532 Planarity : 0.004 0.052 3812 Dihedral : 14.273 153.993 5283 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.32 % Allowed : 15.56 % Favored : 81.12 % 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: 1.39 (0.15), residues: 1186 sheet: -0.81 (0.33), residues: 266 loop : -1.09 (0.17), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 392 HIS 0.003 0.001 HIS A 557 PHE 0.021 0.002 PHE C 585 TYR 0.016 0.001 TYR D 44 ARG 0.007 0.000 ARG C 61 *********************** 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 241 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 166 time to evaluate : 2.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 MET cc_start: 0.8128 (mmm) cc_final: 0.7833 (mtp) REVERT: A 391 MET cc_start: 0.7829 (mtt) cc_final: 0.7573 (mtt) REVERT: A 470 MET cc_start: 0.8501 (mpp) cc_final: 0.7127 (mpp) REVERT: A 473 ARG cc_start: 0.7456 (ttp-110) cc_final: 0.7077 (tpt90) REVERT: A 615 MET cc_start: 0.8623 (tpp) cc_final: 0.8306 (ttt) REVERT: A 1007 PHE cc_start: 0.8005 (OUTLIER) cc_final: 0.7720 (t80) REVERT: B 37 PHE cc_start: 0.8123 (t80) cc_final: 0.7888 (t80) REVERT: B 55 ILE cc_start: 0.8164 (OUTLIER) cc_final: 0.7517 (tp) REVERT: B 73 VAL cc_start: 0.8018 (OUTLIER) cc_final: 0.7664 (p) REVERT: B 156 TRP cc_start: 0.8870 (OUTLIER) cc_final: 0.7821 (m-90) REVERT: C 58 ASP cc_start: 0.7265 (t0) cc_final: 0.6730 (m-30) REVERT: C 351 MET cc_start: 0.8076 (mmm) cc_final: 0.7782 (mtp) REVERT: C 392 TRP cc_start: 0.7612 (t60) cc_final: 0.6887 (t60) REVERT: C 473 ARG cc_start: 0.7489 (ttm170) cc_final: 0.7260 (tpt90) REVERT: C 507 MET cc_start: 0.6766 (ptp) cc_final: 0.6516 (ttp) REVERT: C 615 MET cc_start: 0.8624 (tpp) cc_final: 0.8310 (ttt) REVERT: C 1007 PHE cc_start: 0.8078 (OUTLIER) cc_final: 0.7821 (t80) REVERT: D 37 PHE cc_start: 0.8142 (t80) cc_final: 0.7934 (t80) REVERT: D 55 ILE cc_start: 0.8148 (OUTLIER) cc_final: 0.7507 (tp) REVERT: D 224 GLU cc_start: 0.7474 (mm-30) cc_final: 0.7150 (mp0) REVERT: D 255 LYS cc_start: 0.8413 (mttt) cc_final: 0.8065 (mmtm) outliers start: 75 outliers final: 55 residues processed: 228 average time/residue: 0.3500 time to fit residues: 126.3396 Evaluate side-chains 218 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 157 time to evaluate : 2.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain A residue 656 ASN Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 737 SER Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 846 ASN Chi-restraints excluded: chain A residue 894 TRP Chi-restraints excluded: chain A residue 986 SER Chi-restraints excluded: chain A residue 1007 PHE Chi-restraints excluded: chain A residue 1011 ARG Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 156 TRP Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain C residue 61 ARG Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 127 ASN Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain C residue 197 ASP Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 601 ASP Chi-restraints excluded: chain C residue 639 GLU Chi-restraints excluded: chain C residue 656 ASN Chi-restraints excluded: chain C residue 675 THR Chi-restraints excluded: chain C residue 737 SER Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 894 TRP Chi-restraints excluded: chain C residue 1007 PHE Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 64 ASP Chi-restraints excluded: chain D residue 116 SER Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 156 TRP Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 159 ASN Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 203 GLN Chi-restraints excluded: chain D residue 210 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 85 optimal weight: 1.9990 chunk 229 optimal weight: 1.9990 chunk 50 optimal weight: 7.9990 chunk 149 optimal weight: 0.9980 chunk 62 optimal weight: 8.9990 chunk 255 optimal weight: 5.9990 chunk 212 optimal weight: 10.0000 chunk 118 optimal weight: 0.0970 chunk 21 optimal weight: 7.9990 chunk 84 optimal weight: 0.5980 chunk 134 optimal weight: 6.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.4628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 23148 Z= 0.154 Angle : 0.511 8.822 31252 Z= 0.243 Chirality : 0.042 0.450 3532 Planarity : 0.004 0.040 3812 Dihedral : 13.726 150.822 5277 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.70 % Allowed : 16.40 % Favored : 80.90 % 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: 0.36 (0.16), residues: 2636 helix: 1.64 (0.16), residues: 1188 sheet: -0.69 (0.33), residues: 266 loop : -1.00 (0.17), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 392 HIS 0.003 0.001 HIS A 557 PHE 0.026 0.001 PHE A 585 TYR 0.014 0.001 TYR C 684 ARG 0.007 0.000 ARG C 61 *********************** 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 223 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 162 time to evaluate : 2.649 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 470 MET cc_start: 0.8497 (mpp) cc_final: 0.7155 (mpp) REVERT: A 473 ARG cc_start: 0.7506 (ttp-110) cc_final: 0.7060 (tpt90) REVERT: A 615 MET cc_start: 0.8634 (tpp) cc_final: 0.8242 (ttt) REVERT: A 1007 PHE cc_start: 0.7930 (OUTLIER) cc_final: 0.7659 (t80) REVERT: B 73 VAL cc_start: 0.7974 (OUTLIER) cc_final: 0.7677 (p) REVERT: C 46 LEU cc_start: 0.7185 (mp) cc_final: 0.6883 (mt) REVERT: C 351 MET cc_start: 0.8123 (mmm) cc_final: 0.7906 (mtp) REVERT: C 392 TRP cc_start: 0.7550 (t60) cc_final: 0.6882 (t60) REVERT: C 473 ARG cc_start: 0.7496 (ttm170) cc_final: 0.7259 (tpt90) REVERT: C 615 MET cc_start: 0.8640 (tpp) cc_final: 0.8252 (ttt) REVERT: C 1007 PHE cc_start: 0.8001 (OUTLIER) cc_final: 0.7727 (t80) REVERT: D 255 LYS cc_start: 0.8329 (mttt) cc_final: 0.7920 (mmtm) outliers start: 61 outliers final: 45 residues processed: 212 average time/residue: 0.3581 time to fit residues: 120.2038 Evaluate side-chains 205 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 157 time to evaluate : 2.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain A residue 639 GLU Chi-restraints excluded: chain A residue 656 ASN Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 894 TRP Chi-restraints excluded: chain A residue 986 SER Chi-restraints excluded: chain A residue 1007 PHE Chi-restraints excluded: chain A residue 1011 ARG Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 156 TRP Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 180 LYS Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain C residue 127 ASN Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain C residue 197 ASP Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 601 ASP Chi-restraints excluded: chain C residue 639 GLU Chi-restraints excluded: chain C residue 656 ASN Chi-restraints excluded: chain C residue 737 SER Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 846 ASN Chi-restraints excluded: chain C residue 894 TRP Chi-restraints excluded: chain C residue 1007 PHE Chi-restraints excluded: chain D residue 64 ASP Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 156 TRP Chi-restraints excluded: chain D residue 159 ASN Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 203 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 246 optimal weight: 6.9990 chunk 28 optimal weight: 8.9990 chunk 145 optimal weight: 20.0000 chunk 186 optimal weight: 30.0000 chunk 144 optimal weight: 1.9990 chunk 215 optimal weight: 0.9990 chunk 142 optimal weight: 6.9990 chunk 254 optimal weight: 6.9990 chunk 159 optimal weight: 6.9990 chunk 155 optimal weight: 8.9990 chunk 117 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 946 GLN ** C 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 946 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.5050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 23148 Z= 0.433 Angle : 0.696 17.760 31252 Z= 0.334 Chirality : 0.048 0.421 3532 Planarity : 0.004 0.057 3812 Dihedral : 14.229 140.896 5269 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 3.32 % Allowed : 16.14 % Favored : 80.55 % 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: -0.13 (0.16), residues: 2636 helix: 1.03 (0.15), residues: 1204 sheet: -0.59 (0.33), residues: 262 loop : -1.13 (0.16), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 392 HIS 0.004 0.001 HIS D 80 PHE 0.024 0.002 PHE C 585 TYR 0.028 0.002 TYR B 40 ARG 0.011 0.001 ARG C 61 *********************** 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 245 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 170 time to evaluate : 2.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LEU cc_start: 0.7297 (mp) cc_final: 0.7004 (mt) REVERT: A 391 MET cc_start: 0.8029 (mtt) cc_final: 0.7739 (mtt) REVERT: A 470 MET cc_start: 0.8581 (mpp) cc_final: 0.7429 (mpp) REVERT: A 473 ARG cc_start: 0.7449 (ttp-110) cc_final: 0.7002 (tpt90) REVERT: A 615 MET cc_start: 0.8712 (tpp) cc_final: 0.8446 (ttt) REVERT: B 37 PHE cc_start: 0.8305 (t80) cc_final: 0.8026 (t80) REVERT: B 55 ILE cc_start: 0.8309 (OUTLIER) cc_final: 0.7703 (tp) REVERT: C 65 ASN cc_start: 0.5156 (OUTLIER) cc_final: 0.4825 (m-40) REVERT: C 351 MET cc_start: 0.8241 (mmm) cc_final: 0.7908 (mtp) REVERT: C 392 TRP cc_start: 0.7722 (t60) cc_final: 0.7243 (t60) REVERT: C 473 ARG cc_start: 0.7526 (ttm170) cc_final: 0.7290 (tpt90) REVERT: C 615 MET cc_start: 0.8725 (tpp) cc_final: 0.8462 (ttt) REVERT: C 748 MET cc_start: 0.8626 (ttm) cc_final: 0.8387 (ttt) REVERT: D 13 TRP cc_start: 0.5228 (t60) cc_final: 0.4974 (m100) REVERT: D 37 PHE cc_start: 0.8306 (t80) cc_final: 0.8048 (t80) REVERT: D 55 ILE cc_start: 0.8249 (OUTLIER) cc_final: 0.7649 (tp) outliers start: 75 outliers final: 55 residues processed: 231 average time/residue: 0.3485 time to fit residues: 127.0518 Evaluate side-chains 218 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 160 time to evaluate : 2.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain A residue 639 GLU Chi-restraints excluded: chain A residue 656 ASN Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 737 SER Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 846 ASN Chi-restraints excluded: chain A residue 894 TRP Chi-restraints excluded: chain A residue 1011 ARG Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 156 TRP Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain G residue 35 ILE Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 127 ASN Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain C residue 197 ASP Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 601 ASP Chi-restraints excluded: chain C residue 639 GLU Chi-restraints excluded: chain C residue 656 ASN Chi-restraints excluded: chain C residue 675 THR Chi-restraints excluded: chain C residue 737 SER Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 846 ASN Chi-restraints excluded: chain C residue 894 TRP Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 64 ASP Chi-restraints excluded: chain D residue 116 SER Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 156 TRP Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 203 GLN Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain E residue 35 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 157 optimal weight: 0.7980 chunk 101 optimal weight: 4.9990 chunk 151 optimal weight: 8.9990 chunk 76 optimal weight: 0.9990 chunk 49 optimal weight: 6.9990 chunk 161 optimal weight: 1.9990 chunk 173 optimal weight: 3.9990 chunk 125 optimal weight: 4.9990 chunk 23 optimal weight: 7.9990 chunk 200 optimal weight: 4.9990 chunk 231 optimal weight: 0.4980 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 181 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.5114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23148 Z= 0.191 Angle : 0.560 15.613 31252 Z= 0.265 Chirality : 0.043 0.428 3532 Planarity : 0.004 0.039 3812 Dihedral : 13.592 137.250 5268 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.03 % Allowed : 17.02 % Favored : 80.95 % 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: 0.31 (0.16), residues: 2636 helix: 1.52 (0.15), residues: 1188 sheet: -0.58 (0.32), residues: 282 loop : -0.97 (0.16), residues: 1166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 392 HIS 0.010 0.001 HIS C 493 PHE 0.025 0.001 PHE A 585 TYR 0.013 0.001 TYR C 869 ARG 0.009 0.000 ARG A 61 *********************** 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 212 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 166 time to evaluate : 2.487 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 46 LEU cc_start: 0.7251 (mp) cc_final: 0.7026 (mt) REVERT: A 470 MET cc_start: 0.8594 (mpp) cc_final: 0.7432 (mpp) REVERT: A 473 ARG cc_start: 0.7461 (ttp-110) cc_final: 0.7028 (tpt90) REVERT: A 615 MET cc_start: 0.8756 (tpp) cc_final: 0.8330 (ttt) REVERT: B 110 MET cc_start: 0.8559 (mmt) cc_final: 0.8217 (mmt) REVERT: C 65 ASN cc_start: 0.4898 (OUTLIER) cc_final: 0.4525 (m-40) REVERT: C 351 MET cc_start: 0.8157 (mmm) cc_final: 0.7940 (mtp) REVERT: C 392 TRP cc_start: 0.7685 (t60) cc_final: 0.7166 (t60) REVERT: C 470 MET cc_start: 0.8554 (mpp) cc_final: 0.7499 (mpp) REVERT: C 615 MET cc_start: 0.8765 (tpp) cc_final: 0.8321 (ttt) outliers start: 46 outliers final: 39 residues processed: 205 average time/residue: 0.3399 time to fit residues: 110.4104 Evaluate side-chains 199 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 159 time to evaluate : 2.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain A residue 639 GLU Chi-restraints excluded: chain A residue 656 ASN Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 894 TRP Chi-restraints excluded: chain A residue 1011 ARG Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 156 TRP Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 127 ASN Chi-restraints excluded: chain C residue 197 ASP Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 601 ASP Chi-restraints excluded: chain C residue 639 GLU Chi-restraints excluded: chain C residue 656 ASN Chi-restraints excluded: chain C residue 737 SER Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 846 ASN Chi-restraints excluded: chain C residue 894 TRP Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 64 ASP Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 156 TRP Chi-restraints excluded: chain D residue 203 GLN Chi-restraints excluded: chain D residue 210 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 243 optimal weight: 0.8980 chunk 222 optimal weight: 0.0270 chunk 237 optimal weight: 3.9990 chunk 142 optimal weight: 0.5980 chunk 103 optimal weight: 2.9990 chunk 186 optimal weight: 8.9990 chunk 72 optimal weight: 0.7980 chunk 214 optimal weight: 6.9990 chunk 224 optimal weight: 5.9990 chunk 236 optimal weight: 0.7980 chunk 155 optimal weight: 3.9990 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 ASN ** A 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 577 ASN C 577 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.5232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 23148 Z= 0.132 Angle : 0.517 15.651 31252 Z= 0.241 Chirality : 0.041 0.430 3532 Planarity : 0.003 0.039 3812 Dihedral : 12.821 127.963 5268 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.64 % Allowed : 17.60 % Favored : 80.77 % 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: 1.90 (0.16), residues: 1184 sheet: -0.24 (0.32), residues: 290 loop : -0.89 (0.16), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 392 HIS 0.006 0.001 HIS C 493 PHE 0.026 0.001 PHE C 585 TYR 0.015 0.001 TYR A 869 ARG 0.008 0.000 ARG A 61 *********************** 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 207 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 170 time to evaluate : 2.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LEU cc_start: 0.7201 (mp) cc_final: 0.6924 (mt) REVERT: A 470 MET cc_start: 0.8602 (mpp) cc_final: 0.7457 (mpp) REVERT: A 473 ARG cc_start: 0.7434 (ttp-110) cc_final: 0.6999 (tpt90) REVERT: A 534 MET cc_start: 0.7656 (mmm) cc_final: 0.7443 (mmp) REVERT: A 615 MET cc_start: 0.8773 (tpp) cc_final: 0.8228 (ttt) REVERT: B 180 LYS cc_start: 0.8347 (OUTLIER) cc_final: 0.8054 (ttpt) REVERT: C 65 ASN cc_start: 0.4784 (OUTLIER) cc_final: 0.4456 (m-40) REVERT: C 392 TRP cc_start: 0.7592 (t60) cc_final: 0.7262 (t60) REVERT: C 615 MET cc_start: 0.8771 (tpp) cc_final: 0.8210 (ttt) REVERT: D 224 GLU cc_start: 0.7569 (mm-30) cc_final: 0.7259 (mp0) REVERT: D 255 LYS cc_start: 0.8323 (mttt) cc_final: 0.7917 (mmtt) outliers start: 37 outliers final: 30 residues processed: 202 average time/residue: 0.3363 time to fit residues: 108.3856 Evaluate side-chains 194 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 162 time to evaluate : 2.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain A residue 639 GLU Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 1011 ARG Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 156 TRP Chi-restraints excluded: chain B residue 180 LYS Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 127 ASN Chi-restraints excluded: chain C residue 197 ASP Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 601 ASP Chi-restraints excluded: chain C residue 639 GLU Chi-restraints excluded: chain C residue 737 SER Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 64 ASP Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 156 TRP Chi-restraints excluded: chain D residue 203 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 250 optimal weight: 4.9990 chunk 153 optimal weight: 10.0000 chunk 118 optimal weight: 0.7980 chunk 174 optimal weight: 10.0000 chunk 263 optimal weight: 7.9990 chunk 242 optimal weight: 9.9990 chunk 209 optimal weight: 4.9990 chunk 21 optimal weight: 8.9990 chunk 161 optimal weight: 4.9990 chunk 128 optimal weight: 0.0670 chunk 166 optimal weight: 7.9990 overall best weight: 3.1724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 577 ASN C 577 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.5366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 23148 Z= 0.292 Angle : 0.598 15.568 31252 Z= 0.284 Chirality : 0.044 0.400 3532 Planarity : 0.004 0.043 3812 Dihedral : 13.012 126.388 5264 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.81 % Allowed : 17.73 % Favored : 80.46 % 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: 0.47 (0.16), residues: 2636 helix: 1.63 (0.16), residues: 1192 sheet: -0.18 (0.33), residues: 270 loop : -0.96 (0.16), residues: 1174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 392 HIS 0.004 0.001 HIS D 80 PHE 0.026 0.002 PHE A 585 TYR 0.018 0.001 TYR B 40 ARG 0.008 0.000 ARG C 473 ********************** 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 203 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 162 time to evaluate : 2.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LEU cc_start: 0.7268 (mp) cc_final: 0.6982 (mt) REVERT: A 470 MET cc_start: 0.8605 (mpp) cc_final: 0.7495 (mpp) REVERT: A 473 ARG cc_start: 0.7459 (ttp-110) cc_final: 0.7107 (tpt90) REVERT: A 615 MET cc_start: 0.8772 (tpp) cc_final: 0.8091 (ttt) REVERT: B 37 PHE cc_start: 0.8193 (t80) cc_final: 0.7970 (t80) REVERT: B 223 ARG cc_start: 0.8037 (ttm110) cc_final: 0.7288 (ttm110) REVERT: C 65 ASN cc_start: 0.4762 (OUTLIER) cc_final: 0.4499 (m-40) REVERT: C 392 TRP cc_start: 0.7684 (t60) cc_final: 0.7158 (t60) REVERT: C 446 SER cc_start: 0.8658 (m) cc_final: 0.8262 (t) REVERT: C 615 MET cc_start: 0.8768 (tpp) cc_final: 0.8080 (ttt) REVERT: D 37 PHE cc_start: 0.8186 (t80) cc_final: 0.7962 (t80) outliers start: 41 outliers final: 34 residues processed: 193 average time/residue: 0.3476 time to fit residues: 106.3811 Evaluate side-chains 193 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 158 time to evaluate : 2.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain A residue 639 GLU Chi-restraints excluded: chain A residue 656 ASN Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 846 ASN Chi-restraints excluded: chain A residue 894 TRP Chi-restraints excluded: chain A residue 1011 ARG Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 156 TRP Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 127 ASN Chi-restraints excluded: chain C residue 197 ASP Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 601 ASP Chi-restraints excluded: chain C residue 639 GLU Chi-restraints excluded: chain C residue 675 THR Chi-restraints excluded: chain C residue 737 SER Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 894 TRP Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 64 ASP Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 203 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 223 optimal weight: 0.5980 chunk 64 optimal weight: 4.9990 chunk 193 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 209 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 215 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 184 optimal weight: 8.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 577 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.127156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.087636 restraints weight = 37046.804| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 2.38 r_work: 0.2923 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.5410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 23148 Z= 0.138 Angle : 0.527 15.067 31252 Z= 0.245 Chirality : 0.041 0.411 3532 Planarity : 0.003 0.038 3812 Dihedral : 12.458 125.248 5264 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.59 % Allowed : 17.95 % Favored : 80.46 % 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: 0.72 (0.17), residues: 2636 helix: 1.93 (0.16), residues: 1188 sheet: -0.26 (0.31), residues: 310 loop : -0.89 (0.17), residues: 1138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 392 HIS 0.005 0.001 HIS C 493 PHE 0.024 0.001 PHE C 538 TYR 0.013 0.001 TYR A 869 ARG 0.012 0.000 ARG C 473 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4538.10 seconds wall clock time: 83 minutes 30.29 seconds (5010.29 seconds total)