Starting phenix.real_space_refine on Sun Feb 18 18:03:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wyw_32896/02_2024/7wyw_32896_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wyw_32896/02_2024/7wyw_32896.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wyw_32896/02_2024/7wyw_32896.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wyw_32896/02_2024/7wyw_32896.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wyw_32896/02_2024/7wyw_32896_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wyw_32896/02_2024/7wyw_32896_updated.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 26 5.49 5 Mg 6 5.21 5 S 118 5.16 5 C 14632 2.51 5 N 3514 2.21 5 O 4310 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: 22606 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: 15, 477 Unusual residues: {' MG': 3, 'CLR': 3, 'PCW': 9} Classifications: {'undetermined': 15} Link IDs: {None: 14} 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 162 Unusual residues: {'PCW': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 477 Unusual residues: {' MG': 3, 'CLR': 3, 'PCW': 9} Classifications: {'undetermined': 15} Link IDs: {None: 14} 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 162 Unusual residues: {'PCW': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Time building chain proxies: 12.44, per 1000 atoms: 0.55 Number of scatterers: 22606 At special positions: 0 Unit cell: (216.276, 180.768, 103.296, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 118 16.00 P 26 15.00 Mg 6 11.99 O 4310 8.00 N 3514 7.00 C 14632 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS B 127 " - pdb=" SG CYS B 150 " distance=2.04 Simple disulfide: pdb=" SG CYS B 160 " - pdb=" SG CYS B 176 " distance=2.03 Simple disulfide: pdb=" SG CYS B 215 " - pdb=" SG CYS B 278 " distance=2.03 Simple disulfide: pdb=" SG CYS D 127 " - pdb=" SG CYS D 150 " distance=2.04 Simple disulfide: pdb=" SG CYS D 160 " - pdb=" SG CYS D 176 " distance=2.03 Simple disulfide: pdb=" SG CYS D 215 " - pdb=" SG CYS D 278 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA F 3 " - " MAN F 4 " " BMA H 3 " - " MAN H 4 " " BMA I 3 " - " MAN I 4 " " BMA K 3 " - " MAN K 4 " " BMA L 3 " - " MAN L 4 " " BMA M 3 " - " MAN M 4 " ALPHA1-6 " BMA F 3 " - " MAN F 5 " " BMA H 3 " - " MAN H 6 " " BMA K 3 " - " MAN K 5 " " BMA L 3 " - " MAN L 6 " BETA1-2 " MAN H 4 " - " NAG H 5 " " MAN L 4 " - " NAG L 5 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " BETA1-6 " NAG F 1 " - " FUC F 6 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG I 1 " - " FUC I 5 " " NAG K 1 " - " FUC K 6 " " NAG M 1 " - " FUC M 5 " NAG-ASN " NAG F 1 " - " ASN B 114 " " NAG H 1 " - " ASN B 159 " " NAG I 1 " - " ASN B 194 " " NAG J 1 " - " ASN B 267 " " NAG K 1 " - " ASN D 114 " " NAG L 1 " - " ASN D 159 " " NAG M 1 " - " ASN D 194 " " NAG N 1 " - " ASN D 267 " Time building additional restraints: 9.18 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: 105 helices and 16 sheets defined 43.7% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.24 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 90 through 96 removed outlier: 3.831A pdb=" N GLN A 95 " --> pdb=" O LYS A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 121 Processing helix chain 'A' and resid 128 through 161 removed outlier: 4.501A 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 331 removed outlier: 3.676A pdb=" N ILE A 322 " --> pdb=" O LEU A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 354 removed outlier: 4.483A pdb=" N ALA A 338 " --> pdb=" O GLU A 334 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR A 347 " --> pdb=" O CYS A 343 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG A 350 " --> pdb=" O LEU A 346 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N MET A 351 " --> pdb=" O THR A 347 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS A 354 " --> pdb=" O ARG A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 364 No H-bonds generated for 'chain 'A' and resid 362 through 364' Processing helix chain 'A' and resid 366 through 369 No H-bonds generated for 'chain 'A' and resid 366 through 369' Processing helix chain 'A' and resid 416 through 427 Processing helix chain 'A' and resid 451 through 463 Processing helix chain 'A' and resid 467 through 472 Processing helix chain 'A' and resid 511 through 517 removed outlier: 3.517A pdb=" N ARG A 517 " --> pdb=" O ARG A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 547 Processing helix chain 'A' and resid 599 through 608 Processing helix chain 'A' and resid 621 through 631 removed outlier: 3.853A 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: 4.168A 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: 4.143A pdb=" N LYS A 726 " --> pdb=" O PRO A 723 " (cutoff:3.500A) removed outlier: 3.881A 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 796 removed outlier: 3.752A pdb=" N ARG A 766 " --> pdb=" O VAL A 762 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N PHE A 769 " --> pdb=" O GLY A 765 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N SER A 782 " --> pdb=" O TYR A 778 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ASN A 783 " --> pdb=" O THR A 779 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N ILE A 784 " --> pdb=" O LEU A 780 " (cutoff:3.500A) Proline residue: A 785 - end of helix Proline residue: A 789 - end of helix 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: 4.309A pdb=" N ALA A 823 " --> pdb=" O ALA A 819 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N TYR A 824 " --> pdb=" O ILE A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 847 through 853 removed outlier: 3.634A pdb=" N MET A 852 " --> pdb=" O ARG A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 875 Processing helix chain 'A' and resid 880 through 883 No H-bonds generated for 'chain 'A' and resid 880 through 883' Processing helix chain 'A' and resid 887 through 891 Processing helix chain 'A' and resid 908 through 938 removed outlier: 3.512A pdb=" N VAL A 914 " --> pdb=" O GLN A 910 " (cutoff:3.500A) removed outlier: 4.043A 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: 3.519A pdb=" N PHE A1007 " --> pdb=" O GLU A1003 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE A1008 " --> pdb=" O MET A1004 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE A1009 " --> pdb=" O ARG A1005 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ARG A1010 " --> pdb=" O ARG A1006 " (cutoff:3.500A) Processing helix chain 'A' and resid 1016 through 1021 Processing helix chain 'B' and resid 15 through 17 No H-bonds generated for 'chain 'B' and resid 15 through 17' Processing helix chain 'B' and resid 30 through 61 removed outlier: 3.977A pdb=" N PHE B 34 " --> pdb=" O GLY B 30 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS B 35 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 3.805A 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: 3.576A pdb=" N SER B 105 " --> pdb=" O SER B 101 " (cutoff:3.500A) removed outlier: 4.275A 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 '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 90 through 96 removed outlier: 3.832A pdb=" N GLN C 95 " --> pdb=" O LYS C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 121 Processing helix chain 'C' and resid 128 through 161 removed outlier: 4.501A 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 331 removed outlier: 3.677A pdb=" N ILE C 322 " --> pdb=" O LEU C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 354 removed outlier: 4.483A pdb=" N ALA C 338 " --> pdb=" O GLU C 334 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR C 347 " --> pdb=" O CYS C 343 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG C 350 " --> pdb=" O LEU C 346 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N MET C 351 " --> pdb=" O THR C 347 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS C 354 " --> pdb=" O ARG C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 364 No H-bonds generated for 'chain 'C' and resid 362 through 364' Processing helix chain 'C' and resid 366 through 369 No H-bonds generated for 'chain 'C' and resid 366 through 369' Processing helix chain 'C' and resid 416 through 427 Processing helix chain 'C' and resid 451 through 463 Processing helix chain 'C' and resid 467 through 472 Processing helix chain 'C' and resid 511 through 517 removed outlier: 3.517A 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: 3.854A 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: 4.168A 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: 4.142A pdb=" N LYS C 726 " --> pdb=" O PRO C 723 " (cutoff:3.500A) removed outlier: 3.882A 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 796 removed outlier: 3.752A pdb=" N ARG C 766 " --> pdb=" O VAL C 762 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N PHE C 769 " --> pdb=" O GLY C 765 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N SER C 782 " --> pdb=" O TYR C 778 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ASN C 783 " --> pdb=" O THR C 779 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N ILE C 784 " --> pdb=" O LEU C 780 " (cutoff:3.500A) Proline residue: C 785 - end of helix Proline residue: C 789 - end of helix 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: 4.308A pdb=" N ALA C 823 " --> pdb=" O ALA C 819 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N TYR C 824 " --> pdb=" O ILE C 820 " (cutoff:3.500A) Processing helix chain 'C' and resid 847 through 853 removed outlier: 3.635A pdb=" N MET C 852 " --> pdb=" O ARG C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 857 through 875 Processing helix chain 'C' and resid 880 through 883 No H-bonds generated for 'chain 'C' and resid 880 through 883' Processing helix chain 'C' and resid 887 through 891 Processing helix chain 'C' and resid 908 through 938 removed outlier: 3.511A pdb=" N VAL C 914 " --> pdb=" O GLN C 910 " (cutoff:3.500A) removed outlier: 4.043A 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: 3.594A 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: 3.518A pdb=" N PHE C1007 " --> pdb=" O GLU C1003 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE C1008 " --> pdb=" O MET C1004 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE C1009 " --> pdb=" O ARG C1005 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ARG C1010 " --> pdb=" O ARG C1006 " (cutoff:3.500A) Processing helix chain 'C' and resid 1016 through 1021 Processing helix chain 'D' and resid 15 through 17 No H-bonds generated for 'chain 'D' and resid 15 through 17' Processing helix chain 'D' and resid 30 through 61 removed outlier: 3.977A pdb=" N PHE D 34 " --> pdb=" O GLY D 30 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS D 35 " --> pdb=" O SER D 31 " (cutoff:3.500A) removed outlier: 3.804A 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: 3.577A pdb=" N SER D 105 " --> pdb=" O SER D 101 " (cutoff:3.500A) removed outlier: 4.274A 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 250 through 253 No H-bonds generated for 'chain 'D' and resid 250 through 253' Processing helix chain 'E' and resid 10 through 12 No H-bonds generated for 'chain 'E' and resid 10 through 12' Processing helix chain 'E' and resid 16 through 39 Processing sheet with id= A, first strand: chain 'A' and resid 176 through 181 removed outlier: 11.684A pdb=" N GLN A 168 " --> pdb=" O LYS A 194 " (cutoff:3.500A) removed outlier: 9.219A pdb=" N LYS A 194 " --> pdb=" O GLN A 168 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N LEU A 170 " --> pdb=" O GLU A 192 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LEU A 190 " --> pdb=" O ILE A 172 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR A 253 " --> pdb=" O HIS A 209 " (cutoff:3.500A) removed outlier: 3.880A 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: 6.701A pdb=" N THR A 372 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N THR A 715 " --> pdb=" O THR A 372 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N CYS A 374 " --> pdb=" O THR A 715 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LYS A 612 " --> pdb=" O ILE A 373 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N SER A 375 " --> pdb=" O LYS A 612 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ILE A 614 " --> pdb=" O SER A 375 " (cutoff:3.500A) removed outlier: 4.764A 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: 7.262A pdb=" N LEU A 583 " --> pdb=" O SER A 519 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N ILE A 521 " --> pdb=" O LEU A 583 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N PHE A 585 " --> pdb=" O ILE A 521 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N LEU A 523 " --> pdb=" O PHE A 585 " (cutoff:3.500A) removed outlier: 11.235A pdb=" N GLY A 587 " --> pdb=" O LEU A 523 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N PHE A 555 " --> pdb=" O VAL A 586 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N LEU A 588 " --> pdb=" O LEU A 553 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N LEU A 553 " --> pdb=" O LEU A 588 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ALA A 590 " --> pdb=" O ARG A 551 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ARG A 551 " --> pdb=" O ALA A 590 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N TYR A 503 " --> pdb=" O LEU A 560 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU A 490 " --> pdb=" O ILE A 480 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N GLU A 494 " --> pdb=" O LYS A 476 " (cutoff:3.500A) removed outlier: 6.454A 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: 6.397A pdb=" N ARG A 204 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N VAL A 258 " --> pdb=" O ARG A 204 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 78 through 80 removed outlier: 3.562A pdb=" N THR B 266 " --> pdb=" O SER B 228 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 88 through 92 removed outlier: 7.921A pdb=" N ILE B 89 " --> pdb=" O GLU B 298 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N LYS B 300 " --> pdb=" O ILE B 89 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N PHE B 91 " --> pdb=" O LYS B 300 " (cutoff:3.500A) removed outlier: 6.742A 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: 11.683A pdb=" N GLN C 168 " --> pdb=" O LYS C 194 " (cutoff:3.500A) removed outlier: 9.219A pdb=" N LYS C 194 " --> pdb=" O GLN C 168 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N LEU C 170 " --> pdb=" O GLU C 192 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LEU C 190 " --> pdb=" O ILE C 172 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR C 253 " --> pdb=" O HIS C 209 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N SER C 207 " --> pdb=" O ARG C 255 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 356 through 358 removed outlier: 6.702A pdb=" N THR C 372 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N THR C 715 " --> pdb=" O THR C 372 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N CYS C 374 " --> pdb=" O THR C 715 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LYS C 612 " --> pdb=" O ILE C 373 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N SER C 375 " --> pdb=" O LYS C 612 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ILE C 614 " --> pdb=" O SER C 375 " (cutoff:3.500A) removed outlier: 4.764A 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: 7.264A pdb=" N LEU C 583 " --> pdb=" O SER C 519 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N ILE C 521 " --> pdb=" O LEU C 583 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N PHE C 585 " --> pdb=" O ILE C 521 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N LEU C 523 " --> pdb=" O PHE C 585 " (cutoff:3.500A) removed outlier: 11.235A pdb=" N GLY C 587 " --> pdb=" O LEU C 523 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N PHE C 555 " --> pdb=" O VAL C 586 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N LEU C 588 " --> pdb=" O LEU C 553 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N LEU C 553 " --> pdb=" O LEU C 588 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ALA C 590 " --> pdb=" O ARG C 551 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ARG C 551 " --> pdb=" O ALA C 590 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N TYR C 503 " --> pdb=" O LEU C 560 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU C 490 " --> pdb=" O ILE C 480 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N GLU C 494 " --> pdb=" O LYS C 476 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LYS C 476 " --> pdb=" O GLU C 494 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 202 through 205 removed outlier: 6.397A pdb=" N ARG C 204 " --> pdb=" O VAL C 258 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N VAL C 258 " --> pdb=" O ARG C 204 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 78 through 80 removed outlier: 3.563A pdb=" N THR D 266 " --> pdb=" O SER D 228 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 88 through 92 removed outlier: 7.921A pdb=" N ILE D 89 " --> pdb=" O GLU D 298 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N LYS D 300 " --> pdb=" O ILE D 89 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N PHE D 91 " --> pdb=" O LYS D 300 " (cutoff:3.500A) removed outlier: 6.742A 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 212 838 hydrogen bonds defined for protein. 2448 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.08 Time building geometry restraints manager: 9.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6617 1.34 - 1.46: 4989 1.46 - 1.58: 11190 1.58 - 1.71: 56 1.71 - 1.83: 172 Bond restraints: 23024 Sorted by residual: bond pdb=" OD1 PHD C 376 " pdb=" P PHD C 376 " ideal model delta sigma weight residual 1.816 1.509 0.307 2.00e-02 2.50e+03 2.36e+02 bond pdb=" 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 2.35e+02 bond pdb=" C39 PCW G 103 " pdb=" C40 PCW G 103 " ideal model delta sigma weight residual 1.333 1.544 -0.211 2.00e-02 2.50e+03 1.11e+02 bond pdb=" C39 PCW E 103 " pdb=" C40 PCW E 103 " ideal model delta sigma weight residual 1.333 1.543 -0.210 2.00e-02 2.50e+03 1.10e+02 bond pdb=" C19 PCW C1114 " pdb=" C20 PCW C1114 " ideal model delta sigma weight residual 1.333 1.541 -0.208 2.00e-02 2.50e+03 1.08e+02 ... (remaining 23019 not shown) Histogram of bond angle deviations from ideal: 98.29 - 105.45: 613 105.45 - 112.60: 12071 112.60 - 119.76: 8330 119.76 - 126.92: 9834 126.92 - 134.08: 210 Bond angle restraints: 31058 Sorted by residual: angle pdb=" N PHE A 92 " pdb=" CA PHE A 92 " pdb=" C PHE A 92 " ideal model delta sigma weight residual 113.12 104.67 8.45 1.25e+00 6.40e-01 4.57e+01 angle pdb=" N PHE C 92 " pdb=" CA PHE C 92 " pdb=" C PHE C 92 " ideal model delta sigma weight residual 113.12 104.67 8.45 1.25e+00 6.40e-01 4.57e+01 angle pdb=" N LEU D 157 " pdb=" CA LEU D 157 " pdb=" C LEU D 157 " ideal model delta sigma weight residual 108.67 98.29 10.38 1.55e+00 4.16e-01 4.49e+01 angle pdb=" N LEU B 157 " pdb=" CA LEU B 157 " pdb=" C LEU B 157 " ideal model delta sigma weight residual 108.67 98.33 10.34 1.55e+00 4.16e-01 4.45e+01 angle pdb=" N LEU B 202 " pdb=" CA LEU B 202 " pdb=" C LEU B 202 " ideal model delta sigma weight residual 112.38 118.76 -6.38 1.22e+00 6.72e-01 2.74e+01 ... (remaining 31053 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.88: 14047 35.88 - 71.76: 761 71.76 - 107.64: 86 107.64 - 143.52: 40 143.52 - 179.41: 2 Dihedral angle restraints: 14936 sinusoidal: 7280 harmonic: 7656 Sorted by residual: dihedral pdb=" C33 PCW G 102 " pdb=" C31 PCW G 102 " pdb=" C32 PCW G 102 " pdb=" O2 PCW G 102 " ideal model delta sinusoidal sigma weight residual -168.17 11.24 -179.41 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C33 PCW E 102 " pdb=" C31 PCW E 102 " pdb=" C32 PCW E 102 " pdb=" O2 PCW E 102 " ideal model delta sinusoidal sigma weight residual -168.17 11.23 -179.40 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C33 PCW C1112 " pdb=" C31 PCW C1112 " pdb=" C32 PCW C1112 " pdb=" O2 PCW C1112 " ideal model delta sinusoidal sigma weight residual -168.17 -29.80 -138.37 1 3.00e+01 1.11e-03 1.86e+01 ... (remaining 14933 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 2807 0.075 - 0.150: 592 0.150 - 0.224: 65 0.224 - 0.299: 31 0.299 - 0.374: 17 Chirality restraints: 3512 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 -2.23 -0.17 2.00e-02 2.50e+03 7.30e+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 -2.23 -0.17 2.00e-02 2.50e+03 6.93e+01 chirality pdb=" C1 FUC F 6 " pdb=" O6 NAG F 1 " pdb=" C2 FUC F 6 " pdb=" O5 FUC F 6 " both_signs ideal model delta sigma weight residual False -2.40 -2.34 -0.06 2.00e-02 2.50e+03 1.05e+01 ... (remaining 3509 not shown) Planarity restraints: 3812 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU C 124 " 0.064 5.00e-02 4.00e+02 9.64e-02 1.49e+01 pdb=" N PRO C 125 " -0.167 5.00e-02 4.00e+02 pdb=" CA PRO C 125 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO C 125 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 124 " 0.064 5.00e-02 4.00e+02 9.61e-02 1.48e+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 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR C 569 " 0.059 5.00e-02 4.00e+02 9.07e-02 1.32e+01 pdb=" N PRO C 570 " -0.157 5.00e-02 4.00e+02 pdb=" CA PRO C 570 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO C 570 " 0.049 5.00e-02 4.00e+02 ... (remaining 3809 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 104 2.47 - 3.08: 15068 3.08 - 3.68: 30888 3.68 - 4.29: 48374 4.29 - 4.90: 78473 Nonbonded interactions: 172907 Sorted by model distance: nonbonded pdb=" OP3 PHD C 376 " pdb="MG MG C1101 " model vdw 1.861 2.170 nonbonded pdb=" OP3 PHD A 376 " pdb="MG MG A1101 " model vdw 1.861 2.170 nonbonded pdb="MG MG C1101 " pdb=" O HOH C1204 " model vdw 1.990 2.170 nonbonded pdb="MG MG A1101 " pdb=" O HOH A1204 " model vdw 1.995 2.170 nonbonded pdb=" O THR A 378 " pdb="MG MG A1101 " model vdw 1.998 2.170 ... (remaining 172902 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'G' } ncs_group { reference = (chain 'F' and resid 1 through 4) selection = (chain 'H' and resid 1 through 4) selection = (chain 'K' and resid 1 through 4) selection = (chain 'L' and resid 1 through 4) } ncs_group { reference = chain 'I' selection = chain 'M' } ncs_group { reference = chain 'J' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.310 Check model and map are aligned: 0.350 Set scattering table: 0.230 Process input model: 60.070 Find NCS groups from input model: 1.160 Set up NCS constraints: 0.200 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 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 0.307 23024 Z= 0.652 Angle : 1.448 12.318 31058 Z= 0.744 Chirality : 0.067 0.374 3512 Planarity : 0.009 0.096 3804 Dihedral : 20.107 179.406 10006 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.61 % Allowed : 8.69 % Favored : 90.71 % Rotamer: Outliers : 10.30 % Allowed : 9.24 % 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: -3.47 (0.14), residues: 2636 helix: -1.87 (0.13), residues: 1194 sheet: -2.32 (0.29), residues: 260 loop : -2.69 (0.16), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP D 33 HIS 0.012 0.002 HIS C 493 PHE 0.030 0.002 PHE B 297 TYR 0.039 0.002 TYR D 40 ARG 0.013 0.001 ARG A 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 545 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 233 poor density : 312 time to evaluate : 2.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 LEU cc_start: 0.6633 (OUTLIER) cc_final: 0.5855 (tp) REVERT: A 127 ASN cc_start: 0.6438 (OUTLIER) cc_final: 0.5915 (p0) REVERT: A 158 MET cc_start: 0.8245 (OUTLIER) cc_final: 0.7646 (tmm) REVERT: A 231 PHE cc_start: 0.8385 (OUTLIER) cc_final: 0.8039 (t80) REVERT: A 460 ILE cc_start: 0.8630 (mm) cc_final: 0.8306 (mt) REVERT: A 493 HIS cc_start: 0.7832 (OUTLIER) cc_final: 0.7290 (m-70) REVERT: A 708 GLN cc_start: 0.7901 (OUTLIER) cc_final: 0.7505 (mp10) REVERT: A 933 ASP cc_start: 0.8789 (t70) cc_final: 0.8466 (t0) REVERT: A 1002 ASP cc_start: 0.8151 (t0) cc_final: 0.7932 (t0) REVERT: A 1011 ARG cc_start: 0.7940 (OUTLIER) cc_final: 0.7436 (tpt90) REVERT: A 1016 TRP cc_start: 0.8497 (t60) cc_final: 0.8236 (t60) REVERT: B 20 SER cc_start: 0.7883 (OUTLIER) cc_final: 0.7380 (m) REVERT: B 137 ARG cc_start: 0.8085 (OUTLIER) cc_final: 0.7469 (mtt180) REVERT: B 266 THR cc_start: 0.8367 (OUTLIER) cc_final: 0.7927 (p) REVERT: G 13 THR cc_start: 0.8410 (OUTLIER) cc_final: 0.8040 (p) REVERT: C 52 HIS cc_start: 0.7591 (m170) cc_final: 0.7215 (m90) REVERT: C 63 LEU cc_start: 0.6489 (OUTLIER) cc_final: 0.5935 (tp) REVERT: C 64 THR cc_start: 0.6943 (OUTLIER) cc_final: 0.6679 (t) REVERT: C 127 ASN cc_start: 0.6446 (OUTLIER) cc_final: 0.5983 (p0) REVERT: C 158 MET cc_start: 0.8194 (OUTLIER) cc_final: 0.7652 (tmm) REVERT: C 231 PHE cc_start: 0.8412 (OUTLIER) cc_final: 0.8167 (t80) REVERT: C 267 MET cc_start: 0.8448 (ppp) cc_final: 0.8074 (ppp) REVERT: C 460 ILE cc_start: 0.8686 (mm) cc_final: 0.8342 (tp) REVERT: C 708 GLN cc_start: 0.8010 (OUTLIER) cc_final: 0.7621 (mp10) REVERT: C 837 ARG cc_start: 0.8698 (OUTLIER) cc_final: 0.7337 (ptt-90) REVERT: C 852 MET cc_start: 0.6667 (mmm) cc_final: 0.6368 (mmm) REVERT: C 933 ASP cc_start: 0.8887 (t70) cc_final: 0.8579 (t0) REVERT: D 20 SER cc_start: 0.8206 (OUTLIER) cc_final: 0.7833 (m) REVERT: D 266 THR cc_start: 0.8112 (OUTLIER) cc_final: 0.7498 (p) REVERT: E 13 THR cc_start: 0.8515 (OUTLIER) cc_final: 0.8203 (p) outliers start: 233 outliers final: 34 residues processed: 502 average time/residue: 0.4352 time to fit residues: 312.4295 Evaluate side-chains 197 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 142 time to evaluate : 2.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 343 CYS Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 493 HIS Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 708 GLN Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 846 ASN Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 1011 ARG Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 160 CYS Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain C residue 127 ASN Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 343 CYS Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 708 GLN Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 837 ARG Chi-restraints excluded: chain C residue 846 ASN Chi-restraints excluded: chain C residue 943 SER Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 64 ASP Chi-restraints excluded: chain D residue 160 CYS Chi-restraints excluded: chain D residue 203 GLN Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 33 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 222 optimal weight: 6.9990 chunk 200 optimal weight: 5.9990 chunk 111 optimal weight: 0.0000 chunk 68 optimal weight: 5.9990 chunk 134 optimal weight: 5.9990 chunk 106 optimal weight: 5.9990 chunk 206 optimal weight: 5.9990 chunk 80 optimal weight: 9.9990 chunk 125 optimal weight: 8.9990 chunk 154 optimal weight: 20.0000 chunk 239 optimal weight: 0.2980 overall best weight: 3.6590 ------------------------------------------------------------------------------- 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 167 GLN A 360 ASN ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 ASN A 486 ASN A 557 HIS A 783 ASN A1019 GLN B 56 GLN B 107 HIS B 203 GLN B 243 GLN B 258 GLN B 284 ASN ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 129 ASN C 167 GLN C 360 ASN ** C 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 474 ASN C 486 ASN C 493 HIS C 557 HIS C 783 ASN C1019 GLN D 107 HIS D 203 GLN D 243 GLN D 258 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 23024 Z= 0.311 Angle : 0.715 10.283 31058 Z= 0.348 Chirality : 0.047 0.418 3512 Planarity : 0.005 0.058 3804 Dihedral : 17.321 172.502 5151 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.85 % Allowed : 11.89 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.15), residues: 2636 helix: -0.04 (0.15), residues: 1164 sheet: -1.77 (0.28), residues: 270 loop : -1.86 (0.16), residues: 1202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 156 HIS 0.013 0.002 HIS C 493 PHE 0.017 0.002 PHE C 793 TYR 0.019 0.002 TYR C 569 ARG 0.010 0.001 ARG A 430 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 137 time to evaluate : 2.433 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 52 HIS cc_start: 0.7632 (m170) cc_final: 0.7310 (m-70) REVERT: A 127 ASN cc_start: 0.6913 (OUTLIER) cc_final: 0.6287 (p0) REVERT: A 158 MET cc_start: 0.8293 (mmp) cc_final: 0.7741 (tmm) REVERT: A 231 PHE cc_start: 0.8498 (OUTLIER) cc_final: 0.8260 (t80) REVERT: A 351 MET cc_start: 0.8161 (mmm) cc_final: 0.7847 (mtt) REVERT: A 493 HIS cc_start: 0.7732 (OUTLIER) cc_final: 0.6948 (m170) REVERT: A 967 PHE cc_start: 0.7835 (t80) cc_final: 0.7472 (t80) REVERT: B 20 SER cc_start: 0.7936 (OUTLIER) cc_final: 0.7611 (m) REVERT: B 85 ILE cc_start: 0.7702 (mt) cc_final: 0.6571 (mm) REVERT: G 13 THR cc_start: 0.8934 (m) cc_final: 0.8464 (p) REVERT: C 48 LEU cc_start: 0.8408 (mt) cc_final: 0.8038 (tp) REVERT: C 127 ASN cc_start: 0.6905 (OUTLIER) cc_final: 0.6327 (p0) REVERT: C 158 MET cc_start: 0.8269 (mmp) cc_final: 0.7815 (tmm) REVERT: C 209 HIS cc_start: 0.6986 (OUTLIER) cc_final: 0.6295 (m-70) REVERT: C 507 MET cc_start: 0.8141 (ttp) cc_final: 0.7829 (tmm) REVERT: C 530 LEU cc_start: 0.7177 (OUTLIER) cc_final: 0.6929 (tp) REVERT: C 967 PHE cc_start: 0.7851 (t80) cc_final: 0.7549 (t80) REVERT: D 20 SER cc_start: 0.8110 (OUTLIER) cc_final: 0.7808 (m) REVERT: D 85 ILE cc_start: 0.7507 (mt) cc_final: 0.6235 (mm) REVERT: E 13 THR cc_start: 0.8970 (m) cc_final: 0.8572 (p) outliers start: 87 outliers final: 46 residues processed: 210 average time/residue: 0.3382 time to fit residues: 112.8455 Evaluate side-chains 159 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 105 time to evaluate : 2.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 209 HIS Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 493 HIS Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 846 ASN Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 901 SER Chi-restraints excluded: chain A residue 935 ILE Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 160 CYS Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain C residue 127 ASN Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 209 HIS Chi-restraints excluded: chain C residue 267 MET Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 783 ASN Chi-restraints excluded: chain C residue 837 ARG Chi-restraints excluded: chain C residue 846 ASN Chi-restraints excluded: chain C residue 847 GLU Chi-restraints excluded: chain C residue 901 SER Chi-restraints excluded: chain C residue 935 ILE Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 64 ASP Chi-restraints excluded: chain D residue 71 ASP Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 160 CYS Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 203 GLN Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 269 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 133 optimal weight: 5.9990 chunk 74 optimal weight: 6.9990 chunk 199 optimal weight: 10.0000 chunk 163 optimal weight: 7.9990 chunk 66 optimal weight: 9.9990 chunk 240 optimal weight: 10.0000 chunk 259 optimal weight: 4.9990 chunk 213 optimal weight: 9.9990 chunk 238 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 192 optimal weight: 7.9990 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 52 HIS A 383 GLN A 904 GLN ** A1019 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 904 GLN ** C1019 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.3806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 23024 Z= 0.340 Angle : 0.673 9.869 31058 Z= 0.329 Chirality : 0.046 0.391 3512 Planarity : 0.005 0.044 3804 Dihedral : 15.915 161.838 5097 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.45 % Allowed : 12.91 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.16), residues: 2636 helix: 0.38 (0.15), residues: 1182 sheet: -1.23 (0.29), residues: 270 loop : -1.24 (0.17), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP C 894 HIS 0.008 0.001 HIS C 52 PHE 0.018 0.002 PHE C 793 TYR 0.019 0.002 TYR C 684 ARG 0.010 0.001 ARG C 61 *********************** 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 192 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 114 time to evaluate : 2.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 MET cc_start: 0.8235 (mmp) cc_final: 0.7702 (tmm) REVERT: A 404 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7231 (tt0) REVERT: A 413 LYS cc_start: 0.6976 (OUTLIER) cc_final: 0.6349 (ptpp) REVERT: A 493 HIS cc_start: 0.7648 (OUTLIER) cc_final: 0.7188 (m-70) REVERT: B 20 SER cc_start: 0.8121 (OUTLIER) cc_final: 0.7874 (m) REVERT: C 52 HIS cc_start: 0.7940 (m170) cc_final: 0.7630 (m-70) REVERT: C 158 MET cc_start: 0.8261 (mmp) cc_final: 0.7820 (tmm) REVERT: C 404 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7231 (tt0) REVERT: C 413 LYS cc_start: 0.6927 (OUTLIER) cc_final: 0.6252 (ptpp) REVERT: C 417 THR cc_start: 0.7821 (OUTLIER) cc_final: 0.7560 (p) REVERT: C 530 LEU cc_start: 0.7171 (OUTLIER) cc_final: 0.6838 (tp) REVERT: D 20 SER cc_start: 0.8232 (OUTLIER) cc_final: 0.7978 (m) REVERT: E 10 GLU cc_start: 0.8033 (pm20) cc_final: 0.7824 (pm20) outliers start: 78 outliers final: 50 residues processed: 184 average time/residue: 0.3194 time to fit residues: 95.7911 Evaluate side-chains 158 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 99 time to evaluate : 2.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 413 LYS Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 493 HIS Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 846 ASN Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 886 LYS Chi-restraints excluded: chain A residue 901 SER Chi-restraints excluded: chain A residue 935 ILE Chi-restraints excluded: chain A residue 949 MET Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 127 ASN Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 267 MET Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 404 GLU Chi-restraints excluded: chain C residue 413 LYS Chi-restraints excluded: chain C residue 417 THR Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 650 ILE Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 846 ASN Chi-restraints excluded: chain C residue 847 GLU Chi-restraints excluded: chain C residue 901 SER Chi-restraints excluded: chain C residue 935 ILE 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 47 LEU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 203 GLN Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 303 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 237 optimal weight: 1.9990 chunk 180 optimal weight: 8.9990 chunk 124 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 114 optimal weight: 2.9990 chunk 161 optimal weight: 0.9980 chunk 241 optimal weight: 6.9990 chunk 255 optimal weight: 1.9990 chunk 125 optimal weight: 4.9990 chunk 228 optimal weight: 3.9990 chunk 68 optimal weight: 8.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1019 GLN ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1019 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.4047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 23024 Z= 0.172 Angle : 0.560 10.188 31058 Z= 0.269 Chirality : 0.043 0.415 3512 Planarity : 0.004 0.041 3804 Dihedral : 14.989 160.148 5077 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.87 % Allowed : 14.01 % Favored : 83.11 % 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: -0.27 (0.16), residues: 2636 helix: 0.90 (0.16), residues: 1184 sheet: -0.92 (0.31), residues: 252 loop : -1.07 (0.17), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.002 TRP C 894 HIS 0.004 0.001 HIS C 52 PHE 0.017 0.001 PHE C 793 TYR 0.023 0.001 TYR C 684 ARG 0.006 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 174 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 109 time to evaluate : 2.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 ASN cc_start: 0.7285 (OUTLIER) cc_final: 0.6107 (p0) REVERT: A 158 MET cc_start: 0.8142 (mmp) cc_final: 0.7755 (tmm) REVERT: A 404 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7246 (tt0) REVERT: A 413 LYS cc_start: 0.6920 (OUTLIER) cc_final: 0.6331 (ptpp) REVERT: A 571 PHE cc_start: 0.5592 (OUTLIER) cc_final: 0.5062 (p90) REVERT: B 20 SER cc_start: 0.8007 (OUTLIER) cc_final: 0.7772 (m) REVERT: C 158 MET cc_start: 0.8177 (mmp) cc_final: 0.7859 (tmm) REVERT: C 404 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7245 (tt0) REVERT: C 413 LYS cc_start: 0.6856 (OUTLIER) cc_final: 0.6218 (ptpp) REVERT: C 530 LEU cc_start: 0.7122 (OUTLIER) cc_final: 0.6808 (tp) REVERT: C 897 ASP cc_start: 0.8983 (OUTLIER) cc_final: 0.8409 (p0) REVERT: D 20 SER cc_start: 0.8095 (OUTLIER) cc_final: 0.7875 (m) outliers start: 65 outliers final: 39 residues processed: 168 average time/residue: 0.3136 time to fit residues: 86.9661 Evaluate side-chains 143 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 94 time to evaluate : 2.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 209 HIS Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 413 LYS Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 571 PHE Chi-restraints excluded: chain A residue 846 ASN Chi-restraints excluded: chain A residue 935 ILE Chi-restraints excluded: chain A residue 949 MET Chi-restraints excluded: chain A residue 1007 PHE Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 127 ASN Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 404 GLU Chi-restraints excluded: chain C residue 413 LYS Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 846 ASN Chi-restraints excluded: chain C residue 897 ASP Chi-restraints excluded: chain C residue 935 ILE Chi-restraints excluded: chain C residue 1007 PHE Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 203 GLN Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 303 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 212 optimal weight: 0.8980 chunk 144 optimal weight: 1.9990 chunk 3 optimal weight: 9.9990 chunk 190 optimal weight: 7.9990 chunk 105 optimal weight: 4.9990 chunk 217 optimal weight: 10.0000 chunk 176 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 130 optimal weight: 8.9990 chunk 229 optimal weight: 3.9990 chunk 64 optimal weight: 9.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 744 GLN B 107 HIS ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 577 ASN C 744 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.4488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 23024 Z= 0.292 Angle : 0.619 10.256 31058 Z= 0.298 Chirality : 0.045 0.427 3512 Planarity : 0.004 0.041 3804 Dihedral : 14.587 155.604 5072 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.45 % Allowed : 13.57 % Favored : 82.98 % 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: -0.26 (0.16), residues: 2636 helix: 0.85 (0.15), residues: 1176 sheet: -0.90 (0.31), residues: 252 loop : -1.01 (0.17), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.077 0.002 TRP C 894 HIS 0.014 0.002 HIS A 493 PHE 0.018 0.002 PHE C 793 TYR 0.019 0.002 TYR C 684 ARG 0.007 0.001 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 175 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 97 time to evaluate : 2.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 ASN cc_start: 0.7600 (OUTLIER) cc_final: 0.6452 (p0) REVERT: A 158 MET cc_start: 0.8214 (mmp) cc_final: 0.7841 (tmm) REVERT: A 404 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7226 (tt0) REVERT: A 413 LYS cc_start: 0.6904 (OUTLIER) cc_final: 0.6324 (ptpp) REVERT: A 571 PHE cc_start: 0.5506 (OUTLIER) cc_final: 0.5250 (p90) REVERT: A 748 MET cc_start: 0.8945 (ttt) cc_final: 0.8723 (ttt) REVERT: B 55 ILE cc_start: 0.9050 (OUTLIER) cc_final: 0.8812 (tp) REVERT: C 158 MET cc_start: 0.8210 (mmp) cc_final: 0.7857 (tmm) REVERT: C 404 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7249 (tt0) REVERT: C 413 LYS cc_start: 0.6771 (OUTLIER) cc_final: 0.6218 (ptpp) REVERT: C 530 LEU cc_start: 0.7217 (OUTLIER) cc_final: 0.6883 (tp) REVERT: D 55 ILE cc_start: 0.8989 (OUTLIER) cc_final: 0.8717 (tp) outliers start: 78 outliers final: 57 residues processed: 166 average time/residue: 0.3185 time to fit residues: 87.5340 Evaluate side-chains 157 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 91 time to evaluate : 2.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 413 LYS Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 571 PHE Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 846 ASN Chi-restraints excluded: chain A residue 886 LYS Chi-restraints excluded: chain A residue 901 SER Chi-restraints excluded: chain A residue 935 ILE Chi-restraints excluded: chain A residue 949 MET Chi-restraints excluded: chain A residue 1007 PHE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 127 ASN Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 267 MET Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 404 GLU Chi-restraints excluded: chain C residue 413 LYS Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 781 THR Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 846 ASN Chi-restraints excluded: chain C residue 901 SER Chi-restraints excluded: chain C residue 935 ILE Chi-restraints excluded: chain C residue 949 MET Chi-restraints excluded: chain C residue 1007 PHE Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 167 THR 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 D residue 234 LEU Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 305 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 85 optimal weight: 6.9990 chunk 229 optimal weight: 0.7980 chunk 50 optimal weight: 6.9990 chunk 149 optimal weight: 9.9990 chunk 62 optimal weight: 8.9990 chunk 255 optimal weight: 7.9990 chunk 212 optimal weight: 0.0670 chunk 118 optimal weight: 1.9990 chunk 21 optimal weight: 7.9990 chunk 84 optimal weight: 0.9990 chunk 134 optimal weight: 2.9990 overall best weight: 1.3724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 146 GLN C 577 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.4603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 23024 Z= 0.148 Angle : 0.536 12.373 31058 Z= 0.253 Chirality : 0.043 0.453 3512 Planarity : 0.003 0.038 3804 Dihedral : 13.829 157.387 5068 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.56 % Allowed : 15.56 % 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: 0.13 (0.16), residues: 2636 helix: 1.25 (0.16), residues: 1170 sheet: -0.61 (0.33), residues: 240 loop : -0.90 (0.16), residues: 1226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.076 0.002 TRP A 894 HIS 0.009 0.001 HIS C 52 PHE 0.015 0.001 PHE C 793 TYR 0.020 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 160 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 102 time to evaluate : 2.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 ASN cc_start: 0.7628 (OUTLIER) cc_final: 0.6454 (p0) REVERT: A 158 MET cc_start: 0.8113 (OUTLIER) cc_final: 0.7876 (tmm) REVERT: A 164 MET cc_start: 0.5797 (OUTLIER) cc_final: 0.5567 (ptp) REVERT: A 404 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.7107 (tt0) REVERT: A 571 PHE cc_start: 0.5629 (OUTLIER) cc_final: 0.5391 (p90) REVERT: C 52 HIS cc_start: 0.8089 (m90) cc_final: 0.7475 (m170) REVERT: C 158 MET cc_start: 0.8114 (OUTLIER) cc_final: 0.7892 (tmm) REVERT: C 404 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7169 (tt0) REVERT: C 488 TYR cc_start: 0.7747 (p90) cc_final: 0.7184 (p90) REVERT: C 530 LEU cc_start: 0.7163 (OUTLIER) cc_final: 0.6851 (tp) REVERT: C 734 MET cc_start: 0.8254 (mmm) cc_final: 0.7839 (mmp) REVERT: C 897 ASP cc_start: 0.8908 (OUTLIER) cc_final: 0.8279 (p0) outliers start: 58 outliers final: 38 residues processed: 150 average time/residue: 0.3391 time to fit residues: 84.1478 Evaluate side-chains 148 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 101 time to evaluate : 2.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 571 PHE Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 846 ASN Chi-restraints excluded: chain A residue 935 ILE Chi-restraints excluded: chain A residue 949 MET Chi-restraints excluded: chain A residue 1007 PHE Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 267 MET Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 404 GLU Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain C residue 758 ILE Chi-restraints excluded: chain C residue 846 ASN Chi-restraints excluded: chain C residue 897 ASP Chi-restraints excluded: chain C residue 935 ILE Chi-restraints excluded: chain C residue 949 MET Chi-restraints excluded: chain C residue 1007 PHE Chi-restraints excluded: chain D residue 203 GLN Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 303 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 246 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 chunk 145 optimal weight: 50.0000 chunk 186 optimal weight: 0.0270 chunk 144 optimal weight: 5.9990 chunk 215 optimal weight: 3.9990 chunk 142 optimal weight: 9.9990 chunk 254 optimal weight: 0.5980 chunk 159 optimal weight: 7.9990 chunk 155 optimal weight: 6.9990 chunk 117 optimal weight: 6.9990 overall best weight: 2.7244 ------------------------------------------------------------------------------- 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: 0.8205 moved from start: 0.4865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 23024 Z= 0.215 Angle : 0.569 12.582 31058 Z= 0.269 Chirality : 0.043 0.455 3512 Planarity : 0.003 0.040 3804 Dihedral : 13.360 153.880 5066 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.65 % Allowed : 15.56 % Favored : 81.79 % 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: 0.22 (0.16), residues: 2636 helix: 1.27 (0.15), residues: 1178 sheet: -0.54 (0.34), residues: 240 loop : -0.80 (0.16), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.086 0.002 TRP A 894 HIS 0.008 0.001 HIS A 493 PHE 0.016 0.001 PHE C 793 TYR 0.017 0.001 TYR C 684 ARG 0.004 0.000 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 162 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 102 time to evaluate : 2.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 ASN cc_start: 0.7754 (OUTLIER) cc_final: 0.6642 (p0) REVERT: A 158 MET cc_start: 0.8153 (mmp) cc_final: 0.7845 (tmm) REVERT: A 404 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.7070 (tt0) REVERT: A 413 LYS cc_start: 0.6847 (OUTLIER) cc_final: 0.6367 (ptpp) REVERT: A 473 ARG cc_start: 0.6969 (mtt180) cc_final: 0.6637 (mtm110) REVERT: A 734 MET cc_start: 0.8234 (mmm) cc_final: 0.7709 (mmp) REVERT: C 52 HIS cc_start: 0.8263 (m90) cc_final: 0.7695 (m170) REVERT: C 267 MET cc_start: 0.8515 (OUTLIER) cc_final: 0.8184 (tmm) REVERT: C 404 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7150 (tt0) REVERT: C 413 LYS cc_start: 0.6767 (OUTLIER) cc_final: 0.6259 (ptpp) REVERT: C 488 TYR cc_start: 0.7860 (p90) cc_final: 0.7198 (p90) REVERT: C 530 LEU cc_start: 0.7185 (OUTLIER) cc_final: 0.6838 (tp) outliers start: 60 outliers final: 46 residues processed: 153 average time/residue: 0.3328 time to fit residues: 82.5268 Evaluate side-chains 148 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 95 time to evaluate : 2.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 413 LYS Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 846 ASN Chi-restraints excluded: chain A residue 886 LYS Chi-restraints excluded: chain A residue 935 ILE Chi-restraints excluded: chain A residue 949 MET Chi-restraints excluded: chain A residue 1007 PHE Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 267 MET Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 404 GLU Chi-restraints excluded: chain C residue 413 LYS Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain C residue 846 ASN Chi-restraints excluded: chain C residue 935 ILE Chi-restraints excluded: chain C residue 949 MET Chi-restraints excluded: chain C residue 1007 PHE Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 203 GLN Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 303 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 157 optimal weight: 0.9990 chunk 101 optimal weight: 5.9990 chunk 151 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 161 optimal weight: 0.7980 chunk 173 optimal weight: 10.0000 chunk 125 optimal weight: 0.0980 chunk 23 optimal weight: 0.9990 chunk 200 optimal weight: 0.0470 chunk 231 optimal weight: 20.0000 overall best weight: 0.5882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 577 ASN D 146 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.4965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 23024 Z= 0.130 Angle : 0.529 13.665 31058 Z= 0.248 Chirality : 0.042 0.463 3512 Planarity : 0.003 0.038 3804 Dihedral : 12.658 150.609 5066 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.90 % Allowed : 16.62 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.16), residues: 2636 helix: 1.51 (0.15), residues: 1194 sheet: -0.42 (0.34), residues: 244 loop : -0.75 (0.16), residues: 1198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.002 TRP A 894 HIS 0.005 0.001 HIS A 52 PHE 0.022 0.001 PHE C 578 TYR 0.019 0.001 TYR C 684 ARG 0.008 0.000 ARG D 223 *********************** 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 162 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 119 time to evaluate : 2.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 ASN cc_start: 0.7823 (OUTLIER) cc_final: 0.6660 (p0) REVERT: A 158 MET cc_start: 0.8056 (OUTLIER) cc_final: 0.7850 (tmm) REVERT: A 267 MET cc_start: 0.8383 (OUTLIER) cc_final: 0.7950 (tmm) REVERT: A 334 GLU cc_start: 0.7321 (mt-10) cc_final: 0.7035 (mp0) REVERT: A 473 ARG cc_start: 0.7080 (mtt180) cc_final: 0.6723 (mtm180) REVERT: C 52 HIS cc_start: 0.8220 (m90) cc_final: 0.7737 (m170) REVERT: C 61 ARG cc_start: 0.7459 (tpt90) cc_final: 0.7219 (tpt90) REVERT: C 267 MET cc_start: 0.8444 (OUTLIER) cc_final: 0.8092 (tmm) REVERT: C 488 TYR cc_start: 0.7814 (p90) cc_final: 0.7199 (p90) REVERT: C 530 LEU cc_start: 0.7095 (OUTLIER) cc_final: 0.6814 (tp) REVERT: C 578 PHE cc_start: 0.7056 (OUTLIER) cc_final: 0.6726 (m-80) outliers start: 43 outliers final: 31 residues processed: 156 average time/residue: 0.3481 time to fit residues: 87.0781 Evaluate side-chains 142 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 105 time to evaluate : 2.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 846 ASN Chi-restraints excluded: chain A residue 1007 PHE Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 267 MET Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain C residue 578 PHE Chi-restraints excluded: chain C residue 758 ILE Chi-restraints excluded: chain C residue 846 ASN Chi-restraints excluded: chain C residue 901 SER Chi-restraints excluded: chain C residue 1007 PHE Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 203 GLN Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 303 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 243 optimal weight: 2.9990 chunk 222 optimal weight: 6.9990 chunk 237 optimal weight: 0.9990 chunk 142 optimal weight: 10.0000 chunk 103 optimal weight: 3.9990 chunk 186 optimal weight: 0.0170 chunk 72 optimal weight: 10.0000 chunk 214 optimal weight: 6.9990 chunk 224 optimal weight: 0.7980 chunk 236 optimal weight: 4.9990 chunk 155 optimal weight: 9.9990 overall best weight: 1.7624 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.5095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23024 Z= 0.163 Angle : 0.535 13.319 31058 Z= 0.250 Chirality : 0.042 0.461 3512 Planarity : 0.003 0.038 3804 Dihedral : 12.318 147.973 5066 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.90 % Allowed : 16.58 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.55 (0.16), residues: 2636 helix: 1.54 (0.16), residues: 1186 sheet: -0.38 (0.33), residues: 254 loop : -0.64 (0.17), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP C 894 HIS 0.005 0.001 HIS A 52 PHE 0.017 0.001 PHE C 578 TYR 0.016 0.001 TYR C 684 ARG 0.006 0.000 ARG D 223 *********************** 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 145 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 102 time to evaluate : 2.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 ASN cc_start: 0.7872 (OUTLIER) cc_final: 0.6729 (p0) REVERT: A 267 MET cc_start: 0.8416 (OUTLIER) cc_final: 0.8042 (tmm) REVERT: A 334 GLU cc_start: 0.7374 (mt-10) cc_final: 0.6997 (mp0) REVERT: A 413 LYS cc_start: 0.6755 (OUTLIER) cc_final: 0.6344 (ptpp) REVERT: A 734 MET cc_start: 0.8217 (mmm) cc_final: 0.7601 (mmp) REVERT: C 52 HIS cc_start: 0.8251 (m90) cc_final: 0.7793 (m170) REVERT: C 61 ARG cc_start: 0.7413 (tpt90) cc_final: 0.7157 (tpt90) REVERT: C 267 MET cc_start: 0.8465 (OUTLIER) cc_final: 0.8099 (tmm) REVERT: C 404 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.7095 (tt0) REVERT: C 413 LYS cc_start: 0.6826 (OUTLIER) cc_final: 0.6369 (ptpp) REVERT: C 488 TYR cc_start: 0.7871 (p90) cc_final: 0.7282 (p90) REVERT: C 530 LEU cc_start: 0.7122 (OUTLIER) cc_final: 0.6812 (tp) REVERT: C 578 PHE cc_start: 0.6973 (m-80) cc_final: 0.6619 (m-80) REVERT: C 897 ASP cc_start: 0.8778 (OUTLIER) cc_final: 0.7978 (p0) outliers start: 43 outliers final: 31 residues processed: 140 average time/residue: 0.3389 time to fit residues: 76.9378 Evaluate side-chains 139 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 100 time to evaluate : 2.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 413 LYS Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 846 ASN Chi-restraints excluded: chain A residue 886 LYS Chi-restraints excluded: chain A residue 1007 PHE Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 267 MET Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 404 GLU Chi-restraints excluded: chain C residue 413 LYS Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain C residue 758 ILE Chi-restraints excluded: chain C residue 846 ASN Chi-restraints excluded: chain C residue 897 ASP Chi-restraints excluded: chain C residue 949 MET Chi-restraints excluded: chain C residue 1007 PHE Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 203 GLN Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 303 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 250 optimal weight: 9.9990 chunk 153 optimal weight: 0.9980 chunk 118 optimal weight: 9.9990 chunk 174 optimal weight: 9.9990 chunk 263 optimal weight: 4.9990 chunk 242 optimal weight: 9.9990 chunk 209 optimal weight: 7.9990 chunk 21 optimal weight: 2.9990 chunk 161 optimal weight: 9.9990 chunk 128 optimal weight: 8.9990 chunk 166 optimal weight: 9.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN C 248 ASN C 683 HIS D 107 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.5340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 23024 Z= 0.354 Angle : 0.675 14.195 31058 Z= 0.321 Chirality : 0.046 0.467 3512 Planarity : 0.004 0.041 3804 Dihedral : 12.669 143.331 5066 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.30 % Allowed : 16.18 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.16), residues: 2636 helix: 1.24 (0.15), residues: 1166 sheet: -0.55 (0.33), residues: 254 loop : -0.74 (0.16), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 156 HIS 0.005 0.001 HIS A 52 PHE 0.020 0.002 PHE C 923 TYR 0.018 0.002 TYR C 994 ARG 0.008 0.001 ARG C 893 ********************** 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 149 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 97 time to evaluate : 2.634 Fit side-chains REVERT: A 127 ASN cc_start: 0.7858 (OUTLIER) cc_final: 0.6876 (p0) REVERT: A 267 MET cc_start: 0.8497 (OUTLIER) cc_final: 0.8161 (tmm) REVERT: A 334 GLU cc_start: 0.7471 (mt-10) cc_final: 0.7069 (mp0) REVERT: A 404 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.7043 (tt0) REVERT: A 413 LYS cc_start: 0.6892 (OUTLIER) cc_final: 0.6391 (ptpp) REVERT: A 734 MET cc_start: 0.8221 (mmm) cc_final: 0.7742 (mmp) REVERT: B 266 THR cc_start: 0.8337 (OUTLIER) cc_final: 0.7883 (p) REVERT: C 52 HIS cc_start: 0.8311 (m90) cc_final: 0.7848 (m-70) REVERT: C 267 MET cc_start: 0.8481 (OUTLIER) cc_final: 0.8095 (tmm) REVERT: C 404 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7165 (tt0) REVERT: C 413 LYS cc_start: 0.6856 (OUTLIER) cc_final: 0.6318 (ptpp) REVERT: C 488 TYR cc_start: 0.7703 (p90) cc_final: 0.6975 (p90) REVERT: C 507 MET cc_start: 0.7476 (mmm) cc_final: 0.7150 (tpp) REVERT: C 530 LEU cc_start: 0.7167 (OUTLIER) cc_final: 0.6783 (tp) REVERT: C 734 MET cc_start: 0.8174 (mmm) cc_final: 0.7817 (mmp) REVERT: D 85 ILE cc_start: 0.8555 (mm) cc_final: 0.8146 (mm) outliers start: 52 outliers final: 36 residues processed: 144 average time/residue: 0.3181 time to fit residues: 75.2435 Evaluate side-chains 141 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 96 time to evaluate : 2.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 413 LYS Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 846 ASN Chi-restraints excluded: chain A residue 949 MET Chi-restraints excluded: chain A residue 1007 PHE Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 267 MET Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 404 GLU Chi-restraints excluded: chain C residue 413 LYS Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 484 SER Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain C residue 758 ILE Chi-restraints excluded: chain C residue 781 THR Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 846 ASN Chi-restraints excluded: chain C residue 949 MET Chi-restraints excluded: chain C residue 1007 PHE Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 203 GLN Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 303 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 223 optimal weight: 0.9990 chunk 64 optimal weight: 10.0000 chunk 193 optimal weight: 10.0000 chunk 30 optimal weight: 2.9990 chunk 58 optimal weight: 10.0000 chunk 209 optimal weight: 0.7980 chunk 87 optimal weight: 0.9980 chunk 215 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 184 optimal weight: 9.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.089617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.068081 restraints weight = 67196.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.068043 restraints weight = 51408.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.068792 restraints weight = 38114.872| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.5371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 23024 Z= 0.137 Angle : 0.547 14.170 31058 Z= 0.255 Chirality : 0.042 0.466 3512 Planarity : 0.003 0.038 3804 Dihedral : 11.951 138.694 5066 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.81 % Allowed : 16.62 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.16), residues: 2636 helix: 1.48 (0.15), residues: 1194 sheet: -0.42 (0.33), residues: 258 loop : -0.60 (0.17), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 906 HIS 0.006 0.001 HIS A 493 PHE 0.017 0.001 PHE C 578 TYR 0.016 0.001 TYR C 684 ARG 0.006 0.000 ARG B 223 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3526.90 seconds wall clock time: 66 minutes 7.49 seconds (3967.49 seconds total)