Starting phenix.real_space_refine on Tue Jul 23 17:11:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mf3_23810/07_2024/7mf3_23810_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mf3_23810/07_2024/7mf3_23810.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mf3_23810/07_2024/7mf3_23810.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mf3_23810/07_2024/7mf3_23810.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mf3_23810/07_2024/7mf3_23810_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mf3_23810/07_2024/7mf3_23810_neut.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 4 5.21 5 S 129 5.16 5 C 14359 2.51 5 N 3965 2.21 5 O 4475 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 746": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 22938 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 890, 7230 Classifications: {'peptide': 890} Link IDs: {'PTRANS': 24, 'TRANS': 865} Chain breaks: 2 Chain: "B" Number of atoms: 7276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 896, 7276 Classifications: {'peptide': 896} Link IDs: {'PTRANS': 24, 'TRANS': 871} Chain breaks: 2 Chain: "C" Number of atoms: 1169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1169 Classifications: {'peptide': 149} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 145} Chain: "D" Number of atoms: 1277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1277 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 5, 'TRANS': 152} Chain: "E" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1270 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 5, 'TRANS': 151} Chain: "F" Number of atoms: 1169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1169 Classifications: {'peptide': 149} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 145} Chain: "G" Number of atoms: 1742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1742 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 211} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 1737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1737 Classifications: {'peptide': 211} Link IDs: {'TRANS': 210} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 15.21, per 1000 atoms: 0.66 Number of scatterers: 22938 At special positions: 0 Unit cell: (101.587, 172.608, 229.245, 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 129 16.00 P 6 15.00 Mg 4 11.99 O 4475 8.00 N 3965 7.00 C 14359 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.64 Conformation dependent library (CDL) restraints added in 4.5 seconds 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5380 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 14 sheets defined 64.0% alpha, 4.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.27 Creating SS restraints... Processing helix chain 'A' and resid 88 through 92 removed outlier: 3.676A pdb=" N GLU A 91 " --> pdb=" O ASP A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 110 removed outlier: 3.907A pdb=" N PHE A 109 " --> pdb=" O ARG A 105 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER A 110 " --> pdb=" O GLU A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 139 Processing helix chain 'A' and resid 140 through 142 No H-bonds generated for 'chain 'A' and resid 140 through 142' Processing helix chain 'A' and resid 152 through 168 removed outlier: 3.555A pdb=" N ILE A 156 " --> pdb=" O HIS A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 198 Processing helix chain 'A' and resid 219 through 235 removed outlier: 3.860A pdb=" N GLN A 223 " --> pdb=" O GLU A 219 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N ASN A 228 " --> pdb=" O LEU A 224 " (cutoff:3.500A) Proline residue: A 229 - end of helix removed outlier: 3.834A pdb=" N PHE A 234 " --> pdb=" O ILE A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 295 removed outlier: 4.023A pdb=" N TYR A 291 " --> pdb=" O PHE A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 304 Processing helix chain 'A' and resid 309 through 313 removed outlier: 3.568A pdb=" N ASN A 312 " --> pdb=" O GLY A 309 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TYR A 313 " --> pdb=" O PHE A 310 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 309 through 313' Processing helix chain 'A' and resid 327 through 343 removed outlier: 3.907A pdb=" N MET A 331 " --> pdb=" O GLN A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 362 removed outlier: 3.610A pdb=" N GLN A 349 " --> pdb=" O THR A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 365 No H-bonds generated for 'chain 'A' and resid 363 through 365' Processing helix chain 'A' and resid 381 through 392 Processing helix chain 'A' and resid 394 through 404 Processing helix chain 'A' and resid 419 through 449 Processing helix chain 'A' and resid 476 through 498 Processing helix chain 'A' and resid 498 through 508 removed outlier: 3.603A pdb=" N GLU A 508 " --> pdb=" O GLU A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 529 Processing helix chain 'A' and resid 537 through 546 removed outlier: 4.179A pdb=" N TRP A 546 " --> pdb=" O ASP A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 564 removed outlier: 3.670A pdb=" N VAL A 556 " --> pdb=" O ASP A 552 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU A 557 " --> pdb=" O THR A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 603 Processing helix chain 'A' and resid 606 through 615 removed outlier: 4.073A pdb=" N GLN A 615 " --> pdb=" O SER A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 627 removed outlier: 3.938A pdb=" N TRP A 625 " --> pdb=" O VAL A 621 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ASP A 627 " --> pdb=" O ASP A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 677 removed outlier: 3.966A pdb=" N LEU A 662 " --> pdb=" O THR A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 707 removed outlier: 4.878A pdb=" N GLU A 703 " --> pdb=" O HIS A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 719 Processing helix chain 'A' and resid 727 through 735 Processing helix chain 'A' and resid 748 through 761 removed outlier: 3.879A pdb=" N CYS A 753 " --> pdb=" O GLY A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 763 through 765 No H-bonds generated for 'chain 'A' and resid 763 through 765' Processing helix chain 'A' and resid 778 through 783 removed outlier: 4.039A pdb=" N LEU A 781 " --> pdb=" O THR A 778 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N HIS A 783 " --> pdb=" O VAL A 780 " (cutoff:3.500A) Processing helix chain 'A' and resid 784 through 792 removed outlier: 4.020A pdb=" N ARG A 788 " --> pdb=" O LEU A 784 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 840 removed outlier: 4.464A pdb=" N TRP A 838 " --> pdb=" O LYS A 834 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N TRP A 840 " --> pdb=" O ARG A 836 " (cutoff:3.500A) Processing helix chain 'A' and resid 840 through 846 Processing helix chain 'A' and resid 847 through 854 removed outlier: 4.244A pdb=" N LEU A 851 " --> pdb=" O VAL A 847 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLN A 852 " --> pdb=" O LYS A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 949 removed outlier: 4.016A pdb=" N LYS A 871 " --> pdb=" O LEU A 867 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLU A 872 " --> pdb=" O GLN A 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 110 removed outlier: 3.547A pdb=" N SER B 110 " --> pdb=" O GLU B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 141 Processing helix chain 'B' and resid 152 through 167 removed outlier: 3.725A pdb=" N TYR B 161 " --> pdb=" O ALA B 157 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG B 162 " --> pdb=" O ASP B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 198 Processing helix chain 'B' and resid 218 through 234 removed outlier: 4.056A pdb=" N ASN B 228 " --> pdb=" O LEU B 224 " (cutoff:3.500A) Proline residue: B 229 - end of helix Processing helix chain 'B' and resid 273 through 277 removed outlier: 3.586A pdb=" N ALA B 277 " --> pdb=" O LYS B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 294 removed outlier: 3.672A pdb=" N TYR B 291 " --> pdb=" O PHE B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 305 Processing helix chain 'B' and resid 328 through 343 removed outlier: 3.984A pdb=" N PHE B 332 " --> pdb=" O ASP B 328 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N THR B 335 " --> pdb=" O MET B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 364 Processing helix chain 'B' and resid 381 through 390 removed outlier: 3.797A pdb=" N GLN B 385 " --> pdb=" O ASN B 381 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N CYS B 388 " --> pdb=" O ALA B 384 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LEU B 390 " --> pdb=" O LYS B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 404 Processing helix chain 'B' and resid 419 through 450 Processing helix chain 'B' and resid 476 through 509 removed outlier: 3.684A pdb=" N LEU B 480 " --> pdb=" O SER B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 527 removed outlier: 3.773A pdb=" N LEU B 527 " --> pdb=" O PRO B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 547 removed outlier: 4.128A pdb=" N TRP B 546 " --> pdb=" O ASP B 542 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE B 547 " --> pdb=" O GLU B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 564 Processing helix chain 'B' and resid 596 through 602 removed outlier: 3.688A pdb=" N MET B 602 " --> pdb=" O LEU B 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 615 removed outlier: 3.892A pdb=" N GLN B 615 " --> pdb=" O SER B 611 " (cutoff:3.500A) Processing helix chain 'B' and resid 620 through 627 removed outlier: 3.984A pdb=" N LEU B 624 " --> pdb=" O PHE B 620 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TRP B 625 " --> pdb=" O VAL B 621 " (cutoff:3.500A) Processing helix chain 'B' and resid 661 through 675 Processing helix chain 'B' and resid 697 through 709 removed outlier: 4.073A pdb=" N VAL B 701 " --> pdb=" O ASP B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 709 through 720 removed outlier: 3.704A pdb=" N GLY B 713 " --> pdb=" O GLY B 709 " (cutoff:3.500A) Processing helix chain 'B' and resid 727 through 734 Processing helix chain 'B' and resid 748 through 761 Processing helix chain 'B' and resid 763 through 767 Processing helix chain 'B' and resid 779 through 839 removed outlier: 3.873A pdb=" N THR B 793 " --> pdb=" O ASP B 789 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ASP B 794 " --> pdb=" O LEU B 790 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N VAL B 795 " --> pdb=" O LYS B 791 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ASN B 828 " --> pdb=" O VAL B 824 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ALA B 830 " --> pdb=" O GLN B 826 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ALA B 831 " --> pdb=" O ARG B 827 " (cutoff:3.500A) Processing helix chain 'B' and resid 839 through 845 removed outlier: 3.984A pdb=" N PHE B 844 " --> pdb=" O TRP B 840 " (cutoff:3.500A) Processing helix chain 'B' and resid 847 through 853 Processing helix chain 'B' and resid 855 through 948 removed outlier: 4.227A pdb=" N GLU B 859 " --> pdb=" O ARG B 855 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 18 removed outlier: 4.241A pdb=" N THR C 8 " --> pdb=" O SER C 4 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 38 Processing helix chain 'C' and resid 45 through 52 removed outlier: 4.129A pdb=" N LYS C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 78 removed outlier: 3.617A pdb=" N LEU C 70 " --> pdb=" O PHE C 66 " (cutoff:3.500A) Proline residue: C 71 - end of helix Processing helix chain 'C' and resid 84 through 96 removed outlier: 4.005A pdb=" N TYR C 88 " --> pdb=" O CYS C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 114 removed outlier: 3.574A pdb=" N ARG C 109 " --> pdb=" O GLY C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 127 Processing helix chain 'C' and resid 140 through 148 Processing helix chain 'D' and resid 27 through 41 removed outlier: 3.500A pdb=" N GLN D 31 " --> pdb=" O GLN D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 61 removed outlier: 3.870A pdb=" N ASP D 55 " --> pdb=" O GLU D 51 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ALA D 58 " --> pdb=" O HIS D 54 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N MET D 60 " --> pdb=" O MET D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 76 Processing helix chain 'D' and resid 81 through 91 Processing helix chain 'D' and resid 98 through 110 removed outlier: 4.115A pdb=" N ILE D 102 " --> pdb=" O PRO D 98 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ASP D 110 " --> pdb=" O PHE D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 128 removed outlier: 3.709A pdb=" N THR D 128 " --> pdb=" O GLU D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 139 Processing helix chain 'D' and resid 139 through 144 Processing helix chain 'D' and resid 155 through 163 Processing helix chain 'E' and resid 26 through 41 removed outlier: 4.419A pdb=" N GLN E 31 " --> pdb=" O GLN E 27 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N GLU E 32 " --> pdb=" O SER E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 61 removed outlier: 3.834A pdb=" N ASP E 55 " --> pdb=" O GLU E 51 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N MET E 56 " --> pdb=" O ASP E 52 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER E 59 " --> pdb=" O ASP E 55 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N MET E 60 " --> pdb=" O MET E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 74 Processing helix chain 'E' and resid 83 through 93 removed outlier: 3.866A pdb=" N THR E 87 " --> pdb=" O THR E 83 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N PHE E 89 " --> pdb=" O PHE E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 110 removed outlier: 4.454A pdb=" N PHE E 109 " --> pdb=" O ALA E 105 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ASP E 110 " --> pdb=" O PHE E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 119 through 127 Processing helix chain 'E' and resid 135 through 145 removed outlier: 3.588A pdb=" N GLU E 140 " --> pdb=" O GLU E 136 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N MET E 141 " --> pdb=" O GLU E 137 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA E 145 " --> pdb=" O MET E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 150 No H-bonds generated for 'chain 'E' and resid 148 through 150' Processing helix chain 'E' and resid 154 through 164 Processing helix chain 'F' and resid 4 through 18 removed outlier: 4.250A pdb=" N THR F 8 " --> pdb=" O SER F 4 " (cutoff:3.500A) Processing helix chain 'F' and resid 27 through 38 Processing helix chain 'F' and resid 45 through 50 Processing helix chain 'F' and resid 65 through 77 Proline residue: F 71 - end of helix Processing helix chain 'F' and resid 84 through 96 removed outlier: 3.978A pdb=" N TYR F 88 " --> pdb=" O CYS F 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 115 Processing helix chain 'F' and resid 120 through 128 removed outlier: 3.674A pdb=" N VAL F 124 " --> pdb=" O THR F 120 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL F 128 " --> pdb=" O VAL F 124 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 148 Processing helix chain 'G' and resid 1413 through 1527 removed outlier: 3.507A pdb=" N LYS G1417 " --> pdb=" O GLN G1413 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP G1527 " --> pdb=" O VAL G1523 " (cutoff:3.500A) Processing helix chain 'G' and resid 1532 through 1623 removed outlier: 4.041A pdb=" N LEU G1536 " --> pdb=" O ASN G1532 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N THR G1542 " --> pdb=" O LYS G1538 " (cutoff:3.500A) Processing helix chain 'H' and resid 1414 through 1524 removed outlier: 4.358A pdb=" N ALA H1418 " --> pdb=" O PHE H1414 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA H1419 " --> pdb=" O GLU H1415 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N SER H1524 " --> pdb=" O GLU H1520 " (cutoff:3.500A) Processing helix chain 'H' and resid 1535 through 1621 removed outlier: 3.620A pdb=" N SER H1539 " --> pdb=" O GLU H1535 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 67 through 71 removed outlier: 4.290A pdb=" N GLN A 76 " --> pdb=" O TRP A 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 115 through 117 removed outlier: 6.087A pdb=" N CYS A 121 " --> pdb=" O ARG A 683 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ILE A 685 " --> pdb=" O CYS A 121 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N VAL A 123 " --> pdb=" O ILE A 685 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LEU A 174 " --> pdb=" O VAL A 682 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N CYS A 684 " --> pdb=" O LEU A 174 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N THR A 176 " --> pdb=" O CYS A 684 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 171 through 172 removed outlier: 7.449A pdb=" N GLN A 171 " --> pdb=" O GLY A 462 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 249 through 255 removed outlier: 3.518A pdb=" N GLY A 264 " --> pdb=" O ASN A 255 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 368 through 369 Processing sheet with id=AA6, first strand: chain 'A' and resid 406 through 407 removed outlier: 3.899A pdb=" N VAL A 414 " --> pdb=" O ILE A 407 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 583 through 584 removed outlier: 3.783A pdb=" N ILE A 583 " --> pdb=" O VAL A 590 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 723 through 726 removed outlier: 3.634A pdb=" N ASN A 723 " --> pdb=" O PHE A 776 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE A 775 " --> pdb=" O ARG A 768 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 35 through 38 Processing sheet with id=AB1, first strand: chain 'B' and resid 57 through 60 Processing sheet with id=AB2, first strand: chain 'B' and resid 116 through 117 removed outlier: 6.619A pdb=" N CYS B 121 " --> pdb=" O ARG B 683 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N ILE B 685 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL B 123 " --> pdb=" O ILE B 685 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N VAL B 682 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N LEU B 174 " --> pdb=" O VAL B 682 " (cutoff:3.500A) removed outlier: 8.563A pdb=" N CYS B 684 " --> pdb=" O LEU B 174 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N THR B 176 " --> pdb=" O CYS B 684 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLN B 171 " --> pdb=" O PHE B 460 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU B 464 " --> pdb=" O ILE B 173 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N CYS B 175 " --> pdb=" O LEU B 464 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N SER B 459 " --> pdb=" O PHE B 256 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N PHE B 251 " --> pdb=" O GLU B 268 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLU B 268 " --> pdb=" O PHE B 251 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 579 through 585 removed outlier: 5.985A pdb=" N PHE B 581 " --> pdb=" O TYR B 592 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N TYR B 592 " --> pdb=" O PHE B 581 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY B 588 " --> pdb=" O HIS B 585 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 724 through 726 removed outlier: 3.691A pdb=" N ILE B 725 " --> pdb=" O ILE B 774 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 117 through 118 removed outlier: 3.571A pdb=" N ILE E 117 " --> pdb=" O PHE E 153 " (cutoff:3.500A) 1349 hydrogen bonds defined for protein. 3999 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.36 Time building geometry restraints manager: 11.32 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: 7480 1.34 - 1.46: 2872 1.46 - 1.58: 12700 1.58 - 1.70: 6 1.70 - 1.82: 220 Bond restraints: 23278 Sorted by residual: bond pdb=" O3 PO4 A2002 " pdb=" P PO4 A2002 " ideal model delta sigma weight residual 1.569 1.507 0.062 2.00e-02 2.50e+03 9.47e+00 bond pdb=" O3 PO4 B2002 " pdb=" P PO4 B2002 " ideal model delta sigma weight residual 1.569 1.509 0.060 2.00e-02 2.50e+03 8.95e+00 bond pdb=" O4 PO4 A2002 " pdb=" P PO4 A2002 " ideal model delta sigma weight residual 1.568 1.509 0.059 2.00e-02 2.50e+03 8.70e+00 bond pdb=" O2 PO4 A2002 " pdb=" P PO4 A2002 " ideal model delta sigma weight residual 1.567 1.509 0.058 2.00e-02 2.50e+03 8.47e+00 bond pdb=" O4 PO4 B2002 " pdb=" P PO4 B2002 " ideal model delta sigma weight residual 1.568 1.510 0.058 2.00e-02 2.50e+03 8.30e+00 ... (remaining 23273 not shown) Histogram of bond angle deviations from ideal: 97.38 - 105.13: 292 105.13 - 112.87: 12160 112.87 - 120.62: 10854 120.62 - 128.36: 7854 128.36 - 136.11: 106 Bond angle restraints: 31266 Sorted by residual: angle pdb=" C GLN B 327 " pdb=" N ASP B 328 " pdb=" CA ASP B 328 " ideal model delta sigma weight residual 121.54 129.99 -8.45 1.91e+00 2.74e-01 1.96e+01 angle pdb=" C THR B 176 " pdb=" CA THR B 176 " pdb=" CB THR B 176 " ideal model delta sigma weight residual 109.80 102.34 7.46 1.70e+00 3.46e-01 1.93e+01 angle pdb=" N GLY B 182 " pdb=" CA GLY B 182 " pdb=" C GLY B 182 " ideal model delta sigma weight residual 115.36 109.63 5.73 1.33e+00 5.65e-01 1.86e+01 angle pdb=" N LYS B 183 " pdb=" CA LYS B 183 " pdb=" C LYS B 183 " ideal model delta sigma weight residual 113.19 108.39 4.80 1.19e+00 7.06e-01 1.63e+01 angle pdb=" O ARG A 815 " pdb=" C ARG A 815 " pdb=" N GLN A 816 " ideal model delta sigma weight residual 122.03 126.10 -4.07 1.04e+00 9.25e-01 1.53e+01 ... (remaining 31261 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.84: 14110 35.84 - 71.68: 260 71.68 - 107.51: 38 107.51 - 143.35: 2 143.35 - 179.19: 1 Dihedral angle restraints: 14411 sinusoidal: 6156 harmonic: 8255 Sorted by residual: dihedral pdb=" C5' ADP A2001 " pdb=" O5' ADP A2001 " pdb=" PA ADP A2001 " pdb=" O2A ADP A2001 " ideal model delta sinusoidal sigma weight residual 300.00 120.81 179.19 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' ADP B2001 " pdb=" O5' ADP B2001 " pdb=" PA ADP B2001 " pdb=" O2A ADP B2001 " ideal model delta sinusoidal sigma weight residual -60.00 -176.24 116.24 1 2.00e+01 2.50e-03 3.46e+01 dihedral pdb=" O2A ADP A2001 " pdb=" O3A ADP A2001 " pdb=" PA ADP A2001 " pdb=" PB ADP A2001 " ideal model delta sinusoidal sigma weight residual -60.00 49.62 -109.62 1 2.00e+01 2.50e-03 3.21e+01 ... (remaining 14408 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 3050 0.067 - 0.134: 331 0.134 - 0.202: 17 0.202 - 0.269: 0 0.269 - 0.336: 2 Chirality restraints: 3400 Sorted by residual: chirality pdb=" CA ARG A 815 " pdb=" N ARG A 815 " pdb=" C ARG A 815 " pdb=" CB ARG A 815 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.34 2.00e-01 2.50e+01 2.82e+00 chirality pdb=" CA THR B 176 " pdb=" N THR B 176 " pdb=" C THR B 176 " pdb=" CB THR B 176 " both_signs ideal model delta sigma weight residual False 2.53 2.80 -0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" CB THR A 404 " pdb=" CA THR A 404 " pdb=" OG1 THR A 404 " pdb=" CG2 THR A 404 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 9.80e-01 ... (remaining 3397 not shown) Planarity restraints: 4115 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN B 327 " 0.015 2.00e-02 2.50e+03 2.98e-02 8.86e+00 pdb=" C GLN B 327 " -0.051 2.00e-02 2.50e+03 pdb=" O GLN B 327 " 0.020 2.00e-02 2.50e+03 pdb=" N ASP B 328 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP E 97 " 0.035 5.00e-02 4.00e+02 5.25e-02 4.41e+00 pdb=" N PRO E 98 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO E 98 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO E 98 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 228 " 0.034 5.00e-02 4.00e+02 5.13e-02 4.21e+00 pdb=" N PRO B 229 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO B 229 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 229 " 0.029 5.00e-02 4.00e+02 ... (remaining 4112 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 285 2.57 - 3.15: 19789 3.15 - 3.73: 37739 3.73 - 4.32: 47656 4.32 - 4.90: 74084 Nonbonded interactions: 179553 Sorted by model distance: nonbonded pdb=" O ILE D 48 " pdb=" OD1 ASP D 49 " model vdw 1.985 3.040 nonbonded pdb=" OD1 ASP E 41 " pdb="MG MG E 200 " model vdw 2.078 2.170 nonbonded pdb=" OD1 ASP E 45 " pdb="MG MG E 200 " model vdw 2.100 2.170 nonbonded pdb=" CB SER A 246 " pdb="MG MG A2003 " model vdw 2.129 2.570 nonbonded pdb=" O ASP B 618 " pdb=" OD1 ASP B 618 " model vdw 2.152 3.040 ... (remaining 179548 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 'B' and (resid 29 through 200 or resid 218 through 636 or resid 651 throu \ gh 949 or resid 2001 through 2003)) } ncs_group { reference = chain 'C' selection = chain 'F' } ncs_group { reference = (chain 'D' and (resid 15 through 171 or resid 200)) selection = chain 'E' } ncs_group { reference = (chain 'G' and resid 1413 through 1623) selection = chain 'H' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 13.030 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: 0.000 Extract box with map and model: 0.050 Check model and map are aligned: 0.200 Set scattering table: 0.300 Process input model: 66.450 Find NCS groups from input model: 2.030 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 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 : 0.003 0.062 23278 Z= 0.184 Angle : 0.682 10.266 31266 Z= 0.361 Chirality : 0.042 0.336 3400 Planarity : 0.004 0.052 4115 Dihedral : 15.412 179.189 9031 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 17.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 0.04 % Allowed : 0.28 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.34 (0.16), residues: 2798 helix: 1.04 (0.13), residues: 1601 sheet: -1.60 (0.41), residues: 148 loop : -2.05 (0.18), residues: 1049 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 840 HIS 0.006 0.001 HIS B 783 PHE 0.018 0.001 PHE A 493 TYR 0.029 0.001 TYR G1473 ARG 0.012 0.000 ARG H1477 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 250 time to evaluate : 3.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 MET cc_start: 0.8015 (mpp) cc_final: 0.7812 (mpp) REVERT: B 637 MET cc_start: 0.6967 (mtp) cc_final: 0.5942 (mmm) REVERT: C 16 GLN cc_start: 0.9014 (mp10) cc_final: 0.8714 (pp30) REVERT: C 73 MET cc_start: 0.8597 (mmp) cc_final: 0.8230 (mmp) REVERT: D 24 MET cc_start: 0.6846 (ppp) cc_final: 0.6189 (ppp) REVERT: E 141 MET cc_start: 0.8018 (mpp) cc_final: 0.7516 (tmm) REVERT: G 1462 MET cc_start: 0.9103 (mmp) cc_final: 0.8843 (mpp) REVERT: G 1578 MET cc_start: 0.9529 (mtm) cc_final: 0.9262 (tpp) REVERT: H 1462 MET cc_start: 0.9455 (mmp) cc_final: 0.9042 (mmm) REVERT: H 1514 MET cc_start: 0.8759 (mmm) cc_final: 0.8370 (tmm) outliers start: 1 outliers final: 0 residues processed: 251 average time/residue: 0.4329 time to fit residues: 158.7436 Evaluate side-chains 144 residues out of total 2479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 2.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 234 optimal weight: 3.9990 chunk 210 optimal weight: 5.9990 chunk 116 optimal weight: 6.9990 chunk 71 optimal weight: 0.0670 chunk 142 optimal weight: 5.9990 chunk 112 optimal weight: 7.9990 chunk 217 optimal weight: 10.0000 chunk 84 optimal weight: 5.9990 chunk 132 optimal weight: 6.9990 chunk 162 optimal weight: 1.9990 chunk 252 optimal weight: 5.9990 overall best weight: 3.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 228 ASN ** A 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 502 GLN ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 ASN ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 ASN ** G1432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1605 HIS ** H1607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.104 23278 Z= 0.387 Angle : 0.815 13.035 31266 Z= 0.430 Chirality : 0.045 0.197 3400 Planarity : 0.006 0.060 4115 Dihedral : 7.158 168.533 3051 Min Nonbonded Distance : 1.766 Molprobity Statistics. All-atom Clashscore : 27.84 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.54 % Favored : 91.42 % Rotamer: Outliers : 1.29 % Allowed : 11.46 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.81 (0.15), residues: 2798 helix: 0.59 (0.13), residues: 1591 sheet: -2.03 (0.41), residues: 132 loop : -2.06 (0.18), residues: 1075 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 597 HIS 0.010 0.002 HIS A 102 PHE 0.030 0.002 PHE B 287 TYR 0.042 0.003 TYR G1473 ARG 0.013 0.001 ARG B 168 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 2479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 136 time to evaluate : 2.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 MET cc_start: 0.8127 (tmm) cc_final: 0.7916 (ppp) REVERT: C 20 ARG cc_start: 0.8271 (mtm-85) cc_final: 0.7984 (mtm-85) REVERT: D 89 PHE cc_start: 0.8653 (OUTLIER) cc_final: 0.8269 (m-80) REVERT: E 141 MET cc_start: 0.8108 (mpp) cc_final: 0.7680 (tmm) REVERT: F 73 MET cc_start: 0.3011 (mmm) cc_final: 0.2769 (tpt) REVERT: G 1575 MET cc_start: 0.9293 (ppp) cc_final: 0.9052 (ppp) REVERT: H 1462 MET cc_start: 0.9447 (mmp) cc_final: 0.9074 (mmm) REVERT: H 1514 MET cc_start: 0.8732 (mmm) cc_final: 0.8300 (tmm) REVERT: H 1550 MET cc_start: 0.8655 (ppp) cc_final: 0.8279 (ppp) outliers start: 32 outliers final: 21 residues processed: 163 average time/residue: 0.3639 time to fit residues: 95.5326 Evaluate side-chains 149 residues out of total 2479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 127 time to evaluate : 2.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 428 GLU Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 542 ASP Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 388 CYS Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 495 HIS Chi-restraints excluded: chain B residue 510 ILE Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 95 PHE Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 133 ASP Chi-restraints excluded: chain D residue 89 PHE Chi-restraints excluded: chain F residue 48 MET Chi-restraints excluded: chain F residue 110 HIS Chi-restraints excluded: chain G residue 1605 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 140 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 210 optimal weight: 3.9990 chunk 171 optimal weight: 9.9990 chunk 69 optimal weight: 1.9990 chunk 252 optimal weight: 7.9990 chunk 273 optimal weight: 5.9990 chunk 225 optimal weight: 10.0000 chunk 250 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 202 optimal weight: 10.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 680 ASN ** A 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 817 GLN ** C 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 ASN ** G1447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1605 HIS ** H1607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.098 23278 Z= 0.361 Angle : 0.775 12.343 31266 Z= 0.408 Chirality : 0.044 0.170 3400 Planarity : 0.005 0.049 4115 Dihedral : 7.330 166.041 3051 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 29.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.40 % Favored : 90.60 % Rotamer: Outliers : 2.30 % Allowed : 17.64 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.16 (0.15), residues: 2798 helix: 0.39 (0.13), residues: 1586 sheet: -2.48 (0.37), residues: 140 loop : -2.32 (0.17), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 625 HIS 0.021 0.002 HIS G1605 PHE 0.022 0.002 PHE A 493 TYR 0.036 0.002 TYR G1473 ARG 0.014 0.001 ARG A 916 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 132 time to evaluate : 2.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 339 MET cc_start: 0.9264 (mmp) cc_final: 0.8926 (mmp) REVERT: B 756 MET cc_start: 0.8317 (mmt) cc_final: 0.8055 (mmt) REVERT: B 785 GLU cc_start: 0.8765 (OUTLIER) cc_final: 0.8463 (mp0) REVERT: C 48 MET cc_start: 0.8942 (ppp) cc_final: 0.8628 (ppp) REVERT: D 73 MET cc_start: 0.6715 (mmt) cc_final: 0.6194 (mtt) REVERT: E 141 MET cc_start: 0.8083 (mpp) cc_final: 0.7640 (tmm) REVERT: F 35 MET cc_start: 0.8789 (tpp) cc_final: 0.8395 (tpp) REVERT: F 61 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8874 (mm) REVERT: G 1488 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7440 (mt-10) REVERT: G 1578 MET cc_start: 0.9335 (ttm) cc_final: 0.8900 (tpp) REVERT: H 1462 MET cc_start: 0.9410 (mmp) cc_final: 0.9046 (mmm) REVERT: H 1514 MET cc_start: 0.8805 (mmm) cc_final: 0.8424 (tmm) outliers start: 57 outliers final: 32 residues processed: 182 average time/residue: 0.3225 time to fit residues: 97.0775 Evaluate side-chains 164 residues out of total 2479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 129 time to evaluate : 2.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 331 MET Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 542 ASP Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 388 CYS Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 495 HIS Chi-restraints excluded: chain B residue 510 ILE Chi-restraints excluded: chain B residue 513 ASN Chi-restraints excluded: chain B residue 676 ASN Chi-restraints excluded: chain B residue 730 PHE Chi-restraints excluded: chain B residue 785 GLU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 95 PHE Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain F residue 4 SER Chi-restraints excluded: chain F residue 48 MET Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 100 ASN Chi-restraints excluded: chain F residue 110 HIS Chi-restraints excluded: chain G residue 1488 GLU Chi-restraints excluded: chain G residue 1605 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 249 optimal weight: 0.6980 chunk 190 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 120 optimal weight: 0.7980 chunk 169 optimal weight: 7.9990 chunk 253 optimal weight: 1.9990 chunk 268 optimal weight: 20.0000 chunk 132 optimal weight: 2.9990 chunk 240 optimal weight: 0.5980 chunk 72 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 GLN ** B 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 708 ASN B 817 GLN C 41 ASN ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1432 GLN ** G1447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 23278 Z= 0.166 Angle : 0.652 11.019 31266 Z= 0.333 Chirality : 0.040 0.187 3400 Planarity : 0.004 0.060 4115 Dihedral : 6.830 158.488 3051 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 18.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 1.98 % Allowed : 19.01 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.60 (0.16), residues: 2798 helix: 0.88 (0.13), residues: 1644 sheet: -2.23 (0.40), residues: 150 loop : -2.30 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 36 HIS 0.010 0.001 HIS G1605 PHE 0.022 0.001 PHE G1459 TYR 0.027 0.002 TYR G1473 ARG 0.007 0.000 ARG A 916 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 137 time to evaluate : 2.895 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: B 391 MET cc_start: 0.7361 (tpp) cc_final: 0.7056 (tpt) REVERT: B 747 MET cc_start: 0.7600 (pmm) cc_final: 0.6952 (pmm) REVERT: B 756 MET cc_start: 0.8322 (mmt) cc_final: 0.8087 (mmt) REVERT: B 785 GLU cc_start: 0.8739 (OUTLIER) cc_final: 0.8452 (mp0) REVERT: C 48 MET cc_start: 0.8701 (ppp) cc_final: 0.8461 (ppp) REVERT: C 140 TYR cc_start: 0.8372 (OUTLIER) cc_final: 0.7905 (m-80) REVERT: D 60 MET cc_start: 0.7024 (mmp) cc_final: 0.6410 (pmm) REVERT: D 73 MET cc_start: 0.6942 (mmt) cc_final: 0.6468 (mtt) REVERT: D 89 PHE cc_start: 0.8609 (OUTLIER) cc_final: 0.8205 (m-80) REVERT: E 141 MET cc_start: 0.8072 (mpp) cc_final: 0.7669 (tmm) REVERT: F 61 LEU cc_start: 0.9264 (OUTLIER) cc_final: 0.8931 (mm) REVERT: G 1462 MET cc_start: 0.9179 (mmp) cc_final: 0.8668 (ppp) REVERT: G 1488 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7434 (mt-10) REVERT: G 1578 MET cc_start: 0.9352 (ttm) cc_final: 0.8923 (tpp) REVERT: H 1462 MET cc_start: 0.9358 (mmp) cc_final: 0.8973 (mmm) REVERT: H 1514 MET cc_start: 0.8860 (mmm) cc_final: 0.8527 (tmm) REVERT: H 1575 MET cc_start: 0.9275 (tpp) cc_final: 0.8966 (tpp) outliers start: 49 outliers final: 25 residues processed: 177 average time/residue: 0.3428 time to fit residues: 98.6063 Evaluate side-chains 160 residues out of total 2479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 130 time to evaluate : 2.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 HIS Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 428 GLU Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain B residue 89 MET Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 349 GLN Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain B residue 472 PHE Chi-restraints excluded: chain B residue 495 HIS Chi-restraints excluded: chain B residue 510 ILE Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 676 ASN Chi-restraints excluded: chain B residue 730 PHE Chi-restraints excluded: chain B residue 785 GLU Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 95 PHE Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 133 ASP Chi-restraints excluded: chain C residue 140 TYR Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 89 PHE Chi-restraints excluded: chain F residue 4 SER Chi-restraints excluded: chain F residue 48 MET Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 110 HIS Chi-restraints excluded: chain G residue 1488 GLU Chi-restraints excluded: chain G residue 1605 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 223 optimal weight: 1.9990 chunk 152 optimal weight: 1.9990 chunk 3 optimal weight: 0.0770 chunk 200 optimal weight: 2.9990 chunk 110 optimal weight: 0.9990 chunk 229 optimal weight: 5.9990 chunk 185 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 137 optimal weight: 4.9990 chunk 241 optimal weight: 2.9990 chunk 67 optimal weight: 6.9990 overall best weight: 1.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 ASN ** G1429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1605 HIS ** H1607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23278 Z= 0.205 Angle : 0.657 10.803 31266 Z= 0.336 Chirality : 0.041 0.370 3400 Planarity : 0.004 0.125 4115 Dihedral : 6.780 157.948 3051 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 21.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.54 % Favored : 91.46 % Rotamer: Outliers : 2.74 % Allowed : 20.26 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.16), residues: 2798 helix: 0.95 (0.13), residues: 1638 sheet: -2.27 (0.39), residues: 150 loop : -2.29 (0.19), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 625 HIS 0.006 0.001 HIS A 102 PHE 0.029 0.002 PHE F 66 TYR 0.021 0.001 TYR G1473 ARG 0.008 0.000 ARG H1597 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 129 time to evaluate : 2.818 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 135 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7684 (mt-10) REVERT: B 747 MET cc_start: 0.7704 (pmm) cc_final: 0.6962 (pmm) REVERT: C 48 MET cc_start: 0.8744 (ppp) cc_final: 0.8515 (ppp) REVERT: C 140 TYR cc_start: 0.8397 (OUTLIER) cc_final: 0.8178 (m-80) REVERT: D 24 MET cc_start: 0.7327 (ppp) cc_final: 0.6925 (ppp) REVERT: D 73 MET cc_start: 0.7001 (mmt) cc_final: 0.6558 (mtt) REVERT: D 89 PHE cc_start: 0.8672 (OUTLIER) cc_final: 0.8211 (m-80) REVERT: E 141 MET cc_start: 0.8106 (mpp) cc_final: 0.7625 (tmm) REVERT: F 7 GLN cc_start: 0.5496 (mp10) cc_final: 0.5288 (mp10) REVERT: F 61 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.8974 (mm) REVERT: G 1488 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7495 (mt-10) REVERT: G 1578 MET cc_start: 0.9426 (OUTLIER) cc_final: 0.8967 (tpp) REVERT: H 1462 MET cc_start: 0.9335 (mmp) cc_final: 0.8960 (mmm) REVERT: H 1514 MET cc_start: 0.8979 (mmm) cc_final: 0.8672 (tmm) outliers start: 68 outliers final: 42 residues processed: 187 average time/residue: 0.3074 time to fit residues: 95.0438 Evaluate side-chains 173 residues out of total 2479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 125 time to evaluate : 2.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 102 HIS Chi-restraints excluded: chain A residue 120 PHE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 135 GLU Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 428 GLU Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 581 PHE Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 89 MET Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 349 GLN Chi-restraints excluded: chain B residue 388 CYS Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 472 PHE Chi-restraints excluded: chain B residue 495 HIS Chi-restraints excluded: chain B residue 510 ILE Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 676 ASN Chi-restraints excluded: chain B residue 730 PHE Chi-restraints excluded: chain B residue 785 GLU Chi-restraints excluded: chain B residue 793 THR Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 95 PHE Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 133 ASP Chi-restraints excluded: chain C residue 140 TYR Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 89 PHE Chi-restraints excluded: chain F residue 4 SER Chi-restraints excluded: chain F residue 48 MET Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 100 ASN Chi-restraints excluded: chain F residue 110 HIS Chi-restraints excluded: chain G residue 1488 GLU Chi-restraints excluded: chain G residue 1578 MET Chi-restraints excluded: chain G residue 1605 HIS Chi-restraints excluded: chain G residue 1620 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 90 optimal weight: 2.9990 chunk 241 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 157 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 268 optimal weight: 3.9990 chunk 223 optimal weight: 0.7980 chunk 124 optimal weight: 8.9990 chunk 22 optimal weight: 0.9990 chunk 88 optimal weight: 4.9990 chunk 141 optimal weight: 10.0000 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 491 GLN ** A 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 GLN ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 ASN ** G1429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1605 HIS H1607 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23278 Z= 0.198 Angle : 0.655 10.954 31266 Z= 0.334 Chirality : 0.040 0.277 3400 Planarity : 0.004 0.058 4115 Dihedral : 6.724 155.681 3051 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 21.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 3.11 % Allowed : 21.07 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.16), residues: 2798 helix: 0.99 (0.13), residues: 1631 sheet: -2.26 (0.39), residues: 149 loop : -2.21 (0.19), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 625 HIS 0.006 0.001 HIS B 152 PHE 0.024 0.001 PHE F 66 TYR 0.019 0.001 TYR G1473 ARG 0.005 0.000 ARG B 168 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 131 time to evaluate : 2.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 822 MET cc_start: 0.7473 (tpt) cc_final: 0.7220 (tpt) REVERT: A 933 MET cc_start: 0.9477 (ppp) cc_final: 0.8829 (mmm) REVERT: B 391 MET cc_start: 0.7371 (tpp) cc_final: 0.7139 (tpp) REVERT: B 747 MET cc_start: 0.7679 (pmm) cc_final: 0.6937 (pmm) REVERT: C 48 MET cc_start: 0.8740 (ppp) cc_final: 0.8496 (ppp) REVERT: D 24 MET cc_start: 0.7386 (ppp) cc_final: 0.6960 (ppp) REVERT: D 60 MET cc_start: 0.7722 (mmp) cc_final: 0.7207 (pmm) REVERT: D 73 MET cc_start: 0.7029 (mmt) cc_final: 0.6591 (mtt) REVERT: D 89 PHE cc_start: 0.8642 (OUTLIER) cc_final: 0.8091 (m-80) REVERT: E 141 MET cc_start: 0.8166 (mpp) cc_final: 0.7606 (tmm) REVERT: F 35 MET cc_start: 0.8676 (tpp) cc_final: 0.8290 (tpp) REVERT: F 61 LEU cc_start: 0.9321 (OUTLIER) cc_final: 0.8980 (mm) REVERT: G 1462 MET cc_start: 0.9163 (mmp) cc_final: 0.8533 (ppp) REVERT: G 1488 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7521 (mt-10) REVERT: G 1578 MET cc_start: 0.9448 (ttm) cc_final: 0.8963 (tpp) REVERT: H 1462 MET cc_start: 0.9313 (mmp) cc_final: 0.8917 (mmm) REVERT: H 1514 MET cc_start: 0.8978 (mmm) cc_final: 0.8692 (tmm) outliers start: 77 outliers final: 55 residues processed: 198 average time/residue: 0.3170 time to fit residues: 103.6748 Evaluate side-chains 184 residues out of total 2479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 126 time to evaluate : 2.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 102 HIS Chi-restraints excluded: chain A residue 120 PHE Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 331 MET Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 428 GLU Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 581 PHE Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 868 GLN Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 89 MET Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 141 TYR Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 349 GLN Chi-restraints excluded: chain B residue 388 CYS Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 472 PHE Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 495 HIS Chi-restraints excluded: chain B residue 510 ILE Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 676 ASN Chi-restraints excluded: chain B residue 702 LEU Chi-restraints excluded: chain B residue 730 PHE Chi-restraints excluded: chain B residue 785 GLU Chi-restraints excluded: chain B residue 793 THR Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 95 PHE Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 133 ASP Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 89 PHE Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain F residue 4 SER Chi-restraints excluded: chain F residue 48 MET Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 100 ASN Chi-restraints excluded: chain F residue 110 HIS Chi-restraints excluded: chain G residue 1488 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 259 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 196 optimal weight: 0.7980 chunk 152 optimal weight: 0.0010 chunk 226 optimal weight: 0.0770 chunk 150 optimal weight: 0.8980 chunk 267 optimal weight: 5.9990 chunk 167 optimal weight: 0.5980 chunk 163 optimal weight: 0.9990 chunk 123 optimal weight: 0.1980 overall best weight: 0.3344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 375 GLN ** A 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 800 GLN ** B 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 ASN ** G1429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 23278 Z= 0.151 Angle : 0.640 10.940 31266 Z= 0.321 Chirality : 0.040 0.174 3400 Planarity : 0.004 0.061 4115 Dihedral : 6.465 149.510 3051 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 16.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 2.22 % Allowed : 21.99 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.28 (0.16), residues: 2798 helix: 1.13 (0.13), residues: 1631 sheet: -2.12 (0.39), residues: 152 loop : -2.11 (0.19), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 36 HIS 0.005 0.001 HIS B 152 PHE 0.018 0.001 PHE F 66 TYR 0.019 0.001 TYR C 140 ARG 0.004 0.000 ARG H1496 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 2479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 133 time to evaluate : 2.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 ILE cc_start: 0.9037 (OUTLIER) cc_final: 0.8829 (mm) REVERT: A 339 MET cc_start: 0.9190 (mmp) cc_final: 0.8941 (mmp) REVERT: A 655 MET cc_start: 0.8707 (ppp) cc_final: 0.8506 (ppp) REVERT: B 655 MET cc_start: 0.6638 (ttt) cc_final: 0.6197 (ptt) REVERT: B 747 MET cc_start: 0.7446 (pmm) cc_final: 0.6836 (pmm) REVERT: C 48 MET cc_start: 0.8744 (ppp) cc_final: 0.8538 (ppp) REVERT: D 24 MET cc_start: 0.7103 (ppp) cc_final: 0.6677 (ppp) REVERT: D 60 MET cc_start: 0.7468 (mmp) cc_final: 0.6877 (ptp) REVERT: D 73 MET cc_start: 0.7011 (mmt) cc_final: 0.6596 (mtt) REVERT: D 89 PHE cc_start: 0.8518 (OUTLIER) cc_final: 0.7938 (m-80) REVERT: E 141 MET cc_start: 0.8143 (mpp) cc_final: 0.7616 (tmm) REVERT: G 1462 MET cc_start: 0.9193 (mmp) cc_final: 0.8599 (ppp) REVERT: G 1488 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7567 (mt-10) REVERT: G 1578 MET cc_start: 0.9451 (ttm) cc_final: 0.8999 (tpp) REVERT: H 1462 MET cc_start: 0.9292 (mmp) cc_final: 0.8900 (mmm) REVERT: H 1514 MET cc_start: 0.8977 (mmm) cc_final: 0.8680 (tmm) outliers start: 55 outliers final: 36 residues processed: 183 average time/residue: 0.3166 time to fit residues: 95.2355 Evaluate side-chains 168 residues out of total 2479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 129 time to evaluate : 2.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 HIS Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 428 GLU Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 868 GLN Chi-restraints excluded: chain B residue 89 MET Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 349 GLN Chi-restraints excluded: chain B residue 388 CYS Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain B residue 472 PHE Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 510 ILE Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 702 LEU Chi-restraints excluded: chain B residue 730 PHE Chi-restraints excluded: chain B residue 785 GLU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 89 PHE Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain F residue 4 SER Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 100 ASN Chi-restraints excluded: chain F residue 110 HIS Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain G residue 1477 ARG Chi-restraints excluded: chain G residue 1488 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 165 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 160 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 52 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 170 optimal weight: 10.0000 chunk 182 optimal weight: 4.9990 chunk 132 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 210 optimal weight: 5.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 23278 Z= 0.171 Angle : 0.641 10.688 31266 Z= 0.322 Chirality : 0.040 0.348 3400 Planarity : 0.004 0.058 4115 Dihedral : 6.427 147.298 3051 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 18.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 2.46 % Allowed : 22.20 % Favored : 75.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.28 (0.16), residues: 2798 helix: 1.13 (0.13), residues: 1636 sheet: -2.09 (0.40), residues: 152 loop : -2.13 (0.19), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 625 HIS 0.005 0.001 HIS B 152 PHE 0.015 0.001 PHE C 95 TYR 0.015 0.001 TYR B 832 ARG 0.003 0.000 ARG B 630 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 128 time to evaluate : 2.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.5809 (OUTLIER) cc_final: 0.4778 (mpt) REVERT: A 655 MET cc_start: 0.8717 (ppp) cc_final: 0.8506 (ppp) REVERT: A 915 MET cc_start: 0.9188 (ppp) cc_final: 0.8352 (ttt) REVERT: A 933 MET cc_start: 0.9451 (ppp) cc_final: 0.8763 (mmm) REVERT: B 655 MET cc_start: 0.6631 (ttt) cc_final: 0.6211 (ptt) REVERT: B 747 MET cc_start: 0.7539 (pmm) cc_final: 0.6858 (pmm) REVERT: B 933 MET cc_start: 0.7334 (mmm) cc_final: 0.7110 (mmm) REVERT: C 48 MET cc_start: 0.8739 (ppp) cc_final: 0.8532 (ppp) REVERT: D 24 MET cc_start: 0.7280 (ppp) cc_final: 0.6766 (ppp) REVERT: D 60 MET cc_start: 0.7482 (mmp) cc_final: 0.6858 (ptp) REVERT: D 73 MET cc_start: 0.7049 (mmt) cc_final: 0.6649 (mtt) REVERT: D 89 PHE cc_start: 0.8480 (OUTLIER) cc_final: 0.7958 (m-80) REVERT: E 141 MET cc_start: 0.8260 (mpp) cc_final: 0.7631 (tmm) REVERT: F 61 LEU cc_start: 0.9354 (pt) cc_final: 0.9087 (mm) REVERT: G 1462 MET cc_start: 0.9178 (mmp) cc_final: 0.8571 (ppp) REVERT: G 1488 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7557 (mt-10) REVERT: G 1578 MET cc_start: 0.9474 (ttm) cc_final: 0.9003 (tpp) REVERT: H 1462 MET cc_start: 0.9298 (mmp) cc_final: 0.8898 (mmm) REVERT: H 1514 MET cc_start: 0.8991 (mmm) cc_final: 0.8693 (tmm) outliers start: 61 outliers final: 48 residues processed: 181 average time/residue: 0.3120 time to fit residues: 93.3146 Evaluate side-chains 177 residues out of total 2479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 126 time to evaluate : 2.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 102 HIS Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 428 GLU Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 868 GLN Chi-restraints excluded: chain B residue 89 MET Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 141 TYR Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 349 GLN Chi-restraints excluded: chain B residue 388 CYS Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 472 PHE Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 510 ILE Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 702 LEU Chi-restraints excluded: chain B residue 730 PHE Chi-restraints excluded: chain B residue 785 GLU Chi-restraints excluded: chain B residue 793 THR Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 95 PHE Chi-restraints excluded: chain C residue 133 ASP Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 89 PHE Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain F residue 4 SER Chi-restraints excluded: chain F residue 48 MET Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 110 HIS Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain G residue 1477 ARG Chi-restraints excluded: chain G residue 1488 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 62.3622 > 50: distance: 28 - 33: 9.389 distance: 33 - 34: 14.138 distance: 34 - 35: 22.118 distance: 34 - 37: 18.480 distance: 35 - 36: 10.449 distance: 35 - 42: 31.329 distance: 36 - 67: 14.484 distance: 37 - 38: 16.254 distance: 38 - 39: 15.060 distance: 39 - 40: 23.744 distance: 39 - 41: 18.681 distance: 42 - 43: 22.296 distance: 43 - 44: 19.185 distance: 43 - 46: 18.602 distance: 44 - 45: 25.178 distance: 44 - 51: 15.455 distance: 45 - 76: 17.740 distance: 46 - 47: 6.459 distance: 47 - 48: 16.703 distance: 48 - 49: 14.435 distance: 48 - 50: 9.726 distance: 51 - 52: 4.609 distance: 52 - 53: 4.376 distance: 52 - 55: 4.454 distance: 53 - 54: 17.919 distance: 53 - 60: 15.234 distance: 54 - 85: 38.564 distance: 55 - 56: 21.358 distance: 56 - 57: 14.691 distance: 57 - 58: 13.520 distance: 57 - 59: 4.309 distance: 60 - 61: 27.412 distance: 61 - 62: 20.319 distance: 61 - 64: 7.381 distance: 62 - 63: 26.245 distance: 62 - 67: 29.799 distance: 64 - 65: 28.951 distance: 64 - 66: 12.759 distance: 67 - 68: 23.064 distance: 68 - 69: 7.655 distance: 68 - 71: 15.452 distance: 69 - 70: 11.887 distance: 69 - 76: 17.038 distance: 71 - 72: 14.453 distance: 72 - 73: 6.039 distance: 73 - 74: 7.133 distance: 73 - 75: 9.507 distance: 76 - 77: 21.235 distance: 77 - 78: 20.002 distance: 77 - 80: 28.532 distance: 78 - 79: 20.878 distance: 78 - 85: 9.496 distance: 80 - 81: 15.298 distance: 81 - 82: 12.549 distance: 82 - 83: 12.264 distance: 82 - 84: 14.956 distance: 85 - 86: 13.288 distance: 86 - 87: 13.887 distance: 86 - 89: 20.565 distance: 87 - 88: 21.666 distance: 87 - 93: 28.710 distance: 89 - 90: 7.606 distance: 90 - 91: 7.248 distance: 90 - 92: 37.765 distance: 93 - 94: 25.212 distance: 94 - 95: 25.476 distance: 94 - 97: 50.760 distance: 95 - 96: 12.496 distance: 95 - 100: 12.717 distance: 97 - 98: 11.314 distance: 97 - 99: 7.908 distance: 100 - 101: 22.287 distance: 101 - 102: 24.540 distance: 101 - 104: 55.997 distance: 102 - 103: 20.656 distance: 102 - 105: 13.658 distance: 105 - 106: 45.012 distance: 106 - 107: 16.792 distance: 107 - 108: 3.820 distance: 107 - 109: 32.422