Starting phenix.real_space_refine on Sun Sep 29 18:11:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mf3_23810/09_2024/7mf3_23810.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mf3_23810/09_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_23810/09_2024/7mf3_23810.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mf3_23810/09_2024/7mf3_23810.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mf3_23810/09_2024/7mf3_23810.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mf3_23810/09_2024/7mf3_23810.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. Time to flip 2 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 18.21, per 1000 atoms: 0.79 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 - 3.00 Amino acid : True - 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: 7.15 Conformation dependent library (CDL) restraints added in 3.1 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: 2.21 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: 7.74 Time building geometry restraints manager: 7.95 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: 0.00 - 2.05: 30600 2.05 - 4.11: 537 4.11 - 6.16: 104 6.16 - 8.21: 20 8.21 - 10.27: 5 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 Time spend for trying shortcut: 0.00 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: 11.740 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.940 Check model and map are aligned: 0.160 Set scattering table: 0.220 Process input model: 56.120 Find NCS groups from input model: 0.980 Set up NCS constraints: 0.110 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:3.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.530 ------------------------------------------------------------------------------- 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 : 2.769 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: 0.4279 time to fit residues: 157.2528 Evaluate side-chains 144 residues out of total 2479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 2.807 ------------------------------------------------------------------------------- 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: 3.9990 chunk 116 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 chunk 142 optimal weight: 3.9990 chunk 112 optimal weight: 6.9990 chunk 217 optimal weight: 9.9990 chunk 84 optimal weight: 5.9990 chunk 132 optimal weight: 4.9990 chunk 162 optimal weight: 0.9990 chunk 252 optimal weight: 7.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- 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** ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 502 GLN B 636 GLN D 27 GLN ** E 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 ASN G1447 GLN G1605 HIS H1607 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 23278 Z= 0.308 Angle : 0.750 11.006 31266 Z= 0.392 Chirality : 0.044 0.189 3400 Planarity : 0.005 0.068 4115 Dihedral : 6.731 144.030 3051 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 19.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 1.09 % Allowed : 9.93 % Favored : 88.98 % 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: -0.67 (0.16), residues: 2798 helix: 0.70 (0.13), residues: 1602 sheet: -2.02 (0.40), residues: 145 loop : -2.01 (0.18), residues: 1051 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 840 HIS 0.008 0.002 HIS A 102 PHE 0.023 0.002 PHE A 493 TYR 0.041 0.002 TYR G1473 ARG 0.010 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 166 residues out of total 2479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 139 time to evaluate : 2.787 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: B 391 MET cc_start: 0.7149 (tpp) cc_final: 0.6938 (tpt) REVERT: B 655 MET cc_start: 0.6993 (ttt) cc_final: 0.6319 (ptt) REVERT: B 747 MET cc_start: 0.7641 (pmm) cc_final: 0.7053 (pmm) REVERT: D 73 MET cc_start: 0.6929 (mmt) cc_final: 0.6241 (ptp) REVERT: D 89 PHE cc_start: 0.8662 (OUTLIER) cc_final: 0.8323 (m-80) REVERT: E 141 MET cc_start: 0.8120 (mpp) cc_final: 0.7651 (tmm) REVERT: F 59 MET cc_start: 0.7342 (mmp) cc_final: 0.7124 (mmp) REVERT: F 61 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8761 (mm) REVERT: F 73 MET cc_start: 0.2913 (mmm) cc_final: 0.2660 (tpt) REVERT: G 1578 MET cc_start: 0.9567 (mtm) cc_final: 0.9360 (ttm) REVERT: H 1462 MET cc_start: 0.9441 (mmp) cc_final: 0.9004 (mmm) REVERT: H 1514 MET cc_start: 0.8750 (mmm) cc_final: 0.8330 (tmm) REVERT: H 1550 MET cc_start: 0.8676 (ppp) cc_final: 0.8024 (ppp) outliers start: 27 outliers final: 14 residues processed: 161 average time/residue: 0.3546 time to fit residues: 91.1848 Evaluate side-chains 143 residues out of total 2479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 127 time to evaluate : 2.807 ------------------------------------------------------------------------------- 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 537 VAL 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 495 HIS Chi-restraints excluded: chain B residue 510 ILE Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 95 PHE Chi-restraints excluded: chain D residue 89 PHE Chi-restraints excluded: chain F residue 48 MET Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 125 GLU 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: 0.9980 chunk 78 optimal weight: 0.8980 chunk 210 optimal weight: 0.0370 chunk 171 optimal weight: 9.9990 chunk 69 optimal weight: 2.9990 chunk 252 optimal weight: 9.9990 chunk 273 optimal weight: 3.9990 chunk 225 optimal weight: 6.9990 chunk 250 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 202 optimal weight: 5.9990 overall best weight: 1.5862 ------------------------------------------------------------------------------- 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 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 661 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 23278 Z= 0.208 Angle : 0.676 13.165 31266 Z= 0.347 Chirality : 0.041 0.149 3400 Planarity : 0.004 0.055 4115 Dihedral : 6.566 135.360 3051 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 1.21 % Allowed : 13.68 % Favored : 85.11 % 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: -0.59 (0.16), residues: 2798 helix: 0.81 (0.13), residues: 1595 sheet: -2.03 (0.39), residues: 152 loop : -2.03 (0.18), residues: 1051 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 625 HIS 0.005 0.001 HIS A 102 PHE 0.021 0.002 PHE G1459 TYR 0.034 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 167 residues out of total 2479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 137 time to evaluate : 2.728 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: A 339 MET cc_start: 0.9196 (mmp) cc_final: 0.8870 (mmp) REVERT: A 497 MET cc_start: 0.8066 (mmm) cc_final: 0.7855 (mtp) REVERT: B 747 MET cc_start: 0.7581 (pmm) cc_final: 0.6942 (pmm) REVERT: D 89 PHE cc_start: 0.8668 (OUTLIER) cc_final: 0.8286 (m-80) REVERT: D 129 MET cc_start: 0.8057 (tpt) cc_final: 0.7063 (tpp) REVERT: E 141 MET cc_start: 0.8146 (mpp) cc_final: 0.7591 (tmm) REVERT: F 35 MET cc_start: 0.8794 (tpp) cc_final: 0.8448 (tpp) REVERT: F 61 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8683 (mm) REVERT: G 1488 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7515 (mt-10) REVERT: H 1462 MET cc_start: 0.9395 (mmp) cc_final: 0.9029 (mmm) REVERT: H 1514 MET cc_start: 0.8757 (mmm) cc_final: 0.8350 (tmm) REVERT: H 1550 MET cc_start: 0.8723 (ppp) cc_final: 0.8126 (ppp) outliers start: 30 outliers final: 18 residues processed: 159 average time/residue: 0.3238 time to fit residues: 85.0468 Evaluate side-chains 153 residues out of total 2479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 132 time to evaluate : 2.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 349 GLN 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 60 ASN Chi-restraints excluded: chain C residue 95 PHE Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 89 PHE 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 F residue 125 GLU 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: 1.9990 chunk 190 optimal weight: 0.9990 chunk 131 optimal weight: 0.0670 chunk 27 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 chunk 169 optimal weight: 5.9990 chunk 253 optimal weight: 10.0000 chunk 268 optimal weight: 8.9990 chunk 132 optimal weight: 3.9990 chunk 240 optimal weight: 5.9990 chunk 72 optimal weight: 0.5980 overall best weight: 1.5324 ------------------------------------------------------------------------------- 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 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 888 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1432 GLN G1605 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23278 Z= 0.203 Angle : 0.657 10.248 31266 Z= 0.337 Chirality : 0.041 0.222 3400 Planarity : 0.004 0.056 4115 Dihedral : 6.489 129.627 3051 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 15.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.76 % Favored : 92.24 % Rotamer: Outliers : 1.74 % Allowed : 15.74 % Favored : 82.53 % 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: -0.45 (0.16), residues: 2798 helix: 0.96 (0.13), residues: 1636 sheet: -1.98 (0.40), residues: 150 loop : -2.16 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 625 HIS 0.008 0.001 HIS B 147 PHE 0.016 0.001 PHE C 69 TYR 0.026 0.002 TYR G1473 ARG 0.005 0.000 ARG B 168 *********************** 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 183 residues out of total 2479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 140 time to evaluate : 2.894 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: symmetry clash REVERT: B 391 MET cc_start: 0.6523 (tpt) cc_final: 0.6314 (tpp) REVERT: B 655 MET cc_start: 0.6777 (ttt) cc_final: 0.6247 (ptt) REVERT: B 747 MET cc_start: 0.7605 (pmm) cc_final: 0.6934 (pmm) REVERT: D 60 MET cc_start: 0.7605 (mmp) cc_final: 0.6353 (pmm) REVERT: D 73 MET cc_start: 0.7048 (mmt) cc_final: 0.6464 (mtt) REVERT: D 89 PHE cc_start: 0.8649 (OUTLIER) cc_final: 0.8123 (m-80) REVERT: E 141 MET cc_start: 0.8099 (mpp) cc_final: 0.7562 (tmm) REVERT: F 61 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8667 (mm) REVERT: G 1488 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7508 (mt-10) REVERT: G 1578 MET cc_start: 0.9303 (ttm) cc_final: 0.8833 (tpp) REVERT: H 1462 MET cc_start: 0.9367 (mmp) cc_final: 0.9001 (mmm) REVERT: H 1514 MET cc_start: 0.8779 (mmm) cc_final: 0.8386 (tmm) REVERT: H 1550 MET cc_start: 0.8760 (ppp) cc_final: 0.8280 (ppp) outliers start: 43 outliers final: 26 residues processed: 171 average time/residue: 0.3422 time to fit residues: 95.3933 Evaluate side-chains 161 residues out of total 2479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 132 time to evaluate : 2.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 137 ILE 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 553 THR Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 101 LEU 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 495 HIS Chi-restraints excluded: chain B residue 510 ILE Chi-restraints excluded: chain B residue 730 PHE Chi-restraints excluded: chain C residue 47 VAL 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 32 GLU Chi-restraints excluded: chain D residue 89 PHE 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 1565 GLU Chi-restraints excluded: chain G residue 1605 HIS Chi-restraints excluded: chain H residue 1597 ARG 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: 0.5980 chunk 3 optimal weight: 0.9980 chunk 200 optimal weight: 0.9990 chunk 110 optimal weight: 0.7980 chunk 229 optimal weight: 7.9990 chunk 185 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 137 optimal weight: 5.9990 chunk 241 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 491 GLN ** A 888 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 636 GLN ** B 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 74 GLN F 100 ASN ** G1429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 23278 Z= 0.160 Angle : 0.637 10.198 31266 Z= 0.325 Chirality : 0.040 0.198 3400 Planarity : 0.004 0.057 4115 Dihedral : 6.321 123.234 3051 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 1.90 % Allowed : 17.19 % Favored : 80.91 % 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: -0.32 (0.16), residues: 2798 helix: 1.05 (0.13), residues: 1634 sheet: -1.78 (0.41), residues: 148 loop : -2.11 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 625 HIS 0.010 0.001 HIS B 147 PHE 0.015 0.001 PHE C 69 TYR 0.022 0.001 TYR G1473 ARG 0.004 0.000 ARG A 916 *********************** 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 185 residues out of total 2479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 138 time to evaluate : 2.709 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 766 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8147 (mm) REVERT: B 342 MET cc_start: 0.8283 (mmt) cc_final: 0.7832 (mmt) REVERT: B 391 MET cc_start: 0.6519 (tpt) cc_final: 0.6259 (tpp) REVERT: B 747 MET cc_start: 0.7488 (pmm) cc_final: 0.6868 (pmm) REVERT: C 48 MET cc_start: 0.8835 (ppp) cc_final: 0.8553 (ppp) REVERT: D 60 MET cc_start: 0.7464 (mmp) cc_final: 0.6202 (pmm) REVERT: D 73 MET cc_start: 0.7022 (mmt) cc_final: 0.6448 (mtt) REVERT: D 89 PHE cc_start: 0.8540 (OUTLIER) cc_final: 0.8034 (m-80) REVERT: E 73 MET cc_start: 0.8031 (mpp) cc_final: 0.7713 (ptp) REVERT: E 141 MET cc_start: 0.8097 (mpp) cc_final: 0.7512 (tmm) REVERT: F 61 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8586 (mm) REVERT: G 1462 MET cc_start: 0.9173 (mmp) cc_final: 0.8660 (ppp) REVERT: G 1488 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7566 (mt-10) REVERT: G 1578 MET cc_start: 0.9324 (ttm) cc_final: 0.8862 (tpp) REVERT: H 1462 MET cc_start: 0.9353 (mmp) cc_final: 0.8951 (mmm) REVERT: H 1514 MET cc_start: 0.8805 (mmm) cc_final: 0.8432 (tmm) REVERT: H 1550 MET cc_start: 0.8735 (ppp) cc_final: 0.8306 (ppp) outliers start: 47 outliers final: 25 residues processed: 180 average time/residue: 0.3520 time to fit residues: 102.8120 Evaluate side-chains 162 residues out of total 2479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 133 time to evaluate : 3.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 VAL 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 624 LEU Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 868 GLN Chi-restraints excluded: chain B residue 349 GLN 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 495 HIS Chi-restraints excluded: chain B residue 510 ILE Chi-restraints excluded: chain B residue 730 PHE Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 95 PHE Chi-restraints excluded: chain D residue 89 PHE Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 74 GLN 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 126 GLN Chi-restraints excluded: chain G residue 1488 GLU Chi-restraints excluded: chain G residue 1565 GLU Chi-restraints excluded: chain G residue 1605 HIS Chi-restraints excluded: chain H residue 1597 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 90 optimal weight: 0.9990 chunk 241 optimal weight: 0.7980 chunk 53 optimal weight: 5.9990 chunk 157 optimal weight: 0.3980 chunk 66 optimal weight: 0.6980 chunk 268 optimal weight: 9.9990 chunk 223 optimal weight: 0.9990 chunk 124 optimal weight: 0.0270 chunk 22 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 141 optimal weight: 4.9990 overall best weight: 0.5840 ------------------------------------------------------------------------------- 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 888 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 HIS ** 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** G1605 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 23278 Z= 0.160 Angle : 0.646 10.774 31266 Z= 0.324 Chirality : 0.040 0.292 3400 Planarity : 0.004 0.057 4115 Dihedral : 6.194 117.147 3051 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 1.98 % Allowed : 17.96 % 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: -0.27 (0.16), residues: 2798 helix: 1.09 (0.13), residues: 1635 sheet: -1.70 (0.41), residues: 148 loop : -2.10 (0.19), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 36 HIS 0.009 0.001 HIS B 147 PHE 0.033 0.001 PHE F 66 TYR 0.020 0.001 TYR G1473 ARG 0.003 0.000 ARG A 247 *********************** 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 185 residues out of total 2479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 136 time to evaluate : 2.838 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: 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: 0.9068 (OUTLIER) cc_final: 0.8864 (mm) REVERT: A 766 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.8136 (mm) REVERT: A 933 MET cc_start: 0.9344 (ppp) cc_final: 0.8784 (mmp) REVERT: B 342 MET cc_start: 0.8287 (mmt) cc_final: 0.7867 (mmt) REVERT: B 391 MET cc_start: 0.6577 (tpt) cc_final: 0.6307 (tpp) REVERT: C 48 MET cc_start: 0.8804 (ppp) cc_final: 0.8581 (ppp) REVERT: D 24 MET cc_start: 0.6863 (ppp) cc_final: 0.6521 (ppp) REVERT: D 60 MET cc_start: 0.7453 (mmp) cc_final: 0.6158 (pmm) REVERT: D 73 MET cc_start: 0.6980 (mmt) cc_final: 0.6450 (mtt) REVERT: D 89 PHE cc_start: 0.8441 (OUTLIER) cc_final: 0.7922 (m-80) REVERT: E 141 MET cc_start: 0.8070 (mpp) cc_final: 0.7462 (tmm) REVERT: F 61 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8585 (mm) REVERT: G 1488 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7580 (mt-10) REVERT: G 1557 LEU cc_start: 0.9365 (mt) cc_final: 0.9009 (pp) REVERT: G 1578 MET cc_start: 0.9346 (ttm) cc_final: 0.8923 (tpp) REVERT: H 1462 MET cc_start: 0.9339 (mmp) cc_final: 0.8942 (mmm) REVERT: H 1514 MET cc_start: 0.8835 (mmm) cc_final: 0.8474 (tmm) REVERT: H 1523 VAL cc_start: 0.6891 (OUTLIER) cc_final: 0.6673 (t) REVERT: H 1550 MET cc_start: 0.8748 (ppp) cc_final: 0.8339 (ppp) outliers start: 49 outliers final: 35 residues processed: 178 average time/residue: 0.3420 time to fit residues: 100.7577 Evaluate side-chains 174 residues out of total 2479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 133 time to evaluate : 2.756 ------------------------------------------------------------------------------- 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 137 ILE 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 553 THR Chi-restraints excluded: chain A residue 585 HIS Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 766 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 349 GLN 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 495 HIS Chi-restraints excluded: chain B residue 510 ILE Chi-restraints excluded: chain B residue 730 PHE Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 95 PHE Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 89 PHE Chi-restraints excluded: chain F residue 48 MET Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 74 GLN 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 126 GLN Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain G residue 1488 GLU Chi-restraints excluded: chain G residue 1565 GLU Chi-restraints excluded: chain G residue 1605 HIS Chi-restraints excluded: chain G residue 1612 GLU Chi-restraints excluded: chain H residue 1523 VAL Chi-restraints excluded: chain H residue 1597 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 259 optimal weight: 8.9990 chunk 30 optimal weight: 5.9990 chunk 153 optimal weight: 0.8980 chunk 196 optimal weight: 8.9990 chunk 152 optimal weight: 0.9980 chunk 226 optimal weight: 0.3980 chunk 150 optimal weight: 2.9990 chunk 267 optimal weight: 0.9990 chunk 167 optimal weight: 5.9990 chunk 163 optimal weight: 3.9990 chunk 123 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 888 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23278 Z= 0.171 Angle : 0.642 10.334 31266 Z= 0.324 Chirality : 0.040 0.182 3400 Planarity : 0.004 0.055 4115 Dihedral : 6.166 113.064 3051 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 2.10 % Allowed : 18.89 % 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: -0.26 (0.16), residues: 2798 helix: 1.11 (0.13), residues: 1635 sheet: -1.80 (0.40), residues: 150 loop : -2.10 (0.19), residues: 1013 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 625 HIS 0.009 0.001 HIS B 147 PHE 0.026 0.001 PHE F 66 TYR 0.018 0.001 TYR G1473 ARG 0.003 0.000 ARG B 168 *********************** 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 189 residues out of total 2479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 137 time to evaluate : 2.571 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 766 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8197 (mm) REVERT: A 933 MET cc_start: 0.9367 (ppp) cc_final: 0.8867 (mmt) REVERT: B 342 MET cc_start: 0.8275 (mmt) cc_final: 0.7879 (mmt) REVERT: B 391 MET cc_start: 0.6671 (tpt) cc_final: 0.6382 (tpp) REVERT: B 655 MET cc_start: 0.6461 (ttt) cc_final: 0.6089 (ptt) REVERT: D 24 MET cc_start: 0.6996 (ppp) cc_final: 0.6546 (ppp) REVERT: D 60 MET cc_start: 0.7474 (mmp) cc_final: 0.6134 (pmm) REVERT: D 73 MET cc_start: 0.7042 (mmt) cc_final: 0.6522 (mtt) REVERT: D 89 PHE cc_start: 0.8467 (OUTLIER) cc_final: 0.7952 (m-80) REVERT: E 141 MET cc_start: 0.8060 (mpp) cc_final: 0.7498 (tmm) REVERT: F 40 GLN cc_start: 0.8444 (OUTLIER) cc_final: 0.8235 (mp10) REVERT: F 61 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8604 (mm) REVERT: G 1462 MET cc_start: 0.9200 (mmp) cc_final: 0.8611 (ppp) REVERT: G 1488 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7574 (mt-10) REVERT: G 1578 MET cc_start: 0.9357 (ttm) cc_final: 0.8923 (tpp) REVERT: H 1462 MET cc_start: 0.9335 (mmp) cc_final: 0.8921 (mmm) REVERT: H 1514 MET cc_start: 0.8822 (mmm) cc_final: 0.8475 (tmm) REVERT: H 1550 MET cc_start: 0.8798 (ppp) cc_final: 0.8381 (ppp) outliers start: 52 outliers final: 33 residues processed: 181 average time/residue: 0.3085 time to fit residues: 91.3979 Evaluate side-chains 172 residues out of total 2479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 134 time to evaluate : 2.981 ------------------------------------------------------------------------------- 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 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 553 THR Chi-restraints excluded: chain A residue 585 HIS Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 89 MET 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 495 HIS Chi-restraints excluded: chain B residue 510 ILE Chi-restraints excluded: chain B residue 730 PHE Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 95 PHE 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 40 GLN 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 F residue 126 GLN Chi-restraints excluded: chain G residue 1488 GLU Chi-restraints excluded: chain G residue 1565 GLU Chi-restraints excluded: chain G residue 1605 HIS Chi-restraints excluded: chain G residue 1612 GLU Chi-restraints excluded: chain H residue 1597 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 165 optimal weight: 0.9990 chunk 107 optimal weight: 0.0370 chunk 160 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 52 optimal weight: 9.9990 chunk 51 optimal weight: 0.0770 chunk 170 optimal weight: 0.9980 chunk 182 optimal weight: 4.9990 chunk 132 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 210 optimal weight: 7.9990 overall best weight: 0.6018 ------------------------------------------------------------------------------- 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 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 888 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 HIS ** 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** G1605 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 23278 Z= 0.156 Angle : 0.650 13.191 31266 Z= 0.324 Chirality : 0.041 0.412 3400 Planarity : 0.004 0.056 4115 Dihedral : 6.045 102.676 3051 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 1.86 % Allowed : 19.41 % Favored : 78.73 % 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: -0.24 (0.16), residues: 2798 helix: 1.13 (0.13), residues: 1646 sheet: -1.64 (0.41), residues: 150 loop : -2.15 (0.19), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 36 HIS 0.007 0.001 HIS B 147 PHE 0.017 0.001 PHE C 69 TYR 0.017 0.001 TYR G1473 ARG 0.003 0.000 ARG D 44 *********************** 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 183 residues out of total 2479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 137 time to evaluate : 2.963 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 339 MET cc_start: 0.9120 (mmp) cc_final: 0.8858 (mmp) REVERT: A 766 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.8111 (mm) REVERT: A 933 MET cc_start: 0.9390 (ppp) cc_final: 0.8842 (mmp) REVERT: B 342 MET cc_start: 0.8252 (mmt) cc_final: 0.7873 (mmt) REVERT: B 391 MET cc_start: 0.6739 (tpt) cc_final: 0.6458 (tpp) REVERT: B 655 MET cc_start: 0.6514 (ttt) cc_final: 0.6122 (ptt) REVERT: B 933 MET cc_start: 0.7243 (mmm) cc_final: 0.7018 (mmm) REVERT: D 24 MET cc_start: 0.7004 (ppp) cc_final: 0.6551 (ppp) REVERT: D 56 MET cc_start: 0.8369 (mmm) cc_final: 0.7452 (mpp) REVERT: D 60 MET cc_start: 0.7425 (mmp) cc_final: 0.6355 (pmm) REVERT: D 73 MET cc_start: 0.7109 (mmt) cc_final: 0.6652 (mtt) REVERT: D 89 PHE cc_start: 0.8410 (OUTLIER) cc_final: 0.7867 (m-80) REVERT: E 73 MET cc_start: 0.7907 (mpp) cc_final: 0.7507 (ptp) REVERT: E 141 MET cc_start: 0.8035 (mpp) cc_final: 0.7495 (tmm) REVERT: F 40 GLN cc_start: 0.8388 (OUTLIER) cc_final: 0.8112 (mp10) REVERT: F 61 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8623 (mm) REVERT: G 1462 MET cc_start: 0.9185 (mmp) cc_final: 0.8563 (ppp) REVERT: G 1488 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7571 (mt-10) REVERT: G 1578 MET cc_start: 0.9373 (ttm) cc_final: 0.8939 (tpp) REVERT: H 1462 MET cc_start: 0.9316 (mmp) cc_final: 0.8915 (mmm) REVERT: H 1514 MET cc_start: 0.8882 (mmm) cc_final: 0.8553 (tmm) REVERT: H 1550 MET cc_start: 0.8756 (ppp) cc_final: 0.8337 (ppp) outliers start: 46 outliers final: 36 residues processed: 175 average time/residue: 0.3191 time to fit residues: 91.4011 Evaluate side-chains 173 residues out of total 2479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 132 time to evaluate : 2.559 ------------------------------------------------------------------------------- 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 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 553 THR Chi-restraints excluded: chain A residue 585 HIS Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 766 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 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 510 ILE Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 730 PHE 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 40 GLN 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 F residue 126 GLN Chi-restraints excluded: chain G residue 1488 GLU Chi-restraints excluded: chain G residue 1565 GLU Chi-restraints excluded: chain G residue 1605 HIS Chi-restraints excluded: chain G residue 1612 GLU Chi-restraints excluded: chain H residue 1597 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 243 optimal weight: 0.9980 chunk 256 optimal weight: 1.9990 chunk 234 optimal weight: 0.3980 chunk 249 optimal weight: 7.9990 chunk 150 optimal weight: 0.6980 chunk 108 optimal weight: 0.7980 chunk 196 optimal weight: 7.9990 chunk 76 optimal weight: 9.9990 chunk 225 optimal weight: 0.9980 chunk 236 optimal weight: 7.9990 chunk 248 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 888 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 HIS ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 23278 Z= 0.162 Angle : 0.663 19.059 31266 Z= 0.329 Chirality : 0.040 0.319 3400 Planarity : 0.004 0.054 4115 Dihedral : 5.986 103.306 3051 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 1.86 % Allowed : 19.65 % Favored : 78.49 % 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: -0.24 (0.16), residues: 2798 helix: 1.12 (0.13), residues: 1646 sheet: -1.63 (0.41), residues: 150 loop : -2.14 (0.19), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 625 HIS 0.008 0.001 HIS B 147 PHE 0.016 0.001 PHE C 69 TYR 0.050 0.001 TYR G1473 ARG 0.006 0.000 ARG F 20 *********************** REFINEMENT MACRO_CYCLE 9 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 179 residues out of total 2479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 133 time to evaluate : 2.840 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 766 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8148 (mm) REVERT: A 933 MET cc_start: 0.9373 (ppp) cc_final: 0.8822 (mmp) REVERT: B 342 MET cc_start: 0.8263 (mmt) cc_final: 0.7894 (mmt) REVERT: B 391 MET cc_start: 0.6822 (tpt) cc_final: 0.6538 (tpp) REVERT: B 655 MET cc_start: 0.6513 (ttt) cc_final: 0.6126 (ptt) REVERT: D 24 MET cc_start: 0.7029 (ppp) cc_final: 0.6550 (ppp) REVERT: D 56 MET cc_start: 0.8423 (mmm) cc_final: 0.7887 (mpp) REVERT: D 73 MET cc_start: 0.7132 (mmt) cc_final: 0.6692 (mtt) REVERT: D 89 PHE cc_start: 0.8380 (OUTLIER) cc_final: 0.7849 (m-80) REVERT: E 73 MET cc_start: 0.7819 (mpp) cc_final: 0.7335 (ptp) REVERT: E 141 MET cc_start: 0.8101 (mpp) cc_final: 0.7503 (tmm) REVERT: F 61 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8656 (mm) REVERT: G 1578 MET cc_start: 0.9377 (ttm) cc_final: 0.8947 (tpp) REVERT: H 1462 MET cc_start: 0.9319 (mmp) cc_final: 0.8930 (mmm) REVERT: H 1514 MET cc_start: 0.9016 (mmm) cc_final: 0.8735 (tmm) REVERT: H 1550 MET cc_start: 0.8763 (ppp) cc_final: 0.8345 (ppp) outliers start: 46 outliers final: 37 residues processed: 171 average time/residue: 0.3218 time to fit residues: 90.5129 Evaluate side-chains 171 residues out of total 2479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 131 time to evaluate : 2.943 ------------------------------------------------------------------------------- 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 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 553 THR Chi-restraints excluded: chain A residue 585 HIS Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 766 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 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 466 ILE Chi-restraints excluded: chain B residue 472 PHE Chi-restraints excluded: chain B residue 510 ILE Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 730 PHE Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 60 ASN 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 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 F residue 126 GLN Chi-restraints excluded: chain G residue 1565 GLU Chi-restraints excluded: chain G residue 1605 HIS Chi-restraints excluded: chain G residue 1612 GLU Chi-restraints excluded: chain H residue 1581 GLN Chi-restraints excluded: chain H residue 1597 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 163 optimal weight: 5.9990 chunk 264 optimal weight: 0.9980 chunk 161 optimal weight: 6.9990 chunk 125 optimal weight: 3.9990 chunk 183 optimal weight: 10.0000 chunk 276 optimal weight: 10.0000 chunk 254 optimal weight: 4.9990 chunk 220 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 170 optimal weight: 10.0000 chunk 135 optimal weight: 5.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- 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 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 888 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 79 ASN ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 561 GLN B 636 GLN ** B 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 723 ASN D 42 GLN D 104 ASN ** E 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1605 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.3572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 23278 Z= 0.432 Angle : 0.908 17.870 31266 Z= 0.468 Chirality : 0.047 0.233 3400 Planarity : 0.006 0.053 4115 Dihedral : 6.920 116.407 3051 Min Nonbonded Distance : 1.767 Molprobity Statistics. All-atom Clashscore : 25.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.54 % Favored : 91.46 % Rotamer: Outliers : 1.69 % Allowed : 20.06 % Favored : 78.25 % 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: -1.10 (0.15), residues: 2798 helix: 0.48 (0.12), residues: 1618 sheet: -2.45 (0.40), residues: 135 loop : -2.44 (0.18), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP A 597 HIS 0.011 0.002 HIS B 147 PHE 0.028 0.003 PHE A 493 TYR 0.058 0.003 TYR G1473 ARG 0.010 0.001 ARG F 20 ********************** REFINEMENT MACRO_CYCLE 10 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 169 residues out of total 2479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 127 time to evaluate : 2.843 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: 0.5919 (mpp) cc_final: 0.5002 (mpt) REVERT: A 915 MET cc_start: 0.9174 (ppp) cc_final: 0.8247 (ttt) REVERT: A 933 MET cc_start: 0.9396 (ppp) cc_final: 0.8870 (mmt) REVERT: B 342 MET cc_start: 0.8402 (mmt) cc_final: 0.8090 (mmt) REVERT: B 391 MET cc_start: 0.7330 (tpt) cc_final: 0.6945 (tpt) REVERT: B 933 MET cc_start: 0.7173 (mmm) cc_final: 0.6846 (mmm) REVERT: D 73 MET cc_start: 0.7050 (mmt) cc_final: 0.6359 (mtt) REVERT: D 89 PHE cc_start: 0.8612 (OUTLIER) cc_final: 0.8067 (m-80) REVERT: D 129 MET cc_start: 0.7728 (tpt) cc_final: 0.6607 (tpt) REVERT: E 141 MET cc_start: 0.8144 (mpp) cc_final: 0.7527 (tmm) REVERT: G 1578 MET cc_start: 0.9352 (ttm) cc_final: 0.8909 (tpp) REVERT: H 1462 MET cc_start: 0.9355 (mmp) cc_final: 0.8955 (mmm) REVERT: H 1514 MET cc_start: 0.9051 (mmm) cc_final: 0.8770 (tmm) outliers start: 42 outliers final: 31 residues processed: 164 average time/residue: 0.3175 time to fit residues: 86.4489 Evaluate side-chains 154 residues out of total 2479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 122 time to evaluate : 2.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 239 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 553 THR Chi-restraints excluded: chain A residue 624 LEU 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 345 THR 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 466 ILE Chi-restraints excluded: chain B residue 472 PHE Chi-restraints excluded: chain B residue 603 ASP Chi-restraints excluded: chain B residue 730 PHE Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 95 PHE 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 48 MET Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 110 HIS Chi-restraints excluded: chain F residue 126 GLN Chi-restraints excluded: chain G residue 1605 HIS Chi-restraints excluded: chain G residue 1612 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 175 optimal weight: 1.9990 chunk 234 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 203 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 220 optimal weight: 20.0000 chunk 92 optimal weight: 2.9990 chunk 226 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN ** A 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 888 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 GLN ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 ASN ** G1429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1433 GLN ** G1605 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.052896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.042001 restraints weight = 247499.788| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 7.42 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.3380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23278 Z= 0.201 Angle : 0.730 18.071 31266 Z= 0.365 Chirality : 0.042 0.197 3400 Planarity : 0.004 0.102 4115 Dihedral : 6.423 113.977 3051 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 16.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 1.25 % Allowed : 20.70 % Favored : 78.05 % 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: -0.77 (0.16), residues: 2798 helix: 0.72 (0.13), residues: 1637 sheet: -2.27 (0.40), residues: 142 loop : -2.32 (0.18), residues: 1019 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 625 HIS 0.008 0.001 HIS B 147 PHE 0.019 0.002 PHE F 66 TYR 0.049 0.002 TYR G1473 ARG 0.016 0.001 ARG H1597 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4657.49 seconds wall clock time: 85 minutes 29.52 seconds (5129.52 seconds total)