Starting phenix.real_space_refine on Fri Jun 13 17:28:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7eg1_31104/06_2025/7eg1_31104_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7eg1_31104/06_2025/7eg1_31104.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7eg1_31104/06_2025/7eg1_31104.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7eg1_31104/06_2025/7eg1_31104.map" model { file = "/net/cci-nas-00/data/ceres_data/7eg1_31104/06_2025/7eg1_31104_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7eg1_31104/06_2025/7eg1_31104_trim.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 Zn 2 6.06 5 Mg 4 5.21 5 S 98 5.16 5 C 9766 2.51 5 N 2584 2.21 5 O 2806 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 80 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 15260 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 3004 Classifications: {'peptide': 372} Link IDs: {'PTRANS': 18, 'TRANS': 353} Chain breaks: 2 Chain: "B" Number of atoms: 4601 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 567, 4600 Classifications: {'peptide': 567} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 550} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Conformer: "B" Number of residues, atoms: 567, 4600 Classifications: {'peptide': 567} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 550} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 bond proxies already assigned to first conformer: 4689 Chain: "C" Number of atoms: 3004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 3004 Classifications: {'peptide': 372} Link IDs: {'PTRANS': 18, 'TRANS': 353} Chain breaks: 2 Chain: "D" Number of atoms: 4601 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 567, 4600 Classifications: {'peptide': 567} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 550} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Conformer: "B" Number of residues, atoms: 567, 4600 Classifications: {'peptide': 567} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 550} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 bond proxies already assigned to first conformer: 4689 Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 24 Unusual residues: {' MG': 2, 'X5M': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 24 Unusual residues: {' MG': 2, 'X5M': 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: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5222 SG CYS B 277 75.199 72.840 74.712 1.00 40.55 S ATOM 5495 SG CYS B 311 74.956 74.493 78.226 1.00 33.93 S ATOM 5501 SG CYS B 312 72.082 71.970 76.521 1.00 28.39 S ATOM 12827 SG CYS D 277 24.929 60.113 74.543 1.00 41.45 S ATOM 13100 SG CYS D 311 25.437 58.632 78.226 1.00 33.13 S ATOM 13106 SG CYS D 312 28.303 61.099 76.520 1.00 27.35 S Time building chain proxies: 12.00, per 1000 atoms: 0.79 Number of scatterers: 15260 At special positions: 0 Unit cell: (101.463, 134.193, 129.829, 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) Zn 2 29.99 S 98 16.00 Mg 4 11.99 O 2806 8.00 N 2584 7.00 C 9766 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 381 " - pdb=" SG CYS B 411 " distance=2.03 Simple disulfide: pdb=" SG CYS D 381 " - pdb=" SG CYS D 411 " distance=2.03 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: 4.04 Conformation dependent library (CDL) restraints added in 3.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 601 " pdb="ZN ZN B 601 " - pdb=" ND1 HIS B 275 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 277 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 311 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 312 " pdb=" ZN D 601 " pdb="ZN ZN D 601 " - pdb=" ND1 HIS D 275 " pdb="ZN ZN D 601 " - pdb=" SG CYS D 277 " pdb="ZN ZN D 601 " - pdb=" SG CYS D 311 " pdb="ZN ZN D 601 " - pdb=" SG CYS D 312 " Number of angles added : 6 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3572 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 17 sheets defined 48.9% alpha, 7.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.89 Creating SS restraints... Processing helix chain 'A' and resid 686 through 690 removed outlier: 4.282A pdb=" N ASN A 690 " --> pdb=" O GLU A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 703 removed outlier: 3.653A pdb=" N GLU A 701 " --> pdb=" O PHE A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 723 removed outlier: 3.578A pdb=" N ARG A 717 " --> pdb=" O GLN A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 728 removed outlier: 3.650A pdb=" N ALA A 727 " --> pdb=" O GLY A 723 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE A 728 " --> pdb=" O LEU A 724 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 723 through 728' Processing helix chain 'A' and resid 731 through 746 removed outlier: 3.717A pdb=" N GLY A 745 " --> pdb=" O ALA A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 753 through 769 removed outlier: 3.557A pdb=" N THR A 758 " --> pdb=" O ARG A 754 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL A 764 " --> pdb=" O VAL A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 820 Processing helix chain 'A' and resid 822 through 835 Processing helix chain 'A' and resid 844 through 851 Processing helix chain 'A' and resid 853 through 859 Processing helix chain 'A' and resid 865 through 878 removed outlier: 3.508A pdb=" N LEU A 876 " --> pdb=" O ALA A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 880 through 884 removed outlier: 3.752A pdb=" N TYR A 883 " --> pdb=" O ARG A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 906 removed outlier: 3.562A pdb=" N PHE A 894 " --> pdb=" O ASP A 890 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 922 removed outlier: 3.531A pdb=" N PHE A 916 " --> pdb=" O LYS A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 934 through 951 Processing helix chain 'A' and resid 952 through 956 Processing helix chain 'A' and resid 957 through 981 removed outlier: 3.628A pdb=" N GLU A 974 " --> pdb=" O ASN A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 996 through 1008 Processing helix chain 'A' and resid 1008 through 1019 removed outlier: 3.557A pdb=" N LEU A1012 " --> pdb=" O ILE A1008 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER A1015 " --> pdb=" O PRO A1011 " (cutoff:3.500A) Processing helix chain 'A' and resid 1073 through 1101 removed outlier: 3.517A pdb=" N LEU A1079 " --> pdb=" O ILE A1075 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL A1089 " --> pdb=" O MET A1085 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 30 Processing helix chain 'B' and resid 33 through 54 Processing helix chain 'B' and resid 77 through 87 removed outlier: 3.542A pdb=" N ILE B 86 " --> pdb=" O SER B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 152 removed outlier: 3.628A pdb=" N ASP B 148 " --> pdb=" O GLU B 144 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N MET B 149 " --> pdb=" O PHE B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 186 removed outlier: 3.743A pdb=" N ASP B 186 " --> pdb=" O GLY B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 222 removed outlier: 4.413A pdb=" N GLU B 220 " --> pdb=" O GLN B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 232 Processing helix chain 'B' and resid 255 through 271 removed outlier: 3.948A pdb=" N ASP B 259 " --> pdb=" O SER B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 343 removed outlier: 3.570A pdb=" N GLU B 343 " --> pdb=" O GLN B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 359 removed outlier: 3.586A pdb=" N ILE B 359 " --> pdb=" O VAL B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 362 No H-bonds generated for 'chain 'B' and resid 360 through 362' Processing helix chain 'B' and resid 394 through 402 removed outlier: 3.536A pdb=" N PHE B 400 " --> pdb=" O CYS B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 414 removed outlier: 3.887A pdb=" N LYS B 407 " --> pdb=" O HIS B 403 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N GLN B 408 " --> pdb=" O GLU B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 417 No H-bonds generated for 'chain 'B' and resid 415 through 417' Processing helix chain 'B' and resid 429 through 433 Processing helix chain 'B' and resid 466 through 484 removed outlier: 3.765A pdb=" N ALA B 482 " --> pdb=" O LYS B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 516 removed outlier: 4.036A pdb=" N VAL B 516 " --> pdb=" O ARG B 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 513 through 516' Processing helix chain 'B' and resid 519 through 524 removed outlier: 3.573A pdb=" N TYR B 522 " --> pdb=" O PRO B 519 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TYR B 523 " --> pdb=" O GLU B 520 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N PHE B 524 " --> pdb=" O SER B 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 519 through 524' Processing helix chain 'B' and resid 528 through 541 Processing helix chain 'B' and resid 552 through 559 removed outlier: 3.612A pdb=" N ILE B 557 " --> pdb=" O ASN B 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 686 through 690 removed outlier: 4.281A pdb=" N ASN C 690 " --> pdb=" O GLU C 687 " (cutoff:3.500A) Processing helix chain 'C' and resid 695 through 703 removed outlier: 3.652A pdb=" N GLU C 701 " --> pdb=" O PHE C 697 " (cutoff:3.500A) Processing helix chain 'C' and resid 709 through 723 removed outlier: 3.580A pdb=" N ARG C 717 " --> pdb=" O GLN C 713 " (cutoff:3.500A) Processing helix chain 'C' and resid 723 through 728 removed outlier: 3.649A pdb=" N ALA C 727 " --> pdb=" O GLY C 723 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE C 728 " --> pdb=" O LEU C 724 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 723 through 728' Processing helix chain 'C' and resid 731 through 746 removed outlier: 3.718A pdb=" N GLY C 745 " --> pdb=" O ALA C 741 " (cutoff:3.500A) Processing helix chain 'C' and resid 753 through 769 removed outlier: 3.558A pdb=" N THR C 758 " --> pdb=" O ARG C 754 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL C 764 " --> pdb=" O VAL C 760 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 820 Processing helix chain 'C' and resid 822 through 835 Processing helix chain 'C' and resid 844 through 851 Processing helix chain 'C' and resid 853 through 859 Processing helix chain 'C' and resid 865 through 878 removed outlier: 3.508A pdb=" N LEU C 876 " --> pdb=" O ALA C 872 " (cutoff:3.500A) Processing helix chain 'C' and resid 880 through 884 removed outlier: 3.753A pdb=" N TYR C 883 " --> pdb=" O ARG C 880 " (cutoff:3.500A) Processing helix chain 'C' and resid 890 through 906 removed outlier: 3.561A pdb=" N PHE C 894 " --> pdb=" O ASP C 890 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 922 removed outlier: 3.531A pdb=" N PHE C 916 " --> pdb=" O LYS C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 934 through 951 Processing helix chain 'C' and resid 952 through 956 Processing helix chain 'C' and resid 957 through 981 removed outlier: 3.627A pdb=" N GLU C 974 " --> pdb=" O ASN C 970 " (cutoff:3.500A) Processing helix chain 'C' and resid 996 through 1008 Processing helix chain 'C' and resid 1008 through 1019 removed outlier: 3.557A pdb=" N LEU C1012 " --> pdb=" O ILE C1008 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER C1015 " --> pdb=" O PRO C1011 " (cutoff:3.500A) Processing helix chain 'C' and resid 1073 through 1101 removed outlier: 3.516A pdb=" N LEU C1079 " --> pdb=" O ILE C1075 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL C1089 " --> pdb=" O MET C1085 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 30 Processing helix chain 'D' and resid 33 through 54 Processing helix chain 'D' and resid 76 through 87 removed outlier: 3.735A pdb=" N GLU D 80 " --> pdb=" O GLY D 76 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER D 82 " --> pdb=" O ASP D 78 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE D 86 " --> pdb=" O SER D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 152 removed outlier: 3.755A pdb=" N ASP D 148 " --> pdb=" O GLU D 144 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N MET D 149 " --> pdb=" O PHE D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 186 removed outlier: 3.749A pdb=" N ASP D 186 " --> pdb=" O GLY D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 222 removed outlier: 4.439A pdb=" N GLU D 220 " --> pdb=" O GLN D 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 232 Processing helix chain 'D' and resid 256 through 271 removed outlier: 3.508A pdb=" N MET D 271 " --> pdb=" O SER D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 343 removed outlier: 3.817A pdb=" N ILE D 338 " --> pdb=" O ARG D 334 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLN D 339 " --> pdb=" O LYS D 335 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU D 343 " --> pdb=" O GLN D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 358 removed outlier: 3.629A pdb=" N VAL D 355 " --> pdb=" O ALA D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 362 removed outlier: 4.132A pdb=" N SER D 362 " --> pdb=" O ILE D 359 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 359 through 362' Processing helix chain 'D' and resid 394 through 402 removed outlier: 3.989A pdb=" N PHE D 400 " --> pdb=" O CYS D 396 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 414 removed outlier: 3.855A pdb=" N LYS D 407 " --> pdb=" O HIS D 403 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N GLN D 408 " --> pdb=" O GLU D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 417 No H-bonds generated for 'chain 'D' and resid 415 through 417' Processing helix chain 'D' and resid 429 through 433 Processing helix chain 'D' and resid 466 through 484 removed outlier: 4.038A pdb=" N ALA D 482 " --> pdb=" O LYS D 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 516 removed outlier: 4.020A pdb=" N VAL D 516 " --> pdb=" O ARG D 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 513 through 516' Processing helix chain 'D' and resid 519 through 524 removed outlier: 3.564A pdb=" N TYR D 522 " --> pdb=" O PRO D 519 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR D 523 " --> pdb=" O GLU D 520 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N PHE D 524 " --> pdb=" O SER D 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 519 through 524' Processing helix chain 'D' and resid 528 through 541 Processing helix chain 'D' and resid 552 through 558 removed outlier: 3.638A pdb=" N ILE D 557 " --> pdb=" O ASN D 553 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 772 through 773 Processing sheet with id=AA2, first strand: chain 'A' and resid 1025 through 1026 Processing sheet with id=AA3, first strand: chain 'B' and resid 4 through 5 removed outlier: 4.021A pdb=" N SER B 4 " --> pdb=" O ASP B 17 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N LEU B 16 " --> pdb=" O LYS B 60 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N GLU B 62 " --> pdb=" O LEU B 16 " (cutoff:3.500A) removed outlier: 8.340A pdb=" N VAL B 18 " --> pdb=" O GLU B 62 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 127 through 129 Processing sheet with id=AA5, first strand: chain 'B' and resid 172 through 173 removed outlier: 6.056A pdb=" N LEU D 16 " --> pdb=" O LYS D 60 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N GLU D 62 " --> pdb=" O LEU D 16 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N VAL D 18 " --> pdb=" O GLU D 62 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N SER D 4 " --> pdb=" O ASP D 17 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 204 through 207 removed outlier: 6.584A pdb=" N GLU B 205 " --> pdb=" O PHE B 238 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 274 Processing sheet with id=AA8, first strand: chain 'B' and resid 322 through 323 Processing sheet with id=AA9, first strand: chain 'B' and resid 442 through 443 removed outlier: 3.651A pdb=" N CYS B 442 " --> pdb=" O PHE B 458 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE B 458 " --> pdb=" O CYS B 442 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N THR B 457 " --> pdb=" O PHE B 498 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N TYR B 499 " --> pdb=" O CYS B 508 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N CYS B 508 " --> pdb=" O TYR B 499 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 772 through 773 Processing sheet with id=AB2, first strand: chain 'C' and resid 1025 through 1026 Processing sheet with id=AB3, first strand: chain 'D' and resid 127 through 129 Processing sheet with id=AB4, first strand: chain 'D' and resid 204 through 207 removed outlier: 6.578A pdb=" N GLU D 205 " --> pdb=" O PHE D 238 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 204 through 207 removed outlier: 6.578A pdb=" N GLU D 205 " --> pdb=" O PHE D 238 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 273 through 274 Processing sheet with id=AB7, first strand: chain 'D' and resid 322 through 323 Processing sheet with id=AB8, first strand: chain 'D' and resid 442 through 443 removed outlier: 3.650A pdb=" N CYS D 442 " --> pdb=" O PHE D 458 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE D 458 " --> pdb=" O CYS D 442 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N TYR D 499 " --> pdb=" O CYS D 508 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N CYS D 508 " --> pdb=" O TYR D 499 " (cutoff:3.500A) 625 hydrogen bonds defined for protein. 1782 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: 4.84 Time building geometry restraints manager: 4.53 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: 4927 1.34 - 1.46: 3347 1.46 - 1.58: 7170 1.58 - 1.69: 0 1.69 - 1.81: 150 Bond restraints: 15594 Sorted by residual: bond pdb=" C ALA B 344 " pdb=" N GLU B 345 " ideal model delta sigma weight residual 1.327 1.422 -0.095 2.86e-02 1.22e+03 1.10e+01 bond pdb=" N GLU D 345 " pdb=" CA GLU D 345 " ideal model delta sigma weight residual 1.453 1.487 -0.034 1.32e-02 5.74e+03 6.55e+00 bond pdb=" N LYS C1088 " pdb=" CA LYS C1088 " ideal model delta sigma weight residual 1.459 1.483 -0.023 1.19e-02 7.06e+03 3.85e+00 bond pdb=" N LYS A1088 " pdb=" CA LYS A1088 " ideal model delta sigma weight residual 1.459 1.482 -0.023 1.19e-02 7.06e+03 3.79e+00 bond pdb=" N GLU B 345 " pdb=" CA GLU B 345 " ideal model delta sigma weight residual 1.453 1.482 -0.029 1.51e-02 4.39e+03 3.71e+00 ... (remaining 15589 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.87: 20922 2.87 - 5.75: 122 5.75 - 8.62: 8 8.62 - 11.50: 0 11.50 - 14.37: 2 Bond angle restraints: 21054 Sorted by residual: angle pdb=" CA GLU A 959 " pdb=" CB GLU A 959 " pdb=" CG GLU A 959 " ideal model delta sigma weight residual 114.10 128.47 -14.37 2.00e+00 2.50e-01 5.16e+01 angle pdb=" CA GLU C 959 " pdb=" CB GLU C 959 " pdb=" CG GLU C 959 " ideal model delta sigma weight residual 114.10 128.43 -14.33 2.00e+00 2.50e-01 5.13e+01 angle pdb=" CB GLU C 959 " pdb=" CG GLU C 959 " pdb=" CD GLU C 959 " ideal model delta sigma weight residual 112.60 119.01 -6.41 1.70e+00 3.46e-01 1.42e+01 angle pdb=" CB GLU A 959 " pdb=" CG GLU A 959 " pdb=" CD GLU A 959 " ideal model delta sigma weight residual 112.60 119.00 -6.40 1.70e+00 3.46e-01 1.42e+01 angle pdb=" N GLU C 726 " pdb=" CA GLU C 726 " pdb=" C GLU C 726 " ideal model delta sigma weight residual 114.04 110.04 4.00 1.24e+00 6.50e-01 1.04e+01 ... (remaining 21049 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 8452 17.91 - 35.82: 815 35.82 - 53.73: 111 53.73 - 71.65: 31 71.65 - 89.56: 13 Dihedral angle restraints: 9422 sinusoidal: 3902 harmonic: 5520 Sorted by residual: dihedral pdb=" CA TYR B 390 " pdb=" C TYR B 390 " pdb=" N THR B 391 " pdb=" CA THR B 391 " ideal model delta harmonic sigma weight residual -180.00 -149.99 -30.01 0 5.00e+00 4.00e-02 3.60e+01 dihedral pdb=" CA TYR D 390 " pdb=" C TYR D 390 " pdb=" N THR D 391 " pdb=" CA THR D 391 " ideal model delta harmonic sigma weight residual -180.00 -150.02 -29.98 0 5.00e+00 4.00e-02 3.60e+01 dihedral pdb=" CA ARG D 159 " pdb=" C ARG D 159 " pdb=" N PRO D 160 " pdb=" CA PRO D 160 " ideal model delta harmonic sigma weight residual -180.00 -157.90 -22.10 0 5.00e+00 4.00e-02 1.95e+01 ... (remaining 9419 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1510 0.034 - 0.068: 553 0.068 - 0.103: 158 0.103 - 0.137: 63 0.137 - 0.171: 6 Chirality restraints: 2290 Sorted by residual: chirality pdb=" CA THR D 391 " pdb=" N THR D 391 " pdb=" C THR D 391 " pdb=" CB THR D 391 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.17 2.00e-01 2.50e+01 7.32e-01 chirality pdb=" CA THR B 391 " pdb=" N THR B 391 " pdb=" C THR B 391 " pdb=" CB THR B 391 " both_signs ideal model delta sigma weight residual False 2.53 2.36 0.17 2.00e-01 2.50e+01 7.26e-01 chirality pdb=" CA PHE D 550 " pdb=" N PHE D 550 " pdb=" C PHE D 550 " pdb=" CB PHE D 550 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.39e-01 ... (remaining 2287 not shown) Planarity restraints: 2694 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C02 X5M C1201 " -0.066 2.00e-02 2.50e+03 1.12e-01 1.25e+02 pdb=" C04 X5M C1201 " -0.063 2.00e-02 2.50e+03 pdb=" C06 X5M C1201 " -0.065 2.00e-02 2.50e+03 pdb=" N03 X5M C1201 " 0.193 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C02 X5M A1201 " 0.066 2.00e-02 2.50e+03 1.11e-01 1.24e+02 pdb=" C04 X5M A1201 " 0.063 2.00e-02 2.50e+03 pdb=" C06 X5M A1201 " 0.065 2.00e-02 2.50e+03 pdb=" N03 X5M A1201 " -0.193 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C06 X5M A1201 " -0.012 2.00e-02 2.50e+03 4.14e-02 3.86e+01 pdb=" C07 X5M A1201 " -0.015 2.00e-02 2.50e+03 pdb=" C08 X5M A1201 " 0.004 2.00e-02 2.50e+03 pdb=" C09 X5M A1201 " -0.022 2.00e-02 2.50e+03 pdb=" C10 X5M A1201 " -0.074 2.00e-02 2.50e+03 pdb=" C11 X5M A1201 " -0.032 2.00e-02 2.50e+03 pdb=" C15 X5M A1201 " 0.067 2.00e-02 2.50e+03 pdb=" N03 X5M A1201 " 0.036 2.00e-02 2.50e+03 pdb=" N12 X5M A1201 " 0.048 2.00e-02 2.50e+03 ... (remaining 2691 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 139 2.60 - 3.18: 13566 3.18 - 3.75: 21020 3.75 - 4.33: 33088 4.33 - 4.90: 54377 Nonbonded interactions: 122190 Sorted by model distance: nonbonded pdb=" OD2 ASP C 837 " pdb="MG MG C1202 " model vdw 2.026 2.170 nonbonded pdb=" OD1 ASP A 950 " pdb="MG MG A1202 " model vdw 2.046 2.170 nonbonded pdb=" OD2 ASP A 837 " pdb="MG MG A1202 " model vdw 2.058 2.170 nonbonded pdb=" OD1 ASP C 950 " pdb="MG MG C1202 " model vdw 2.089 2.170 nonbonded pdb=" NE2 HIS A 836 " pdb="MG MG A1202 " model vdw 2.158 2.250 ... (remaining 122185 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = (chain 'B' and (resid 2 through 439 or resid 441 through 568 or resid 601)) selection = (chain 'D' and (resid 2 through 439 or resid 441 through 568 or resid 601)) } 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=0.35 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.570 Check model and map are aligned: 0.110 Set scattering table: 0.120 Process input model: 43.280 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 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 : 0.009 0.621 15604 Z= 0.360 Angle : 0.684 21.913 21064 Z= 0.380 Chirality : 0.042 0.171 2290 Planarity : 0.005 0.112 2694 Dihedral : 14.261 89.557 5844 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 16.04 Ramachandran Plot: Outliers : 0.11 % Allowed : 11.92 % Favored : 87.97 % Rotamer: Outliers : 0.36 % Allowed : 3.29 % Favored : 96.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -5.05 (0.15), residues: 1862 helix: -3.47 (0.12), residues: 836 sheet: -2.17 (0.38), residues: 160 loop : -3.41 (0.18), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1026 HIS 0.009 0.001 HIS D 323 PHE 0.033 0.001 PHE D 550 TYR 0.024 0.002 TYR D 70 ARG 0.003 0.000 ARG B 309 Details of bonding type rmsd hydrogen bonds : bond 0.29721 ( 619) hydrogen bonds : angle 9.81496 ( 1782) metal coordination : bond 0.29639 ( 8) metal coordination : angle 12.11512 ( 6) SS BOND : bond 0.00085 ( 2) SS BOND : angle 0.88426 ( 4) covalent geometry : bond 0.00604 (15594) covalent geometry : angle 0.65312 (21054) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 199 time to evaluate : 1.637 Fit side-chains REVERT: A 679 MET cc_start: 0.7210 (ptp) cc_final: 0.6758 (ptp) REVERT: A 944 MET cc_start: 0.8314 (mmm) cc_final: 0.7962 (mmm) REVERT: B 48 MET cc_start: 0.8549 (ttp) cc_final: 0.8263 (ttp) REVERT: B 101 ASN cc_start: 0.8010 (t0) cc_final: 0.7689 (t0) REVERT: B 341 MET cc_start: 0.8455 (mmm) cc_final: 0.8123 (mmm) REVERT: B 412 GLU cc_start: 0.8370 (tm-30) cc_final: 0.7937 (tm-30) REVERT: B 494 MET cc_start: 0.8833 (mmt) cc_final: 0.8466 (mmt) REVERT: B 520 GLU cc_start: 0.8007 (mm-30) cc_final: 0.7683 (mm-30) REVERT: C 679 MET cc_start: 0.7209 (ptp) cc_final: 0.6937 (ptp) REVERT: C 944 MET cc_start: 0.8547 (mmm) cc_final: 0.8210 (mmm) REVERT: D 31 MET cc_start: 0.9011 (ttm) cc_final: 0.8800 (ttp) REVERT: D 48 MET cc_start: 0.8555 (ttp) cc_final: 0.8247 (ttp) REVERT: D 341 MET cc_start: 0.8442 (mmm) cc_final: 0.8126 (mmm) REVERT: D 412 GLU cc_start: 0.8361 (tm-30) cc_final: 0.7929 (tm-30) REVERT: D 494 MET cc_start: 0.8819 (mmt) cc_final: 0.8406 (mmt) REVERT: D 520 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7638 (mm-30) outliers start: 6 outliers final: 0 residues processed: 204 average time/residue: 0.2960 time to fit residues: 86.9892 Evaluate side-chains 156 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 1.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 157 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 48 optimal weight: 0.7980 chunk 95 optimal weight: 1.9990 chunk 75 optimal weight: 0.5980 chunk 145 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 chunk 108 optimal weight: 3.9990 chunk 168 optimal weight: 0.0570 overall best weight: 0.6902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1078 HIS A1081 GLN B 125 ASN B 172 GLN B 358 GLN B 360 ASN C1081 GLN D 125 ASN D 172 GLN D 360 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.142223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.110720 restraints weight = 19578.677| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 1.99 r_work: 0.3027 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2801 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2801 r_free = 0.2801 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2801 r_free = 0.2801 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2801 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15604 Z= 0.126 Angle : 0.588 8.756 21064 Z= 0.308 Chirality : 0.041 0.146 2290 Planarity : 0.005 0.046 2694 Dihedral : 4.930 37.440 2064 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.88 % Favored : 90.12 % Rotamer: Outliers : 0.66 % Allowed : 6.04 % Favored : 93.30 % 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: -2.79 (0.17), residues: 1862 helix: -0.98 (0.16), residues: 858 sheet: -1.34 (0.41), residues: 158 loop : -2.90 (0.19), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 369 HIS 0.004 0.001 HIS C 869 PHE 0.034 0.001 PHE D 550 TYR 0.013 0.001 TYR D 499 ARG 0.005 0.001 ARG B 387 Details of bonding type rmsd hydrogen bonds : bond 0.04707 ( 619) hydrogen bonds : angle 4.29089 ( 1782) metal coordination : bond 0.02109 ( 8) metal coordination : angle 4.36414 ( 6) SS BOND : bond 0.00420 ( 2) SS BOND : angle 1.69406 ( 4) covalent geometry : bond 0.00271 (15594) covalent geometry : angle 0.58260 (21054) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 164 time to evaluate : 1.672 Fit side-chains REVERT: A 679 MET cc_start: 0.6996 (ptp) cc_final: 0.6727 (ptp) REVERT: A 944 MET cc_start: 0.8711 (mmm) cc_final: 0.8265 (mmm) REVERT: B 48 MET cc_start: 0.8892 (ttp) cc_final: 0.8686 (ttp) REVERT: B 101 ASN cc_start: 0.8601 (t0) cc_final: 0.8092 (t0) REVERT: B 494 MET cc_start: 0.9161 (mmt) cc_final: 0.8930 (mmt) REVERT: C 679 MET cc_start: 0.7009 (ptp) cc_final: 0.6669 (ptp) REVERT: C 944 MET cc_start: 0.8790 (mmm) cc_final: 0.8425 (mmm) REVERT: D 48 MET cc_start: 0.8897 (ttp) cc_final: 0.8681 (ttp) REVERT: D 101 ASN cc_start: 0.8475 (t0) cc_final: 0.8161 (t0) REVERT: D 360 ASN cc_start: 0.7691 (OUTLIER) cc_final: 0.7375 (t0) REVERT: D 412 GLU cc_start: 0.8770 (tm-30) cc_final: 0.8274 (tm-30) REVERT: D 472 GLN cc_start: 0.8774 (tp40) cc_final: 0.8532 (tp40) REVERT: D 494 MET cc_start: 0.9142 (mmt) cc_final: 0.8849 (mmt) outliers start: 11 outliers final: 7 residues processed: 170 average time/residue: 0.2590 time to fit residues: 68.2735 Evaluate side-chains 146 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 138 time to evaluate : 1.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 680 ASP Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 330 MET Chi-restraints excluded: chain C residue 671 ILE Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 360 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 20 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 173 optimal weight: 0.0060 chunk 184 optimal weight: 4.9990 chunk 182 optimal weight: 4.9990 chunk 117 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 150 optimal weight: 0.9980 chunk 112 optimal weight: 0.3980 chunk 104 optimal weight: 8.9990 chunk 55 optimal weight: 7.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.144633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.112163 restraints weight = 19544.974| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 2.03 r_work: 0.3024 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2830 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2830 r_free = 0.2830 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2830 r_free = 0.2830 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2830 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 15604 Z= 0.106 Angle : 0.525 7.954 21064 Z= 0.274 Chirality : 0.041 0.193 2290 Planarity : 0.004 0.047 2694 Dihedral : 4.576 34.467 2064 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.86 % Favored : 91.14 % Rotamer: Outliers : 1.50 % Allowed : 7.24 % Favored : 91.27 % 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: -1.44 (0.19), residues: 1862 helix: 0.56 (0.18), residues: 860 sheet: -0.97 (0.42), residues: 160 loop : -2.68 (0.20), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C1086 HIS 0.006 0.001 HIS D 274 PHE 0.029 0.001 PHE D 550 TYR 0.012 0.001 TYR B 293 ARG 0.006 0.000 ARG D 387 Details of bonding type rmsd hydrogen bonds : bond 0.03773 ( 619) hydrogen bonds : angle 3.79780 ( 1782) metal coordination : bond 0.01124 ( 8) metal coordination : angle 2.66789 ( 6) SS BOND : bond 0.00063 ( 2) SS BOND : angle 1.32929 ( 4) covalent geometry : bond 0.00233 (15594) covalent geometry : angle 0.52269 (21054) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 158 time to evaluate : 1.750 Fit side-chains REVERT: A 835 MET cc_start: 0.8649 (ptt) cc_final: 0.8414 (ptt) REVERT: A 944 MET cc_start: 0.8766 (mmm) cc_final: 0.8363 (mmm) REVERT: B 48 MET cc_start: 0.8911 (ttp) cc_final: 0.8707 (ttp) REVERT: B 101 ASN cc_start: 0.8593 (t0) cc_final: 0.8082 (t0) REVERT: B 494 MET cc_start: 0.9158 (mmt) cc_final: 0.8937 (mmt) REVERT: C 944 MET cc_start: 0.8818 (mmm) cc_final: 0.8474 (mmm) REVERT: D 101 ASN cc_start: 0.8535 (t0) cc_final: 0.8103 (t0) REVERT: D 412 GLU cc_start: 0.8629 (tm-30) cc_final: 0.8171 (tm-30) REVERT: D 494 MET cc_start: 0.9176 (mmt) cc_final: 0.8922 (mmt) outliers start: 25 outliers final: 19 residues processed: 175 average time/residue: 0.2602 time to fit residues: 72.2927 Evaluate side-chains 157 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 138 time to evaluate : 1.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 933 THR Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1096 LEU Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 330 MET Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain C residue 671 ILE Chi-restraints excluded: chain C residue 826 LEU Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1096 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 330 MET Chi-restraints excluded: chain D residue 506 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 42 optimal weight: 2.9990 chunk 78 optimal weight: 9.9990 chunk 184 optimal weight: 4.9990 chunk 61 optimal weight: 9.9990 chunk 3 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 55 optimal weight: 9.9990 chunk 172 optimal weight: 0.6980 chunk 77 optimal weight: 6.9990 chunk 115 optimal weight: 5.9990 chunk 106 optimal weight: 6.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 936 ASN ** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 936 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.137302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.104964 restraints weight = 19667.812| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 1.95 r_work: 0.2942 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2749 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2749 r_free = 0.2749 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2749 r_free = 0.2749 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2749 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.081 15604 Z= 0.286 Angle : 0.671 7.722 21064 Z= 0.347 Chirality : 0.048 0.204 2290 Planarity : 0.005 0.063 2694 Dihedral : 5.107 38.421 2064 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.74 % Favored : 89.26 % Rotamer: Outliers : 1.85 % Allowed : 9.45 % Favored : 88.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.40 (0.19), residues: 1862 helix: 0.56 (0.18), residues: 858 sheet: -0.71 (0.42), residues: 158 loop : -2.67 (0.20), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 110 HIS 0.008 0.001 HIS D 323 PHE 0.030 0.002 PHE D 550 TYR 0.020 0.002 TYR B 157 ARG 0.008 0.001 ARG C 709 Details of bonding type rmsd hydrogen bonds : bond 0.05416 ( 619) hydrogen bonds : angle 4.16633 ( 1782) metal coordination : bond 0.00755 ( 8) metal coordination : angle 2.82832 ( 6) SS BOND : bond 0.00179 ( 2) SS BOND : angle 0.91336 ( 4) covalent geometry : bond 0.00706 (15594) covalent geometry : angle 0.66955 (21054) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 148 time to evaluate : 1.856 Fit side-chains REVERT: A 944 MET cc_start: 0.8851 (mmm) cc_final: 0.8455 (mmm) REVERT: B 48 MET cc_start: 0.8975 (ttp) cc_final: 0.8729 (ttp) REVERT: B 101 ASN cc_start: 0.8585 (t0) cc_final: 0.8023 (t0) REVERT: B 412 GLU cc_start: 0.8988 (tm-30) cc_final: 0.8411 (tm-30) REVERT: B 494 MET cc_start: 0.9113 (mmt) cc_final: 0.8836 (mmt) REVERT: C 944 MET cc_start: 0.8840 (mmm) cc_final: 0.8434 (mmm) REVERT: D 48 MET cc_start: 0.8982 (ttp) cc_final: 0.8731 (ttp) REVERT: D 62 GLU cc_start: 0.8639 (mt-10) cc_final: 0.8400 (mt-10) REVERT: D 101 ASN cc_start: 0.8651 (t0) cc_final: 0.8178 (t0) REVERT: D 326 ASP cc_start: 0.7493 (OUTLIER) cc_final: 0.7097 (p0) REVERT: D 353 GLU cc_start: 0.7117 (mp0) cc_final: 0.6888 (mp0) REVERT: D 412 GLU cc_start: 0.8963 (tm-30) cc_final: 0.8365 (tm-30) REVERT: D 494 MET cc_start: 0.9100 (mmt) cc_final: 0.8790 (mmt) outliers start: 31 outliers final: 22 residues processed: 169 average time/residue: 0.2520 time to fit residues: 66.4770 Evaluate side-chains 169 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 146 time to evaluate : 1.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 680 ASP Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 933 THR Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1096 LEU Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain C residue 671 ILE Chi-restraints excluded: chain C residue 680 ASP Chi-restraints excluded: chain C residue 777 THR Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1096 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 326 ASP Chi-restraints excluded: chain D residue 491 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 57 optimal weight: 0.9990 chunk 62 optimal weight: 9.9990 chunk 172 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 124 optimal weight: 0.8980 chunk 64 optimal weight: 0.0980 chunk 27 optimal weight: 0.7980 chunk 138 optimal weight: 0.6980 chunk 111 optimal weight: 0.9980 chunk 74 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 360 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.142772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.111148 restraints weight = 19877.088| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.95 r_work: 0.3023 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2857 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2857 r_free = 0.2857 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2857 r_free = 0.2857 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2857 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 15604 Z= 0.103 Angle : 0.520 8.146 21064 Z= 0.271 Chirality : 0.040 0.154 2290 Planarity : 0.004 0.047 2694 Dihedral : 4.747 48.767 2064 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.29 % Favored : 90.71 % Rotamer: Outliers : 1.67 % Allowed : 10.35 % Favored : 87.98 % 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: -0.84 (0.20), residues: 1862 helix: 1.20 (0.19), residues: 862 sheet: -0.62 (0.42), residues: 160 loop : -2.56 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 369 HIS 0.006 0.001 HIS D 274 PHE 0.033 0.001 PHE D 550 TYR 0.012 0.001 TYR D 293 ARG 0.005 0.000 ARG D 387 Details of bonding type rmsd hydrogen bonds : bond 0.03413 ( 619) hydrogen bonds : angle 3.69099 ( 1782) metal coordination : bond 0.00742 ( 8) metal coordination : angle 2.08708 ( 6) SS BOND : bond 0.00022 ( 2) SS BOND : angle 1.10555 ( 4) covalent geometry : bond 0.00225 (15594) covalent geometry : angle 0.51881 (21054) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 151 time to evaluate : 1.674 Fit side-chains REVERT: A 726 GLU cc_start: 0.7754 (mp0) cc_final: 0.7491 (mp0) REVERT: A 944 MET cc_start: 0.8796 (mmm) cc_final: 0.8469 (mmm) REVERT: B 48 MET cc_start: 0.8770 (ttp) cc_final: 0.8569 (ttp) REVERT: B 101 ASN cc_start: 0.8609 (t0) cc_final: 0.8116 (t0) REVERT: B 412 GLU cc_start: 0.8930 (tm-30) cc_final: 0.8415 (tm-30) REVERT: B 494 MET cc_start: 0.9058 (mmt) cc_final: 0.8811 (mmt) REVERT: C 944 MET cc_start: 0.8791 (mmm) cc_final: 0.8458 (mmm) REVERT: D 101 ASN cc_start: 0.8682 (t0) cc_final: 0.8169 (t0) REVERT: D 412 GLU cc_start: 0.8906 (tm-30) cc_final: 0.8361 (tm-30) outliers start: 28 outliers final: 26 residues processed: 166 average time/residue: 0.2649 time to fit residues: 67.4045 Evaluate side-chains 173 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 147 time to evaluate : 1.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 680 ASP Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 933 THR Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1096 LEU Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 330 MET Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain C residue 671 ILE Chi-restraints excluded: chain C residue 680 ASP Chi-restraints excluded: chain C residue 777 THR Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 826 LEU Chi-restraints excluded: chain C residue 933 THR Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1096 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 491 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 21 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 82 optimal weight: 5.9990 chunk 148 optimal weight: 10.0000 chunk 182 optimal weight: 5.9990 chunk 138 optimal weight: 0.9990 chunk 122 optimal weight: 4.9990 chunk 140 optimal weight: 4.9990 chunk 131 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 22 optimal weight: 4.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.139443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.107222 restraints weight = 19826.945| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 1.91 r_work: 0.2960 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2785 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2785 r_free = 0.2785 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2785 r_free = 0.2785 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2785 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 15604 Z= 0.191 Angle : 0.583 7.556 21064 Z= 0.301 Chirality : 0.044 0.164 2290 Planarity : 0.004 0.057 2694 Dihedral : 4.891 50.754 2064 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.31 % Favored : 89.69 % Rotamer: Outliers : 2.03 % Allowed : 10.89 % Favored : 87.08 % 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: -0.83 (0.20), residues: 1862 helix: 1.17 (0.18), residues: 860 sheet: -0.42 (0.42), residues: 158 loop : -2.54 (0.20), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 369 HIS 0.006 0.001 HIS D 323 PHE 0.028 0.002 PHE D 550 TYR 0.013 0.002 TYR D 70 ARG 0.006 0.000 ARG D 387 Details of bonding type rmsd hydrogen bonds : bond 0.04360 ( 619) hydrogen bonds : angle 3.82863 ( 1782) metal coordination : bond 0.00630 ( 8) metal coordination : angle 2.38611 ( 6) SS BOND : bond 0.00124 ( 2) SS BOND : angle 0.81856 ( 4) covalent geometry : bond 0.00468 (15594) covalent geometry : angle 0.58145 (21054) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 148 time to evaluate : 1.954 Fit side-chains REVERT: A 944 MET cc_start: 0.8857 (mmm) cc_final: 0.8523 (mmm) REVERT: B 48 MET cc_start: 0.8822 (ttp) cc_final: 0.8604 (ttp) REVERT: B 101 ASN cc_start: 0.8613 (t0) cc_final: 0.8106 (t0) REVERT: B 158 LEU cc_start: 0.5369 (OUTLIER) cc_final: 0.5114 (tp) REVERT: B 412 GLU cc_start: 0.8948 (tm-30) cc_final: 0.8414 (tm-30) REVERT: B 494 MET cc_start: 0.9040 (mmt) cc_final: 0.8770 (mmt) REVERT: C 944 MET cc_start: 0.8867 (mmm) cc_final: 0.8525 (mmm) REVERT: D 48 MET cc_start: 0.8809 (ttp) cc_final: 0.8572 (ttp) REVERT: D 101 ASN cc_start: 0.8716 (t0) cc_final: 0.8188 (t0) REVERT: D 326 ASP cc_start: 0.6863 (OUTLIER) cc_final: 0.6393 (p0) REVERT: D 412 GLU cc_start: 0.8901 (tm-30) cc_final: 0.8347 (tm-30) outliers start: 34 outliers final: 28 residues processed: 168 average time/residue: 0.3148 time to fit residues: 80.3947 Evaluate side-chains 177 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 147 time to evaluate : 2.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 680 ASP Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 933 THR Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1096 LEU Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 330 MET Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain C residue 671 ILE Chi-restraints excluded: chain C residue 680 ASP Chi-restraints excluded: chain C residue 777 THR Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 826 LEU Chi-restraints excluded: chain C residue 933 THR Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1096 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 195 LYS Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 326 ASP Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain D residue 506 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 96 optimal weight: 5.9990 chunk 145 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 chunk 98 optimal weight: 0.8980 chunk 151 optimal weight: 0.5980 chunk 176 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 83 optimal weight: 7.9990 chunk 60 optimal weight: 8.9990 chunk 100 optimal weight: 5.9990 chunk 92 optimal weight: 0.8980 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.139808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.107477 restraints weight = 19847.269| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 1.94 r_work: 0.2965 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2799 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2799 r_free = 0.2799 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2799 r_free = 0.2799 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2799 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 15604 Z= 0.173 Angle : 0.568 8.627 21064 Z= 0.294 Chirality : 0.043 0.170 2290 Planarity : 0.004 0.051 2694 Dihedral : 4.924 53.470 2064 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.15 % Favored : 89.85 % Rotamer: Outliers : 2.15 % Allowed : 11.66 % Favored : 86.18 % 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: -0.74 (0.20), residues: 1862 helix: 1.26 (0.18), residues: 862 sheet: -0.38 (0.42), residues: 160 loop : -2.52 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 369 HIS 0.005 0.001 HIS D 274 PHE 0.032 0.001 PHE D 550 TYR 0.015 0.002 TYR D 70 ARG 0.005 0.000 ARG C 709 Details of bonding type rmsd hydrogen bonds : bond 0.04178 ( 619) hydrogen bonds : angle 3.79215 ( 1782) metal coordination : bond 0.00631 ( 8) metal coordination : angle 2.36190 ( 6) SS BOND : bond 0.00092 ( 2) SS BOND : angle 0.82480 ( 4) covalent geometry : bond 0.00421 (15594) covalent geometry : angle 0.56687 (21054) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 144 time to evaluate : 1.656 Fit side-chains REVERT: A 733 ARG cc_start: 0.8086 (tpp80) cc_final: 0.7868 (tpp80) REVERT: A 944 MET cc_start: 0.8848 (mmm) cc_final: 0.8514 (mmm) REVERT: B 48 MET cc_start: 0.8812 (ttp) cc_final: 0.8598 (ttp) REVERT: B 177 MET cc_start: 0.8360 (mtt) cc_final: 0.8106 (mtt) REVERT: B 326 ASP cc_start: 0.7049 (OUTLIER) cc_final: 0.6667 (p0) REVERT: B 412 GLU cc_start: 0.8927 (tm-30) cc_final: 0.8386 (tm-30) REVERT: B 494 MET cc_start: 0.9044 (mmt) cc_final: 0.8774 (mmt) REVERT: C 686 MET cc_start: 0.8495 (OUTLIER) cc_final: 0.7981 (mtp) REVERT: C 944 MET cc_start: 0.8859 (mmm) cc_final: 0.8520 (mmm) REVERT: D 48 MET cc_start: 0.8809 (ttp) cc_final: 0.8584 (ttp) REVERT: D 101 ASN cc_start: 0.8689 (t0) cc_final: 0.8244 (t0) REVERT: D 326 ASP cc_start: 0.6807 (OUTLIER) cc_final: 0.6319 (p0) REVERT: D 412 GLU cc_start: 0.8920 (tm-30) cc_final: 0.8356 (tm-30) outliers start: 36 outliers final: 29 residues processed: 166 average time/residue: 0.2514 time to fit residues: 64.5997 Evaluate side-chains 176 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 144 time to evaluate : 1.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 679 MET Chi-restraints excluded: chain A residue 680 ASP Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 933 THR Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1096 LEU Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 330 MET Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain C residue 671 ILE Chi-restraints excluded: chain C residue 680 ASP Chi-restraints excluded: chain C residue 686 MET Chi-restraints excluded: chain C residue 777 THR Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 826 LEU Chi-restraints excluded: chain C residue 933 THR Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1096 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 195 LYS Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 326 ASP Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain D residue 506 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 52 optimal weight: 8.9990 chunk 90 optimal weight: 4.9990 chunk 181 optimal weight: 2.9990 chunk 55 optimal weight: 9.9990 chunk 103 optimal weight: 8.9990 chunk 35 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 134 optimal weight: 0.7980 chunk 48 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 89 optimal weight: 0.0000 overall best weight: 1.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.140231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.106321 restraints weight = 19526.938| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 2.08 r_work: 0.2971 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2753 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2753 r_free = 0.2753 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2753 r_free = 0.2753 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2753 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 15604 Z= 0.154 Angle : 0.553 8.017 21064 Z= 0.286 Chirality : 0.042 0.150 2290 Planarity : 0.004 0.052 2694 Dihedral : 4.855 54.241 2064 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.10 % Favored : 89.90 % Rotamer: Outliers : 2.03 % Allowed : 11.66 % Favored : 86.30 % 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: -0.63 (0.20), residues: 1862 helix: 1.34 (0.18), residues: 864 sheet: -0.32 (0.42), residues: 160 loop : -2.48 (0.20), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 369 HIS 0.005 0.001 HIS D 274 PHE 0.029 0.001 PHE D 550 TYR 0.015 0.001 TYR D 70 ARG 0.006 0.000 ARG C 709 Details of bonding type rmsd hydrogen bonds : bond 0.03959 ( 619) hydrogen bonds : angle 3.73604 ( 1782) metal coordination : bond 0.00633 ( 8) metal coordination : angle 2.26269 ( 6) SS BOND : bond 0.00083 ( 2) SS BOND : angle 0.84685 ( 4) covalent geometry : bond 0.00372 (15594) covalent geometry : angle 0.55127 (21054) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 146 time to evaluate : 1.630 Fit side-chains REVERT: A 733 ARG cc_start: 0.8063 (tpp80) cc_final: 0.7812 (tpp-160) REVERT: A 944 MET cc_start: 0.8840 (mmm) cc_final: 0.8502 (mmm) REVERT: B 48 MET cc_start: 0.8935 (ttp) cc_final: 0.8713 (ttp) REVERT: B 326 ASP cc_start: 0.7118 (OUTLIER) cc_final: 0.6703 (p0) REVERT: B 412 GLU cc_start: 0.9010 (tm-30) cc_final: 0.8398 (tm-30) REVERT: B 494 MET cc_start: 0.9093 (mmt) cc_final: 0.8850 (mmt) REVERT: C 944 MET cc_start: 0.8809 (mmm) cc_final: 0.8451 (mmm) REVERT: D 48 MET cc_start: 0.8945 (ttp) cc_final: 0.8708 (ttp) REVERT: D 101 ASN cc_start: 0.8719 (t0) cc_final: 0.8266 (t0) REVERT: D 326 ASP cc_start: 0.6841 (OUTLIER) cc_final: 0.6372 (p0) REVERT: D 412 GLU cc_start: 0.8993 (tm-30) cc_final: 0.8394 (tm-30) outliers start: 34 outliers final: 28 residues processed: 167 average time/residue: 0.2576 time to fit residues: 66.0195 Evaluate side-chains 175 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 145 time to evaluate : 1.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 680 ASP Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1096 LEU Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 330 MET Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain C residue 671 ILE Chi-restraints excluded: chain C residue 680 ASP Chi-restraints excluded: chain C residue 777 THR Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 826 LEU Chi-restraints excluded: chain C residue 933 THR Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1096 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 195 LYS Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 326 ASP Chi-restraints excluded: chain D residue 330 MET Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain D residue 506 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 18 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 132 optimal weight: 7.9990 chunk 67 optimal weight: 3.9990 chunk 117 optimal weight: 3.9990 chunk 62 optimal weight: 0.0670 chunk 173 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 149 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 overall best weight: 1.8124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 360 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.141580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.108920 restraints weight = 19428.777| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 1.95 r_work: 0.2941 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2776 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2776 r_free = 0.2776 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2776 r_free = 0.2776 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2776 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 15604 Z= 0.158 Angle : 0.558 8.450 21064 Z= 0.288 Chirality : 0.042 0.152 2290 Planarity : 0.004 0.051 2694 Dihedral : 4.906 55.867 2064 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.42 % Favored : 89.58 % Rotamer: Outliers : 1.85 % Allowed : 12.08 % Favored : 86.06 % 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: -0.59 (0.20), residues: 1862 helix: 1.36 (0.18), residues: 864 sheet: -0.29 (0.42), residues: 160 loop : -2.44 (0.20), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 369 HIS 0.005 0.001 HIS D 274 PHE 0.031 0.001 PHE D 550 TYR 0.014 0.001 TYR B 70 ARG 0.005 0.000 ARG D 387 Details of bonding type rmsd hydrogen bonds : bond 0.04009 ( 619) hydrogen bonds : angle 3.74067 ( 1782) metal coordination : bond 0.00626 ( 8) metal coordination : angle 2.23201 ( 6) SS BOND : bond 0.00091 ( 2) SS BOND : angle 0.79948 ( 4) covalent geometry : bond 0.00383 (15594) covalent geometry : angle 0.55653 (21054) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 147 time to evaluate : 1.935 Fit side-chains REVERT: A 733 ARG cc_start: 0.8017 (tpp80) cc_final: 0.7770 (tpp-160) REVERT: A 944 MET cc_start: 0.8819 (mmm) cc_final: 0.8474 (mmm) REVERT: B 48 MET cc_start: 0.8932 (ttp) cc_final: 0.8702 (ttp) REVERT: B 326 ASP cc_start: 0.7118 (OUTLIER) cc_final: 0.6705 (p0) REVERT: B 412 GLU cc_start: 0.8993 (tm-30) cc_final: 0.8357 (tm-30) REVERT: B 494 MET cc_start: 0.9077 (mmt) cc_final: 0.8816 (mmt) REVERT: C 944 MET cc_start: 0.8794 (mmm) cc_final: 0.8433 (mmm) REVERT: D 48 MET cc_start: 0.8931 (ttp) cc_final: 0.8687 (ttp) REVERT: D 101 ASN cc_start: 0.8685 (t0) cc_final: 0.8223 (t0) REVERT: D 326 ASP cc_start: 0.6665 (OUTLIER) cc_final: 0.6209 (p0) REVERT: D 412 GLU cc_start: 0.8958 (tm-30) cc_final: 0.8326 (tm-30) outliers start: 31 outliers final: 28 residues processed: 164 average time/residue: 0.2893 time to fit residues: 73.1020 Evaluate side-chains 177 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 147 time to evaluate : 2.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 933 THR Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1096 LEU Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 330 MET Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain C residue 671 ILE Chi-restraints excluded: chain C residue 680 ASP Chi-restraints excluded: chain C residue 777 THR Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 826 LEU Chi-restraints excluded: chain C residue 933 THR Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1096 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 195 LYS Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 326 ASP Chi-restraints excluded: chain D residue 330 MET Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain D residue 506 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 8 optimal weight: 0.6980 chunk 6 optimal weight: 0.0870 chunk 96 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 169 optimal weight: 0.3980 chunk 136 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 46 optimal weight: 0.2980 chunk 58 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.144779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.112086 restraints weight = 19594.858| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.98 r_work: 0.3045 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2849 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2849 r_free = 0.2849 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2849 r_free = 0.2849 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2849 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 15604 Z= 0.096 Angle : 0.501 7.566 21064 Z= 0.259 Chirality : 0.040 0.139 2290 Planarity : 0.004 0.047 2694 Dihedral : 4.636 56.634 2064 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.34 % Favored : 90.66 % Rotamer: Outliers : 1.73 % Allowed : 12.32 % Favored : 85.94 % 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: -0.25 (0.20), residues: 1862 helix: 1.65 (0.19), residues: 862 sheet: -0.14 (0.42), residues: 160 loop : -2.25 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1086 HIS 0.004 0.001 HIS D 274 PHE 0.028 0.001 PHE D 550 TYR 0.015 0.001 TYR B 293 ARG 0.005 0.000 ARG C 709 Details of bonding type rmsd hydrogen bonds : bond 0.03027 ( 619) hydrogen bonds : angle 3.51298 ( 1782) metal coordination : bond 0.00594 ( 8) metal coordination : angle 1.80956 ( 6) SS BOND : bond 0.00023 ( 2) SS BOND : angle 0.86469 ( 4) covalent geometry : bond 0.00211 (15594) covalent geometry : angle 0.50023 (21054) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 156 time to evaluate : 1.894 Fit side-chains REVERT: A 733 ARG cc_start: 0.7975 (tpp80) cc_final: 0.7695 (tpp80) REVERT: B 48 MET cc_start: 0.8859 (ttp) cc_final: 0.8640 (ttp) REVERT: B 326 ASP cc_start: 0.6532 (OUTLIER) cc_final: 0.6155 (p0) REVERT: B 412 GLU cc_start: 0.9010 (tm-30) cc_final: 0.8388 (tm-30) REVERT: D 48 MET cc_start: 0.8809 (ttp) cc_final: 0.8566 (ttp) REVERT: D 101 ASN cc_start: 0.8640 (t0) cc_final: 0.8214 (t0) REVERT: D 326 ASP cc_start: 0.6433 (OUTLIER) cc_final: 0.5941 (p0) REVERT: D 353 GLU cc_start: 0.7200 (mp0) cc_final: 0.6908 (mp0) REVERT: D 412 GLU cc_start: 0.8825 (tm-30) cc_final: 0.8293 (tm-30) outliers start: 29 outliers final: 23 residues processed: 171 average time/residue: 0.2608 time to fit residues: 68.6283 Evaluate side-chains 173 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 148 time to evaluate : 1.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 933 THR Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1096 LEU Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 330 MET Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain C residue 680 ASP Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 826 LEU Chi-restraints excluded: chain C residue 933 THR Chi-restraints excluded: chain C residue 1096 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 195 LYS Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 326 ASP Chi-restraints excluded: chain D residue 330 MET Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain D residue 506 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 49 optimal weight: 4.9990 chunk 116 optimal weight: 0.0020 chunk 79 optimal weight: 0.7980 chunk 129 optimal weight: 2.9990 chunk 62 optimal weight: 7.9990 chunk 180 optimal weight: 0.1980 chunk 87 optimal weight: 0.0670 chunk 83 optimal weight: 4.9990 chunk 53 optimal weight: 0.0770 chunk 150 optimal weight: 3.9990 chunk 154 optimal weight: 0.9990 overall best weight: 0.2284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 820 ASN A 943 GLN B 380 HIS C 820 ASN D 41 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.147395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.116040 restraints weight = 19593.841| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 1.89 r_work: 0.3094 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2919 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2919 r_free = 0.2919 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2919 r_free = 0.2919 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2919 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 15604 Z= 0.089 Angle : 0.491 9.274 21064 Z= 0.252 Chirality : 0.039 0.141 2290 Planarity : 0.004 0.046 2694 Dihedral : 4.490 59.627 2064 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.08 % Favored : 90.92 % Rotamer: Outliers : 1.50 % Allowed : 12.80 % Favored : 85.71 % 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: -0.04 (0.21), residues: 1862 helix: 1.81 (0.19), residues: 860 sheet: 0.05 (0.42), residues: 160 loop : -2.15 (0.21), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1086 HIS 0.003 0.000 HIS D 274 PHE 0.026 0.001 PHE D 550 TYR 0.017 0.001 TYR D 293 ARG 0.005 0.000 ARG B 387 Details of bonding type rmsd hydrogen bonds : bond 0.02791 ( 619) hydrogen bonds : angle 3.41159 ( 1782) metal coordination : bond 0.00540 ( 8) metal coordination : angle 1.81906 ( 6) SS BOND : bond 0.00021 ( 2) SS BOND : angle 0.64175 ( 4) covalent geometry : bond 0.00190 (15594) covalent geometry : angle 0.49019 (21054) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8969.01 seconds wall clock time: 158 minutes 27.54 seconds (9507.54 seconds total)