Starting phenix.real_space_refine on Wed Mar 4 17:45:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7eg1_31104/03_2026/7eg1_31104_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7eg1_31104/03_2026/7eg1_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_31104/03_2026/7eg1_31104.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7eg1_31104/03_2026/7eg1_31104.map" model { file = "/net/cci-nas-00/data/ceres_data/7eg1_31104/03_2026/7eg1_31104_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7eg1_31104/03_2026/7eg1_31104_trim.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 5.27, per 1000 atoms: 0.35 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: 1.14 Conformation dependent library (CDL) restraints added in 933.2 milliseconds 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: 0.51 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: 2.65 Time building geometry restraints manager: 1.55 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: 0.03 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 601)) selection = (chain 'D' and (resid 2 through 439 or resid 441 through 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: 0.540 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: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 18.220 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.050 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.770 ------------------------------------------------------------------------------- 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 : 16.12 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.003 0.000 ARG B 309 TYR 0.024 0.002 TYR D 70 PHE 0.033 0.001 PHE D 550 TRP 0.010 0.001 TRP A1026 HIS 0.009 0.001 HIS D 323 Details of bonding type rmsd covalent geometry : bond 0.00604 (15594) covalent geometry : angle 0.65312 (21054) SS BOND : bond 0.00085 ( 2) SS BOND : angle 0.88426 ( 4) hydrogen bonds : bond 0.29721 ( 619) hydrogen bonds : angle 9.81496 ( 1782) metal coordination : bond 0.29639 ( 8) metal coordination : angle 12.11512 ( 6) *********************** 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 : 0.478 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: 0.8550 (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: 0.8124 (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: 0.8546 (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: 0.8248 (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: 0.1419 time to fit residues: 41.9601 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 : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.4980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.0870 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.0270 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 6.9990 overall best weight: 0.5216 ------------------------------------------------------------------------------- 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 = 0.3624 r_free = 0.3624 target = 0.142614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.111106 restraints weight = 19579.623| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 1.99 r_work: 0.3032 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2808 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2808 r_free = 0.2808 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2808 r_free = 0.2808 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2808 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15604 Z= 0.121 Angle : 0.586 8.847 21064 Z= 0.307 Chirality : 0.041 0.146 2290 Planarity : 0.005 0.046 2694 Dihedral : 4.916 38.102 2064 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.45 % Favored : 90.55 % Rotamer: Outliers : 0.72 % Allowed : 5.92 % Favored : 93.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.72 (0.18), residues: 1862 helix: -0.91 (0.16), residues: 858 sheet: -1.34 (0.41), residues: 158 loop : -2.89 (0.19), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 387 TYR 0.013 0.001 TYR D 499 PHE 0.034 0.001 PHE B 550 TRP 0.011 0.001 TRP B 369 HIS 0.004 0.001 HIS C 869 Details of bonding type rmsd covalent geometry : bond 0.00257 (15594) covalent geometry : angle 0.58080 (21054) SS BOND : bond 0.00752 ( 2) SS BOND : angle 1.47565 ( 4) hydrogen bonds : bond 0.04574 ( 619) hydrogen bonds : angle 4.24987 ( 1782) metal coordination : bond 0.02062 ( 8) metal coordination : angle 4.52535 ( 6) *********************** 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 176 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 164 time to evaluate : 0.462 Fit side-chains REVERT: A 679 MET cc_start: 0.6953 (ptp) cc_final: 0.6709 (ptp) REVERT: A 944 MET cc_start: 0.8704 (mmm) cc_final: 0.8251 (mmm) REVERT: B 101 ASN cc_start: 0.8593 (t0) cc_final: 0.8079 (t0) REVERT: B 352 TYR cc_start: 0.7196 (t80) cc_final: 0.6307 (t80) REVERT: B 494 MET cc_start: 0.9166 (mmt) cc_final: 0.8936 (mmt) REVERT: C 679 MET cc_start: 0.7005 (ptp) cc_final: 0.6676 (ptp) REVERT: C 944 MET cc_start: 0.8804 (mmm) cc_final: 0.8442 (mmm) REVERT: D 48 MET cc_start: 0.8889 (ttp) cc_final: 0.8674 (ttp) REVERT: D 101 ASN cc_start: 0.8470 (t0) cc_final: 0.8157 (t0) REVERT: D 360 ASN cc_start: 0.7685 (OUTLIER) cc_final: 0.7381 (t0) REVERT: D 412 GLU cc_start: 0.8767 (tm-30) cc_final: 0.8271 (tm-30) REVERT: D 472 GLN cc_start: 0.8780 (tp40) cc_final: 0.8538 (tp40) REVERT: D 494 MET cc_start: 0.9170 (mmt) cc_final: 0.8890 (mmt) outliers start: 12 outliers final: 9 residues processed: 170 average time/residue: 0.1100 time to fit residues: 28.9702 Evaluate side-chains 147 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 137 time to evaluate : 0.561 ------------------------------------------------------------------------------- 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 1096 LEU 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 C residue 1096 LEU 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 148 optimal weight: 10.0000 chunk 130 optimal weight: 7.9990 chunk 131 optimal weight: 1.9990 chunk 142 optimal weight: 0.9990 chunk 174 optimal weight: 7.9990 chunk 182 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 133 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 154 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 360 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.140442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.107156 restraints weight = 19867.562| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 2.02 r_work: 0.2973 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2759 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2759 r_free = 0.2759 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2759 r_free = 0.2759 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2759 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.1933 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= 0.163 Angle : 0.576 8.079 21064 Z= 0.300 Chirality : 0.043 0.209 2290 Planarity : 0.004 0.055 2694 Dihedral : 4.790 33.610 2064 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.31 % Favored : 89.69 % Rotamer: Outliers : 1.85 % Allowed : 7.89 % Favored : 90.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.19), residues: 1862 helix: 0.39 (0.18), residues: 860 sheet: -0.91 (0.42), residues: 158 loop : -2.74 (0.19), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 387 TYR 0.012 0.002 TYR D 70 PHE 0.030 0.001 PHE D 550 TRP 0.007 0.001 TRP D 369 HIS 0.006 0.001 HIS D 274 Details of bonding type rmsd covalent geometry : bond 0.00391 (15594) covalent geometry : angle 0.57378 (21054) SS BOND : bond 0.00062 ( 2) SS BOND : angle 1.32286 ( 4) hydrogen bonds : bond 0.04620 ( 619) hydrogen bonds : angle 3.99123 ( 1782) metal coordination : bond 0.01073 ( 8) metal coordination : angle 2.93255 ( 6) *********************** 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 174 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 143 time to evaluate : 0.469 Fit side-chains REVERT: A 679 MET cc_start: 0.6936 (ptp) cc_final: 0.6722 (ptp) REVERT: A 944 MET cc_start: 0.8824 (mmm) cc_final: 0.8423 (mmm) REVERT: B 101 ASN cc_start: 0.8653 (t0) cc_final: 0.8099 (t0) REVERT: B 360 ASN cc_start: 0.7866 (OUTLIER) cc_final: 0.7616 (t0) REVERT: B 494 MET cc_start: 0.9144 (mmt) cc_final: 0.8887 (mmt) REVERT: C 944 MET cc_start: 0.8856 (mmm) cc_final: 0.8476 (mmm) REVERT: D 48 MET cc_start: 0.8996 (ttp) cc_final: 0.8784 (ttp) REVERT: D 101 ASN cc_start: 0.8583 (t0) cc_final: 0.8142 (t0) REVERT: D 412 GLU cc_start: 0.8810 (tm-30) cc_final: 0.8245 (tm-30) REVERT: D 494 MET cc_start: 0.9148 (mmt) cc_final: 0.8892 (mmt) outliers start: 31 outliers final: 22 residues processed: 164 average time/residue: 0.0946 time to fit residues: 25.1723 Evaluate side-chains 159 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 136 time to evaluate : 0.352 ------------------------------------------------------------------------------- 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 360 ASN Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain C residue 671 ILE Chi-restraints excluded: chain C residue 777 THR 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 460 MET Chi-restraints excluded: chain D residue 491 VAL 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 62 optimal weight: 1.9990 chunk 125 optimal weight: 0.9980 chunk 176 optimal weight: 6.9990 chunk 124 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 162 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 chunk 33 optimal weight: 8.9990 chunk 24 optimal weight: 0.3980 chunk 158 optimal weight: 9.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 936 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.143011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.110993 restraints weight = 19870.560| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 1.97 r_work: 0.3016 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2841 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2841 r_free = 0.2841 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 = 0.2841 r_free = 0.2841 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2841 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 15604 Z= 0.106 Angle : 0.520 7.912 21064 Z= 0.270 Chirality : 0.041 0.175 2290 Planarity : 0.004 0.048 2694 Dihedral : 4.626 36.333 2064 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.97 % Favored : 91.03 % Rotamer: Outliers : 1.50 % Allowed : 8.97 % Favored : 89.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.20), residues: 1862 helix: 1.04 (0.18), residues: 862 sheet: -0.75 (0.42), residues: 160 loop : -2.58 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 709 TYR 0.012 0.001 TYR B 293 PHE 0.031 0.001 PHE D 550 TRP 0.008 0.001 TRP B 369 HIS 0.005 0.001 HIS D 274 Details of bonding type rmsd covalent geometry : bond 0.00236 (15594) covalent geometry : angle 0.51835 (21054) SS BOND : bond 0.00035 ( 2) SS BOND : angle 1.04898 ( 4) hydrogen bonds : bond 0.03483 ( 619) hydrogen bonds : angle 3.69973 ( 1782) metal coordination : bond 0.00942 ( 8) metal coordination : angle 2.42484 ( 6) *********************** 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 183 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 158 time to evaluate : 0.464 Fit side-chains REVERT: A 944 MET cc_start: 0.8831 (mmm) cc_final: 0.8482 (mmm) REVERT: B 101 ASN cc_start: 0.8663 (t0) cc_final: 0.8170 (t0) REVERT: B 412 GLU cc_start: 0.8859 (tm-30) cc_final: 0.8358 (tm-30) REVERT: B 494 MET cc_start: 0.9107 (mmt) cc_final: 0.8882 (mmt) REVERT: C 944 MET cc_start: 0.8813 (mmm) cc_final: 0.8478 (mmm) REVERT: D 101 ASN cc_start: 0.8660 (t0) cc_final: 0.8181 (t0) REVERT: D 412 GLU cc_start: 0.8835 (tm-30) cc_final: 0.8327 (tm-30) REVERT: D 494 MET cc_start: 0.9109 (mmt) cc_final: 0.8851 (mmt) outliers start: 25 outliers final: 23 residues processed: 172 average time/residue: 0.1038 time to fit residues: 28.3850 Evaluate side-chains 168 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 145 time to evaluate : 0.597 ------------------------------------------------------------------------------- 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 B residue 506 THR 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 62 optimal weight: 0.5980 chunk 49 optimal weight: 5.9990 chunk 159 optimal weight: 6.9990 chunk 146 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 118 optimal weight: 0.8980 chunk 30 optimal weight: 6.9990 chunk 33 optimal weight: 8.9990 chunk 177 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 936 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.140311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.109173 restraints weight = 19887.048| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 1.92 r_work: 0.2984 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2823 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2823 r_free = 0.2823 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 = 0.2823 r_free = 0.2823 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2823 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 15604 Z= 0.152 Angle : 0.551 7.441 21064 Z= 0.286 Chirality : 0.043 0.155 2290 Planarity : 0.004 0.054 2694 Dihedral : 4.703 45.567 2064 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.04 % Favored : 89.96 % 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 : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.20), residues: 1862 helix: 1.18 (0.18), residues: 864 sheet: -0.58 (0.42), residues: 160 loop : -2.59 (0.20), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 387 TYR 0.013 0.001 TYR D 293 PHE 0.027 0.001 PHE D 550 TRP 0.006 0.001 TRP B 369 HIS 0.006 0.001 HIS D 274 Details of bonding type rmsd covalent geometry : bond 0.00367 (15594) covalent geometry : angle 0.54915 (21054) SS BOND : bond 0.00105 ( 2) SS BOND : angle 0.85486 ( 4) hydrogen bonds : bond 0.04057 ( 619) hydrogen bonds : angle 3.75921 ( 1782) metal coordination : bond 0.00719 ( 8) metal coordination : angle 2.29923 ( 6) *********************** 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 175 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 144 time to evaluate : 0.536 Fit side-chains REVERT: A 686 MET cc_start: 0.8535 (mtp) cc_final: 0.8127 (mmm) REVERT: A 944 MET cc_start: 0.8840 (mmm) cc_final: 0.8481 (mmm) REVERT: B 101 ASN cc_start: 0.8630 (t0) cc_final: 0.8130 (t0) REVERT: B 412 GLU cc_start: 0.8918 (tm-30) cc_final: 0.8378 (tm-30) REVERT: B 494 MET cc_start: 0.9068 (mmt) cc_final: 0.8837 (mmt) REVERT: C 944 MET cc_start: 0.8835 (mmm) cc_final: 0.8487 (mmm) REVERT: D 101 ASN cc_start: 0.8699 (t0) cc_final: 0.8191 (t0) REVERT: D 326 ASP cc_start: 0.6971 (OUTLIER) cc_final: 0.6516 (p0) REVERT: D 360 ASN cc_start: 0.7708 (OUTLIER) cc_final: 0.7480 (t0) REVERT: D 412 GLU cc_start: 0.8890 (tm-30) cc_final: 0.8336 (tm-30) REVERT: D 494 MET cc_start: 0.9090 (mmt) cc_final: 0.8854 (mmt) outliers start: 31 outliers final: 26 residues processed: 163 average time/residue: 0.1126 time to fit residues: 28.8807 Evaluate side-chains 170 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 142 time to evaluate : 0.621 ------------------------------------------------------------------------------- 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 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 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 360 ASN Chi-restraints excluded: chain D residue 460 MET Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain D residue 506 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 66 optimal weight: 10.0000 chunk 67 optimal weight: 9.9990 chunk 32 optimal weight: 0.7980 chunk 90 optimal weight: 0.0770 chunk 50 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 101 optimal weight: 1.9990 chunk 151 optimal weight: 0.0980 chunk 71 optimal weight: 6.9990 chunk 147 optimal weight: 10.0000 overall best weight: 0.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 ASN B 327 ASN ** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.143009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.111047 restraints weight = 19771.619| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 1.92 r_work: 0.3027 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2862 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2862 r_free = 0.2862 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 = 0.2862 r_free = 0.2862 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2862 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 15604 Z= 0.103 Angle : 0.511 7.768 21064 Z= 0.265 Chirality : 0.041 0.140 2290 Planarity : 0.004 0.048 2694 Dihedral : 4.601 48.898 2064 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.34 % Favored : 90.66 % Rotamer: Outliers : 1.97 % Allowed : 10.83 % Favored : 87.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.20), residues: 1862 helix: 1.43 (0.19), residues: 864 sheet: -0.39 (0.41), residues: 164 loop : -2.45 (0.20), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 387 TYR 0.013 0.001 TYR B 293 PHE 0.030 0.001 PHE D 550 TRP 0.008 0.001 TRP B 369 HIS 0.005 0.001 HIS D 274 Details of bonding type rmsd covalent geometry : bond 0.00232 (15594) covalent geometry : angle 0.50971 (21054) SS BOND : bond 0.00019 ( 2) SS BOND : angle 0.84370 ( 4) hydrogen bonds : bond 0.03373 ( 619) hydrogen bonds : angle 3.57858 ( 1782) metal coordination : bond 0.00766 ( 8) metal coordination : angle 2.00607 ( 6) *********************** 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 181 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 148 time to evaluate : 0.604 Fit side-chains REVERT: A 944 MET cc_start: 0.8820 (mmm) cc_final: 0.8476 (mmm) REVERT: B 101 ASN cc_start: 0.8623 (t0) cc_final: 0.8145 (t0) REVERT: B 412 GLU cc_start: 0.8924 (tm-30) cc_final: 0.8386 (tm-30) REVERT: B 494 MET cc_start: 0.9062 (mmt) cc_final: 0.8842 (mmt) REVERT: C 944 MET cc_start: 0.8810 (mmm) cc_final: 0.8468 (mmm) REVERT: D 101 ASN cc_start: 0.8746 (t0) cc_final: 0.8247 (t0) REVERT: D 326 ASP cc_start: 0.6764 (OUTLIER) cc_final: 0.6190 (p0) REVERT: D 360 ASN cc_start: 0.7630 (OUTLIER) cc_final: 0.7374 (t0) REVERT: D 412 GLU cc_start: 0.8886 (tm-30) cc_final: 0.8329 (tm-30) REVERT: D 494 MET cc_start: 0.9075 (mmt) cc_final: 0.8851 (mmt) outliers start: 33 outliers final: 28 residues processed: 168 average time/residue: 0.1165 time to fit residues: 30.2614 Evaluate side-chains 170 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 140 time to evaluate : 0.590 ------------------------------------------------------------------------------- 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 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 B residue 506 THR 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 326 ASP Chi-restraints excluded: chain D residue 330 MET Chi-restraints excluded: chain D residue 360 ASN 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 13 optimal weight: 0.6980 chunk 127 optimal weight: 7.9990 chunk 147 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 107 optimal weight: 4.9990 chunk 148 optimal weight: 3.9990 chunk 79 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 83 optimal weight: 6.9990 chunk 39 optimal weight: 5.9990 chunk 44 optimal weight: 0.9980 overall best weight: 1.2382 ------------------------------------------------------------------------------- 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 = 0.3614 r_free = 0.3614 target = 0.141876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.109761 restraints weight = 19613.350| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 1.92 r_work: 0.3003 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- 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: 0.8526 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 15604 Z= 0.125 Angle : 0.527 7.930 21064 Z= 0.272 Chirality : 0.041 0.144 2290 Planarity : 0.004 0.049 2694 Dihedral : 4.610 51.354 2064 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.72 % Favored : 90.28 % Rotamer: Outliers : 1.79 % Allowed : 11.42 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.20), residues: 1862 helix: 1.48 (0.18), residues: 864 sheet: -0.28 (0.42), residues: 160 loop : -2.40 (0.20), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 387 TYR 0.014 0.001 TYR D 293 PHE 0.026 0.001 PHE D 550 TRP 0.006 0.001 TRP B 369 HIS 0.003 0.001 HIS B 323 Details of bonding type rmsd covalent geometry : bond 0.00297 (15594) covalent geometry : angle 0.52585 (21054) SS BOND : bond 0.00034 ( 2) SS BOND : angle 0.71327 ( 4) hydrogen bonds : bond 0.03596 ( 619) hydrogen bonds : angle 3.59609 ( 1782) metal coordination : bond 0.00628 ( 8) metal coordination : angle 2.02503 ( 6) *********************** 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 173 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 143 time to evaluate : 0.623 Fit side-chains REVERT: A 686 MET cc_start: 0.8610 (mtp) cc_final: 0.8143 (mmm) REVERT: A 944 MET cc_start: 0.8833 (mmm) cc_final: 0.8486 (mmm) REVERT: B 101 ASN cc_start: 0.8627 (t0) cc_final: 0.8155 (t0) REVERT: B 158 LEU cc_start: 0.5274 (OUTLIER) cc_final: 0.5013 (tp) REVERT: B 412 GLU cc_start: 0.8912 (tm-30) cc_final: 0.8358 (tm-30) REVERT: B 494 MET cc_start: 0.9073 (mmt) cc_final: 0.8841 (mmt) REVERT: C 944 MET cc_start: 0.8839 (mmm) cc_final: 0.8491 (mmm) REVERT: D 101 ASN cc_start: 0.8712 (t0) cc_final: 0.8176 (t0) REVERT: D 326 ASP cc_start: 0.6755 (OUTLIER) cc_final: 0.6208 (p0) REVERT: D 360 ASN cc_start: 0.7622 (OUTLIER) cc_final: 0.7313 (t0) REVERT: D 412 GLU cc_start: 0.8885 (tm-30) cc_final: 0.8315 (tm-30) REVERT: D 494 MET cc_start: 0.9082 (mmt) cc_final: 0.8845 (mmt) outliers start: 30 outliers final: 26 residues processed: 161 average time/residue: 0.1187 time to fit residues: 29.7086 Evaluate side-chains 171 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 142 time to evaluate : 0.575 ------------------------------------------------------------------------------- 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 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 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 360 ASN 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 44 optimal weight: 6.9990 chunk 46 optimal weight: 0.9990 chunk 78 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 135 optimal weight: 0.7980 chunk 153 optimal weight: 8.9990 chunk 1 optimal weight: 0.0070 chunk 144 optimal weight: 5.9990 chunk 115 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 overall best weight: 1.5602 ------------------------------------------------------------------------------- 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 = 0.3605 r_free = 0.3605 target = 0.141132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.108959 restraints weight = 19773.986| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 1.93 r_work: 0.2992 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2813 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2813 r_free = 0.2813 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2813 r_free = 0.2813 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2813 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 15604 Z= 0.142 Angle : 0.540 7.673 21064 Z= 0.279 Chirality : 0.042 0.147 2290 Planarity : 0.004 0.048 2694 Dihedral : 4.709 54.918 2064 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.51 % Favored : 90.49 % Rotamer: Outliers : 1.97 % Allowed : 11.42 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.20), residues: 1862 helix: 1.46 (0.18), residues: 864 sheet: -0.24 (0.41), residues: 164 loop : -2.36 (0.20), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 709 TYR 0.014 0.001 TYR B 70 PHE 0.030 0.001 PHE D 550 TRP 0.006 0.001 TRP B 369 HIS 0.004 0.001 HIS D 323 Details of bonding type rmsd covalent geometry : bond 0.00341 (15594) covalent geometry : angle 0.53913 (21054) SS BOND : bond 0.00039 ( 2) SS BOND : angle 0.64697 ( 4) hydrogen bonds : bond 0.03791 ( 619) hydrogen bonds : angle 3.63505 ( 1782) metal coordination : bond 0.00663 ( 8) metal coordination : angle 2.12912 ( 6) *********************** 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 176 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 143 time to evaluate : 0.531 Fit side-chains REVERT: A 686 MET cc_start: 0.8576 (mtp) cc_final: 0.8116 (mmm) REVERT: A 944 MET cc_start: 0.8860 (mmm) cc_final: 0.8512 (mmm) REVERT: B 101 ASN cc_start: 0.8642 (t0) cc_final: 0.8157 (t0) REVERT: B 158 LEU cc_start: 0.5237 (OUTLIER) cc_final: 0.5018 (tp) REVERT: B 412 GLU cc_start: 0.8922 (tm-30) cc_final: 0.8376 (tm-30) REVERT: B 494 MET cc_start: 0.9062 (mmt) cc_final: 0.8797 (mmt) REVERT: C 944 MET cc_start: 0.8851 (mmm) cc_final: 0.8493 (mmm) REVERT: D 101 ASN cc_start: 0.8678 (t0) cc_final: 0.8236 (t0) REVERT: D 326 ASP cc_start: 0.6797 (OUTLIER) cc_final: 0.6236 (p0) REVERT: D 360 ASN cc_start: 0.7651 (OUTLIER) cc_final: 0.7295 (t0) REVERT: D 412 GLU cc_start: 0.8909 (tm-30) cc_final: 0.8309 (tm-30) REVERT: D 494 MET cc_start: 0.9083 (mmt) cc_final: 0.8846 (mmt) outliers start: 33 outliers final: 28 residues processed: 162 average time/residue: 0.1177 time to fit residues: 29.7938 Evaluate side-chains 174 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 143 time to evaluate : 0.588 ------------------------------------------------------------------------------- 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 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 330 MET Chi-restraints excluded: chain D residue 360 ASN 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 114 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 139 optimal weight: 0.6980 chunk 84 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 171 optimal weight: 0.7980 chunk 154 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 94 optimal weight: 6.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.3620 r_free = 0.3620 target = 0.142316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.110440 restraints weight = 19520.407| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 1.93 r_work: 0.3008 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2843 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2843 r_free = 0.2843 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 = 0.2843 r_free = 0.2843 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2843 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15604 Z= 0.116 Angle : 0.520 7.867 21064 Z= 0.269 Chirality : 0.041 0.143 2290 Planarity : 0.004 0.047 2694 Dihedral : 4.622 56.360 2064 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.67 % Favored : 90.33 % Rotamer: Outliers : 2.09 % Allowed : 11.36 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.20), residues: 1862 helix: 1.57 (0.19), residues: 864 sheet: -0.17 (0.41), residues: 164 loop : -2.28 (0.21), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 387 TYR 0.015 0.001 TYR B 293 PHE 0.027 0.001 PHE D 550 TRP 0.007 0.001 TRP B 369 HIS 0.003 0.001 HIS C 836 Details of bonding type rmsd covalent geometry : bond 0.00273 (15594) covalent geometry : angle 0.51902 (21054) SS BOND : bond 0.00043 ( 2) SS BOND : angle 0.74214 ( 4) hydrogen bonds : bond 0.03451 ( 619) hydrogen bonds : angle 3.55365 ( 1782) metal coordination : bond 0.00661 ( 8) metal coordination : angle 1.90246 ( 6) *********************** 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 181 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 146 time to evaluate : 0.704 Fit side-chains REVERT: A 814 TYR cc_start: 0.7708 (OUTLIER) cc_final: 0.7471 (m-10) REVERT: A 944 MET cc_start: 0.8847 (mmm) cc_final: 0.8506 (mmm) REVERT: B 254 MET cc_start: 0.7694 (tpt) cc_final: 0.7413 (tpp) REVERT: B 412 GLU cc_start: 0.8927 (tm-30) cc_final: 0.8361 (tm-30) REVERT: B 494 MET cc_start: 0.9071 (mmt) cc_final: 0.8834 (mmt) REVERT: C 944 MET cc_start: 0.8828 (mmm) cc_final: 0.8474 (mmm) REVERT: D 101 ASN cc_start: 0.8671 (t0) cc_final: 0.8243 (t0) REVERT: D 326 ASP cc_start: 0.6655 (OUTLIER) cc_final: 0.6113 (p0) REVERT: D 353 GLU cc_start: 0.7388 (mp0) cc_final: 0.7082 (mp0) REVERT: D 360 ASN cc_start: 0.7586 (OUTLIER) cc_final: 0.7232 (t0) REVERT: D 412 GLU cc_start: 0.8925 (tm-30) cc_final: 0.8309 (tm-30) REVERT: D 494 MET cc_start: 0.9085 (mmt) cc_final: 0.8844 (mmt) outliers start: 35 outliers final: 27 residues processed: 165 average time/residue: 0.1201 time to fit residues: 30.8250 Evaluate side-chains 173 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 143 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 680 ASP Chi-restraints excluded: chain A residue 814 TYR 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 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 360 ASN 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 53 optimal weight: 0.0980 chunk 64 optimal weight: 0.7980 chunk 92 optimal weight: 0.7980 chunk 137 optimal weight: 0.9990 chunk 59 optimal weight: 0.0050 chunk 13 optimal weight: 0.7980 chunk 79 optimal weight: 5.9990 chunk 71 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 176 optimal weight: 9.9990 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 360 ASN D 41 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.145713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.114216 restraints weight = 19772.463| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 1.93 r_work: 0.3058 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2909 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2909 r_free = 0.2909 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2909 r_free = 0.2909 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2909 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.2950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 15604 Z= 0.094 Angle : 0.501 8.753 21064 Z= 0.258 Chirality : 0.040 0.138 2290 Planarity : 0.004 0.045 2694 Dihedral : 4.460 57.595 2064 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.61 % Favored : 90.39 % Rotamer: Outliers : 1.85 % Allowed : 11.72 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.21), residues: 1862 helix: 1.76 (0.19), residues: 860 sheet: 0.08 (0.42), residues: 160 loop : -2.18 (0.21), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 387 TYR 0.014 0.001 TYR B 293 PHE 0.028 0.001 PHE D 550 TRP 0.009 0.001 TRP A1086 HIS 0.002 0.000 HIS A 869 Details of bonding type rmsd covalent geometry : bond 0.00207 (15594) covalent geometry : angle 0.50029 (21054) SS BOND : bond 0.00028 ( 2) SS BOND : angle 0.70006 ( 4) hydrogen bonds : bond 0.02934 ( 619) hydrogen bonds : angle 3.42733 ( 1782) metal coordination : bond 0.00600 ( 8) metal coordination : angle 1.81566 ( 6) ********************** 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 188 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 157 time to evaluate : 0.571 Fit side-chains REVERT: A 686 MET cc_start: 0.8516 (mtp) cc_final: 0.8207 (mtp) REVERT: A 698 ASP cc_start: 0.8747 (m-30) cc_final: 0.8534 (m-30) REVERT: A 944 MET cc_start: 0.8795 (mmm) cc_final: 0.8461 (mmm) REVERT: B 101 ASN cc_start: 0.8635 (t0) cc_final: 0.8300 (t0) REVERT: B 326 ASP cc_start: 0.6455 (OUTLIER) cc_final: 0.6136 (p0) REVERT: B 330 MET cc_start: 0.8625 (OUTLIER) cc_final: 0.8318 (mtm) REVERT: B 412 GLU cc_start: 0.8926 (tm-30) cc_final: 0.8367 (tm-30) REVERT: C 681 ASN cc_start: 0.7330 (m110) cc_final: 0.7090 (t0) REVERT: C 944 MET cc_start: 0.8794 (mmm) cc_final: 0.8451 (mmm) REVERT: D 101 ASN cc_start: 0.8636 (t0) cc_final: 0.8248 (t0) REVERT: D 326 ASP cc_start: 0.6429 (OUTLIER) cc_final: 0.5968 (p0) REVERT: D 330 MET cc_start: 0.8560 (OUTLIER) cc_final: 0.8257 (mtm) REVERT: D 353 GLU cc_start: 0.7322 (mp0) cc_final: 0.7080 (mp0) REVERT: D 360 ASN cc_start: 0.7459 (OUTLIER) cc_final: 0.7130 (t0) REVERT: D 412 GLU cc_start: 0.8786 (tm-30) cc_final: 0.8332 (tm-30) REVERT: D 494 MET cc_start: 0.9074 (mmt) cc_final: 0.8852 (mmt) outliers start: 31 outliers final: 23 residues processed: 176 average time/residue: 0.1168 time to fit residues: 31.9255 Evaluate side-chains 174 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 146 time to evaluate : 0.628 ------------------------------------------------------------------------------- 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 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 326 ASP Chi-restraints excluded: chain D residue 330 MET Chi-restraints excluded: chain D residue 360 ASN 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 178 optimal weight: 4.9990 chunk 167 optimal weight: 7.9990 chunk 107 optimal weight: 0.9980 chunk 181 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 137 optimal weight: 2.9990 chunk 146 optimal weight: 10.0000 chunk 9 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 = 0.3621 r_free = 0.3621 target = 0.142320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.110883 restraints weight = 19542.243| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 1.99 r_work: 0.3010 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2827 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2827 r_free = 0.2827 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 = 0.2827 r_free = 0.2827 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2827 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 15604 Z= 0.131 Angle : 0.527 7.381 21064 Z= 0.272 Chirality : 0.041 0.144 2290 Planarity : 0.004 0.061 2694 Dihedral : 4.584 59.492 2064 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.94 % Favored : 90.06 % Rotamer: Outliers : 1.73 % Allowed : 11.72 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.20), residues: 1862 helix: 1.67 (0.19), residues: 864 sheet: 0.06 (0.42), residues: 160 loop : -2.19 (0.21), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 387 TYR 0.017 0.001 TYR D 293 PHE 0.025 0.001 PHE D 550 TRP 0.007 0.001 TRP B 369 HIS 0.003 0.001 HIS D 323 Details of bonding type rmsd covalent geometry : bond 0.00313 (15594) covalent geometry : angle 0.52635 (21054) SS BOND : bond 0.00084 ( 2) SS BOND : angle 0.58626 ( 4) hydrogen bonds : bond 0.03545 ( 619) hydrogen bonds : angle 3.52387 ( 1782) metal coordination : bond 0.00567 ( 8) metal coordination : angle 1.88315 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4009.26 seconds wall clock time: 69 minutes 19.61 seconds (4159.61 seconds total)