Starting phenix.real_space_refine on Sun Dec 10 19:08:04 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eg1_31104/12_2023/7eg1_31104_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eg1_31104/12_2023/7eg1_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eg1_31104/12_2023/7eg1_31104.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eg1_31104/12_2023/7eg1_31104.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eg1_31104/12_2023/7eg1_31104_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eg1_31104/12_2023/7eg1_31104_trim_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 Mg 4 5.21 5 S 98 5.16 5 C 9766 2.51 5 N 2584 2.21 5 O 2806 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 675": "OE1" <-> "OE2" Residue "A GLU 687": "OE1" <-> "OE2" Residue "A ARG 705": "NH1" <-> "NH2" Residue "A ARG 709": "NH1" <-> "NH2" Residue "A ARG 717": "NH1" <-> "NH2" Residue "A ARG 733": "NH1" <-> "NH2" Residue "A GLU 743": "OE1" <-> "OE2" Residue "A GLU 893": "OE1" <-> "OE2" Residue "A GLU 903": "OE1" <-> "OE2" Residue "A GLU 935": "OE1" <-> "OE2" Residue "A GLU 959": "OE1" <-> "OE2" Residue "A GLU 1092": "OE1" <-> "OE2" Residue "A GLU 1100": "OE1" <-> "OE2" Residue "B ARG 20": "NH1" <-> "NH2" Residue "B GLU 25": "OE1" <-> "OE2" Residue "B ARG 28": "NH1" <-> "NH2" Residue "B ARG 37": "NH1" <-> "NH2" Residue "B GLU 42": "OE1" <-> "OE2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B ARG 118": "NH1" <-> "NH2" Residue "B ARG 129": "NH1" <-> "NH2" Residue "B ARG 166": "NH1" <-> "NH2" Residue "B ARG 187": "NH1" <-> "NH2" Residue "B GLU 189": "OE1" <-> "OE2" Residue "B GLU 212": "OE1" <-> "OE2" Residue "B ARG 217": "NH1" <-> "NH2" Residue "B GLU 253": "OE1" <-> "OE2" Residue "B ARG 262": "NH1" <-> "NH2" Residue "B ARG 269": "NH1" <-> "NH2" Residue "B ARG 306": "NH1" <-> "NH2" Residue "B GLU 308": "OE1" <-> "OE2" Residue "B GLU 318": "OE1" <-> "OE2" Residue "B ARG 328": "NH1" <-> "NH2" Residue "B ARG 334": "NH1" <-> "NH2" Residue "B GLU 345": "OE1" <-> "OE2" Residue "B GLU 354": "OE1" <-> "OE2" Residue "B ARG 378": "NH1" <-> "NH2" Residue "B GLU 404": "OE1" <-> "OE2" Residue "B ARG 426": "NH1" <-> "NH2" Residue "B GLU 464": "OE1" <-> "OE2" Residue "B GLU 520": "OE1" <-> "OE2" Residue "B ARG 527": "NH1" <-> "NH2" Residue "C GLU 675": "OE1" <-> "OE2" Residue "C GLU 687": "OE1" <-> "OE2" Residue "C ARG 705": "NH1" <-> "NH2" Residue "C ARG 709": "NH1" <-> "NH2" Residue "C ARG 717": "NH1" <-> "NH2" Residue "C ARG 733": "NH1" <-> "NH2" Residue "C GLU 743": "OE1" <-> "OE2" Residue "C GLU 893": "OE1" <-> "OE2" Residue "C GLU 903": "OE1" <-> "OE2" Residue "C GLU 935": "OE1" <-> "OE2" Residue "C GLU 959": "OE1" <-> "OE2" Residue "C GLU 1092": "OE1" <-> "OE2" Residue "C GLU 1100": "OE1" <-> "OE2" Residue "D ARG 20": "NH1" <-> "NH2" Residue "D ARG 28": "NH1" <-> "NH2" Residue "D ARG 37": "NH1" <-> "NH2" Residue "D ARG 46": "NH1" <-> "NH2" Residue "D ARG 118": "NH1" <-> "NH2" Residue "D ARG 129": "NH1" <-> "NH2" Residue "D ARG 166": "NH1" <-> "NH2" Residue "D ARG 187": "NH1" <-> "NH2" Residue "D GLU 212": "OE1" <-> "OE2" Residue "D ARG 217": "NH1" <-> "NH2" Residue "D GLU 246": "OE1" <-> "OE2" Residue "D ARG 262": "NH1" <-> "NH2" Residue "D ARG 269": "NH1" <-> "NH2" Residue "D ARG 306": "NH1" <-> "NH2" Residue "D GLU 308": "OE1" <-> "OE2" Residue "D GLU 318": "OE1" <-> "OE2" Residue "D ARG 328": "NH1" <-> "NH2" Residue "D ARG 334": "NH1" <-> "NH2" Residue "D GLU 336": "OE1" <-> "OE2" Residue "D ARG 378": "NH1" <-> "NH2" Residue "D GLU 404": "OE1" <-> "OE2" Residue "D ARG 426": "NH1" <-> "NH2" Residue "D GLU 464": "OE1" <-> "OE2" Residue "D GLU 520": "OE1" <-> "OE2" Residue "D ARG 527": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 15260 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 3004 Classifications: {'peptide': 372} Link IDs: {'PTRANS': 18, 'TRANS': 353} Chain breaks: 2 Chain: "B" Number of atoms: 4601 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 567, 4600 Classifications: {'peptide': 567} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 550} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Conformer: "B" Number of residues, atoms: 567, 4600 Classifications: {'peptide': 567} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 550} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 bond proxies already assigned to first conformer: 4689 Chain: "C" Number of atoms: 3004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 3004 Classifications: {'peptide': 372} Link IDs: {'PTRANS': 18, 'TRANS': 353} Chain breaks: 2 Chain: "D" Number of atoms: 4601 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 567, 4600 Classifications: {'peptide': 567} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 550} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Conformer: "B" Number of residues, atoms: 567, 4600 Classifications: {'peptide': 567} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 550} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 bond proxies already assigned to first conformer: 4689 Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 24 Unusual residues: {' MG': 2, 'X5M': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 24 Unusual residues: {' MG': 2, 'X5M': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5222 SG CYS B 277 75.199 72.840 74.712 1.00 40.55 S ATOM 5495 SG CYS B 311 74.956 74.493 78.226 1.00 33.93 S ATOM 5501 SG CYS B 312 72.082 71.970 76.521 1.00 28.39 S ATOM 12827 SG CYS D 277 24.929 60.113 74.543 1.00 41.45 S ATOM 13100 SG CYS D 311 25.437 58.632 78.226 1.00 33.13 S ATOM 13106 SG CYS D 312 28.303 61.099 76.520 1.00 27.35 S Time building chain proxies: 11.56, per 1000 atoms: 0.76 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.67 Conformation dependent library (CDL) restraints added in 4.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 601 " pdb="ZN ZN B 601 " - pdb=" ND1 HIS B 275 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 277 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 311 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 312 " pdb=" ZN D 601 " pdb="ZN ZN D 601 " - pdb=" ND1 HIS D 275 " pdb="ZN ZN D 601 " - pdb=" SG CYS D 277 " pdb="ZN ZN D 601 " - pdb=" SG CYS D 311 " pdb="ZN ZN D 601 " - pdb=" SG CYS D 312 " Number of angles added : 6 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3572 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 76 helices and 10 sheets defined 41.4% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.95 Creating SS restraints... Processing helix chain 'A' and resid 687 through 689 No H-bonds generated for 'chain 'A' and resid 687 through 689' Processing helix chain 'A' and resid 696 through 702 removed outlier: 3.653A pdb=" N GLU A 701 " --> pdb=" O PHE A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 722 removed outlier: 3.578A pdb=" N ARG A 717 " --> pdb=" O GLN A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 727 No H-bonds generated for 'chain 'A' and resid 724 through 727' Processing helix chain 'A' and resid 732 through 745 removed outlier: 3.717A pdb=" N GLY A 745 " --> pdb=" O ALA A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 754 through 768 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 817 through 819 No H-bonds generated for 'chain 'A' and resid 817 through 819' Processing helix chain 'A' and resid 823 through 834 Processing helix chain 'A' and resid 845 through 850 Processing helix chain 'A' and resid 854 through 858 Processing helix chain 'A' and resid 866 through 877 removed outlier: 3.508A pdb=" N LEU A 876 " --> pdb=" O ALA A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 881 through 883 No H-bonds generated for 'chain 'A' and resid 881 through 883' Processing helix chain 'A' and resid 891 through 905 Processing helix chain 'A' and resid 913 through 923 removed outlier: 3.511A pdb=" N LYS A 923 " --> pdb=" O LYS A 919 " (cutoff:3.500A) Processing helix chain 'A' and resid 935 through 950 Processing helix chain 'A' and resid 953 through 955 No H-bonds generated for 'chain 'A' and resid 953 through 955' Processing helix chain 'A' and resid 958 through 980 removed outlier: 3.628A pdb=" N GLU A 974 " --> pdb=" O ASN A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1007 Processing helix chain 'A' and resid 1009 through 1018 removed outlier: 3.503A pdb=" N SER A1015 " --> pdb=" O PRO A1011 " (cutoff:3.500A) Processing helix chain 'A' and resid 1074 through 1100 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 25 through 29 Processing helix chain 'B' and resid 34 through 53 Processing helix chain 'B' and resid 78 through 86 removed outlier: 3.542A pdb=" N ILE B 86 " --> pdb=" O SER B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 151 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 215 through 221 removed outlier: 4.413A pdb=" N GLU B 220 " --> pdb=" O GLN B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 231 Processing helix chain 'B' and resid 256 through 270 Processing helix chain 'B' and resid 334 through 342 Processing helix chain 'B' and resid 351 through 361 removed outlier: 3.586A pdb=" N ILE B 359 " --> pdb=" O VAL B 355 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N ASN B 360 " --> pdb=" O ILE B 356 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N THR B 361 " --> pdb=" O SER B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 401 removed outlier: 3.536A pdb=" N PHE B 400 " --> pdb=" O CYS B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 416 removed outlier: 4.412A pdb=" N GLN B 408 " --> pdb=" O GLU B 404 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER B 415 " --> pdb=" O CYS B 411 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N SER B 416 " --> pdb=" O GLU B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 432 No H-bonds generated for 'chain 'B' and resid 430 through 432' Processing helix chain 'B' and resid 467 through 483 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 515 No H-bonds generated for 'chain 'B' and resid 513 through 515' Processing helix chain 'B' and resid 520 through 523 removed outlier: 3.698A pdb=" N TYR B 523 " --> pdb=" O GLU B 520 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 520 through 523' Processing helix chain 'B' and resid 529 through 540 Processing helix chain 'B' and resid 553 through 558 removed outlier: 3.612A pdb=" N ILE B 557 " --> pdb=" O ASN B 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 689 No H-bonds generated for 'chain 'C' and resid 687 through 689' Processing helix chain 'C' and resid 696 through 702 removed outlier: 3.652A pdb=" N GLU C 701 " --> pdb=" O PHE C 697 " (cutoff:3.500A) Processing helix chain 'C' and resid 710 through 722 removed outlier: 3.580A pdb=" N ARG C 717 " --> pdb=" O GLN C 713 " (cutoff:3.500A) Processing helix chain 'C' and resid 724 through 727 No H-bonds generated for 'chain 'C' and resid 724 through 727' Processing helix chain 'C' and resid 732 through 745 removed outlier: 3.718A pdb=" N GLY C 745 " --> pdb=" O ALA C 741 " (cutoff:3.500A) Processing helix chain 'C' and resid 754 through 768 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 817 through 819 No H-bonds generated for 'chain 'C' and resid 817 through 819' Processing helix chain 'C' and resid 823 through 834 Processing helix chain 'C' and resid 845 through 850 Processing helix chain 'C' and resid 854 through 858 Processing helix chain 'C' and resid 866 through 877 removed outlier: 3.508A pdb=" N LEU C 876 " --> pdb=" O ALA C 872 " (cutoff:3.500A) Processing helix chain 'C' and resid 881 through 883 No H-bonds generated for 'chain 'C' and resid 881 through 883' Processing helix chain 'C' and resid 891 through 905 Processing helix chain 'C' and resid 913 through 923 removed outlier: 3.510A pdb=" N LYS C 923 " --> pdb=" O LYS C 919 " (cutoff:3.500A) Processing helix chain 'C' and resid 935 through 950 Processing helix chain 'C' and resid 953 through 955 No H-bonds generated for 'chain 'C' and resid 953 through 955' Processing helix chain 'C' and resid 958 through 980 removed outlier: 3.627A pdb=" N GLU C 974 " --> pdb=" O ASN C 970 " (cutoff:3.500A) Processing helix chain 'C' and resid 997 through 1007 Processing helix chain 'C' and resid 1009 through 1018 removed outlier: 3.502A pdb=" N SER C1015 " --> pdb=" O PRO C1011 " (cutoff:3.500A) Processing helix chain 'C' and resid 1074 through 1100 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 25 through 29 Processing helix chain 'D' and resid 34 through 53 Processing helix chain 'D' and resid 77 through 86 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 139 through 151 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 215 through 221 removed outlier: 4.439A pdb=" N GLU D 220 " --> pdb=" O GLN D 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 231 Processing helix chain 'D' and resid 257 through 270 Processing helix chain 'D' and resid 334 through 342 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) Processing helix chain 'D' and resid 351 through 361 removed outlier: 3.629A pdb=" N VAL D 355 " --> pdb=" O ALA D 351 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ILE D 359 " --> pdb=" O VAL D 355 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N ASN D 360 " --> pdb=" O ILE D 356 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N THR D 361 " --> pdb=" O SER D 357 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 401 removed outlier: 3.989A pdb=" N PHE D 400 " --> pdb=" O CYS D 396 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 416 removed outlier: 4.372A pdb=" N GLN D 408 " --> pdb=" O GLU D 404 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER D 415 " --> pdb=" O CYS D 411 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N SER D 416 " --> pdb=" O GLU D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 467 through 483 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 515 No H-bonds generated for 'chain 'D' and resid 513 through 515' Processing helix chain 'D' and resid 520 through 523 removed outlier: 3.662A pdb=" N TYR D 523 " --> pdb=" O GLU D 520 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 520 through 523' Processing helix chain 'D' and resid 529 through 540 Processing helix chain 'D' and resid 553 through 558 removed outlier: 3.638A pdb=" N ILE D 557 " --> pdb=" O ASN D 553 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 15 through 17 removed outlier: 6.762A pdb=" N VAL B 58 " --> pdb=" O LEU B 16 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 127 through 129 Processing sheet with id= C, first strand: chain 'B' and resid 204 through 207 removed outlier: 6.500A pdb=" N TYR B 236 " --> pdb=" O GLU B 205 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N LYS B 207 " --> pdb=" O TYR B 236 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N PHE B 238 " --> pdb=" O LYS B 207 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 420 through 422 Processing sheet with id= E, first strand: chain 'B' and resid 456 through 459 removed outlier: 6.757A pdb=" N LYS B 496 " --> pdb=" O THR B 457 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N HIS B 459 " --> pdb=" O LYS B 496 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N PHE B 498 " --> pdb=" O HIS B 459 " (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= F, first strand: chain 'D' and resid 15 through 17 removed outlier: 6.789A pdb=" N VAL D 58 " --> pdb=" O LEU D 16 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 127 through 129 Processing sheet with id= H, first strand: chain 'D' and resid 204 through 207 removed outlier: 6.504A pdb=" N TYR D 236 " --> pdb=" O GLU D 205 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N LYS D 207 " --> pdb=" O TYR D 236 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N PHE D 238 " --> pdb=" O LYS D 207 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 420 through 422 Processing sheet with id= J, first strand: chain 'D' and resid 456 through 459 removed outlier: 6.795A pdb=" N LYS D 496 " --> pdb=" O THR D 457 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N HIS D 459 " --> pdb=" O LYS D 496 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N PHE D 498 " --> pdb=" O HIS D 459 " (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) 480 hydrogen bonds defined for protein. 1428 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.66 Time building geometry restraints manager: 6.13 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: 99.75 - 106.60: 393 106.60 - 113.45: 8493 113.45 - 120.30: 5798 120.30 - 127.16: 6202 127.16 - 134.01: 168 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: 141 2.60 - 3.18: 13637 3.18 - 3.75: 21139 3.75 - 4.33: 33378 4.33 - 4.90: 54451 Nonbonded interactions: 122746 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 122741 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = (chain 'B' and (resid 2 through 439 or resid 441 through 568 or resid 601)) selection = (chain 'D' and (resid 2 through 439 or resid 441 through 568 or resid 601)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.35 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.380 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: 2.560 Check model and map are aligned: 0.220 Set scattering table: 0.140 Process input model: 49.770 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.820 ------------------------------------------------------------------------------- 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 : 0.006 0.095 15594 Z= 0.388 Angle : 0.653 14.372 21054 Z= 0.376 Chirality : 0.042 0.171 2290 Planarity : 0.005 0.112 2694 Dihedral : 14.261 89.557 5844 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 16.04 Ramachandran Plot: Outliers : 0.11 % Allowed : 11.92 % Favored : 87.97 % Rotamer: Outliers : 0.36 % Allowed : 3.29 % Favored : 96.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.05 (0.15), residues: 1862 helix: -3.47 (0.12), residues: 836 sheet: -2.17 (0.38), residues: 160 loop : -3.41 (0.18), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1026 HIS 0.009 0.001 HIS D 323 PHE 0.033 0.001 PHE D 550 TYR 0.024 0.002 TYR D 70 ARG 0.003 0.000 ARG B 309 *********************** 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 fitting. rotamer outliers: 6 poor density : 199 time to evaluate : 1.792 Fit side-chains outliers start: 6 outliers final: 0 residues processed: 204 average time/residue: 0.3106 time to fit residues: 91.3934 Evaluate side-chains 154 residues out of total 1674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 1.850 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 157 optimal weight: 3.9990 chunk 140 optimal weight: 0.8980 chunk 78 optimal weight: 8.9990 chunk 48 optimal weight: 0.7980 chunk 95 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 145 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 chunk 108 optimal weight: 0.0770 chunk 168 optimal weight: 2.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 15594 Z= 0.157 Angle : 0.553 8.484 21054 Z= 0.286 Chirality : 0.041 0.176 2290 Planarity : 0.004 0.044 2694 Dihedral : 4.758 37.644 2064 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.24 % Favored : 90.76 % Rotamer: Outliers : 0.72 % Allowed : 6.88 % Favored : 92.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.96 (0.17), residues: 1862 helix: -1.12 (0.16), residues: 852 sheet: -1.44 (0.41), residues: 160 loop : -2.99 (0.19), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 369 HIS 0.003 0.001 HIS D 380 PHE 0.033 0.001 PHE D 550 TYR 0.013 0.001 TYR D 499 ARG 0.004 0.000 ARG D 376 *********************** 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 180 residues out of total 1674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 168 time to evaluate : 1.897 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 7 residues processed: 174 average time/residue: 0.2576 time to fit residues: 69.3496 Evaluate side-chains 151 residues out of total 1674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 144 time to evaluate : 1.818 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1540 time to fit residues: 4.5069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 93 optimal weight: 10.0000 chunk 52 optimal weight: 10.0000 chunk 140 optimal weight: 3.9990 chunk 115 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 169 optimal weight: 5.9990 chunk 182 optimal weight: 4.9990 chunk 150 optimal weight: 0.0170 chunk 167 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 135 optimal weight: 0.4980 overall best weight: 1.7024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 936 ASN C 936 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 15594 Z= 0.233 Angle : 0.545 8.047 21054 Z= 0.282 Chirality : 0.042 0.149 2290 Planarity : 0.004 0.055 2694 Dihedral : 4.633 32.267 2064 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.04 % Favored : 89.90 % Rotamer: Outliers : 1.20 % Allowed : 9.09 % Favored : 89.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.19), residues: 1862 helix: 0.16 (0.18), residues: 850 sheet: -1.03 (0.41), residues: 160 loop : -2.83 (0.19), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C1026 HIS 0.006 0.001 HIS D 274 PHE 0.030 0.001 PHE D 550 TYR 0.013 0.002 TYR D 70 ARG 0.004 0.000 ARG C 709 *********************** 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 175 residues out of total 1674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 155 time to evaluate : 1.769 Fit side-chains outliers start: 20 outliers final: 15 residues processed: 168 average time/residue: 0.2442 time to fit residues: 64.4911 Evaluate side-chains 158 residues out of total 1674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 143 time to evaluate : 1.710 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1491 time to fit residues: 6.4347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 167 optimal weight: 9.9990 chunk 127 optimal weight: 2.9990 chunk 87 optimal weight: 9.9990 chunk 18 optimal weight: 3.9990 chunk 80 optimal weight: 6.9990 chunk 113 optimal weight: 0.6980 chunk 169 optimal weight: 1.9990 chunk 179 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 160 optimal weight: 7.9990 chunk 48 optimal weight: 1.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 15594 Z= 0.251 Angle : 0.547 7.905 21054 Z= 0.282 Chirality : 0.042 0.152 2290 Planarity : 0.004 0.054 2694 Dihedral : 4.737 44.170 2064 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.10 % Favored : 89.90 % Rotamer: Outliers : 0.90 % Allowed : 10.47 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.19), residues: 1862 helix: 0.63 (0.18), residues: 850 sheet: -0.80 (0.41), residues: 160 loop : -2.66 (0.19), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 369 HIS 0.004 0.001 HIS D 274 PHE 0.030 0.001 PHE D 550 TYR 0.012 0.002 TYR D 70 ARG 0.005 0.000 ARG C 709 *********************** 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 164 residues out of total 1674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 149 time to evaluate : 1.891 Fit side-chains outliers start: 15 outliers final: 8 residues processed: 159 average time/residue: 0.2539 time to fit residues: 63.7471 Evaluate side-chains 151 residues out of total 1674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 143 time to evaluate : 1.781 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1512 time to fit residues: 4.7123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 149 optimal weight: 3.9990 chunk 102 optimal weight: 0.4980 chunk 2 optimal weight: 6.9990 chunk 133 optimal weight: 4.9990 chunk 74 optimal weight: 8.9990 chunk 153 optimal weight: 9.9990 chunk 124 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 91 optimal weight: 0.8980 chunk 161 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 15594 Z= 0.286 Angle : 0.560 8.035 21054 Z= 0.288 Chirality : 0.043 0.159 2290 Planarity : 0.004 0.057 2694 Dihedral : 4.833 48.237 2064 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.42 % Favored : 89.58 % Rotamer: Outliers : 0.78 % Allowed : 11.30 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.20), residues: 1862 helix: 0.80 (0.18), residues: 850 sheet: -0.70 (0.41), residues: 160 loop : -2.59 (0.19), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C1026 HIS 0.005 0.001 HIS B 323 PHE 0.031 0.001 PHE D 550 TYR 0.014 0.002 TYR D 70 ARG 0.005 0.000 ARG C 709 *********************** 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 160 residues out of total 1674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 147 time to evaluate : 1.938 Fit side-chains outliers start: 13 outliers final: 6 residues processed: 153 average time/residue: 0.2596 time to fit residues: 62.1062 Evaluate side-chains 150 residues out of total 1674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 144 time to evaluate : 1.947 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1407 time to fit residues: 4.1646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 60 optimal weight: 9.9990 chunk 161 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 105 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 179 optimal weight: 2.9990 chunk 149 optimal weight: 5.9990 chunk 83 optimal weight: 7.9990 chunk 14 optimal weight: 0.9980 chunk 59 optimal weight: 0.3980 chunk 94 optimal weight: 0.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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** D 360 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15594 Z= 0.160 Angle : 0.501 7.481 21054 Z= 0.258 Chirality : 0.040 0.139 2290 Planarity : 0.003 0.045 2694 Dihedral : 4.602 49.106 2064 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.61 % Favored : 90.39 % Rotamer: Outliers : 0.78 % Allowed : 12.08 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.20), residues: 1862 helix: 1.15 (0.19), residues: 852 sheet: -0.48 (0.42), residues: 160 loop : -2.45 (0.20), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 369 HIS 0.003 0.001 HIS D 274 PHE 0.030 0.001 PHE D 550 TYR 0.013 0.001 TYR D 293 ARG 0.007 0.000 ARG D 387 *********************** 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 165 residues out of total 1674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 152 time to evaluate : 1.937 Fit side-chains outliers start: 13 outliers final: 8 residues processed: 160 average time/residue: 0.2485 time to fit residues: 63.0763 Evaluate side-chains 152 residues out of total 1674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 144 time to evaluate : 1.783 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1569 time to fit residues: 4.7171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 173 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 102 optimal weight: 0.9990 chunk 131 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 151 optimal weight: 10.0000 chunk 100 optimal weight: 1.9990 chunk 179 optimal weight: 0.9980 chunk 112 optimal weight: 2.9990 chunk 109 optimal weight: 0.5980 chunk 82 optimal weight: 0.8980 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15594 Z= 0.168 Angle : 0.502 7.504 21054 Z= 0.258 Chirality : 0.040 0.144 2290 Planarity : 0.003 0.050 2694 Dihedral : 4.500 50.529 2064 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.67 % Favored : 90.33 % Rotamer: Outliers : 0.42 % Allowed : 12.80 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.20), residues: 1862 helix: 1.31 (0.19), residues: 852 sheet: -0.32 (0.42), residues: 160 loop : -2.36 (0.20), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1086 HIS 0.003 0.001 HIS D 274 PHE 0.028 0.001 PHE D 550 TYR 0.015 0.001 TYR D 293 ARG 0.006 0.000 ARG D 387 *********************** 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 155 residues out of total 1674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 148 time to evaluate : 1.876 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 152 average time/residue: 0.2503 time to fit residues: 60.0802 Evaluate side-chains 146 residues out of total 1674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 143 time to evaluate : 1.770 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1611 time to fit residues: 3.5601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 110 optimal weight: 6.9990 chunk 71 optimal weight: 5.9990 chunk 107 optimal weight: 8.9990 chunk 54 optimal weight: 2.9990 chunk 35 optimal weight: 7.9990 chunk 34 optimal weight: 0.9980 chunk 113 optimal weight: 0.9990 chunk 122 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 140 optimal weight: 3.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 15594 Z= 0.195 Angle : 0.512 7.412 21054 Z= 0.262 Chirality : 0.041 0.140 2290 Planarity : 0.003 0.047 2694 Dihedral : 4.548 52.363 2064 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.77 % Favored : 90.23 % Rotamer: Outliers : 0.36 % Allowed : 13.04 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.20), residues: 1862 helix: 1.33 (0.19), residues: 850 sheet: -0.24 (0.42), residues: 160 loop : -2.31 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 369 HIS 0.003 0.001 HIS D 274 PHE 0.029 0.001 PHE D 550 TYR 0.014 0.001 TYR D 293 ARG 0.005 0.000 ARG D 387 *********************** 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 152 residues out of total 1674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 146 time to evaluate : 1.830 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 148 average time/residue: 0.2538 time to fit residues: 59.6660 Evaluate side-chains 146 residues out of total 1674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 142 time to evaluate : 1.695 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1559 time to fit residues: 3.5125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 163 optimal weight: 0.9990 chunk 171 optimal weight: 0.6980 chunk 156 optimal weight: 0.8980 chunk 167 optimal weight: 0.9980 chunk 100 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 131 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 150 optimal weight: 0.9990 chunk 158 optimal weight: 4.9990 chunk 166 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 15594 Z= 0.148 Angle : 0.488 7.822 21054 Z= 0.249 Chirality : 0.040 0.138 2290 Planarity : 0.003 0.047 2694 Dihedral : 4.406 53.123 2064 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.24 % Favored : 90.76 % Rotamer: Outliers : 0.30 % Allowed : 13.34 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.20), residues: 1862 helix: 1.52 (0.19), residues: 848 sheet: -0.13 (0.42), residues: 160 loop : -2.24 (0.21), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1086 HIS 0.003 0.001 HIS D 274 PHE 0.028 0.001 PHE D 550 TYR 0.014 0.001 TYR D 293 ARG 0.005 0.000 ARG D 387 *********************** 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 156 residues out of total 1674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 151 time to evaluate : 1.821 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 154 average time/residue: 0.2541 time to fit residues: 61.8215 Evaluate side-chains 151 residues out of total 1674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 148 time to evaluate : 1.808 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1421 time to fit residues: 3.2965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 109 optimal weight: 0.9990 chunk 176 optimal weight: 2.9990 chunk 107 optimal weight: 7.9990 chunk 83 optimal weight: 2.9990 chunk 122 optimal weight: 5.9990 chunk 185 optimal weight: 3.9990 chunk 170 optimal weight: 4.9990 chunk 147 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 113 optimal weight: 0.8980 chunk 90 optimal weight: 4.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 367 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 15594 Z= 0.233 Angle : 0.527 7.360 21054 Z= 0.270 Chirality : 0.042 0.147 2290 Planarity : 0.004 0.050 2694 Dihedral : 4.576 54.560 2064 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.69 % Favored : 89.31 % Rotamer: Outliers : 0.18 % Allowed : 13.46 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.20), residues: 1862 helix: 1.37 (0.19), residues: 850 sheet: -0.10 (0.42), residues: 160 loop : -2.26 (0.21), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C1026 HIS 0.006 0.001 HIS D 274 PHE 0.029 0.001 PHE D 550 TYR 0.014 0.001 TYR D 293 ARG 0.005 0.000 ARG D 387 ********************** 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 154 residues out of total 1674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 151 time to evaluate : 1.651 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 152 average time/residue: 0.2445 time to fit residues: 58.9869 Evaluate side-chains 150 residues out of total 1674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 147 time to evaluate : 1.720 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1624 time to fit residues: 3.2593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 117 optimal weight: 1.9990 chunk 157 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 136 optimal weight: 6.9990 chunk 21 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 147 optimal weight: 7.9990 chunk 61 optimal weight: 0.8980 chunk 151 optimal weight: 0.0030 chunk 18 optimal weight: 0.8980 chunk 27 optimal weight: 8.9990 overall best weight: 0.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 367 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.143622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.112816 restraints weight = 19715.809| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.90 r_work: 0.3037 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2851 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2851 r_free = 0.2851 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2851 r_free = 0.2851 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2851 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 15594 Z= 0.137 Angle : 0.481 7.595 21054 Z= 0.246 Chirality : 0.039 0.137 2290 Planarity : 0.003 0.043 2694 Dihedral : 4.375 54.018 2064 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.51 % Favored : 90.49 % Rotamer: Outliers : 0.06 % Allowed : 13.76 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.21), residues: 1862 helix: 1.63 (0.19), residues: 848 sheet: 0.02 (0.43), residues: 160 loop : -2.18 (0.21), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1086 HIS 0.004 0.001 HIS D 274 PHE 0.029 0.001 PHE D 550 TYR 0.015 0.001 TYR B 293 ARG 0.005 0.000 ARG D 387 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2921.65 seconds wall clock time: 54 minutes 23.14 seconds (3263.14 seconds total)