Starting phenix.real_space_refine on Sat May 24 12:40:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ydx_39184/05_2025/8ydx_39184.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ydx_39184/05_2025/8ydx_39184.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ydx_39184/05_2025/8ydx_39184.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ydx_39184/05_2025/8ydx_39184.map" model { file = "/net/cci-nas-00/data/ceres_data/8ydx_39184/05_2025/8ydx_39184.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ydx_39184/05_2025/8ydx_39184.cif" } resolution = 4.9 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= 0.002 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: 4 Type Number sf(0) Gaussians S 117 5.16 5 C 16261 2.51 5 N 4204 2.21 5 O 4889 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 25471 Number of models: 1 Model: "" Number of chains: 7 Chain: "D" Number of atoms: 330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 330 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'TRANS': 38} Chain: "C" Number of atoms: 8008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 8008 Classifications: {'peptide': 1024} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 54, 'TRANS': 969} Chain breaks: 7 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 8086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1035, 8086 Classifications: {'peptide': 1035} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 54, 'TRANS': 980} Chain breaks: 6 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 8009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 8009 Classifications: {'peptide': 1024} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 53, 'TRANS': 970} Chain breaks: 9 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Restraints were copied for chains: E, F Time building chain proxies: 15.96, per 1000 atoms: 0.63 Number of scatterers: 25471 At special positions: 0 Unit cell: (182.88, 145.44, 155.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 117 16.00 O 4889 8.00 N 4204 7.00 C 16261 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 282 " " NAG A1302 " - " ASN A 331 " " NAG A1303 " - " ASN A 616 " " NAG A1304 " - " ASN A 709 " " NAG A1305 " - " ASN A 717 " " NAG A1306 " - " ASN A 801 " " NAG A1307 " - " ASN A1074 " " NAG A1308 " - " ASN A1098 " " NAG A1309 " - " ASN A1134 " " NAG B1301 " - " ASN B 282 " " NAG B1302 " - " ASN B 331 " " NAG B1303 " - " ASN B 616 " " NAG B1304 " - " ASN B 709 " " NAG B1305 " - " ASN B 717 " " NAG B1306 " - " ASN B 801 " " NAG B1307 " - " ASN B1074 " " NAG B1308 " - " ASN B1098 " " NAG B1309 " - " ASN B1134 " " NAG C1301 " - " ASN C 282 " " NAG C1302 " - " ASN C 331 " " NAG C1303 " - " ASN C 616 " " NAG C1304 " - " ASN C 709 " " NAG C1305 " - " ASN C 717 " " NAG C1306 " - " ASN C1098 " " NAG C1307 " - " ASN C1074 " " NAG C1308 " - " ASN C1134 " " NAG C1309 " - " ASN C 801 " Time building additional restraints: 6.09 Conformation dependent library (CDL) restraints added in 3.2 seconds 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6002 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 52 sheets defined 28.5% alpha, 28.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.93 Creating SS restraints... Processing helix chain 'D' and resid 1 through 19 removed outlier: 3.873A pdb=" N ILE D 5 " --> pdb=" O ASP D 1 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 38 removed outlier: 3.557A pdb=" N ARG D 38 " --> pdb=" O GLU D 34 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 19 Processing helix chain 'F' and resid 21 through 38 removed outlier: 3.558A pdb=" N ARG F 38 " --> pdb=" O GLU F 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 19 Processing helix chain 'E' and resid 21 through 38 removed outlier: 3.557A pdb=" N ARG E 38 " --> pdb=" O GLU E 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.711A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 383 through 388 removed outlier: 3.953A pdb=" N ASN C 388 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.344A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 755 Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.558A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.287A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.603A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.022A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.870A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.751A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.710A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 383 through 388 removed outlier: 3.953A pdb=" N ASN B 388 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.345A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 757 removed outlier: 3.775A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N TYR B 756 " --> pdb=" O LEU B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.190A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.582A pdb=" N ARG B 983 " --> pdb=" O ASP B 979 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.143A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 4.305A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.711A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 383 through 388 removed outlier: 3.953A pdb=" N ASN A 388 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.345A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.634A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.522A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.221A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.585A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.972A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.975A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.281A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 42 through 43 removed outlier: 5.923A pdb=" N PHE C 43 " --> pdb=" O ARG A 567 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ASP A 568 " --> pdb=" O THR A 573 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N THR A 573 " --> pdb=" O ASP A 568 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.820A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.758A pdb=" N ARG C 237 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N PHE C 106 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N GLN C 239 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N TRP C 104 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 135 through 144 removed outlier: 7.008A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 10.254A pdb=" N ASP C 138 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 9.203A pdb=" N PHE C 157 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 11.177A pdb=" N PHE C 140 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 8.670A pdb=" N SER C 155 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N GLY C 142 " --> pdb=" O MET C 153 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N MET C 153 " --> pdb=" O GLY C 142 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.487A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 325 through 328 removed outlier: 5.489A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 13.319A pdb=" N THR C 572 " --> pdb=" O PRO C 589 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N THR C 573 " --> pdb=" O ASP C 568 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N ASP C 568 " --> pdb=" O THR C 573 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AA9, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.614A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.968A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.968A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 701 through 703 removed outlier: 6.131A pdb=" N ALA C 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AB7, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.906A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 733 through 735 removed outlier: 4.317A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 788 through 790 removed outlier: 5.763A pdb=" N ILE C 788 " --> pdb=" O ASN A 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.435A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AC3, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.567A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ASN B 188 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ILE B 210 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N ARG B 190 " --> pdb=" O THR B 208 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N THR B 208 " --> pdb=" O ARG B 190 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N PHE B 192 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N LYS B 206 " --> pdb=" O PHE B 192 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N PHE B 194 " --> pdb=" O TYR B 204 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N TYR B 204 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N ASN B 196 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N LYS B 202 " --> pdb=" O ASN B 196 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.648A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 83 through 85 removed outlier: 4.708A pdb=" N TYR B 145 " --> pdb=" O ARG B 246 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N TYR B 144 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N GLU B 154 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 83 through 85 removed outlier: 6.102A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 314 through 319 removed outlier: 6.130A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.503A pdb=" N GLU B 583 " --> pdb=" O ASP B 578 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AD1, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.615A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD3, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD4, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.320A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.614A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.320A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.614A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 701 through 703 Processing sheet with id=AD7, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.388A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.388A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.400A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.457A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.379A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.676A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'A' and resid 84 through 85 removed outlier: 5.682A pdb=" N TYR A 144 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N GLU A 154 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.260A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL A 126 " --> pdb=" O TYR A 170 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N TYR A 170 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.734A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AE8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.614A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AF1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AF2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.099A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.456A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.099A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.456A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.557A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.189A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.220A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'A' and resid 1094 through 1097 1136 hydrogen bonds defined for protein. 3162 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: 13.28 Time building geometry restraints manager: 7.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 6641 1.33 - 1.46: 5632 1.46 - 1.59: 13626 1.59 - 1.72: 0 1.72 - 1.85: 153 Bond restraints: 26052 Sorted by residual: bond pdb=" N GLN A 271 " pdb=" CA GLN A 271 " ideal model delta sigma weight residual 1.453 1.484 -0.031 8.30e-03 1.45e+04 1.40e+01 bond pdb=" CA PRO A 792 " pdb=" C PRO A 792 " ideal model delta sigma weight residual 1.514 1.535 -0.021 5.50e-03 3.31e+04 1.40e+01 bond pdb=" N GLN C 271 " pdb=" CA GLN C 271 " ideal model delta sigma weight residual 1.453 1.484 -0.031 8.30e-03 1.45e+04 1.40e+01 bond pdb=" N VAL A 729 " pdb=" CA VAL A 729 " ideal model delta sigma weight residual 1.456 1.491 -0.035 9.50e-03 1.11e+04 1.33e+01 bond pdb=" N ILE B 714 " pdb=" CA ILE B 714 " ideal model delta sigma weight residual 1.457 1.490 -0.032 9.00e-03 1.23e+04 1.29e+01 ... (remaining 26047 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.23: 31897 2.23 - 4.45: 3351 4.45 - 6.68: 167 6.68 - 8.91: 20 8.91 - 11.13: 5 Bond angle restraints: 35440 Sorted by residual: angle pdb=" N THR B 618 " pdb=" CA THR B 618 " pdb=" C THR B 618 " ideal model delta sigma weight residual 112.54 101.96 10.58 1.22e+00 6.72e-01 7.51e+01 angle pdb=" CA THR C 470 " pdb=" CB THR C 470 " pdb=" OG1 THR C 470 " ideal model delta sigma weight residual 109.60 98.94 10.66 1.50e+00 4.44e-01 5.05e+01 angle pdb=" CA THR B 470 " pdb=" CB THR B 470 " pdb=" OG1 THR B 470 " ideal model delta sigma weight residual 109.60 98.94 10.66 1.50e+00 4.44e-01 5.05e+01 angle pdb=" CA THR A 470 " pdb=" CB THR A 470 " pdb=" OG1 THR A 470 " ideal model delta sigma weight residual 109.60 98.94 10.66 1.50e+00 4.44e-01 5.05e+01 angle pdb=" N THR B 761 " pdb=" CA THR B 761 " pdb=" C THR B 761 " ideal model delta sigma weight residual 111.36 104.78 6.58 1.09e+00 8.42e-01 3.64e+01 ... (remaining 35435 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 14133 17.87 - 35.74: 1247 35.74 - 53.61: 280 53.61 - 71.48: 55 71.48 - 89.35: 40 Dihedral angle restraints: 15755 sinusoidal: 6440 harmonic: 9315 Sorted by residual: dihedral pdb=" C CYS B 617 " pdb=" N CYS B 617 " pdb=" CA CYS B 617 " pdb=" CB CYS B 617 " ideal model delta harmonic sigma weight residual -122.60 -142.26 19.66 0 2.50e+00 1.60e-01 6.18e+01 dihedral pdb=" N CYS B 617 " pdb=" C CYS B 617 " pdb=" CA CYS B 617 " pdb=" CB CYS B 617 " ideal model delta harmonic sigma weight residual 122.80 140.95 -18.15 0 2.50e+00 1.60e-01 5.27e+01 dihedral pdb=" CA PHE C 371 " pdb=" C PHE C 371 " pdb=" N ALA C 372 " pdb=" CA ALA C 372 " ideal model delta harmonic sigma weight residual -180.00 -157.49 -22.51 0 5.00e+00 4.00e-02 2.03e+01 ... (remaining 15752 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.162: 3746 0.162 - 0.324: 327 0.324 - 0.486: 4 0.486 - 0.648: 0 0.648 - 0.809: 4 Chirality restraints: 4081 Sorted by residual: chirality pdb=" C1 NAG B1302 " pdb=" ND2 ASN B 331 " pdb=" C2 NAG B1302 " pdb=" O5 NAG B1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.59 -0.81 2.00e-01 2.50e+01 1.64e+01 chirality pdb=" C1 NAG C1302 " pdb=" ND2 ASN C 331 " pdb=" C2 NAG C1302 " pdb=" O5 NAG C1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.62 -0.78 2.00e-01 2.50e+01 1.52e+01 chirality pdb=" CA CYS B 617 " pdb=" N CYS B 617 " pdb=" C CYS B 617 " pdb=" CB CYS B 617 " both_signs ideal model delta sigma weight residual False 2.51 1.76 0.75 2.00e-01 2.50e+01 1.42e+01 ... (remaining 4078 not shown) Planarity restraints: 4585 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1309 " 0.120 2.00e-02 2.50e+03 9.90e-02 1.23e+02 pdb=" C7 NAG C1309 " -0.033 2.00e-02 2.50e+03 pdb=" C8 NAG C1309 " 0.089 2.00e-02 2.50e+03 pdb=" N2 NAG C1309 " -0.159 2.00e-02 2.50e+03 pdb=" O7 NAG C1309 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1302 " 0.051 2.00e-02 2.50e+03 4.25e-02 2.26e+01 pdb=" C7 NAG C1302 " -0.013 2.00e-02 2.50e+03 pdb=" C8 NAG C1302 " 0.038 2.00e-02 2.50e+03 pdb=" N2 NAG C1302 " -0.069 2.00e-02 2.50e+03 pdb=" O7 NAG C1302 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1309 " -0.049 2.00e-02 2.50e+03 4.09e-02 2.09e+01 pdb=" C7 NAG B1309 " 0.018 2.00e-02 2.50e+03 pdb=" C8 NAG B1309 " -0.039 2.00e-02 2.50e+03 pdb=" N2 NAG B1309 " 0.064 2.00e-02 2.50e+03 pdb=" O7 NAG B1309 " 0.007 2.00e-02 2.50e+03 ... (remaining 4582 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 190 2.58 - 3.16: 21294 3.16 - 3.74: 41022 3.74 - 4.32: 57522 4.32 - 4.90: 93855 Nonbonded interactions: 213883 Sorted by model distance: nonbonded pdb=" SG CYS B 738 " pdb=" SG CYS B 760 " model vdw 2.004 3.760 nonbonded pdb=" SG CYS A 743 " pdb=" SG CYS A 749 " model vdw 2.025 3.760 nonbonded pdb=" SG CYS C 738 " pdb=" SG CYS C 760 " model vdw 2.025 3.760 nonbonded pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " model vdw 2.026 3.760 nonbonded pdb=" SG CYS B 617 " pdb=" SG CYS B 649 " model vdw 2.026 3.760 ... (remaining 213878 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 66 or resid 80 through 331 or (resid 332 and (n \ ame N or name CA or name C or name O or name CB )) or resid 334 through 1146 or \ resid 1301 through 1309)) selection = (chain 'B' and (resid 27 through 66 or resid 80 through 145 or resid 152 through \ 173 or resid 186 through 332 or resid 334 through 526 or resid 528 through 620 \ or resid 641 through 1146 or resid 1301 through 1309)) selection = (chain 'C' and (resid 27 through 66 or resid 80 through 331 or (resid 332 and (n \ ame N or name CA or name C or name O or name CB )) or resid 334 through 526 or r \ esid 528 through 620 or resid 641 through 1146 or resid 1301 through 1309)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 2.130 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: 0.020 Extract box with map and model: 0.940 Check model and map are aligned: 0.170 Set scattering table: 0.240 Process input model: 61.330 Find NCS groups from input model: 1.480 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6442 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 : 0.011 0.044 26079 Z= 0.835 Angle : 1.393 14.908 35521 Z= 0.997 Chirality : 0.098 0.809 4081 Planarity : 0.010 0.119 4558 Dihedral : 14.939 89.355 9753 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.61 % Allowed : 14.36 % Favored : 84.03 % Cbeta Deviations : 0.10 % 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: 0.50 (0.14), residues: 3144 helix: 1.90 (0.18), residues: 804 sheet: 0.67 (0.18), residues: 669 loop : -0.59 (0.14), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.006 TRP C 353 HIS 0.013 0.003 HIS A 519 PHE 0.037 0.004 PHE C 515 TYR 0.050 0.006 TYR B 449 ARG 0.017 0.002 ARG B 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00594 ( 27) link_NAG-ASN : angle 3.69755 ( 81) hydrogen bonds : bond 0.14479 ( 1120) hydrogen bonds : angle 7.39998 ( 3162) covalent geometry : bond 0.01143 (26052) covalent geometry : angle 1.38290 (35440) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 2801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 382 time to evaluate : 2.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 13 MET cc_start: 0.4326 (ttp) cc_final: 0.4098 (ttm) REVERT: E 13 MET cc_start: 0.5444 (ttp) cc_final: 0.4984 (ptm) REVERT: C 481 ASN cc_start: 0.6772 (m-40) cc_final: 0.6571 (m-40) REVERT: C 611 LEU cc_start: 0.8634 (tp) cc_final: 0.7951 (tp) REVERT: C 739 THR cc_start: 0.8231 (p) cc_final: 0.8020 (t) REVERT: C 985 ASP cc_start: 0.8567 (p0) cc_final: 0.8255 (p0) REVERT: C 1066 THR cc_start: 0.7622 (OUTLIER) cc_final: 0.6933 (t) REVERT: B 91 TYR cc_start: 0.7542 (t80) cc_final: 0.7166 (t80) REVERT: B 193 VAL cc_start: 0.8476 (t) cc_final: 0.8213 (t) REVERT: B 610 VAL cc_start: 0.8841 (t) cc_final: 0.8448 (p) REVERT: B 731 MET cc_start: 0.7127 (ptp) cc_final: 0.6503 (ptp) REVERT: B 898 PHE cc_start: 0.7393 (t80) cc_final: 0.7006 (t80) REVERT: B 1034 LEU cc_start: 0.9030 (mm) cc_final: 0.8662 (mt) REVERT: B 1054 GLN cc_start: 0.6990 (mm-40) cc_final: 0.6477 (mm-40) REVERT: A 117 LEU cc_start: 0.7738 (tt) cc_final: 0.7392 (mp) REVERT: A 153 MET cc_start: 0.6764 (ppp) cc_final: 0.6258 (pmm) REVERT: A 241 LEU cc_start: 0.7273 (mt) cc_final: 0.6777 (tp) REVERT: A 596 SER cc_start: 0.8888 (m) cc_final: 0.8348 (p) REVERT: A 806 LEU cc_start: 0.8935 (mt) cc_final: 0.8731 (pp) REVERT: A 866 THR cc_start: 0.8457 (p) cc_final: 0.8144 (t) REVERT: A 877 LEU cc_start: 0.8221 (mt) cc_final: 0.7916 (mt) REVERT: A 1004 LEU cc_start: 0.9298 (tp) cc_final: 0.8958 (tp) REVERT: A 1017 GLU cc_start: 0.6953 (tt0) cc_final: 0.6375 (tt0) REVERT: A 1018 ILE cc_start: 0.8524 (mm) cc_final: 0.8144 (mm) REVERT: A 1029 MET cc_start: 0.6569 (ttm) cc_final: 0.6292 (tpp) outliers start: 45 outliers final: 4 residues processed: 418 average time/residue: 0.3792 time to fit residues: 246.6607 Evaluate side-chains 166 residues out of total 2801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 161 time to evaluate : 2.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 266 optimal weight: 4.9990 chunk 239 optimal weight: 0.9990 chunk 132 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 161 optimal weight: 20.0000 chunk 127 optimal weight: 20.0000 chunk 247 optimal weight: 5.9990 chunk 95 optimal weight: 9.9990 chunk 150 optimal weight: 8.9990 chunk 184 optimal weight: 2.9990 chunk 286 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 ASN C 207 HIS C 641 ASN C 762 GLN C 957 GLN C1005 GLN C1054 GLN C1088 HIS B 146 HIS B 218 GLN B 856 ASN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 949 GLN B 955 ASN B1005 GLN A 173 GLN A 935 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 960 ASN A 965 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.047829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.031590 restraints weight = 204051.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.032954 restraints weight = 112879.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.033850 restraints weight = 75640.596| |-----------------------------------------------------------------------------| r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 26079 Z= 0.183 Angle : 0.655 14.979 35521 Z= 0.341 Chirality : 0.048 0.620 4081 Planarity : 0.004 0.058 4558 Dihedral : 5.702 53.272 3994 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.32 % Favored : 97.65 % Rotamer: Outliers : 0.21 % Allowed : 3.72 % Favored : 96.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.14), residues: 3144 helix: 1.74 (0.18), residues: 776 sheet: 0.20 (0.18), residues: 687 loop : -0.61 (0.14), residues: 1681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 64 HIS 0.006 0.001 HIS A 49 PHE 0.019 0.002 PHE B 92 TYR 0.025 0.002 TYR C 170 ARG 0.009 0.001 ARG D 15 Details of bonding type rmsd link_NAG-ASN : bond 0.00595 ( 27) link_NAG-ASN : angle 3.37831 ( 81) hydrogen bonds : bond 0.04816 ( 1120) hydrogen bonds : angle 6.18513 ( 3162) covalent geometry : bond 0.00379 (26052) covalent geometry : angle 0.63579 (35440) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 216 time to evaluate : 2.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 18 GLU cc_start: 0.7971 (mt-10) cc_final: 0.7655 (pp20) REVERT: E 21 HIS cc_start: 0.6825 (m-70) cc_final: 0.6522 (t-170) REVERT: E 37 LYS cc_start: 0.7029 (mmmt) cc_final: 0.6687 (ptpp) REVERT: C 153 MET cc_start: 0.5301 (tmm) cc_final: 0.5048 (tmm) REVERT: C 170 TYR cc_start: 0.8033 (t80) cc_final: 0.7548 (t80) REVERT: C 223 LEU cc_start: 0.8759 (mt) cc_final: 0.8351 (tp) REVERT: C 449 TYR cc_start: 0.8082 (m-80) cc_final: 0.7853 (m-80) REVERT: C 574 ASP cc_start: 0.8863 (t0) cc_final: 0.8263 (t0) REVERT: C 869 MET cc_start: 0.8030 (mtp) cc_final: 0.7629 (mtp) REVERT: C 1050 MET cc_start: 0.8806 (ppp) cc_final: 0.8261 (ppp) REVERT: B 610 VAL cc_start: 0.9107 (t) cc_final: 0.8885 (p) REVERT: B 756 TYR cc_start: 0.8498 (m-80) cc_final: 0.8234 (m-10) REVERT: B 819 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7594 (mm-30) REVERT: B 858 LEU cc_start: 0.8289 (mp) cc_final: 0.7812 (mp) REVERT: B 869 MET cc_start: 0.9496 (mtm) cc_final: 0.8748 (ptp) REVERT: B 912 THR cc_start: 0.8401 (OUTLIER) cc_final: 0.8166 (p) REVERT: B 1001 LEU cc_start: 0.9057 (tt) cc_final: 0.8796 (pp) REVERT: B 1019 ARG cc_start: 0.8146 (tpt-90) cc_final: 0.7907 (tpt-90) REVERT: B 1029 MET cc_start: 0.8579 (ttm) cc_final: 0.7712 (ttm) REVERT: B 1054 GLN cc_start: 0.7474 (mm-40) cc_final: 0.6860 (mm-40) REVERT: A 650 LEU cc_start: 0.8792 (tp) cc_final: 0.8354 (pp) REVERT: A 712 ILE cc_start: 0.8917 (tt) cc_final: 0.8680 (tt) REVERT: A 780 GLU cc_start: 0.8440 (mt-10) cc_final: 0.8224 (pt0) REVERT: A 806 LEU cc_start: 0.9274 (mt) cc_final: 0.8855 (pp) REVERT: A 902 MET cc_start: 0.8510 (mmp) cc_final: 0.8194 (mmm) REVERT: A 1029 MET cc_start: 0.8346 (ttm) cc_final: 0.7705 (tpp) REVERT: A 1050 MET cc_start: 0.8904 (pmm) cc_final: 0.8110 (pmm) outliers start: 6 outliers final: 1 residues processed: 221 average time/residue: 0.3359 time to fit residues: 123.1485 Evaluate side-chains 124 residues out of total 2801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 122 time to evaluate : 3.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 82 optimal weight: 5.9990 chunk 139 optimal weight: 8.9990 chunk 302 optimal weight: 0.7980 chunk 120 optimal weight: 3.9990 chunk 36 optimal weight: 9.9990 chunk 188 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 80 optimal weight: 6.9990 chunk 256 optimal weight: 7.9990 chunk 270 optimal weight: 4.9990 chunk 100 optimal weight: 7.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 21 HIS C 207 HIS C 360 ASN C 580 GLN C 764 ASN C1005 GLN ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B 949 GLN B 955 ASN B1005 GLN ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 GLN A 613 GLN A 703 ASN A 901 GLN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 949 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.046663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.030773 restraints weight = 201364.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.032082 restraints weight = 114059.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.032940 restraints weight = 77147.025| |-----------------------------------------------------------------------------| r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 26079 Z= 0.188 Angle : 0.620 14.661 35521 Z= 0.323 Chirality : 0.046 0.495 4081 Planarity : 0.004 0.041 4558 Dihedral : 5.357 54.390 3994 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.18 % Allowed : 3.98 % Favored : 95.85 % 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: 0.02 (0.14), residues: 3144 helix: 1.42 (0.18), residues: 784 sheet: -0.00 (0.18), residues: 677 loop : -0.62 (0.14), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 886 HIS 0.008 0.001 HIS C 505 PHE 0.022 0.002 PHE A 802 TYR 0.026 0.002 TYR B 904 ARG 0.008 0.001 ARG C1039 Details of bonding type rmsd link_NAG-ASN : bond 0.00478 ( 27) link_NAG-ASN : angle 2.93651 ( 81) hydrogen bonds : bond 0.04346 ( 1120) hydrogen bonds : angle 6.01983 ( 3162) covalent geometry : bond 0.00391 (26052) covalent geometry : angle 0.60508 (35440) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 2801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 174 time to evaluate : 2.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 17 ASP cc_start: 0.8073 (t70) cc_final: 0.7701 (t0) REVERT: F 27 MET cc_start: 0.9559 (mmp) cc_final: 0.9334 (mmt) REVERT: E 18 GLU cc_start: 0.8020 (mt-10) cc_final: 0.7733 (pp20) REVERT: C 153 MET cc_start: 0.5627 (tmm) cc_final: 0.5364 (tmm) REVERT: C 170 TYR cc_start: 0.8050 (t80) cc_final: 0.7564 (t80) REVERT: C 869 MET cc_start: 0.8168 (mtp) cc_final: 0.7853 (mtp) REVERT: C 1050 MET cc_start: 0.8962 (ppp) cc_final: 0.8481 (ppp) REVERT: B 117 LEU cc_start: 0.9417 (tt) cc_final: 0.9187 (mt) REVERT: B 135 PHE cc_start: 0.8217 (m-10) cc_final: 0.7751 (m-80) REVERT: B 153 MET cc_start: 0.7565 (ppp) cc_final: 0.7198 (pmm) REVERT: B 756 TYR cc_start: 0.8394 (m-80) cc_final: 0.8099 (m-10) REVERT: B 869 MET cc_start: 0.9526 (mtm) cc_final: 0.8865 (ptp) REVERT: B 1001 LEU cc_start: 0.9108 (tt) cc_final: 0.8787 (pp) REVERT: B 1029 MET cc_start: 0.8741 (ttm) cc_final: 0.8022 (ttm) REVERT: B 1054 GLN cc_start: 0.7516 (mm-40) cc_final: 0.7152 (mm-40) REVERT: A 650 LEU cc_start: 0.8951 (tp) cc_final: 0.8461 (pp) REVERT: A 712 ILE cc_start: 0.8922 (tt) cc_final: 0.8694 (tt) REVERT: A 780 GLU cc_start: 0.8400 (mt-10) cc_final: 0.8199 (pt0) REVERT: A 806 LEU cc_start: 0.9271 (mt) cc_final: 0.8847 (pp) REVERT: A 868 GLU cc_start: 0.8631 (pp20) cc_final: 0.8405 (tm-30) REVERT: A 902 MET cc_start: 0.8530 (mmp) cc_final: 0.8219 (mmm) REVERT: A 1050 MET cc_start: 0.9140 (pmm) cc_final: 0.8322 (pmm) outliers start: 5 outliers final: 0 residues processed: 177 average time/residue: 0.3476 time to fit residues: 101.7465 Evaluate side-chains 113 residues out of total 2801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 2.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 129 optimal weight: 6.9990 chunk 158 optimal weight: 30.0000 chunk 60 optimal weight: 10.0000 chunk 243 optimal weight: 6.9990 chunk 182 optimal weight: 0.7980 chunk 174 optimal weight: 1.9990 chunk 202 optimal weight: 0.7980 chunk 16 optimal weight: 20.0000 chunk 10 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 chunk 109 optimal weight: 0.1980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 388 ASN ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN B1106 GLN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.046896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.030860 restraints weight = 200344.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.032158 restraints weight = 113831.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.033019 restraints weight = 77499.199| |-----------------------------------------------------------------------------| r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.3455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 26079 Z= 0.133 Angle : 0.568 14.861 35521 Z= 0.294 Chirality : 0.046 0.486 4081 Planarity : 0.004 0.042 4558 Dihedral : 5.054 54.859 3994 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.04 % Allowed : 1.93 % Favored : 98.03 % 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: 0.00 (0.14), residues: 3144 helix: 1.45 (0.19), residues: 776 sheet: -0.00 (0.19), residues: 662 loop : -0.66 (0.14), residues: 1706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 64 HIS 0.002 0.001 HIS A 49 PHE 0.022 0.001 PHE A 135 TYR 0.020 0.001 TYR B 904 ARG 0.005 0.000 ARG A 577 Details of bonding type rmsd link_NAG-ASN : bond 0.00542 ( 27) link_NAG-ASN : angle 2.99582 ( 81) hydrogen bonds : bond 0.03954 ( 1120) hydrogen bonds : angle 5.79841 ( 3162) covalent geometry : bond 0.00280 (26052) covalent geometry : angle 0.55048 (35440) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 2801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 164 time to evaluate : 3.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 17 ASP cc_start: 0.8095 (t70) cc_final: 0.7822 (t70) REVERT: F 27 MET cc_start: 0.9520 (mmp) cc_final: 0.9317 (mmp) REVERT: E 18 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7703 (pp20) REVERT: C 153 MET cc_start: 0.5632 (tmm) cc_final: 0.5362 (tmm) REVERT: C 170 TYR cc_start: 0.8032 (t80) cc_final: 0.7570 (t80) REVERT: C 869 MET cc_start: 0.7992 (mtp) cc_final: 0.7693 (mtp) REVERT: C 900 MET cc_start: 0.9240 (tpp) cc_final: 0.9030 (tpp) REVERT: C 1029 MET cc_start: 0.8552 (ttm) cc_final: 0.8169 (ttm) REVERT: C 1050 MET cc_start: 0.9108 (ppp) cc_final: 0.8577 (ppp) REVERT: B 117 LEU cc_start: 0.9421 (tt) cc_final: 0.9212 (mt) REVERT: B 153 MET cc_start: 0.7551 (ppp) cc_final: 0.7150 (pmm) REVERT: B 855 PHE cc_start: 0.7228 (m-10) cc_final: 0.7027 (m-10) REVERT: B 869 MET cc_start: 0.9478 (mtm) cc_final: 0.8805 (ptp) REVERT: B 1001 LEU cc_start: 0.9152 (tt) cc_final: 0.8796 (pp) REVERT: B 1019 ARG cc_start: 0.8287 (tpt-90) cc_final: 0.8085 (tpt-90) REVERT: B 1029 MET cc_start: 0.8811 (ttm) cc_final: 0.8203 (ttm) REVERT: B 1034 LEU cc_start: 0.8615 (mm) cc_final: 0.7831 (mt) REVERT: B 1054 GLN cc_start: 0.7335 (mm-40) cc_final: 0.6951 (mm-40) REVERT: A 650 LEU cc_start: 0.8906 (tp) cc_final: 0.8461 (pp) REVERT: A 806 LEU cc_start: 0.9286 (mt) cc_final: 0.8857 (pp) REVERT: A 902 MET cc_start: 0.8484 (mmp) cc_final: 0.8130 (mmp) REVERT: A 1050 MET cc_start: 0.9168 (pmm) cc_final: 0.8526 (pmm) outliers start: 1 outliers final: 0 residues processed: 165 average time/residue: 0.3402 time to fit residues: 94.0604 Evaluate side-chains 110 residues out of total 2801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 2.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 303 optimal weight: 0.9980 chunk 198 optimal weight: 0.0040 chunk 206 optimal weight: 6.9990 chunk 38 optimal weight: 10.0000 chunk 246 optimal weight: 10.0000 chunk 115 optimal weight: 6.9990 chunk 81 optimal weight: 0.5980 chunk 282 optimal weight: 3.9990 chunk 127 optimal weight: 5.9990 chunk 285 optimal weight: 0.0670 chunk 61 optimal weight: 9.9990 overall best weight: 1.1332 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN B1010 GLN B1064 HIS A 321 GLN A 926 GLN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.047048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.030881 restraints weight = 198978.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.032198 restraints weight = 112503.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.033067 restraints weight = 76414.132| |-----------------------------------------------------------------------------| r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.3633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 26079 Z= 0.120 Angle : 0.546 14.656 35521 Z= 0.282 Chirality : 0.045 0.469 4081 Planarity : 0.004 0.044 4558 Dihedral : 4.841 54.668 3994 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % 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: 0.06 (0.14), residues: 3144 helix: 1.53 (0.19), residues: 776 sheet: 0.10 (0.19), residues: 645 loop : -0.66 (0.14), residues: 1723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 886 HIS 0.002 0.000 HIS A 49 PHE 0.013 0.001 PHE C 559 TYR 0.027 0.001 TYR A 904 ARG 0.006 0.000 ARG A 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00469 ( 27) link_NAG-ASN : angle 2.78297 ( 81) hydrogen bonds : bond 0.03778 ( 1120) hydrogen bonds : angle 5.67751 ( 3162) covalent geometry : bond 0.00248 (26052) covalent geometry : angle 0.53009 (35440) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 2801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 2.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 17 ASP cc_start: 0.8077 (t70) cc_final: 0.7834 (t70) REVERT: F 27 MET cc_start: 0.9555 (mmp) cc_final: 0.9331 (mmp) REVERT: E 18 GLU cc_start: 0.7912 (mt-10) cc_final: 0.7645 (pp20) REVERT: E 37 LYS cc_start: 0.5779 (mmpt) cc_final: 0.5419 (mmmt) REVERT: C 153 MET cc_start: 0.5709 (tmm) cc_final: 0.5415 (tmm) REVERT: C 170 TYR cc_start: 0.8056 (t80) cc_final: 0.7578 (t80) REVERT: C 869 MET cc_start: 0.7948 (mtp) cc_final: 0.7709 (mtp) REVERT: C 1029 MET cc_start: 0.8543 (ttm) cc_final: 0.8192 (ttm) REVERT: C 1050 MET cc_start: 0.8764 (ppp) cc_final: 0.8450 (ppp) REVERT: B 153 MET cc_start: 0.7770 (ppp) cc_final: 0.7396 (pmm) REVERT: B 869 MET cc_start: 0.9480 (mtm) cc_final: 0.8798 (ptp) REVERT: B 1001 LEU cc_start: 0.9099 (tt) cc_final: 0.8812 (pp) REVERT: B 1019 ARG cc_start: 0.8274 (tpt-90) cc_final: 0.8061 (tpt-90) REVERT: B 1029 MET cc_start: 0.8828 (ttm) cc_final: 0.8202 (ttm) REVERT: B 1034 LEU cc_start: 0.8621 (mm) cc_final: 0.7867 (mt) REVERT: B 1054 GLN cc_start: 0.7232 (mm-40) cc_final: 0.6897 (mm-40) REVERT: A 650 LEU cc_start: 0.9007 (tp) cc_final: 0.8552 (pp) REVERT: A 779 GLN cc_start: 0.8872 (tm-30) cc_final: 0.8509 (tm-30) REVERT: A 806 LEU cc_start: 0.9319 (mt) cc_final: 0.8874 (pp) REVERT: A 902 MET cc_start: 0.8487 (mmp) cc_final: 0.8138 (mmp) REVERT: A 1005 GLN cc_start: 0.8692 (tt0) cc_final: 0.8427 (tt0) REVERT: A 1050 MET cc_start: 0.9236 (pmm) cc_final: 0.8424 (pmm) outliers start: 0 outliers final: 0 residues processed: 158 average time/residue: 0.3295 time to fit residues: 87.1945 Evaluate side-chains 111 residues out of total 2801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 2.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 77 optimal weight: 2.9990 chunk 315 optimal weight: 5.9990 chunk 104 optimal weight: 20.0000 chunk 214 optimal weight: 20.0000 chunk 129 optimal weight: 0.1980 chunk 142 optimal weight: 9.9990 chunk 160 optimal weight: 30.0000 chunk 215 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 262 optimal weight: 20.0000 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN B1064 HIS A 703 ASN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1011 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.046693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.030697 restraints weight = 200126.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.031984 restraints weight = 113795.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.032835 restraints weight = 77493.578| |-----------------------------------------------------------------------------| r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.3860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 26079 Z= 0.136 Angle : 0.556 14.422 35521 Z= 0.287 Chirality : 0.045 0.449 4081 Planarity : 0.004 0.046 4558 Dihedral : 4.744 54.603 3994 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.04 % Allowed : 1.65 % Favored : 98.32 % 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: 0.06 (0.15), residues: 3144 helix: 1.43 (0.19), residues: 782 sheet: 0.15 (0.19), residues: 655 loop : -0.64 (0.14), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 64 HIS 0.004 0.001 HIS B1048 PHE 0.021 0.001 PHE C 927 TYR 0.025 0.001 TYR B 904 ARG 0.005 0.000 ARG A 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00452 ( 27) link_NAG-ASN : angle 2.68747 ( 81) hydrogen bonds : bond 0.03772 ( 1120) hydrogen bonds : angle 5.64751 ( 3162) covalent geometry : bond 0.00287 (26052) covalent geometry : angle 0.54162 (35440) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 2801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 160 time to evaluate : 2.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 17 ASP cc_start: 0.8237 (t70) cc_final: 0.7943 (t0) REVERT: F 27 MET cc_start: 0.9526 (mmp) cc_final: 0.9324 (mmp) REVERT: F 34 GLU cc_start: 0.9222 (mp0) cc_final: 0.9019 (mp0) REVERT: E 18 GLU cc_start: 0.7899 (mt-10) cc_final: 0.7639 (pp20) REVERT: E 37 LYS cc_start: 0.5771 (mmpt) cc_final: 0.5442 (mmmt) REVERT: C 153 MET cc_start: 0.5954 (tmm) cc_final: 0.5633 (tmm) REVERT: C 170 TYR cc_start: 0.8083 (t80) cc_final: 0.7616 (t80) REVERT: C 869 MET cc_start: 0.8067 (mtp) cc_final: 0.7857 (mtp) REVERT: C 1029 MET cc_start: 0.8549 (ttm) cc_final: 0.8251 (ttm) REVERT: C 1050 MET cc_start: 0.8800 (ppp) cc_final: 0.8403 (ppp) REVERT: B 153 MET cc_start: 0.7244 (ppp) cc_final: 0.6912 (pmm) REVERT: B 869 MET cc_start: 0.9471 (mtm) cc_final: 0.8762 (ptp) REVERT: B 902 MET cc_start: 0.9165 (mmp) cc_final: 0.8766 (mmm) REVERT: B 1001 LEU cc_start: 0.9121 (tt) cc_final: 0.8873 (pp) REVERT: B 1029 MET cc_start: 0.8888 (ttm) cc_final: 0.8320 (ttm) REVERT: B 1034 LEU cc_start: 0.8655 (mm) cc_final: 0.7931 (mt) REVERT: B 1050 MET cc_start: 0.8800 (ptp) cc_final: 0.8434 (ptm) REVERT: A 650 LEU cc_start: 0.8875 (tp) cc_final: 0.8364 (pp) REVERT: A 779 GLN cc_start: 0.8857 (tm-30) cc_final: 0.8467 (tm-30) REVERT: A 806 LEU cc_start: 0.9324 (mt) cc_final: 0.8876 (pp) REVERT: A 902 MET cc_start: 0.8463 (mmp) cc_final: 0.8112 (mmp) REVERT: A 1005 GLN cc_start: 0.8707 (tt0) cc_final: 0.8447 (tt0) REVERT: A 1050 MET cc_start: 0.9114 (pmm) cc_final: 0.8664 (pmm) outliers start: 1 outliers final: 0 residues processed: 161 average time/residue: 0.3523 time to fit residues: 95.3310 Evaluate side-chains 107 residues out of total 2801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 3.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 30 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 269 optimal weight: 10.0000 chunk 138 optimal weight: 20.0000 chunk 63 optimal weight: 5.9990 chunk 206 optimal weight: 0.9990 chunk 265 optimal weight: 7.9990 chunk 49 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 chunk 128 optimal weight: 6.9990 chunk 205 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 ASN ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 703 ASN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.046638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.030608 restraints weight = 201969.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.031899 restraints weight = 115044.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.032746 restraints weight = 78329.728| |-----------------------------------------------------------------------------| r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.4022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 26079 Z= 0.135 Angle : 0.554 14.225 35521 Z= 0.286 Chirality : 0.045 0.449 4081 Planarity : 0.004 0.045 4558 Dihedral : 4.706 54.673 3994 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.04 % Allowed : 1.07 % Favored : 98.89 % 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: 0.05 (0.15), residues: 3144 helix: 1.46 (0.19), residues: 785 sheet: 0.19 (0.20), residues: 647 loop : -0.69 (0.14), residues: 1712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 886 HIS 0.003 0.001 HIS A 49 PHE 0.017 0.001 PHE A 374 TYR 0.026 0.001 TYR A 904 ARG 0.004 0.000 ARG A 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00497 ( 27) link_NAG-ASN : angle 2.74659 ( 81) hydrogen bonds : bond 0.03723 ( 1120) hydrogen bonds : angle 5.58170 ( 3162) covalent geometry : bond 0.00285 (26052) covalent geometry : angle 0.53880 (35440) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 2801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 152 time to evaluate : 2.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 27 MET cc_start: 0.9582 (mmp) cc_final: 0.9327 (mmm) REVERT: E 18 GLU cc_start: 0.7891 (mt-10) cc_final: 0.7641 (pp20) REVERT: E 37 LYS cc_start: 0.6001 (mmpt) cc_final: 0.5707 (mmmt) REVERT: C 153 MET cc_start: 0.6006 (tmm) cc_final: 0.5658 (tmm) REVERT: C 170 TYR cc_start: 0.8101 (t80) cc_final: 0.7626 (t80) REVERT: C 869 MET cc_start: 0.8092 (mtp) cc_final: 0.7888 (mtp) REVERT: C 900 MET cc_start: 0.9370 (tpp) cc_final: 0.9058 (tpp) REVERT: C 985 ASP cc_start: 0.9010 (p0) cc_final: 0.8800 (p0) REVERT: C 1029 MET cc_start: 0.8534 (ttm) cc_final: 0.8165 (ttm) REVERT: C 1050 MET cc_start: 0.8887 (ppp) cc_final: 0.8430 (ppp) REVERT: B 106 PHE cc_start: 0.8460 (m-80) cc_final: 0.8257 (m-80) REVERT: B 153 MET cc_start: 0.7348 (ppp) cc_final: 0.7099 (pmm) REVERT: B 724 THR cc_start: 0.9355 (p) cc_final: 0.9115 (p) REVERT: B 725 GLU cc_start: 0.8331 (mm-30) cc_final: 0.7832 (mm-30) REVERT: B 869 MET cc_start: 0.9464 (mtm) cc_final: 0.8813 (ptp) REVERT: B 902 MET cc_start: 0.9221 (mmp) cc_final: 0.8873 (mmp) REVERT: B 1001 LEU cc_start: 0.9120 (tt) cc_final: 0.8884 (pp) REVERT: B 1029 MET cc_start: 0.8867 (ttm) cc_final: 0.8304 (ttm) REVERT: B 1034 LEU cc_start: 0.8685 (mm) cc_final: 0.7968 (mt) REVERT: B 1050 MET cc_start: 0.8755 (ptp) cc_final: 0.8426 (ptm) REVERT: A 650 LEU cc_start: 0.8846 (tp) cc_final: 0.8345 (pp) REVERT: A 779 GLN cc_start: 0.8822 (tm-30) cc_final: 0.8429 (tm-30) REVERT: A 806 LEU cc_start: 0.9314 (mt) cc_final: 0.8870 (pp) REVERT: A 902 MET cc_start: 0.8476 (mmp) cc_final: 0.8120 (mmp) REVERT: A 1050 MET cc_start: 0.9146 (pmm) cc_final: 0.8740 (pmm) REVERT: A 1063 LEU cc_start: 0.9084 (mm) cc_final: 0.8872 (mm) outliers start: 1 outliers final: 0 residues processed: 153 average time/residue: 0.3511 time to fit residues: 91.5513 Evaluate side-chains 110 residues out of total 2801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 2.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 54 optimal weight: 5.9990 chunk 5 optimal weight: 0.7980 chunk 51 optimal weight: 9.9990 chunk 225 optimal weight: 7.9990 chunk 172 optimal weight: 8.9990 chunk 286 optimal weight: 3.9990 chunk 8 optimal weight: 20.0000 chunk 27 optimal weight: 7.9990 chunk 50 optimal weight: 0.0970 chunk 236 optimal weight: 5.9990 chunk 287 optimal weight: 10.0000 overall best weight: 3.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 7 GLN C 487 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 926 GLN B 955 ASN A 703 ASN ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.045825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.029838 restraints weight = 208701.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.031102 restraints weight = 118394.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.031941 restraints weight = 80523.441| |-----------------------------------------------------------------------------| r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.4401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 26079 Z= 0.203 Angle : 0.612 13.823 35521 Z= 0.318 Chirality : 0.046 0.443 4081 Planarity : 0.004 0.063 4558 Dihedral : 4.956 54.258 3994 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % 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: -0.13 (0.15), residues: 3144 helix: 1.31 (0.19), residues: 788 sheet: -0.10 (0.20), residues: 654 loop : -0.72 (0.14), residues: 1702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 886 HIS 0.007 0.001 HIS A 49 PHE 0.020 0.002 PHE C 927 TYR 0.028 0.002 TYR A 904 ARG 0.006 0.001 ARG D 15 Details of bonding type rmsd link_NAG-ASN : bond 0.00457 ( 27) link_NAG-ASN : angle 2.66061 ( 81) hydrogen bonds : bond 0.04040 ( 1120) hydrogen bonds : angle 5.72955 ( 3162) covalent geometry : bond 0.00419 (26052) covalent geometry : angle 0.59962 (35440) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 2801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 3.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 17 ASP cc_start: 0.8178 (t0) cc_final: 0.7946 (t0) REVERT: F 27 MET cc_start: 0.9594 (mmp) cc_final: 0.9346 (mmm) REVERT: E 18 GLU cc_start: 0.7833 (mt-10) cc_final: 0.7574 (pp20) REVERT: E 37 LYS cc_start: 0.6121 (mmpt) cc_final: 0.5781 (mmmt) REVERT: C 153 MET cc_start: 0.5995 (tmm) cc_final: 0.5661 (tmm) REVERT: C 869 MET cc_start: 0.8238 (mtp) cc_final: 0.8020 (mtp) REVERT: C 985 ASP cc_start: 0.8901 (p0) cc_final: 0.8681 (p0) REVERT: C 1029 MET cc_start: 0.8592 (ttm) cc_final: 0.8263 (ttm) REVERT: C 1050 MET cc_start: 0.8955 (ppp) cc_final: 0.8517 (ppp) REVERT: B 106 PHE cc_start: 0.8696 (m-80) cc_final: 0.8350 (m-80) REVERT: B 153 MET cc_start: 0.7334 (ppp) cc_final: 0.7092 (pmm) REVERT: B 724 THR cc_start: 0.9339 (p) cc_final: 0.9096 (p) REVERT: B 725 GLU cc_start: 0.8320 (mm-30) cc_final: 0.7783 (mm-30) REVERT: B 869 MET cc_start: 0.9477 (mtm) cc_final: 0.9125 (mtp) REVERT: B 902 MET cc_start: 0.9192 (mmp) cc_final: 0.8809 (mmp) REVERT: B 1001 LEU cc_start: 0.9131 (tt) cc_final: 0.8879 (pp) REVERT: B 1029 MET cc_start: 0.8890 (ttm) cc_final: 0.8358 (ttm) REVERT: B 1050 MET cc_start: 0.8779 (ptp) cc_final: 0.8430 (ptm) REVERT: A 650 LEU cc_start: 0.8893 (tp) cc_final: 0.8404 (pp) REVERT: A 779 GLN cc_start: 0.8873 (tm-30) cc_final: 0.8480 (tm-30) REVERT: A 806 LEU cc_start: 0.9300 (mt) cc_final: 0.8887 (pp) REVERT: A 902 MET cc_start: 0.8435 (mmp) cc_final: 0.8221 (mmp) REVERT: A 1050 MET cc_start: 0.9086 (pmm) cc_final: 0.8679 (pmm) REVERT: A 1063 LEU cc_start: 0.8937 (mm) cc_final: 0.8717 (mm) outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.3462 time to fit residues: 80.4070 Evaluate side-chains 102 residues out of total 2801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 3.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 51 optimal weight: 5.9990 chunk 227 optimal weight: 8.9990 chunk 238 optimal weight: 0.8980 chunk 234 optimal weight: 30.0000 chunk 295 optimal weight: 7.9990 chunk 25 optimal weight: 0.7980 chunk 41 optimal weight: 5.9990 chunk 243 optimal weight: 8.9990 chunk 137 optimal weight: 9.9990 chunk 155 optimal weight: 0.7980 chunk 278 optimal weight: 1.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 710 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN B 955 ASN A 703 ASN ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.046152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.030145 restraints weight = 204526.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.031415 restraints weight = 118246.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.032260 restraints weight = 81181.235| |-----------------------------------------------------------------------------| r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.4548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 26079 Z= 0.146 Angle : 0.570 13.877 35521 Z= 0.294 Chirality : 0.045 0.447 4081 Planarity : 0.004 0.044 4558 Dihedral : 4.885 59.229 3994 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.15), residues: 3144 helix: 1.40 (0.19), residues: 771 sheet: -0.11 (0.20), residues: 657 loop : -0.67 (0.14), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 104 HIS 0.003 0.001 HIS A 49 PHE 0.020 0.001 PHE A 374 TYR 0.021 0.001 TYR B 904 ARG 0.007 0.000 ARG B1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00446 ( 27) link_NAG-ASN : angle 2.61511 ( 81) hydrogen bonds : bond 0.03790 ( 1120) hydrogen bonds : angle 5.63740 ( 3162) covalent geometry : bond 0.00306 (26052) covalent geometry : angle 0.55652 (35440) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 2801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 3.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 18 GLU cc_start: 0.7941 (tp30) cc_final: 0.7100 (pt0) REVERT: F 27 MET cc_start: 0.9597 (mmp) cc_final: 0.9339 (mmm) REVERT: E 18 GLU cc_start: 0.7837 (mt-10) cc_final: 0.7576 (pp20) REVERT: E 27 MET cc_start: 0.4785 (mtm) cc_final: 0.4086 (tpt) REVERT: C 153 MET cc_start: 0.6047 (tmm) cc_final: 0.5693 (tmm) REVERT: C 170 TYR cc_start: 0.8413 (t80) cc_final: 0.7938 (t80) REVERT: C 869 MET cc_start: 0.8201 (mtp) cc_final: 0.7968 (mtp) REVERT: C 985 ASP cc_start: 0.8885 (p0) cc_final: 0.8650 (p0) REVERT: C 1029 MET cc_start: 0.8589 (ttm) cc_final: 0.8222 (ttm) REVERT: C 1050 MET cc_start: 0.8947 (ppp) cc_final: 0.8475 (ppp) REVERT: B 106 PHE cc_start: 0.8707 (m-80) cc_final: 0.8379 (m-80) REVERT: B 724 THR cc_start: 0.9317 (p) cc_final: 0.9015 (p) REVERT: B 725 GLU cc_start: 0.8385 (mm-30) cc_final: 0.7753 (mm-30) REVERT: B 869 MET cc_start: 0.9494 (mtm) cc_final: 0.8828 (ptp) REVERT: B 902 MET cc_start: 0.9184 (mmp) cc_final: 0.8743 (mmp) REVERT: B 1001 LEU cc_start: 0.9115 (tt) cc_final: 0.8810 (pp) REVERT: B 1029 MET cc_start: 0.8895 (ttm) cc_final: 0.8312 (ttm) REVERT: B 1050 MET cc_start: 0.8771 (ptp) cc_final: 0.8445 (ptp) REVERT: A 650 LEU cc_start: 0.8865 (tp) cc_final: 0.8407 (pp) REVERT: A 779 GLN cc_start: 0.9068 (tm-30) cc_final: 0.8719 (tm-30) REVERT: A 806 LEU cc_start: 0.9295 (mt) cc_final: 0.8878 (pp) REVERT: A 902 MET cc_start: 0.8308 (mmp) cc_final: 0.8038 (mmp) REVERT: A 1019 ARG cc_start: 0.8769 (ttp80) cc_final: 0.8284 (ptm160) REVERT: A 1050 MET cc_start: 0.9159 (pmm) cc_final: 0.8676 (pmm) REVERT: A 1063 LEU cc_start: 0.9036 (mm) cc_final: 0.8833 (mm) outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.3278 time to fit residues: 79.8498 Evaluate side-chains 103 residues out of total 2801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 3.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 133 optimal weight: 1.9990 chunk 287 optimal weight: 9.9990 chunk 220 optimal weight: 5.9990 chunk 47 optimal weight: 10.0000 chunk 127 optimal weight: 0.0770 chunk 104 optimal weight: 8.9990 chunk 89 optimal weight: 0.7980 chunk 185 optimal weight: 9.9990 chunk 138 optimal weight: 3.9990 chunk 291 optimal weight: 0.5980 chunk 148 optimal weight: 30.0000 overall best weight: 1.4942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 655 HIS B 751 ASN A 703 ASN ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.046672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.030878 restraints weight = 213731.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.032225 restraints weight = 124018.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.032863 restraints weight = 79811.963| |-----------------------------------------------------------------------------| r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.4655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 26079 Z= 0.127 Angle : 0.567 13.622 35521 Z= 0.290 Chirality : 0.045 0.445 4081 Planarity : 0.004 0.044 4558 Dihedral : 4.738 57.101 3994 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.15), residues: 3144 helix: 1.44 (0.19), residues: 781 sheet: -0.03 (0.20), residues: 650 loop : -0.66 (0.15), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 886 HIS 0.012 0.001 HIS B 655 PHE 0.022 0.001 PHE C 927 TYR 0.027 0.001 TYR A 904 ARG 0.006 0.000 ARG C 815 Details of bonding type rmsd link_NAG-ASN : bond 0.00543 ( 27) link_NAG-ASN : angle 2.84954 ( 81) hydrogen bonds : bond 0.03669 ( 1120) hydrogen bonds : angle 5.57432 ( 3162) covalent geometry : bond 0.00270 (26052) covalent geometry : angle 0.55102 (35440) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 2801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 3.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 18 GLU cc_start: 0.7974 (tp30) cc_final: 0.7186 (pt0) REVERT: D 19 GLU cc_start: 0.6274 (mt-10) cc_final: 0.6058 (mt-10) REVERT: F 27 MET cc_start: 0.9604 (mmp) cc_final: 0.9347 (mmm) REVERT: E 18 GLU cc_start: 0.7828 (mt-10) cc_final: 0.7570 (pp20) REVERT: E 27 MET cc_start: 0.4817 (mtm) cc_final: 0.4102 (tpt) REVERT: C 153 MET cc_start: 0.5907 (tmm) cc_final: 0.5595 (tmm) REVERT: C 170 TYR cc_start: 0.8409 (t80) cc_final: 0.7928 (t80) REVERT: C 869 MET cc_start: 0.8113 (mtp) cc_final: 0.7877 (mtp) REVERT: C 1029 MET cc_start: 0.8557 (ttm) cc_final: 0.8121 (ttm) REVERT: C 1050 MET cc_start: 0.8910 (ppp) cc_final: 0.8431 (ppp) REVERT: B 106 PHE cc_start: 0.8793 (m-80) cc_final: 0.8423 (m-80) REVERT: B 201 PHE cc_start: 0.8866 (t80) cc_final: 0.8648 (t80) REVERT: B 724 THR cc_start: 0.9315 (p) cc_final: 0.8926 (p) REVERT: B 725 GLU cc_start: 0.8270 (mm-30) cc_final: 0.7794 (mm-30) REVERT: B 869 MET cc_start: 0.9390 (mtm) cc_final: 0.8686 (ptp) REVERT: B 902 MET cc_start: 0.9122 (mmp) cc_final: 0.8621 (mmp) REVERT: B 1001 LEU cc_start: 0.9042 (tt) cc_final: 0.8776 (pp) REVERT: B 1029 MET cc_start: 0.8815 (ttm) cc_final: 0.8237 (ttm) REVERT: B 1034 LEU cc_start: 0.8734 (mm) cc_final: 0.8061 (mt) REVERT: B 1050 MET cc_start: 0.8816 (ptp) cc_final: 0.8449 (ptp) REVERT: A 650 LEU cc_start: 0.8932 (tp) cc_final: 0.8534 (pp) REVERT: A 779 GLN cc_start: 0.8968 (tm-30) cc_final: 0.8610 (tm-30) REVERT: A 806 LEU cc_start: 0.9289 (mt) cc_final: 0.8869 (pp) REVERT: A 902 MET cc_start: 0.8327 (mmp) cc_final: 0.8042 (mmp) REVERT: A 1019 ARG cc_start: 0.8632 (ttp80) cc_final: 0.8196 (ptm160) REVERT: A 1050 MET cc_start: 0.9172 (pmm) cc_final: 0.8669 (pmm) REVERT: A 1067 TYR cc_start: 0.8669 (t80) cc_final: 0.8214 (t80) outliers start: 0 outliers final: 0 residues processed: 143 average time/residue: 0.3359 time to fit residues: 81.4813 Evaluate side-chains 104 residues out of total 2801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 3.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 201 optimal weight: 0.8980 chunk 105 optimal weight: 1.9990 chunk 100 optimal weight: 0.4980 chunk 179 optimal weight: 0.7980 chunk 118 optimal weight: 10.0000 chunk 277 optimal weight: 10.0000 chunk 308 optimal weight: 0.6980 chunk 83 optimal weight: 6.9990 chunk 287 optimal weight: 4.9990 chunk 136 optimal weight: 0.6980 chunk 160 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 751 ASN B1071 GLN ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 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 = 0.3268 r_free = 0.3268 target = 0.046867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.030862 restraints weight = 201674.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.032164 restraints weight = 115981.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.033034 restraints weight = 79281.591| |-----------------------------------------------------------------------------| r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.4739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 26079 Z= 0.107 Angle : 0.551 13.384 35521 Z= 0.282 Chirality : 0.045 0.443 4081 Planarity : 0.004 0.045 4558 Dihedral : 4.536 57.570 3994 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.15), residues: 3144 helix: 1.49 (0.19), residues: 773 sheet: 0.04 (0.20), residues: 643 loop : -0.65 (0.14), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 886 HIS 0.003 0.000 HIS B 655 PHE 0.022 0.001 PHE C 927 TYR 0.024 0.001 TYR A 904 ARG 0.014 0.000 ARG B1019 Details of bonding type rmsd link_NAG-ASN : bond 0.00464 ( 27) link_NAG-ASN : angle 2.64623 ( 81) hydrogen bonds : bond 0.03485 ( 1120) hydrogen bonds : angle 5.45087 ( 3162) covalent geometry : bond 0.00228 (26052) covalent geometry : angle 0.53680 (35440) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7438.66 seconds wall clock time: 132 minutes 13.87 seconds (7933.87 seconds total)