Starting phenix.real_space_refine on Fri Sep 19 11:21:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ydx_39184/09_2025/8ydx_39184.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ydx_39184/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8ydx_39184/09_2025/8ydx_39184.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ydx_39184/09_2025/8ydx_39184.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ydx_39184/09_2025/8ydx_39184.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ydx_39184/09_2025/8ydx_39184.map" } resolution = 4.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 6.74, per 1000 atoms: 0.26 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: 1.97 Conformation dependent library (CDL) restraints added in 846.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 1.21 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: 5.82 Time building geometry restraints manager: 2.67 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 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 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 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: 2.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.280 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 24.940 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.710 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.017 0.002 ARG B 346 TYR 0.050 0.006 TYR B 449 PHE 0.037 0.004 PHE C 515 TRP 0.057 0.006 TRP C 353 HIS 0.013 0.003 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.01143 (26052) covalent geometry : angle 1.38290 (35440) hydrogen bonds : bond 0.14479 ( 1120) hydrogen bonds : angle 7.39998 ( 3162) link_NAG-ASN : bond 0.00594 ( 27) link_NAG-ASN : angle 3.69755 ( 81) *********************** 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 : 1.172 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: D 13 MET cc_start: 0.4326 (ttp) cc_final: 0.4103 (ttm) REVERT: E 13 MET cc_start: 0.5444 (ttp) cc_final: 0.4978 (ptm) REVERT: C 481 ASN cc_start: 0.6772 (m-40) cc_final: 0.6567 (m-40) REVERT: C 611 LEU cc_start: 0.8634 (tp) cc_final: 0.7948 (tp) REVERT: C 985 ASP cc_start: 0.8567 (p0) cc_final: 0.8254 (p0) REVERT: C 1066 THR cc_start: 0.7622 (OUTLIER) cc_final: 0.6927 (t) REVERT: B 91 TYR cc_start: 0.7542 (t80) cc_final: 0.7168 (t80) REVERT: B 193 VAL cc_start: 0.8476 (t) cc_final: 0.8197 (t) REVERT: B 610 VAL cc_start: 0.8841 (t) cc_final: 0.8466 (p) REVERT: B 731 MET cc_start: 0.7127 (ptp) cc_final: 0.6536 (ptp) REVERT: B 898 PHE cc_start: 0.7393 (t80) cc_final: 0.7003 (t80) REVERT: B 1034 LEU cc_start: 0.9030 (mm) cc_final: 0.8653 (mt) REVERT: B 1054 GLN cc_start: 0.6990 (mm-40) cc_final: 0.5796 (mm-40) REVERT: B 1063 LEU cc_start: 0.9102 (mt) cc_final: 0.8820 (mt) REVERT: A 117 LEU cc_start: 0.7738 (tt) cc_final: 0.7386 (mp) REVERT: A 153 MET cc_start: 0.6764 (ppp) cc_final: 0.6264 (pmm) REVERT: A 241 LEU cc_start: 0.7273 (mt) cc_final: 0.6771 (tp) REVERT: A 596 SER cc_start: 0.8888 (m) cc_final: 0.8355 (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: 0.8142 (t) REVERT: A 877 LEU cc_start: 0.8221 (mt) cc_final: 0.7914 (mt) REVERT: A 1004 LEU cc_start: 0.9298 (tp) cc_final: 0.8951 (tp) REVERT: A 1017 GLU cc_start: 0.6953 (tt0) cc_final: 0.6237 (tt0) REVERT: A 1018 ILE cc_start: 0.8524 (mm) cc_final: 0.8095 (mm) REVERT: A 1029 MET cc_start: 0.6569 (ttm) cc_final: 0.6245 (tpp) outliers start: 45 outliers final: 4 residues processed: 418 average time/residue: 0.1750 time to fit residues: 114.6668 Evaluate side-chains 163 residues out of total 2801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 158 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 0.0670 chunk 183 optimal weight: 7.9990 chunk 298 optimal weight: 0.8980 overall best weight: 2.1924 ------------------------------------------------------------------------------- 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 = 0.3294 r_free = 0.3294 target = 0.047787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.031624 restraints weight = 199757.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.032981 restraints weight = 112133.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.033878 restraints weight = 75691.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.034475 restraints weight = 57523.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.034837 restraints weight = 47663.200| |-----------------------------------------------------------------------------| r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 26079 Z= 0.174 Angle : 0.659 15.260 35521 Z= 0.343 Chirality : 0.048 0.619 4081 Planarity : 0.004 0.053 4558 Dihedral : 5.734 53.440 3994 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.32 % Favored : 97.65 % Rotamer: Outliers : 0.18 % Allowed : 3.72 % Favored : 96.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.20 (0.14), residues: 3144 helix: 1.66 (0.18), residues: 778 sheet: 0.24 (0.18), residues: 672 loop : -0.63 (0.14), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C1107 TYR 0.026 0.002 TYR A 904 PHE 0.020 0.002 PHE B 92 TRP 0.023 0.002 TRP A 64 HIS 0.005 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00367 (26052) covalent geometry : angle 0.63895 (35440) hydrogen bonds : bond 0.04802 ( 1120) hydrogen bonds : angle 6.20536 ( 3162) link_NAG-ASN : bond 0.00529 ( 27) link_NAG-ASN : angle 3.43391 ( 81) *********************** 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 216 residues out of total 2801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 211 time to evaluate : 0.988 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: E 13 MET cc_start: 0.6696 (ttp) cc_final: 0.6450 (ptm) REVERT: E 18 GLU cc_start: 0.7965 (mt-10) cc_final: 0.7635 (pp20) REVERT: E 21 HIS cc_start: 0.6747 (m-70) cc_final: 0.6460 (t-170) REVERT: C 129 LYS cc_start: 0.7996 (mttt) cc_final: 0.7772 (mmmm) REVERT: C 153 MET cc_start: 0.5348 (tmm) cc_final: 0.5080 (tmm) REVERT: C 170 TYR cc_start: 0.8057 (t80) cc_final: 0.7790 (t80) REVERT: C 223 LEU cc_start: 0.8732 (mt) cc_final: 0.8347 (tp) REVERT: C 449 TYR cc_start: 0.8040 (m-80) cc_final: 0.7828 (m-80) REVERT: C 869 MET cc_start: 0.8051 (mtp) cc_final: 0.7612 (mtp) REVERT: C 1050 MET cc_start: 0.8754 (ppp) cc_final: 0.8166 (ppp) REVERT: B 206 LYS cc_start: 0.9137 (tptt) cc_final: 0.8801 (mmmt) REVERT: B 610 VAL cc_start: 0.9113 (t) cc_final: 0.8905 (p) REVERT: B 756 TYR cc_start: 0.8416 (m-80) cc_final: 0.8111 (m-10) REVERT: B 858 LEU cc_start: 0.8294 (mp) cc_final: 0.7840 (mp) REVERT: B 869 MET cc_start: 0.9487 (mtm) cc_final: 0.8785 (ptp) REVERT: B 912 THR cc_start: 0.8391 (OUTLIER) cc_final: 0.8139 (p) REVERT: B 1001 LEU cc_start: 0.9051 (tt) cc_final: 0.8798 (pp) REVERT: B 1019 ARG cc_start: 0.8252 (tpt-90) cc_final: 0.7872 (tpt-90) REVERT: B 1029 MET cc_start: 0.8511 (ttm) cc_final: 0.7587 (ttm) REVERT: B 1054 GLN cc_start: 0.7598 (mm-40) cc_final: 0.7108 (mm-40) REVERT: A 650 LEU cc_start: 0.8789 (tp) cc_final: 0.8362 (pp) REVERT: A 712 ILE cc_start: 0.8934 (tt) cc_final: 0.8689 (tt) REVERT: A 780 GLU cc_start: 0.8445 (mt-10) cc_final: 0.8235 (pt0) REVERT: A 806 LEU cc_start: 0.9282 (mt) cc_final: 0.8867 (pp) REVERT: A 902 MET cc_start: 0.8505 (mmp) cc_final: 0.8181 (mmm) REVERT: A 1029 MET cc_start: 0.8342 (ttm) cc_final: 0.7732 (tpp) REVERT: A 1050 MET cc_start: 0.8881 (pmm) cc_final: 0.8124 (pmm) outliers start: 5 outliers final: 0 residues processed: 215 average time/residue: 0.1508 time to fit residues: 53.5349 Evaluate side-chains 128 residues out of total 2801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 127 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 163 optimal weight: 5.9990 chunk 253 optimal weight: 10.0000 chunk 93 optimal weight: 0.8980 chunk 184 optimal weight: 1.9990 chunk 295 optimal weight: 7.9990 chunk 161 optimal weight: 5.9990 chunk 21 optimal weight: 0.3980 chunk 99 optimal weight: 1.9990 chunk 11 optimal weight: 9.9990 chunk 117 optimal weight: 6.9990 chunk 57 optimal weight: 20.0000 overall best weight: 2.2586 ------------------------------------------------------------------------------- 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 207 HIS 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN A 901 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.047045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.031083 restraints weight = 201277.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.032400 restraints weight = 113505.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.033258 restraints weight = 76779.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.033855 restraints weight = 58644.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.034215 restraints weight = 48571.193| |-----------------------------------------------------------------------------| r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.3076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 26079 Z= 0.159 Angle : 0.592 14.749 35521 Z= 0.308 Chirality : 0.046 0.499 4081 Planarity : 0.004 0.046 4558 Dihedral : 5.254 54.597 3994 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.18 % Allowed : 3.51 % Favored : 96.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.11 (0.14), residues: 3144 helix: 1.58 (0.19), residues: 772 sheet: 0.04 (0.19), residues: 666 loop : -0.60 (0.14), residues: 1706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C1039 TYR 0.023 0.001 TYR A 904 PHE 0.023 0.001 PHE A 802 TRP 0.016 0.001 TRP A 886 HIS 0.005 0.001 HIS C 505 Details of bonding type rmsd covalent geometry : bond 0.00331 (26052) covalent geometry : angle 0.57562 (35440) hydrogen bonds : bond 0.04212 ( 1120) hydrogen bonds : angle 5.93887 ( 3162) link_NAG-ASN : bond 0.00477 ( 27) link_NAG-ASN : angle 2.94849 ( 81) *********************** 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 182 residues out of total 2801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 177 time to evaluate : 0.862 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: F 17 ASP cc_start: 0.8010 (t70) cc_final: 0.7620 (t0) REVERT: F 27 MET cc_start: 0.9554 (mmp) cc_final: 0.9316 (mmt) REVERT: E 13 MET cc_start: 0.6397 (ttp) cc_final: 0.6167 (ptm) REVERT: E 18 GLU cc_start: 0.8014 (mt-10) cc_final: 0.7720 (pp20) REVERT: C 153 MET cc_start: 0.5646 (tmm) cc_final: 0.5372 (tmm) REVERT: C 170 TYR cc_start: 0.8065 (t80) cc_final: 0.7477 (t80) REVERT: C 223 LEU cc_start: 0.8798 (mt) cc_final: 0.8327 (tp) REVERT: C 869 MET cc_start: 0.8122 (mtp) cc_final: 0.7838 (mtp) REVERT: C 927 PHE cc_start: 0.9057 (t80) cc_final: 0.8848 (t80) REVERT: C 1050 MET cc_start: 0.8960 (ppp) cc_final: 0.8450 (ppp) REVERT: B 117 LEU cc_start: 0.9381 (tt) cc_final: 0.9147 (mt) REVERT: B 135 PHE cc_start: 0.8197 (m-10) cc_final: 0.7740 (m-80) REVERT: B 756 TYR cc_start: 0.8438 (m-80) cc_final: 0.8133 (m-10) REVERT: B 869 MET cc_start: 0.9602 (mtm) cc_final: 0.8675 (ptp) REVERT: B 1001 LEU cc_start: 0.9080 (tt) cc_final: 0.8763 (pp) REVERT: B 1018 ILE cc_start: 0.9031 (mm) cc_final: 0.8596 (tt) REVERT: B 1029 MET cc_start: 0.8645 (ttm) cc_final: 0.7768 (ttm) REVERT: B 1034 LEU cc_start: 0.8616 (mm) cc_final: 0.7808 (mt) REVERT: A 650 LEU cc_start: 0.8947 (tp) cc_final: 0.8485 (pp) REVERT: A 712 ILE cc_start: 0.8934 (tt) cc_final: 0.8681 (tt) REVERT: A 806 LEU cc_start: 0.9306 (mt) cc_final: 0.8862 (pp) REVERT: A 902 MET cc_start: 0.8526 (mmp) cc_final: 0.8167 (mmm) REVERT: A 1050 MET cc_start: 0.9103 (pmm) cc_final: 0.8457 (pmm) outliers start: 5 outliers final: 0 residues processed: 180 average time/residue: 0.1564 time to fit residues: 46.6676 Evaluate side-chains 115 residues out of total 2801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 218 optimal weight: 0.0370 chunk 174 optimal weight: 1.9990 chunk 40 optimal weight: 0.0970 chunk 97 optimal weight: 3.9990 chunk 126 optimal weight: 0.9980 chunk 176 optimal weight: 0.9980 chunk 137 optimal weight: 8.9990 chunk 14 optimal weight: 9.9990 chunk 163 optimal weight: 8.9990 chunk 57 optimal weight: 20.0000 chunk 186 optimal weight: 1.9990 overall best weight: 0.8258 ------------------------------------------------------------------------------- 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 388 ASN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN A 703 ASN ** 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 = 0.3286 r_free = 0.3286 target = 0.047482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.031347 restraints weight = 197764.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.032690 restraints weight = 111187.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.033575 restraints weight = 75150.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.034136 restraints weight = 57201.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.034546 restraints weight = 47591.178| |-----------------------------------------------------------------------------| r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 26079 Z= 0.114 Angle : 0.553 14.951 35521 Z= 0.286 Chirality : 0.045 0.493 4081 Planarity : 0.004 0.044 4558 Dihedral : 4.910 55.099 3994 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.00 % Allowed : 1.97 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.10 (0.14), residues: 3144 helix: 1.52 (0.19), residues: 771 sheet: 0.12 (0.19), residues: 648 loop : -0.60 (0.14), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 577 TYR 0.018 0.001 TYR B 904 PHE 0.021 0.001 PHE A 135 TRP 0.016 0.001 TRP C 64 HIS 0.003 0.000 HIS C 245 Details of bonding type rmsd covalent geometry : bond 0.00239 (26052) covalent geometry : angle 0.53465 (35440) hydrogen bonds : bond 0.03861 ( 1120) hydrogen bonds : angle 5.73468 ( 3162) link_NAG-ASN : bond 0.00526 ( 27) link_NAG-ASN : angle 2.99293 ( 81) *********************** 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 164 residues out of total 2801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 1.031 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: 0.8119 (t70) cc_final: 0.7863 (t70) REVERT: F 26 LEU cc_start: 0.9656 (mt) cc_final: 0.9296 (pp) REVERT: F 27 MET cc_start: 0.9512 (mmp) cc_final: 0.9207 (mmm) REVERT: E 13 MET cc_start: 0.6483 (ttp) cc_final: 0.6252 (ptm) REVERT: E 18 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7680 (pp20) REVERT: C 153 MET cc_start: 0.5594 (tmm) cc_final: 0.5326 (tmm) REVERT: C 170 TYR cc_start: 0.7979 (t80) cc_final: 0.7492 (t80) REVERT: C 223 LEU cc_start: 0.8802 (mt) cc_final: 0.8277 (tp) REVERT: C 869 MET cc_start: 0.7989 (mtp) cc_final: 0.7759 (mtp) REVERT: C 1029 MET cc_start: 0.8589 (ttm) cc_final: 0.8253 (ttm) REVERT: C 1041 ASP cc_start: 0.8236 (t0) cc_final: 0.8030 (t0) REVERT: C 1050 MET cc_start: 0.9041 (ppp) cc_final: 0.8515 (ppp) REVERT: B 117 LEU cc_start: 0.9406 (tt) cc_final: 0.9181 (mt) REVERT: B 869 MET cc_start: 0.9450 (mtm) cc_final: 0.8547 (ptp) REVERT: B 1018 ILE cc_start: 0.9171 (mm) cc_final: 0.8808 (tt) REVERT: B 1019 ARG cc_start: 0.8332 (tpt-90) cc_final: 0.7993 (tpt-90) REVERT: B 1029 MET cc_start: 0.8823 (ttm) cc_final: 0.8205 (ttm) REVERT: B 1034 LEU cc_start: 0.8640 (mm) cc_final: 0.7908 (mt) REVERT: B 1050 MET cc_start: 0.8750 (ptm) cc_final: 0.8547 (ptp) REVERT: A 650 LEU cc_start: 0.9014 (tp) cc_final: 0.8613 (pp) REVERT: A 712 ILE cc_start: 0.8918 (tt) cc_final: 0.8661 (tt) REVERT: A 902 MET cc_start: 0.8502 (mmp) cc_final: 0.8124 (mmp) REVERT: A 1050 MET cc_start: 0.9117 (pmm) cc_final: 0.8510 (pmm) REVERT: A 1067 TYR cc_start: 0.8724 (t80) cc_final: 0.8364 (t80) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.1440 time to fit residues: 40.4853 Evaluate side-chains 114 residues out of total 2801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 23 optimal weight: 6.9990 chunk 245 optimal weight: 20.0000 chunk 273 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 309 optimal weight: 6.9990 chunk 315 optimal weight: 8.9990 chunk 213 optimal weight: 0.8980 chunk 274 optimal weight: 10.0000 chunk 314 optimal weight: 0.6980 chunk 77 optimal weight: 0.0670 chunk 203 optimal weight: 9.9990 overall best weight: 1.9322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 21 HIS ** F 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN B1010 GLN B1064 HIS ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.046814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.030799 restraints weight = 200151.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.032093 restraints weight = 113984.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.032946 restraints weight = 77669.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.033519 restraints weight = 59428.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.033867 restraints weight = 49464.611| |-----------------------------------------------------------------------------| r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.3632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 26079 Z= 0.141 Angle : 0.558 14.434 35521 Z= 0.290 Chirality : 0.045 0.454 4081 Planarity : 0.004 0.046 4558 Dihedral : 4.789 54.474 3994 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.04 % Allowed : 2.51 % Favored : 97.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.08 (0.14), residues: 3144 helix: 1.46 (0.19), residues: 777 sheet: 0.09 (0.19), residues: 651 loop : -0.60 (0.14), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1019 TYR 0.027 0.001 TYR A 904 PHE 0.017 0.001 PHE C 186 TRP 0.014 0.001 TRP A 886 HIS 0.006 0.001 HIS D 21 Details of bonding type rmsd covalent geometry : bond 0.00293 (26052) covalent geometry : angle 0.54331 (35440) hydrogen bonds : bond 0.03870 ( 1120) hydrogen bonds : angle 5.62106 ( 3162) link_NAG-ASN : bond 0.00450 ( 27) link_NAG-ASN : angle 2.72993 ( 81) *********************** 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 155 residues out of total 2801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 154 time to evaluate : 1.013 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: 0.8139 (t70) cc_final: 0.7869 (t0) REVERT: F 27 MET cc_start: 0.9523 (mmp) cc_final: 0.9311 (mmt) REVERT: E 13 MET cc_start: 0.6282 (ttp) cc_final: 0.5948 (ptm) REVERT: E 18 GLU cc_start: 0.7985 (mt-10) cc_final: 0.7710 (pp20) REVERT: C 153 MET cc_start: 0.5794 (tmm) cc_final: 0.5501 (tmm) REVERT: C 170 TYR cc_start: 0.8050 (t80) cc_final: 0.7574 (t80) REVERT: C 869 MET cc_start: 0.8024 (mtp) cc_final: 0.7711 (mtp) REVERT: C 1029 MET cc_start: 0.8609 (ttm) cc_final: 0.8340 (ttm) REVERT: C 1041 ASP cc_start: 0.8325 (t0) cc_final: 0.8118 (t0) REVERT: C 1050 MET cc_start: 0.9103 (ppp) cc_final: 0.8592 (ppp) REVERT: B 106 PHE cc_start: 0.8879 (m-80) cc_final: 0.8471 (m-80) REVERT: B 869 MET cc_start: 0.9458 (mtm) cc_final: 0.8771 (ptp) REVERT: B 1019 ARG cc_start: 0.8375 (tpt-90) cc_final: 0.8061 (tpt-90) REVERT: B 1029 MET cc_start: 0.8784 (ttm) cc_final: 0.8044 (ttm) REVERT: B 1034 LEU cc_start: 0.8644 (mm) cc_final: 0.7912 (mt) REVERT: B 1054 GLN cc_start: 0.7269 (mm-40) cc_final: 0.6886 (mm-40) REVERT: A 650 LEU cc_start: 0.8901 (tp) cc_final: 0.8387 (pp) REVERT: A 712 ILE cc_start: 0.8935 (tt) cc_final: 0.8659 (tt) REVERT: A 902 MET cc_start: 0.8466 (mmp) cc_final: 0.8081 (mmp) REVERT: A 1050 MET cc_start: 0.9229 (pmm) cc_final: 0.8431 (pmm) REVERT: A 1067 TYR cc_start: 0.8666 (t80) cc_final: 0.8225 (t80) outliers start: 1 outliers final: 0 residues processed: 155 average time/residue: 0.1639 time to fit residues: 42.7685 Evaluate side-chains 105 residues out of total 2801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 232 optimal weight: 6.9990 chunk 268 optimal weight: 10.0000 chunk 293 optimal weight: 2.9990 chunk 183 optimal weight: 6.9990 chunk 287 optimal weight: 4.9990 chunk 186 optimal weight: 7.9990 chunk 159 optimal weight: 6.9990 chunk 304 optimal weight: 0.8980 chunk 200 optimal weight: 0.9990 chunk 294 optimal weight: 0.9990 chunk 10 optimal weight: 10.0000 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.046603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.030649 restraints weight = 201592.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.031937 restraints weight = 114388.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.032793 restraints weight = 77750.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.033366 restraints weight = 59551.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.033722 restraints weight = 49490.619| |-----------------------------------------------------------------------------| r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.3895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 26079 Z= 0.148 Angle : 0.557 14.340 35521 Z= 0.290 Chirality : 0.045 0.447 4081 Planarity : 0.004 0.105 4558 Dihedral : 4.740 54.603 3994 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.03 (0.14), residues: 3144 helix: 1.33 (0.19), residues: 783 sheet: 0.11 (0.19), residues: 654 loop : -0.62 (0.14), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1019 TYR 0.022 0.001 TYR B 904 PHE 0.020 0.001 PHE C 927 TRP 0.017 0.001 TRP C 64 HIS 0.004 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00308 (26052) covalent geometry : angle 0.54283 (35440) hydrogen bonds : bond 0.03859 ( 1120) hydrogen bonds : angle 5.63407 ( 3162) link_NAG-ASN : bond 0.00447 ( 27) link_NAG-ASN : angle 2.65977 ( 81) *********************** 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 150 residues out of total 2801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 27 MET cc_start: 0.9529 (mmp) cc_final: 0.9329 (mmp) REVERT: E 18 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7705 (pp20) REVERT: C 153 MET cc_start: 0.5963 (tmm) cc_final: 0.5632 (tmm) REVERT: C 170 TYR cc_start: 0.8077 (t80) cc_final: 0.7611 (t80) REVERT: C 869 MET cc_start: 0.7948 (mtp) cc_final: 0.7729 (mtp) REVERT: C 1029 MET cc_start: 0.8575 (ttm) cc_final: 0.8284 (ttm) REVERT: C 1041 ASP cc_start: 0.8452 (t0) cc_final: 0.8194 (t0) REVERT: C 1050 MET cc_start: 0.8797 (ppp) cc_final: 0.8364 (ppp) REVERT: B 106 PHE cc_start: 0.8835 (m-80) cc_final: 0.8394 (m-80) REVERT: B 869 MET cc_start: 0.9448 (mtm) cc_final: 0.8797 (ptp) REVERT: B 1001 LEU cc_start: 0.9056 (tt) cc_final: 0.8848 (pp) REVERT: B 1019 ARG cc_start: 0.8332 (tpt-90) cc_final: 0.8069 (tpt-90) REVERT: B 1029 MET cc_start: 0.8836 (ttm) cc_final: 0.8220 (ttm) REVERT: B 1034 LEU cc_start: 0.8663 (mm) cc_final: 0.7937 (mt) REVERT: B 1054 GLN cc_start: 0.7283 (mm-40) cc_final: 0.6885 (mm-40) REVERT: A 650 LEU cc_start: 0.8877 (tp) cc_final: 0.8374 (pp) REVERT: A 712 ILE cc_start: 0.8970 (tt) cc_final: 0.8692 (tt) REVERT: A 902 MET cc_start: 0.8468 (mmp) cc_final: 0.8099 (mmp) REVERT: A 1050 MET cc_start: 0.9081 (pmm) cc_final: 0.8689 (pmm) REVERT: A 1067 TYR cc_start: 0.8705 (t80) cc_final: 0.8229 (t80) outliers start: 0 outliers final: 0 residues processed: 150 average time/residue: 0.1645 time to fit residues: 41.2295 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 : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 52 optimal weight: 7.9990 chunk 287 optimal weight: 7.9990 chunk 301 optimal weight: 2.9990 chunk 236 optimal weight: 5.9990 chunk 153 optimal weight: 6.9990 chunk 304 optimal weight: 4.9990 chunk 116 optimal weight: 0.6980 chunk 74 optimal weight: 0.9980 chunk 299 optimal weight: 1.9990 chunk 122 optimal weight: 6.9990 chunk 181 optimal weight: 4.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 7 GLN C 360 ASN C 487 ASN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN B1064 HIS A 613 GLN A 935 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.046384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.030445 restraints weight = 202287.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.031725 restraints weight = 115244.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.032572 restraints weight = 78569.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.033145 restraints weight = 60239.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.033509 restraints weight = 50116.378| |-----------------------------------------------------------------------------| r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.4136 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= 0.156 Angle : 0.572 14.025 35521 Z= 0.296 Chirality : 0.045 0.448 4081 Planarity : 0.004 0.087 4558 Dihedral : 4.774 54.433 3994 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.04 % Allowed : 1.00 % Favored : 98.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.00 (0.14), residues: 3144 helix: 1.30 (0.19), residues: 791 sheet: 0.11 (0.19), residues: 654 loop : -0.65 (0.14), residues: 1699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 34 TYR 0.024 0.001 TYR A 904 PHE 0.018 0.001 PHE A 135 TRP 0.019 0.001 TRP A 886 HIS 0.004 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00322 (26052) covalent geometry : angle 0.55847 (35440) hydrogen bonds : bond 0.03828 ( 1120) hydrogen bonds : angle 5.61699 ( 3162) link_NAG-ASN : bond 0.00444 ( 27) link_NAG-ASN : angle 2.68333 ( 81) *********************** 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 142 residues out of total 2801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 141 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 17 ASP cc_start: 0.8116 (t0) cc_final: 0.7869 (t0) REVERT: F 27 MET cc_start: 0.9596 (mmp) cc_final: 0.9346 (mmm) REVERT: E 18 GLU cc_start: 0.7941 (mt-10) cc_final: 0.7707 (pp20) REVERT: C 153 MET cc_start: 0.5998 (tmm) cc_final: 0.5669 (tmm) REVERT: C 170 TYR cc_start: 0.8118 (t80) cc_final: 0.7645 (t80) REVERT: C 740 MET cc_start: 0.8298 (ttt) cc_final: 0.8093 (ttt) REVERT: C 869 MET cc_start: 0.8150 (mtp) cc_final: 0.7912 (mtp) REVERT: C 1029 MET cc_start: 0.8583 (ttm) cc_final: 0.8226 (ttm) REVERT: C 1050 MET cc_start: 0.8865 (ppp) cc_final: 0.8405 (ppp) REVERT: B 106 PHE cc_start: 0.8793 (m-80) cc_final: 0.8217 (m-80) REVERT: B 724 THR cc_start: 0.9346 (p) cc_final: 0.9108 (p) REVERT: B 725 GLU cc_start: 0.8463 (mm-30) cc_final: 0.7944 (mm-30) REVERT: B 869 MET cc_start: 0.9453 (mtm) cc_final: 0.8794 (ptp) REVERT: B 1001 LEU cc_start: 0.9158 (tt) cc_final: 0.8938 (pp) REVERT: B 1019 ARG cc_start: 0.8352 (tpt-90) cc_final: 0.8102 (tpt-90) REVERT: B 1029 MET cc_start: 0.8813 (ttm) cc_final: 0.8116 (ttm) REVERT: B 1054 GLN cc_start: 0.7258 (mm-40) cc_final: 0.6914 (mm-40) REVERT: A 650 LEU cc_start: 0.8879 (tp) cc_final: 0.8389 (pp) REVERT: A 712 ILE cc_start: 0.8937 (tt) cc_final: 0.8687 (tt) REVERT: A 902 MET cc_start: 0.8473 (mmp) cc_final: 0.8251 (mmp) REVERT: A 1019 ARG cc_start: 0.8759 (ttp80) cc_final: 0.8323 (ptm160) REVERT: A 1050 MET cc_start: 0.9109 (pmm) cc_final: 0.8642 (pmm) REVERT: A 1063 LEU cc_start: 0.9034 (mm) cc_final: 0.8817 (mm) REVERT: A 1067 TYR cc_start: 0.8591 (t80) cc_final: 0.7968 (t80) outliers start: 1 outliers final: 0 residues processed: 142 average time/residue: 0.1681 time to fit residues: 39.6912 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 : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 194 optimal weight: 0.0570 chunk 43 optimal weight: 7.9990 chunk 133 optimal weight: 1.9990 chunk 129 optimal weight: 7.9990 chunk 237 optimal weight: 0.9990 chunk 263 optimal weight: 7.9990 chunk 225 optimal weight: 8.9990 chunk 278 optimal weight: 9.9990 chunk 280 optimal weight: 2.9990 chunk 293 optimal weight: 5.9990 chunk 162 optimal weight: 0.9980 overall best weight: 1.4104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 935 GLN B 955 ASN A 321 GLN ** 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 = 0.3266 r_free = 0.3266 target = 0.046795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.030740 restraints weight = 201226.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.032041 restraints weight = 114659.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.032902 restraints weight = 78041.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.033486 restraints weight = 59664.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.033859 restraints weight = 49521.517| |-----------------------------------------------------------------------------| r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.4250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 26079 Z= 0.124 Angle : 0.555 13.959 35521 Z= 0.286 Chirality : 0.045 0.447 4081 Planarity : 0.004 0.077 4558 Dihedral : 4.627 54.855 3994 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.03 (0.15), residues: 3144 helix: 1.42 (0.19), residues: 787 sheet: 0.12 (0.19), residues: 652 loop : -0.66 (0.14), residues: 1705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 34 TYR 0.025 0.001 TYR A 904 PHE 0.022 0.001 PHE C 927 TRP 0.016 0.001 TRP A 886 HIS 0.002 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00263 (26052) covalent geometry : angle 0.53881 (35440) hydrogen bonds : bond 0.03659 ( 1120) hydrogen bonds : angle 5.54286 ( 3162) link_NAG-ASN : bond 0.00473 ( 27) link_NAG-ASN : angle 2.86162 ( 81) *********************** 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 148 residues out of total 2801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 27 MET cc_start: 0.9578 (mmp) cc_final: 0.9339 (mmm) REVERT: E 18 GLU cc_start: 0.7916 (mt-10) cc_final: 0.7686 (pp20) REVERT: C 153 MET cc_start: 0.5989 (tmm) cc_final: 0.5649 (tmm) REVERT: C 170 TYR cc_start: 0.8173 (t80) cc_final: 0.7674 (t80) REVERT: C 740 MET cc_start: 0.8354 (ttt) cc_final: 0.8131 (ttt) REVERT: C 869 MET cc_start: 0.8086 (mtp) cc_final: 0.7873 (mtp) REVERT: C 985 ASP cc_start: 0.9061 (p0) cc_final: 0.8845 (p0) REVERT: C 1029 MET cc_start: 0.8649 (ttm) cc_final: 0.8293 (ttm) REVERT: C 1050 MET cc_start: 0.8970 (ppp) cc_final: 0.8485 (ppp) REVERT: B 106 PHE cc_start: 0.8778 (m-80) cc_final: 0.8293 (m-80) REVERT: B 153 MET cc_start: 0.7465 (ppp) cc_final: 0.7180 (pmm) REVERT: B 724 THR cc_start: 0.9362 (p) cc_final: 0.9107 (p) REVERT: B 725 GLU cc_start: 0.8402 (mm-30) cc_final: 0.7872 (mm-30) REVERT: B 751 ASN cc_start: 0.9282 (m110) cc_final: 0.9081 (m-40) REVERT: B 869 MET cc_start: 0.9454 (mtm) cc_final: 0.8796 (ptp) REVERT: B 902 MET cc_start: 0.9270 (mmp) cc_final: 0.8934 (mmp) REVERT: B 1001 LEU cc_start: 0.9134 (tt) cc_final: 0.8771 (pp) REVERT: B 1019 ARG cc_start: 0.8318 (tpt-90) cc_final: 0.8012 (tpt-90) REVERT: B 1029 MET cc_start: 0.8806 (ttm) cc_final: 0.8086 (ttm) REVERT: B 1034 LEU cc_start: 0.8648 (mm) cc_final: 0.7957 (mt) REVERT: B 1050 MET cc_start: 0.8774 (ptp) cc_final: 0.8427 (ptm) REVERT: B 1054 GLN cc_start: 0.7238 (mm-40) cc_final: 0.6882 (mm-40) REVERT: A 650 LEU cc_start: 0.8975 (tp) cc_final: 0.8545 (pp) REVERT: A 779 GLN cc_start: 0.8955 (tm-30) cc_final: 0.8485 (tm-30) REVERT: A 902 MET cc_start: 0.8474 (mmp) cc_final: 0.8208 (mmp) REVERT: A 1019 ARG cc_start: 0.8716 (ttp80) cc_final: 0.8303 (ptm160) REVERT: A 1050 MET cc_start: 0.9198 (pmm) cc_final: 0.8614 (pmm) REVERT: A 1063 LEU cc_start: 0.9044 (mm) cc_final: 0.8811 (mm) REVERT: A 1067 TYR cc_start: 0.8638 (t80) cc_final: 0.8004 (t80) outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.1544 time to fit residues: 39.4032 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 : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 131 optimal weight: 8.9990 chunk 148 optimal weight: 0.1980 chunk 97 optimal weight: 0.7980 chunk 18 optimal weight: 4.9990 chunk 115 optimal weight: 5.9990 chunk 200 optimal weight: 4.9990 chunk 278 optimal weight: 10.0000 chunk 117 optimal weight: 6.9990 chunk 122 optimal weight: 10.0000 chunk 276 optimal weight: 0.5980 chunk 273 optimal weight: 0.7980 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 317 ASN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.046672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.030703 restraints weight = 202803.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.031992 restraints weight = 115674.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.032845 restraints weight = 78914.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.033380 restraints weight = 60392.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.033787 restraints weight = 50557.821| |-----------------------------------------------------------------------------| r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.4402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 26079 Z= 0.126 Angle : 0.555 13.693 35521 Z= 0.287 Chirality : 0.045 0.445 4081 Planarity : 0.004 0.067 4558 Dihedral : 4.571 54.944 3994 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.04 % Allowed : 0.68 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.02 (0.15), residues: 3144 helix: 1.38 (0.19), residues: 783 sheet: 0.17 (0.20), residues: 654 loop : -0.68 (0.14), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 34 TYR 0.023 0.001 TYR A 904 PHE 0.020 0.001 PHE A 374 TRP 0.016 0.001 TRP B 104 HIS 0.002 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00269 (26052) covalent geometry : angle 0.54130 (35440) hydrogen bonds : bond 0.03672 ( 1120) hydrogen bonds : angle 5.50668 ( 3162) link_NAG-ASN : bond 0.00444 ( 27) link_NAG-ASN : angle 2.66639 ( 81) *********************** 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 141 residues out of total 2801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 140 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 27 MET cc_start: 0.9573 (mmp) cc_final: 0.9333 (mmm) REVERT: E 18 GLU cc_start: 0.7915 (mt-10) cc_final: 0.7684 (pp20) REVERT: C 153 MET cc_start: 0.5999 (tmm) cc_final: 0.5659 (tmm) REVERT: C 170 TYR cc_start: 0.8188 (t80) cc_final: 0.7671 (t80) REVERT: C 900 MET cc_start: 0.9088 (tpt) cc_final: 0.8805 (tpp) REVERT: C 985 ASP cc_start: 0.9020 (p0) cc_final: 0.8791 (p0) REVERT: C 1029 MET cc_start: 0.8648 (ttm) cc_final: 0.8294 (ttm) REVERT: C 1050 MET cc_start: 0.8974 (ppp) cc_final: 0.8487 (ppp) REVERT: B 106 PHE cc_start: 0.8787 (m-80) cc_final: 0.8272 (m-80) REVERT: B 153 MET cc_start: 0.7569 (ppp) cc_final: 0.7191 (pmm) REVERT: B 724 THR cc_start: 0.9353 (p) cc_final: 0.9090 (p) REVERT: B 725 GLU cc_start: 0.8447 (mm-30) cc_final: 0.7820 (mm-30) REVERT: B 869 MET cc_start: 0.9425 (mtm) cc_final: 0.8700 (ptp) REVERT: B 902 MET cc_start: 0.9275 (mmp) cc_final: 0.8876 (mmp) REVERT: B 1001 LEU cc_start: 0.8974 (tt) cc_final: 0.8762 (pp) REVERT: B 1019 ARG cc_start: 0.8350 (tpt-90) cc_final: 0.8059 (tpt-90) REVERT: B 1029 MET cc_start: 0.8832 (ttm) cc_final: 0.8130 (ttm) REVERT: B 1034 LEU cc_start: 0.8650 (mm) cc_final: 0.7973 (mt) REVERT: B 1050 MET cc_start: 0.8793 (ptp) cc_final: 0.8498 (ptm) REVERT: A 650 LEU cc_start: 0.8982 (tp) cc_final: 0.8557 (pp) REVERT: A 779 GLN cc_start: 0.8878 (tm-30) cc_final: 0.8484 (tm-30) REVERT: A 902 MET cc_start: 0.8479 (mmp) cc_final: 0.8195 (mmp) REVERT: A 1019 ARG cc_start: 0.8761 (ttp80) cc_final: 0.8371 (ptm160) REVERT: A 1050 MET cc_start: 0.9229 (pmm) cc_final: 0.8591 (pmm) REVERT: A 1063 LEU cc_start: 0.9032 (mm) cc_final: 0.8779 (mm) REVERT: A 1067 TYR cc_start: 0.8649 (t80) cc_final: 0.8100 (t80) outliers start: 1 outliers final: 0 residues processed: 141 average time/residue: 0.1497 time to fit residues: 36.4815 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 : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 53 optimal weight: 9.9990 chunk 207 optimal weight: 4.9990 chunk 231 optimal weight: 0.0170 chunk 56 optimal weight: 0.0770 chunk 305 optimal weight: 0.3980 chunk 245 optimal weight: 6.9990 chunk 147 optimal weight: 9.9990 chunk 113 optimal weight: 10.0000 chunk 52 optimal weight: 9.9990 chunk 135 optimal weight: 0.6980 chunk 304 optimal weight: 0.9980 overall best weight: 0.4376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 762 GLN B 926 GLN ** 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 = 0.3282 r_free = 0.3282 target = 0.047171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.031084 restraints weight = 199433.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.032425 restraints weight = 112848.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.033317 restraints weight = 76468.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.033908 restraints weight = 58220.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.034273 restraints weight = 48197.632| |-----------------------------------------------------------------------------| r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.4495 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= 0.105 Angle : 0.548 13.551 35521 Z= 0.281 Chirality : 0.045 0.445 4081 Planarity : 0.004 0.053 4558 Dihedral : 4.411 55.369 3994 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (0.15), residues: 3144 helix: 1.45 (0.19), residues: 787 sheet: 0.18 (0.20), residues: 638 loop : -0.62 (0.14), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 34 TYR 0.020 0.001 TYR B 904 PHE 0.024 0.001 PHE C 927 TRP 0.019 0.001 TRP A 886 HIS 0.002 0.000 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00224 (26052) covalent geometry : angle 0.53417 (35440) hydrogen bonds : bond 0.03472 ( 1120) hydrogen bonds : angle 5.39045 ( 3162) link_NAG-ASN : bond 0.00478 ( 27) link_NAG-ASN : angle 2.57637 ( 81) ********************** 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 155 residues out of total 2801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 27 MET cc_start: 0.9566 (mmp) cc_final: 0.9308 (mmm) REVERT: E 18 GLU cc_start: 0.7893 (mt-10) cc_final: 0.7670 (pp20) REVERT: C 153 MET cc_start: 0.5954 (tmm) cc_final: 0.5617 (tmm) REVERT: C 170 TYR cc_start: 0.8080 (t80) cc_final: 0.7629 (t80) REVERT: C 900 MET cc_start: 0.9023 (tpt) cc_final: 0.8735 (tpp) REVERT: C 985 ASP cc_start: 0.8954 (p0) cc_final: 0.8731 (p0) REVERT: C 1029 MET cc_start: 0.8405 (ttm) cc_final: 0.8011 (ttm) REVERT: C 1050 MET cc_start: 0.8813 (ppp) cc_final: 0.8428 (ppp) REVERT: B 106 PHE cc_start: 0.8829 (m-80) cc_final: 0.8435 (m-80) REVERT: B 153 MET cc_start: 0.7530 (ppp) cc_final: 0.7177 (pmm) REVERT: B 724 THR cc_start: 0.9362 (p) cc_final: 0.9024 (p) REVERT: B 725 GLU cc_start: 0.8402 (mm-30) cc_final: 0.7937 (mm-30) REVERT: B 819 GLU cc_start: 0.7984 (mt-10) cc_final: 0.7061 (mm-30) REVERT: B 869 MET cc_start: 0.9395 (mtm) cc_final: 0.8778 (ptp) REVERT: B 902 MET cc_start: 0.9272 (mmp) cc_final: 0.8895 (mmp) REVERT: B 1019 ARG cc_start: 0.8289 (tpt-90) cc_final: 0.8032 (tpt-90) REVERT: B 1029 MET cc_start: 0.8839 (ttm) cc_final: 0.8289 (ttm) REVERT: B 1034 LEU cc_start: 0.8712 (mm) cc_final: 0.8140 (mt) REVERT: B 1050 MET cc_start: 0.8768 (ptp) cc_final: 0.8424 (ptp) REVERT: B 1054 GLN cc_start: 0.8489 (mm-40) cc_final: 0.7310 (mm110) REVERT: A 389 ASP cc_start: 0.6926 (m-30) cc_final: 0.6316 (p0) REVERT: A 650 LEU cc_start: 0.8917 (tp) cc_final: 0.8463 (pp) REVERT: A 779 GLN cc_start: 0.8868 (tm-30) cc_final: 0.8490 (tm-30) REVERT: A 902 MET cc_start: 0.8464 (mmp) cc_final: 0.8184 (mmp) REVERT: A 904 TYR cc_start: 0.8361 (t80) cc_final: 0.8097 (t80) REVERT: A 1050 MET cc_start: 0.9236 (pmm) cc_final: 0.8515 (pmm) REVERT: A 1055 SER cc_start: 0.7854 (t) cc_final: 0.7517 (p) REVERT: A 1063 LEU cc_start: 0.9074 (mm) cc_final: 0.8851 (mm) REVERT: A 1067 TYR cc_start: 0.8620 (t80) cc_final: 0.7937 (t80) outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 0.1574 time to fit residues: 41.2493 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 : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 205 optimal weight: 0.8980 chunk 181 optimal weight: 7.9990 chunk 174 optimal weight: 8.9990 chunk 281 optimal weight: 1.9990 chunk 223 optimal weight: 20.0000 chunk 171 optimal weight: 6.9990 chunk 134 optimal weight: 9.9990 chunk 163 optimal weight: 0.9980 chunk 148 optimal weight: 2.9990 chunk 224 optimal weight: 1.9990 chunk 58 optimal weight: 7.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1002 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.046515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.030590 restraints weight = 202521.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.031888 restraints weight = 115877.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.032750 restraints weight = 79089.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.033328 restraints weight = 60442.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.033716 restraints weight = 50128.236| |-----------------------------------------------------------------------------| r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.4635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 26079 Z= 0.134 Angle : 0.562 13.039 35521 Z= 0.288 Chirality : 0.045 0.439 4081 Planarity : 0.004 0.139 4558 Dihedral : 4.444 54.917 3994 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.05 (0.15), residues: 3144 helix: 1.39 (0.19), residues: 793 sheet: 0.15 (0.20), residues: 644 loop : -0.65 (0.14), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 905 TYR 0.041 0.001 TYR A 904 PHE 0.020 0.001 PHE C 927 TRP 0.080 0.002 TRP A 886 HIS 0.003 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00284 (26052) covalent geometry : angle 0.54956 (35440) hydrogen bonds : bond 0.03664 ( 1120) hydrogen bonds : angle 5.41829 ( 3162) link_NAG-ASN : bond 0.00426 ( 27) link_NAG-ASN : angle 2.50609 ( 81) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4270.91 seconds wall clock time: 75 minutes 8.98 seconds (4508.98 seconds total)