Starting phenix.real_space_refine on Fri Jul 3 07:43:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ky5_23068/07_2026/7ky5_23068.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ky5_23068/07_2026/7ky5_23068.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ky5_23068/07_2026/7ky5_23068.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ky5_23068/07_2026/7ky5_23068.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ky5_23068/07_2026/7ky5_23068.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ky5_23068/07_2026/7ky5_23068.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7ky5_23068/07_2026/7ky5_23068.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ky5_23068/07_2026/7ky5_23068.cif" } resolution = 3.98 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: 7 Type Number sf(0) Gaussians Al 1 5.89 5 Mg 1 5.21 5 S 62 5.16 5 C 8022 2.51 5 N 2053 2.21 5 O 2340 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 74 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12483 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 9297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1165, 9297 Classifications: {'peptide': 1165} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 1125} Chain breaks: 4 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2974 Classifications: {'peptide': 369} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 19, 'TRANS': 349} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 62 Unusual residues: {' MG': 1, 'ALF': 1, 'CLR': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 72 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 1.97, per 1000 atoms: 0.16 Number of scatterers: 12483 At special positions: 0 Unit cell: (133.812, 129.682, 137.942, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 62 16.00 Al 1 13.00 Mg 1 11.99 F 4 9.00 O 2340 8.00 N 2053 7.00 C 8022 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 110 " - pdb=" SG CYS B 159 " distance=2.03 Simple disulfide: pdb=" SG CYS B 216 " - pdb=" SG CYS B 231 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Links applied ALPHA1-4 " NAG C 2 " - " MAN C 3 " " NAG D 2 " - " MAN D 3 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG B 501 " - " ASN B 113 " " NAG B 502 " - " ASN B 256 " " NAG B 504 " - " ASN B 332 " " NAG C 1 " - " ASN B 240 " " NAG D 1 " - " ASN B 298 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.83 Conformation dependent library (CDL) restraints added in 451.2 milliseconds 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2882 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 14 sheets defined 46.7% alpha, 13.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 244 through 254 Processing helix chain 'A' and resid 256 through 271 removed outlier: 3.674A pdb=" N TYR A 260 " --> pdb=" O PHE A 256 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ALA A 269 " --> pdb=" O LEU A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 312 removed outlier: 3.777A pdb=" N ILE A 286 " --> pdb=" O SER A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 446 removed outlier: 3.564A pdb=" N ASN A 445 " --> pdb=" O TYR A 442 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL A 446 " --> pdb=" O TRP A 443 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 442 through 446' Processing helix chain 'A' and resid 471 through 473 No H-bonds generated for 'chain 'A' and resid 471 through 473' Processing helix chain 'A' and resid 495 through 499 removed outlier: 3.685A pdb=" N LYS A 499 " --> pdb=" O LYS A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 509 removed outlier: 3.502A pdb=" N ARG A 509 " --> pdb=" O ASP A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 548 No H-bonds generated for 'chain 'A' and resid 546 through 548' Processing helix chain 'A' and resid 570 through 573 removed outlier: 3.876A pdb=" N ASP A 573 " --> pdb=" O THR A 570 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 570 through 573' Processing helix chain 'A' and resid 574 through 581 removed outlier: 4.062A pdb=" N GLY A 581 " --> pdb=" O MET A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 613 removed outlier: 3.908A pdb=" N GLU A 593 " --> pdb=" O ARG A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 616 No H-bonds generated for 'chain 'A' and resid 614 through 616' Processing helix chain 'A' and resid 641 through 654 Processing helix chain 'A' and resid 660 through 680 removed outlier: 4.469A pdb=" N ILE A 664 " --> pdb=" O ILE A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 684 Processing helix chain 'A' and resid 701 through 706 removed outlier: 3.727A pdb=" N GLY A 704 " --> pdb=" O ASP A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 753 through 779 removed outlier: 3.896A pdb=" N SER A 779 " --> pdb=" O LEU A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 801 removed outlier: 4.387A pdb=" N GLU A 798 " --> pdb=" O LYS A 794 " (cutoff:3.500A) Processing helix chain 'A' and resid 806 through 819 Processing helix chain 'A' and resid 843 through 856 Processing helix chain 'A' and resid 918 through 925 Processing helix chain 'A' and resid 934 through 950 Processing helix chain 'A' and resid 962 through 977 Processing helix chain 'A' and resid 983 through 996 Processing helix chain 'A' and resid 1013 through 1024 removed outlier: 3.654A pdb=" N SER A1017 " --> pdb=" O GLY A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1035 through 1046 removed outlier: 3.626A pdb=" N ALA A1039 " --> pdb=" O LYS A1035 " (cutoff:3.500A) Processing helix chain 'A' and resid 1062 through 1068 removed outlier: 3.890A pdb=" N VAL A1065 " --> pdb=" O GLY A1062 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU A1066 " --> pdb=" O GLU A1063 " (cutoff:3.500A) Processing helix chain 'A' and resid 1071 through 1086 Processing helix chain 'A' and resid 1093 through 1102 removed outlier: 4.112A pdb=" N ARG A1102 " --> pdb=" O LYS A1098 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1126 removed outlier: 4.524A pdb=" N GLY A1126 " --> pdb=" O VAL A1122 " (cutoff:3.500A) Processing helix chain 'A' and resid 1126 through 1140 Processing helix chain 'A' and resid 1149 through 1163 Processing helix chain 'A' and resid 1177 through 1185 removed outlier: 4.055A pdb=" N SER A1183 " --> pdb=" O ALA A1179 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ASP A1185 " --> pdb=" O ILE A1181 " (cutoff:3.500A) Processing helix chain 'A' and resid 1208 through 1238 removed outlier: 4.273A pdb=" N VAL A1212 " --> pdb=" O GLN A1208 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N THR A1213 " --> pdb=" O PHE A1209 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ARG A1214 " --> pdb=" O ARG A1210 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LEU A1217 " --> pdb=" O THR A1213 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLY A1220 " --> pdb=" O VAL A1216 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N LYS A1221 " --> pdb=" O LEU A1217 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA A1228 " --> pdb=" O TYR A1224 " (cutoff:3.500A) Proline residue: A1232 - end of helix removed outlier: 3.718A pdb=" N ASN A1238 " --> pdb=" O PHE A1234 " (cutoff:3.500A) Processing helix chain 'A' and resid 1238 through 1249 removed outlier: 4.195A pdb=" N SER A1244 " --> pdb=" O ILE A1240 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU A1245 " --> pdb=" O PHE A1241 " (cutoff:3.500A) Processing helix chain 'A' and resid 1263 through 1272 removed outlier: 5.508A pdb=" N ASN A1269 " --> pdb=" O LEU A1265 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N LEU A1270 " --> pdb=" O THR A1266 " (cutoff:3.500A) Processing helix chain 'A' and resid 1274 through 1283 Processing helix chain 'A' and resid 1288 through 1295 Processing helix chain 'A' and resid 1296 through 1298 No H-bonds generated for 'chain 'A' and resid 1296 through 1298' Processing helix chain 'A' and resid 1299 through 1305 Processing helix chain 'A' and resid 1309 through 1337 Proline residue: A1331 - end of helix removed outlier: 4.477A pdb=" N LYS A1337 " --> pdb=" O LEU A1333 " (cutoff:3.500A) Processing helix chain 'A' and resid 1350 through 1374 removed outlier: 3.552A pdb=" N VAL A1354 " --> pdb=" O HIS A1350 " (cutoff:3.500A) Processing helix chain 'A' and resid 1380 through 1401 Processing helix chain 'A' and resid 1410 through 1417 removed outlier: 3.995A pdb=" N ALA A1417 " --> pdb=" O ALA A1413 " (cutoff:3.500A) Processing helix chain 'A' and resid 1418 through 1447 Proline residue: A1435 - end of helix removed outlier: 3.734A pdb=" N ILE A1445 " --> pdb=" O CYS A1441 " (cutoff:3.500A) Processing helix chain 'A' and resid 1449 through 1461 removed outlier: 3.811A pdb=" N ILE A1453 " --> pdb=" O LYS A1449 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLY A1461 " --> pdb=" O MET A1457 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 98 Proline residue: B 77 - end of helix Processing helix chain 'B' and resid 109 through 114 removed outlier: 3.642A pdb=" N ASN B 113 " --> pdb=" O ASP B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 124 No H-bonds generated for 'chain 'B' and resid 122 through 124' Processing helix chain 'B' and resid 186 through 192 Processing helix chain 'B' and resid 195 through 200 Processing helix chain 'B' and resid 204 through 210 Processing helix chain 'B' and resid 232 through 237 Processing helix chain 'B' and resid 267 through 273 Processing helix chain 'B' and resid 286 through 290 removed outlier: 3.775A pdb=" N GLU B 290 " --> pdb=" O PRO B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 315 removed outlier: 3.542A pdb=" N GLN B 312 " --> pdb=" O TRP B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 354 Processing helix chain 'B' and resid 372 through 398 Processing helix chain 'B' and resid 409 through 413 removed outlier: 3.745A pdb=" N MET B 413 " --> pdb=" O SER B 410 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 206 through 210 Processing sheet with id=AA2, first strand: chain 'A' and resid 318 through 319 Processing sheet with id=AA3, first strand: chain 'A' and resid 451 through 455 removed outlier: 6.473A pdb=" N MET A 566 " --> pdb=" O LEU A 466 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N LEU A 466 " --> pdb=" O MET A 566 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 458 through 459 removed outlier: 4.268A pdb=" N ASP A 458 " --> pdb=" O LEU A 557 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N TYR A 477 " --> pdb=" O ARG A 558 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 693 through 694 removed outlier: 3.521A pdb=" N THR A 693 " --> pdb=" O ALA A1205 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N GLY A1189 " --> pdb=" O ILE A1206 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1054 through 1058 removed outlier: 8.174A pdb=" N PHE A1111 " --> pdb=" O ALA A1142 " (cutoff:3.500A) removed outlier: 8.491A pdb=" N LEU A1144 " --> pdb=" O PHE A1111 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL A1113 " --> pdb=" O LEU A1144 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N VAL A1143 " --> pdb=" O LEU A1028 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL A1030 " --> pdb=" O VAL A1143 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ILE A 709 " --> pdb=" O TRP A1029 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LEU A1031 " --> pdb=" O ILE A 709 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N SER A 711 " --> pdb=" O LEU A1031 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 732 through 734 removed outlier: 5.401A pdb=" N VAL A 721 " --> pdb=" O ARG A1009 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG A1009 " --> pdb=" O VAL A 721 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LYS A 725 " --> pdb=" O ALA A1005 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N ALA A1005 " --> pdb=" O LYS A 725 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N CYS A 727 " --> pdb=" O GLY A1003 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLY A1003 " --> pdb=" O CYS A 727 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N ILE A 729 " --> pdb=" O LEU A1001 " (cutoff:3.500A) removed outlier: 9.540A pdb=" N LEU A1001 " --> pdb=" O ILE A 729 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N LEU A1000 " --> pdb=" O GLN A 958 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N GLN A 958 " --> pdb=" O LEU A1000 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLY A1002 " --> pdb=" O LEU A 956 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ARG A 952 " --> pdb=" O ILE A1006 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N SER A 895 " --> pdb=" O VAL A 884 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N VAL A 884 " --> pdb=" O SER A 895 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ILE A 897 " --> pdb=" O LEU A 882 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN A 880 " --> pdb=" O LYS A 899 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 826 through 827 removed outlier: 3.845A pdb=" N LEU A 826 " --> pdb=" O LYS A 840 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LYS A 840 " --> pdb=" O LEU A 826 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 858 through 864 removed outlier: 5.265A pdb=" N SER A 863 " --> pdb=" O GLY A 867 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N GLY A 867 " --> pdb=" O SER A 863 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1377 through 1378 Processing sheet with id=AB2, first strand: chain 'B' and resid 126 through 129 removed outlier: 7.001A pdb=" N TYR B 177 " --> pdb=" O LEU B 326 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LEU B 326 " --> pdb=" O TYR B 177 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N LEU B 179 " --> pdb=" O THR B 324 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N THR B 324 " --> pdb=" O LEU B 179 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 119 through 120 Processing sheet with id=AB4, first strand: chain 'B' and resid 119 through 120 Processing sheet with id=AB5, first strand: chain 'B' and resid 227 through 228 removed outlier: 6.443A pdb=" N ILE B 227 " --> pdb=" O ALA B 284 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 578 hydrogen bonds defined for protein. 1611 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: 1.81 Time building geometry restraints manager: 1.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3934 1.34 - 1.46: 2193 1.46 - 1.58: 6540 1.58 - 1.69: 0 1.69 - 1.81: 94 Bond restraints: 12761 Sorted by residual: bond pdb=" F1 ALF A1703 " pdb="AL ALF A1703 " ideal model delta sigma weight residual 1.684 1.785 -0.101 2.00e-02 2.50e+03 2.56e+01 bond pdb=" F3 ALF A1703 " pdb="AL ALF A1703 " ideal model delta sigma weight residual 1.685 1.785 -0.100 2.00e-02 2.50e+03 2.49e+01 bond pdb=" F4 ALF A1703 " pdb="AL ALF A1703 " ideal model delta sigma weight residual 1.686 1.786 -0.100 2.00e-02 2.50e+03 2.49e+01 bond pdb=" F2 ALF A1703 " pdb="AL ALF A1703 " ideal model delta sigma weight residual 1.685 1.784 -0.099 2.00e-02 2.50e+03 2.44e+01 bond pdb=" C1 MAN C 3 " pdb=" C2 MAN C 3 " ideal model delta sigma weight residual 1.526 1.560 -0.034 2.00e-02 2.50e+03 2.90e+00 ... (remaining 12756 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.25: 17319 14.25 - 28.49: 4 28.49 - 42.74: 0 42.74 - 56.99: 0 56.99 - 71.23: 2 Bond angle restraints: 17325 Sorted by residual: angle pdb=" F1 ALF A1703 " pdb="AL ALF A1703 " pdb=" F2 ALF A1703 " ideal model delta sigma weight residual 108.68 179.91 -71.23 3.00e+00 1.11e-01 5.64e+02 angle pdb=" F3 ALF A1703 " pdb="AL ALF A1703 " pdb=" F4 ALF A1703 " ideal model delta sigma weight residual 109.63 179.96 -70.33 3.00e+00 1.11e-01 5.50e+02 angle pdb=" F2 ALF A1703 " pdb="AL ALF A1703 " pdb=" F4 ALF A1703 " ideal model delta sigma weight residual 110.21 90.14 20.07 3.00e+00 1.11e-01 4.48e+01 angle pdb=" F2 ALF A1703 " pdb="AL ALF A1703 " pdb=" F3 ALF A1703 " ideal model delta sigma weight residual 109.59 89.89 19.70 3.00e+00 1.11e-01 4.31e+01 angle pdb=" F1 ALF A1703 " pdb="AL ALF A1703 " pdb=" F3 ALF A1703 " ideal model delta sigma weight residual 109.69 90.07 19.62 3.00e+00 1.11e-01 4.28e+01 ... (remaining 17320 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 6829 17.77 - 35.54: 559 35.54 - 53.32: 86 53.32 - 71.09: 8 71.09 - 88.86: 7 Dihedral angle restraints: 7489 sinusoidal: 3010 harmonic: 4479 Sorted by residual: dihedral pdb=" CA ASN B 256 " pdb=" C ASN B 256 " pdb=" N TYR B 257 " pdb=" CA TYR B 257 " ideal model delta harmonic sigma weight residual -180.00 -158.26 -21.74 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" CA TYR A1335 " pdb=" C TYR A1335 " pdb=" N HIS A1336 " pdb=" CA HIS A1336 " ideal model delta harmonic sigma weight residual -180.00 -159.15 -20.85 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CA ASN A1252 " pdb=" C ASN A1252 " pdb=" N ASN A1253 " pdb=" CA ASN A1253 " ideal model delta harmonic sigma weight residual 180.00 159.86 20.14 0 5.00e+00 4.00e-02 1.62e+01 ... (remaining 7486 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.176: 1963 0.176 - 0.352: 9 0.352 - 0.528: 1 0.528 - 0.704: 0 0.704 - 0.880: 1 Chirality restraints: 1974 Sorted by residual: chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN B 240 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -3.28 0.88 2.00e-01 2.50e+01 1.94e+01 chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.34 -0.06 2.00e-02 2.50e+03 1.05e+01 chirality pdb=" C14 CLR A1701 " pdb=" C13 CLR A1701 " pdb=" C15 CLR A1701 " pdb=" C8 CLR A1701 " both_signs ideal model delta sigma weight residual False -2.32 -2.67 0.36 2.00e-01 2.50e+01 3.16e+00 ... (remaining 1971 not shown) Planarity restraints: 2182 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 1 " -0.314 2.00e-02 2.50e+03 2.65e-01 8.79e+02 pdb=" C7 NAG C 1 " 0.082 2.00e-02 2.50e+03 pdb=" C8 NAG C 1 " -0.188 2.00e-02 2.50e+03 pdb=" N2 NAG C 1 " 0.458 2.00e-02 2.50e+03 pdb=" O7 NAG C 1 " -0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 142 " 0.019 2.00e-02 2.50e+03 1.81e-02 8.15e+00 pdb=" CG TRP B 142 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 TRP B 142 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP B 142 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 142 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 142 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 142 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 142 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 142 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP B 142 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG A1477 " 0.042 5.00e-02 4.00e+02 6.34e-02 6.43e+00 pdb=" N PRO A1478 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO A1478 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A1478 " 0.035 5.00e-02 4.00e+02 ... (remaining 2179 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1139 2.74 - 3.28: 13384 3.28 - 3.82: 21173 3.82 - 4.36: 23873 4.36 - 4.90: 40125 Nonbonded interactions: 99694 Sorted by model distance: nonbonded pdb=" CD1 TYR A1409 " pdb=" NH2 ARG B 272 " model vdw 2.200 3.420 nonbonded pdb=" OG1 THR B 248 " pdb=" O GLN B 341 " model vdw 2.236 3.040 nonbonded pdb=" OG1 THR A 953 " pdb=" O THR A1004 " model vdw 2.240 3.040 nonbonded pdb=" OG1 THR A 718 " pdb=" O ARG A1009 " model vdw 2.263 3.040 nonbonded pdb=" O LEU A 703 " pdb=" OH TYR A1299 " model vdw 2.288 3.040 ... (remaining 99689 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 'C' selection = chain 'D' } 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: 1.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.530 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 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 : 0.004 0.207 12773 Z= 0.208 Angle : 1.102 71.235 17356 Z= 0.481 Chirality : 0.052 0.880 1974 Planarity : 0.007 0.265 2177 Dihedral : 12.785 88.860 4601 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 16.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 0.07 % Allowed : 0.37 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.22), residues: 1520 helix: 0.59 (0.22), residues: 617 sheet: -0.47 (0.39), residues: 188 loop : -1.98 (0.23), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A1131 TYR 0.021 0.001 TYR A 260 PHE 0.039 0.002 PHE A1328 TRP 0.048 0.001 TRP B 142 HIS 0.003 0.001 HIS A1350 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.19 (12761) covalent geometry : angle 1.08589 / 0.48 (17325) SS BOND : bond 0.00150 / 0.08 ( 2) SS BOND : angle 0.56534 / 0.41 ( 4) hydrogen bonds : bond 0.12136 / 7.84 ( 562) hydrogen bonds : angle 5.23141 / 3.65 ( 1611) Misc. bond : bond 0.00201 / 0.11 ( 1) link_ALPHA1-4 : bond 0.00560 / 0.29 ( 2) link_ALPHA1-4 : angle 1.96025 / 1.20 ( 6) link_BETA1-4 : bond 0.00488 / 0.23 ( 2) link_BETA1-4 : angle 0.95317 / 0.84 ( 6) link_NAG-ASN : bond 0.09268 / 4.42 ( 5) link_NAG-ASN : angle 6.48871 / 3.29 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 213 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 TYR cc_start: 0.5892 (m-10) cc_final: 0.4875 (m-10) REVERT: A 835 LYS cc_start: 0.9027 (mppt) cc_final: 0.8636 (tptt) REVERT: B 391 ILE cc_start: 0.9036 (tp) cc_final: 0.8516 (tp) REVERT: B 395 PHE cc_start: 0.8008 (m-80) cc_final: 0.7272 (m-80) outliers start: 1 outliers final: 0 residues processed: 214 average time/residue: 0.0767 time to fit residues: 25.7885 Evaluate side-chains 162 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 20.0000 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 8.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 698 ASN ** A 814 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 873 GLN A 888 ASN ** A1252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1323 GLN ** B 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.096021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.077492 restraints weight = 56693.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.079508 restraints weight = 35111.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.080889 restraints weight = 24362.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.081934 restraints weight = 18684.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.082580 restraints weight = 15345.777| |-----------------------------------------------------------------------------| r_work (final): 0.3898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12773 Z= 0.130 Angle : 0.665 10.989 17356 Z= 0.326 Chirality : 0.044 0.227 1974 Planarity : 0.004 0.050 2177 Dihedral : 4.438 46.474 1686 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 1.86 % Allowed : 9.65 % Favored : 88.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.21), residues: 1520 helix: 0.44 (0.21), residues: 623 sheet: -0.52 (0.37), residues: 196 loop : -1.93 (0.23), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 625 TYR 0.022 0.001 TYR A 260 PHE 0.028 0.002 PHE A 602 TRP 0.018 0.001 TRP B 142 HIS 0.004 0.001 HIS A 942 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (12761) covalent geometry : angle 0.65317 / 0.32 (17325) SS BOND : bond 0.00097 / 0.05 ( 2) SS BOND : angle 0.40802 / 0.27 ( 4) hydrogen bonds : bond 0.03860 / 2.57 ( 562) hydrogen bonds : angle 4.63965 / 3.26 ( 1611) Misc. bond : bond 0.00204 / 0.11 ( 1) link_ALPHA1-4 : bond 0.00526 / 0.27 ( 2) link_ALPHA1-4 : angle 1.90599 / 1.15 ( 6) link_BETA1-4 : bond 0.00821 / 0.39 ( 2) link_BETA1-4 : angle 1.49805 / 1.23 ( 6) link_NAG-ASN : bond 0.00594 / 0.30 ( 5) link_NAG-ASN : angle 4.07849 / 2.32 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 183 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 TYR cc_start: 0.7962 (m-10) cc_final: 0.7605 (m-10) REVERT: A 260 TYR cc_start: 0.6207 (m-10) cc_final: 0.5874 (m-10) REVERT: A 525 SER cc_start: 0.8580 (t) cc_final: 0.7964 (p) REVERT: A 566 MET cc_start: 0.7528 (tpp) cc_final: 0.7202 (tpp) REVERT: A 756 GLU cc_start: 0.8176 (mp0) cc_final: 0.7889 (pm20) REVERT: A 778 MET cc_start: 0.6831 (ppp) cc_final: 0.6595 (ppp) REVERT: A 835 LYS cc_start: 0.8964 (mppt) cc_final: 0.8591 (tptt) REVERT: A 1120 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8981 (pp) REVERT: A 1238 ASN cc_start: 0.8666 (p0) cc_final: 0.8379 (p0) REVERT: A 1372 MET cc_start: 0.8487 (tmm) cc_final: 0.7690 (mmt) REVERT: A 1446 PHE cc_start: 0.7195 (t80) cc_final: 0.6940 (t80) REVERT: B 391 ILE cc_start: 0.9031 (tp) cc_final: 0.8507 (tp) REVERT: B 395 PHE cc_start: 0.7885 (m-80) cc_final: 0.7078 (m-80) outliers start: 25 outliers final: 17 residues processed: 191 average time/residue: 0.0754 time to fit residues: 23.1398 Evaluate side-chains 181 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 163 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 771 MET Chi-restraints excluded: chain A residue 1116 ASP Chi-restraints excluded: chain A residue 1120 LEU Chi-restraints excluded: chain A residue 1145 CYS Chi-restraints excluded: chain A residue 1280 LEU Chi-restraints excluded: chain A residue 1309 ASN Chi-restraints excluded: chain A residue 1361 ILE Chi-restraints excluded: chain A residue 1368 PHE Chi-restraints excluded: chain A residue 1370 VAL Chi-restraints excluded: chain A residue 1387 LEU Chi-restraints excluded: chain A residue 1434 LEU Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 346 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 105 optimal weight: 8.9990 chunk 67 optimal weight: 20.0000 chunk 55 optimal weight: 20.0000 chunk 106 optimal weight: 7.9990 chunk 79 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 25 optimal weight: 10.0000 chunk 116 optimal weight: 6.9990 chunk 4 optimal weight: 7.9990 chunk 74 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 814 HIS ** A1208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 GLN ** B 301 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 = 0.4053 r_free = 0.4053 target = 0.090983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.072668 restraints weight = 58748.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.074519 restraints weight = 36029.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.075749 restraints weight = 25055.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.076817 restraints weight = 19283.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.077402 restraints weight = 15901.034| |-----------------------------------------------------------------------------| r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12773 Z= 0.188 Angle : 0.668 9.046 17356 Z= 0.337 Chirality : 0.045 0.208 1974 Planarity : 0.004 0.051 2177 Dihedral : 4.573 46.114 1686 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 16.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 2.82 % Allowed : 12.62 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.21), residues: 1520 helix: 0.36 (0.21), residues: 617 sheet: -0.50 (0.36), residues: 208 loop : -2.00 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 625 TYR 0.020 0.002 TYR A1248 PHE 0.024 0.002 PHE A 602 TRP 0.025 0.002 TRP B 126 HIS 0.004 0.001 HIS A 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.19 (12761) covalent geometry : angle 0.65851 / 0.33 (17325) SS BOND : bond 0.00245 / 0.12 ( 2) SS BOND : angle 0.55767 / 0.45 ( 4) hydrogen bonds : bond 0.03717 / 2.46 ( 562) hydrogen bonds : angle 4.67789 / 3.27 ( 1611) Misc. bond : bond 0.00296 / 0.16 ( 1) link_ALPHA1-4 : bond 0.00691 / 0.35 ( 2) link_ALPHA1-4 : angle 1.90193 / 1.16 ( 6) link_BETA1-4 : bond 0.01060 / 0.51 ( 2) link_BETA1-4 : angle 1.84554 / 1.75 ( 6) link_NAG-ASN : bond 0.00545 / 0.27 ( 5) link_NAG-ASN : angle 3.58857 / 2.05 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 169 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 TYR cc_start: 0.7962 (m-10) cc_final: 0.7632 (m-10) REVERT: A 464 MET cc_start: 0.8030 (tpp) cc_final: 0.7534 (mmm) REVERT: A 566 MET cc_start: 0.7473 (tpp) cc_final: 0.7245 (tpp) REVERT: A 756 GLU cc_start: 0.8259 (mp0) cc_final: 0.8018 (pm20) REVERT: A 835 LYS cc_start: 0.8966 (mppt) cc_final: 0.8492 (tptt) REVERT: A 1120 LEU cc_start: 0.9283 (OUTLIER) cc_final: 0.9061 (pp) REVERT: A 1200 MET cc_start: 0.8780 (mmm) cc_final: 0.7939 (mmm) REVERT: A 1303 ILE cc_start: 0.9307 (mm) cc_final: 0.9088 (mt) REVERT: A 1372 MET cc_start: 0.8561 (tmm) cc_final: 0.7732 (mmt) REVERT: A 1378 ASP cc_start: 0.8296 (p0) cc_final: 0.7763 (p0) REVERT: A 1446 PHE cc_start: 0.7206 (t80) cc_final: 0.6939 (t80) REVERT: B 391 ILE cc_start: 0.9073 (tp) cc_final: 0.8428 (tt) REVERT: B 395 PHE cc_start: 0.7794 (m-80) cc_final: 0.7139 (m-80) outliers start: 38 outliers final: 29 residues processed: 184 average time/residue: 0.0767 time to fit residues: 22.3374 Evaluate side-chains 181 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 151 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 771 MET Chi-restraints excluded: chain A residue 1028 LEU Chi-restraints excluded: chain A residue 1097 LEU Chi-restraints excluded: chain A residue 1106 LEU Chi-restraints excluded: chain A residue 1116 ASP Chi-restraints excluded: chain A residue 1120 LEU Chi-restraints excluded: chain A residue 1145 CYS Chi-restraints excluded: chain A residue 1278 ILE Chi-restraints excluded: chain A residue 1280 LEU Chi-restraints excluded: chain A residue 1298 LEU Chi-restraints excluded: chain A residue 1309 ASN Chi-restraints excluded: chain A residue 1321 VAL Chi-restraints excluded: chain A residue 1361 ILE Chi-restraints excluded: chain A residue 1370 VAL Chi-restraints excluded: chain A residue 1384 PHE Chi-restraints excluded: chain A residue 1387 LEU Chi-restraints excluded: chain A residue 1406 ASN Chi-restraints excluded: chain A residue 1434 LEU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 176 ASN Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 407 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 102 optimal weight: 0.9990 chunk 88 optimal weight: 7.9990 chunk 123 optimal weight: 0.9990 chunk 70 optimal weight: 4.9990 chunk 41 optimal weight: 9.9990 chunk 76 optimal weight: 7.9990 chunk 121 optimal weight: 5.9990 chunk 34 optimal weight: 7.9990 chunk 145 optimal weight: 9.9990 chunk 19 optimal weight: 8.9990 chunk 29 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 809 GLN A1208 GLN ** A1252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1323 GLN ** B 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 301 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 = 0.3907 r_free = 0.3907 target = 0.086893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.067613 restraints weight = 58931.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.069747 restraints weight = 34550.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.071363 restraints weight = 23367.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.072350 restraints weight = 17587.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.073201 restraints weight = 14318.381| |-----------------------------------------------------------------------------| r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12773 Z= 0.186 Angle : 0.663 12.611 17356 Z= 0.336 Chirality : 0.045 0.250 1974 Planarity : 0.004 0.054 2177 Dihedral : 4.645 43.392 1686 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 17.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 3.41 % Allowed : 15.07 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.21), residues: 1520 helix: 0.27 (0.21), residues: 624 sheet: -0.58 (0.36), residues: 209 loop : -1.96 (0.23), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 625 TYR 0.014 0.002 TYR B 360 PHE 0.029 0.002 PHE A 606 TRP 0.017 0.001 TRP A 562 HIS 0.003 0.001 HIS B 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.19 (12761) covalent geometry : angle 0.65408 / 0.33 (17325) SS BOND : bond 0.00183 / 0.09 ( 2) SS BOND : angle 0.61338 / 0.52 ( 4) hydrogen bonds : bond 0.03652 / 2.41 ( 562) hydrogen bonds : angle 4.78157 / 3.33 ( 1611) Misc. bond : bond 0.00273 / 0.14 ( 1) link_ALPHA1-4 : bond 0.00528 / 0.27 ( 2) link_ALPHA1-4 : angle 1.76168 / 1.07 ( 6) link_BETA1-4 : bond 0.00937 / 0.45 ( 2) link_BETA1-4 : angle 1.74362 / 1.63 ( 6) link_NAG-ASN : bond 0.00532 / 0.27 ( 5) link_NAG-ASN : angle 3.54452 / 2.01 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 160 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 TYR cc_start: 0.7953 (m-10) cc_final: 0.7747 (m-10) REVERT: A 314 ARG cc_start: 0.8666 (ttt-90) cc_final: 0.7835 (tpt170) REVERT: A 525 SER cc_start: 0.8745 (t) cc_final: 0.8187 (p) REVERT: A 566 MET cc_start: 0.7551 (tpp) cc_final: 0.7267 (tpp) REVERT: A 702 ASP cc_start: 0.8412 (OUTLIER) cc_final: 0.8059 (t0) REVERT: A 778 MET cc_start: 0.7859 (ppp) cc_final: 0.7627 (ppp) REVERT: A 835 LYS cc_start: 0.9080 (mppt) cc_final: 0.8405 (tptt) REVERT: A 1120 LEU cc_start: 0.9330 (OUTLIER) cc_final: 0.9093 (pp) REVERT: A 1208 GLN cc_start: 0.7767 (OUTLIER) cc_final: 0.7031 (pm20) REVERT: A 1339 MET cc_start: 0.7731 (mmp) cc_final: 0.7157 (mmp) REVERT: A 1372 MET cc_start: 0.8736 (tmm) cc_final: 0.8518 (tmm) REVERT: A 1378 ASP cc_start: 0.8638 (p0) cc_final: 0.8281 (p0) REVERT: A 1446 PHE cc_start: 0.7248 (t80) cc_final: 0.6927 (t80) REVERT: B 102 GLU cc_start: 0.8203 (pp20) cc_final: 0.7234 (pp20) REVERT: B 391 ILE cc_start: 0.9079 (tp) cc_final: 0.8456 (tt) REVERT: B 395 PHE cc_start: 0.7957 (m-80) cc_final: 0.7295 (m-80) outliers start: 46 outliers final: 32 residues processed: 183 average time/residue: 0.0723 time to fit residues: 20.9096 Evaluate side-chains 185 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 150 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 702 ASP Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 771 MET Chi-restraints excluded: chain A residue 1097 LEU Chi-restraints excluded: chain A residue 1106 LEU Chi-restraints excluded: chain A residue 1116 ASP Chi-restraints excluded: chain A residue 1120 LEU Chi-restraints excluded: chain A residue 1145 CYS Chi-restraints excluded: chain A residue 1201 CYS Chi-restraints excluded: chain A residue 1206 ILE Chi-restraints excluded: chain A residue 1208 GLN Chi-restraints excluded: chain A residue 1227 LEU Chi-restraints excluded: chain A residue 1279 LEU Chi-restraints excluded: chain A residue 1280 LEU Chi-restraints excluded: chain A residue 1293 MET Chi-restraints excluded: chain A residue 1309 ASN Chi-restraints excluded: chain A residue 1336 HIS Chi-restraints excluded: chain A residue 1361 ILE Chi-restraints excluded: chain A residue 1370 VAL Chi-restraints excluded: chain A residue 1387 LEU Chi-restraints excluded: chain A residue 1391 VAL Chi-restraints excluded: chain A residue 1434 LEU Chi-restraints excluded: chain A residue 1442 ILE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 176 ASN Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 359 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 81 optimal weight: 6.9990 chunk 117 optimal weight: 9.9990 chunk 21 optimal weight: 0.9980 chunk 55 optimal weight: 20.0000 chunk 84 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 51 optimal weight: 9.9990 chunk 1 optimal weight: 2.9990 chunk 148 optimal weight: 0.9980 chunk 89 optimal weight: 8.9990 chunk 53 optimal weight: 7.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 579 ASN ** A1252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 301 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 = 0.3912 r_free = 0.3912 target = 0.086998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.067840 restraints weight = 57974.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.070037 restraints weight = 33750.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.071531 restraints weight = 22852.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.072654 restraints weight = 17124.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.073350 restraints weight = 13825.509| |-----------------------------------------------------------------------------| r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12773 Z= 0.152 Angle : 0.636 10.776 17356 Z= 0.319 Chirality : 0.044 0.203 1974 Planarity : 0.004 0.055 2177 Dihedral : 4.639 41.851 1686 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 16.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 3.64 % Allowed : 16.63 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.22), residues: 1520 helix: 0.36 (0.21), residues: 623 sheet: -0.45 (0.38), residues: 196 loop : -1.87 (0.23), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 625 TYR 0.014 0.001 TYR A1322 PHE 0.031 0.002 PHE A 647 TRP 0.012 0.001 TRP B 126 HIS 0.003 0.001 HIS B 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (12761) covalent geometry : angle 0.62598 / 0.32 (17325) SS BOND : bond 0.00134 / 0.07 ( 2) SS BOND : angle 0.57614 / 0.50 ( 4) hydrogen bonds : bond 0.03584 / 2.35 ( 562) hydrogen bonds : angle 4.69306 / 3.28 ( 1611) Misc. bond : bond 0.00256 / 0.13 ( 1) link_ALPHA1-4 : bond 0.00679 / 0.34 ( 2) link_ALPHA1-4 : angle 1.77331 / 1.09 ( 6) link_BETA1-4 : bond 0.00927 / 0.44 ( 2) link_BETA1-4 : angle 1.66990 / 1.54 ( 6) link_NAG-ASN : bond 0.00572 / 0.30 ( 5) link_NAG-ASN : angle 3.58926 / 2.05 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 160 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 ARG cc_start: 0.8673 (ttt-90) cc_final: 0.7861 (tpt90) REVERT: A 525 SER cc_start: 0.8781 (t) cc_final: 0.8223 (p) REVERT: A 566 MET cc_start: 0.7642 (tpp) cc_final: 0.7353 (tpp) REVERT: A 722 MET cc_start: 0.7271 (mtm) cc_final: 0.6979 (ptt) REVERT: A 756 GLU cc_start: 0.8214 (mp0) cc_final: 0.7927 (pm20) REVERT: A 968 ARG cc_start: 0.9288 (OUTLIER) cc_final: 0.8954 (ppt170) REVERT: A 1011 GLN cc_start: 0.8579 (OUTLIER) cc_final: 0.8192 (mp10) REVERT: A 1120 LEU cc_start: 0.9315 (OUTLIER) cc_final: 0.9081 (pp) REVERT: A 1200 MET cc_start: 0.8971 (mmm) cc_final: 0.8579 (mmm) REVERT: A 1339 MET cc_start: 0.7719 (mmp) cc_final: 0.7305 (mmp) REVERT: A 1372 MET cc_start: 0.8782 (tmm) cc_final: 0.8512 (tmm) REVERT: A 1378 ASP cc_start: 0.8633 (p0) cc_final: 0.8270 (p0) REVERT: B 391 ILE cc_start: 0.9084 (tp) cc_final: 0.8441 (tt) REVERT: B 395 PHE cc_start: 0.7975 (m-80) cc_final: 0.7291 (m-80) outliers start: 49 outliers final: 37 residues processed: 189 average time/residue: 0.0790 time to fit residues: 22.8941 Evaluate side-chains 195 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 155 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 520 HIS Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 771 MET Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 953 THR Chi-restraints excluded: chain A residue 968 ARG Chi-restraints excluded: chain A residue 1011 GLN Chi-restraints excluded: chain A residue 1097 LEU Chi-restraints excluded: chain A residue 1106 LEU Chi-restraints excluded: chain A residue 1116 ASP Chi-restraints excluded: chain A residue 1120 LEU Chi-restraints excluded: chain A residue 1206 ILE Chi-restraints excluded: chain A residue 1227 LEU Chi-restraints excluded: chain A residue 1280 LEU Chi-restraints excluded: chain A residue 1293 MET Chi-restraints excluded: chain A residue 1298 LEU Chi-restraints excluded: chain A residue 1309 ASN Chi-restraints excluded: chain A residue 1336 HIS Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain A residue 1361 ILE Chi-restraints excluded: chain A residue 1370 VAL Chi-restraints excluded: chain A residue 1387 LEU Chi-restraints excluded: chain A residue 1391 VAL Chi-restraints excluded: chain A residue 1406 ASN Chi-restraints excluded: chain A residue 1434 LEU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 176 ASN Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 407 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 53 optimal weight: 9.9990 chunk 30 optimal weight: 10.0000 chunk 9 optimal weight: 7.9990 chunk 89 optimal weight: 6.9990 chunk 139 optimal weight: 0.2980 chunk 26 optimal weight: 8.9990 chunk 31 optimal weight: 0.7980 chunk 50 optimal weight: 8.9990 chunk 143 optimal weight: 4.9990 chunk 145 optimal weight: 0.0370 chunk 105 optimal weight: 5.9990 overall best weight: 2.4262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 GLN ** B 301 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 = 0.3911 r_free = 0.3911 target = 0.087014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.067949 restraints weight = 58002.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.070049 restraints weight = 33717.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.071586 restraints weight = 22902.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.072636 restraints weight = 17153.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.073134 restraints weight = 13805.080| |-----------------------------------------------------------------------------| r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.3040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12773 Z= 0.146 Angle : 0.634 11.907 17356 Z= 0.317 Chirality : 0.044 0.264 1974 Planarity : 0.004 0.056 2177 Dihedral : 4.604 39.432 1686 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 16.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 4.31 % Allowed : 17.59 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.22), residues: 1520 helix: 0.38 (0.21), residues: 624 sheet: -0.41 (0.38), residues: 196 loop : -1.84 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1009 TYR 0.019 0.001 TYR A 619 PHE 0.025 0.002 PHE A 647 TRP 0.010 0.001 TRP B 126 HIS 0.003 0.001 HIS B 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.15 (12761) covalent geometry : angle 0.62417 / 0.32 (17325) SS BOND : bond 0.00122 / 0.06 ( 2) SS BOND : angle 0.59264 / 0.50 ( 4) hydrogen bonds : bond 0.03488 / 2.30 ( 562) hydrogen bonds : angle 4.63577 / 3.24 ( 1611) Misc. bond : bond 0.00245 / 0.13 ( 1) link_ALPHA1-4 : bond 0.00588 / 0.30 ( 2) link_ALPHA1-4 : angle 1.75133 / 1.08 ( 6) link_BETA1-4 : bond 0.00907 / 0.43 ( 2) link_BETA1-4 : angle 1.65360 / 1.51 ( 6) link_NAG-ASN : bond 0.00557 / 0.28 ( 5) link_NAG-ASN : angle 3.57699 / 2.03 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 163 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 ARG cc_start: 0.8727 (ttt-90) cc_final: 0.7981 (tpt-90) REVERT: A 525 SER cc_start: 0.8770 (t) cc_final: 0.8218 (p) REVERT: A 566 MET cc_start: 0.7776 (tpp) cc_final: 0.7470 (tpp) REVERT: A 702 ASP cc_start: 0.8457 (OUTLIER) cc_final: 0.8087 (t0) REVERT: A 722 MET cc_start: 0.7282 (mtm) cc_final: 0.6936 (ptt) REVERT: A 756 GLU cc_start: 0.8258 (mp0) cc_final: 0.7944 (pm20) REVERT: A 968 ARG cc_start: 0.9280 (OUTLIER) cc_final: 0.8949 (ppt170) REVERT: A 1011 GLN cc_start: 0.8590 (OUTLIER) cc_final: 0.8235 (mp10) REVERT: A 1120 LEU cc_start: 0.9328 (OUTLIER) cc_final: 0.9098 (pp) REVERT: A 1200 MET cc_start: 0.9005 (mmm) cc_final: 0.8627 (mmm) REVERT: A 1339 MET cc_start: 0.7706 (mmp) cc_final: 0.7188 (mmp) REVERT: A 1372 MET cc_start: 0.8877 (tmm) cc_final: 0.7923 (mmt) REVERT: A 1378 ASP cc_start: 0.8667 (p0) cc_final: 0.8272 (p0) REVERT: A 1446 PHE cc_start: 0.7264 (t80) cc_final: 0.6949 (t80) REVERT: B 79 TYR cc_start: 0.8691 (OUTLIER) cc_final: 0.8431 (m-10) REVERT: B 391 ILE cc_start: 0.9114 (tp) cc_final: 0.8458 (tt) REVERT: B 395 PHE cc_start: 0.8031 (m-80) cc_final: 0.7347 (m-80) outliers start: 58 outliers final: 40 residues processed: 201 average time/residue: 0.0811 time to fit residues: 25.5306 Evaluate side-chains 198 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 153 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 520 HIS Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 702 ASP Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 771 MET Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 968 ARG Chi-restraints excluded: chain A residue 1011 GLN Chi-restraints excluded: chain A residue 1028 LEU Chi-restraints excluded: chain A residue 1097 LEU Chi-restraints excluded: chain A residue 1106 LEU Chi-restraints excluded: chain A residue 1116 ASP Chi-restraints excluded: chain A residue 1120 LEU Chi-restraints excluded: chain A residue 1227 LEU Chi-restraints excluded: chain A residue 1280 LEU Chi-restraints excluded: chain A residue 1293 MET Chi-restraints excluded: chain A residue 1298 LEU Chi-restraints excluded: chain A residue 1309 ASN Chi-restraints excluded: chain A residue 1336 HIS Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain A residue 1361 ILE Chi-restraints excluded: chain A residue 1370 VAL Chi-restraints excluded: chain A residue 1387 LEU Chi-restraints excluded: chain A residue 1391 VAL Chi-restraints excluded: chain A residue 1434 LEU Chi-restraints excluded: chain A residue 1451 ILE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 79 TYR Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 176 ASN Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 407 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 8.9990 chunk 80 optimal weight: 8.9990 chunk 114 optimal weight: 9.9990 chunk 34 optimal weight: 1.9990 chunk 42 optimal weight: 7.9990 chunk 60 optimal weight: 9.9990 chunk 142 optimal weight: 10.0000 chunk 143 optimal weight: 0.9980 chunk 64 optimal weight: 7.9990 chunk 30 optimal weight: 10.0000 chunk 71 optimal weight: 0.6980 overall best weight: 3.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 323 ASN ** A1252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 301 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 = 0.3851 r_free = 0.3851 target = 0.083852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.065216 restraints weight = 59250.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.067162 restraints weight = 33965.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.068599 restraints weight = 22997.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.069612 restraints weight = 17186.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.070370 restraints weight = 13933.834| |-----------------------------------------------------------------------------| r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.3507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 12773 Z= 0.211 Angle : 0.709 10.670 17356 Z= 0.355 Chirality : 0.046 0.240 1974 Planarity : 0.004 0.062 2177 Dihedral : 4.833 37.832 1686 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 18.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 4.97 % Allowed : 18.49 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.21), residues: 1520 helix: 0.30 (0.21), residues: 625 sheet: -0.50 (0.38), residues: 190 loop : -1.89 (0.23), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 541 TYR 0.032 0.002 TYR A 229 PHE 0.025 0.002 PHE A1234 TRP 0.011 0.001 TRP A 969 HIS 0.003 0.001 HIS A 807 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.21 (12761) covalent geometry : angle 0.69867 / 0.35 (17325) SS BOND : bond 0.00318 / 0.16 ( 2) SS BOND : angle 0.57368 / 0.55 ( 4) hydrogen bonds : bond 0.03752 / 2.47 ( 562) hydrogen bonds : angle 4.83127 / 3.36 ( 1611) Misc. bond : bond 0.00253 / 0.13 ( 1) link_ALPHA1-4 : bond 0.00594 / 0.30 ( 2) link_ALPHA1-4 : angle 1.81219 / 1.13 ( 6) link_BETA1-4 : bond 0.01319 / 0.65 ( 2) link_BETA1-4 : angle 2.25313 / 1.87 ( 6) link_NAG-ASN : bond 0.00559 / 0.28 ( 5) link_NAG-ASN : angle 3.76313 / 2.08 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 150 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 ARG cc_start: 0.8731 (ttt-90) cc_final: 0.8024 (tpt90) REVERT: A 525 SER cc_start: 0.8798 (t) cc_final: 0.8290 (p) REVERT: A 566 MET cc_start: 0.7761 (tpp) cc_final: 0.7435 (tpp) REVERT: A 702 ASP cc_start: 0.8518 (OUTLIER) cc_final: 0.8200 (t0) REVERT: A 722 MET cc_start: 0.7162 (mtm) cc_final: 0.6844 (ptt) REVERT: A 968 ARG cc_start: 0.9301 (OUTLIER) cc_final: 0.8968 (ppt170) REVERT: A 1011 GLN cc_start: 0.8655 (OUTLIER) cc_final: 0.8313 (mp10) REVERT: A 1120 LEU cc_start: 0.9362 (OUTLIER) cc_final: 0.9133 (pp) REVERT: A 1200 MET cc_start: 0.9068 (mmm) cc_final: 0.8702 (mmm) REVERT: A 1339 MET cc_start: 0.7771 (mmp) cc_final: 0.7390 (mmp) REVERT: A 1372 MET cc_start: 0.8934 (tmm) cc_final: 0.8617 (ppp) REVERT: A 1378 ASP cc_start: 0.8644 (p0) cc_final: 0.8304 (p0) REVERT: A 1446 PHE cc_start: 0.7197 (t80) cc_final: 0.6898 (t80) REVERT: B 292 MET cc_start: 0.8731 (mpp) cc_final: 0.8496 (mpp) REVERT: B 391 ILE cc_start: 0.9149 (tp) cc_final: 0.8805 (tt) REVERT: B 395 PHE cc_start: 0.8135 (m-80) cc_final: 0.7504 (m-80) outliers start: 67 outliers final: 48 residues processed: 193 average time/residue: 0.0737 time to fit residues: 22.4266 Evaluate side-chains 193 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 141 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 520 HIS Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 702 ASP Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 771 MET Chi-restraints excluded: chain A residue 968 ARG Chi-restraints excluded: chain A residue 1011 GLN Chi-restraints excluded: chain A residue 1028 LEU Chi-restraints excluded: chain A residue 1097 LEU Chi-restraints excluded: chain A residue 1099 GLU Chi-restraints excluded: chain A residue 1106 LEU Chi-restraints excluded: chain A residue 1116 ASP Chi-restraints excluded: chain A residue 1120 LEU Chi-restraints excluded: chain A residue 1145 CYS Chi-restraints excluded: chain A residue 1201 CYS Chi-restraints excluded: chain A residue 1227 LEU Chi-restraints excluded: chain A residue 1280 LEU Chi-restraints excluded: chain A residue 1293 MET Chi-restraints excluded: chain A residue 1298 LEU Chi-restraints excluded: chain A residue 1309 ASN Chi-restraints excluded: chain A residue 1336 HIS Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain A residue 1361 ILE Chi-restraints excluded: chain A residue 1370 VAL Chi-restraints excluded: chain A residue 1387 LEU Chi-restraints excluded: chain A residue 1391 VAL Chi-restraints excluded: chain A residue 1406 ASN Chi-restraints excluded: chain A residue 1434 LEU Chi-restraints excluded: chain A residue 1442 ILE Chi-restraints excluded: chain A residue 1451 ILE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 176 ASN Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 407 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 140 optimal weight: 0.9980 chunk 62 optimal weight: 6.9990 chunk 104 optimal weight: 0.9980 chunk 135 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 138 optimal weight: 6.9990 chunk 50 optimal weight: 20.0000 chunk 86 optimal weight: 0.9980 chunk 69 optimal weight: 8.9990 chunk 102 optimal weight: 2.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.088655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.070338 restraints weight = 57212.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.072190 restraints weight = 34958.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.073545 restraints weight = 24355.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.074334 restraints weight = 18695.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.075175 restraints weight = 15566.983| |-----------------------------------------------------------------------------| r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.3484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12773 Z= 0.121 Angle : 0.669 13.978 17356 Z= 0.327 Chirality : 0.045 0.367 1974 Planarity : 0.004 0.054 2177 Dihedral : 4.689 37.376 1686 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 3.41 % Allowed : 20.94 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.22), residues: 1520 helix: 0.45 (0.21), residues: 617 sheet: -0.31 (0.39), residues: 187 loop : -1.82 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1009 TYR 0.018 0.001 TYR A 229 PHE 0.030 0.002 PHE A1328 TRP 0.013 0.001 TRP A 532 HIS 0.003 0.001 HIS A 455 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (12761) covalent geometry : angle 0.65052 / 0.32 (17325) SS BOND : bond 0.00169 / 0.09 ( 2) SS BOND : angle 0.58308 / 0.48 ( 4) hydrogen bonds : bond 0.03493 / 2.30 ( 562) hydrogen bonds : angle 4.57336 / 3.18 ( 1611) Misc. bond : bond 0.00201 / 0.11 ( 1) link_ALPHA1-4 : bond 0.00710 / 0.36 ( 2) link_ALPHA1-4 : angle 1.72066 / 1.07 ( 6) link_BETA1-4 : bond 0.01229 / 0.62 ( 2) link_BETA1-4 : angle 1.83188 / 1.41 ( 6) link_NAG-ASN : bond 0.00576 / 0.30 ( 5) link_NAG-ASN : angle 5.07662 / 2.85 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 162 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 314 ARG cc_start: 0.8629 (ttt-90) cc_final: 0.7996 (tpt-90) REVERT: A 464 MET cc_start: 0.7740 (tpp) cc_final: 0.7269 (mmm) REVERT: A 525 SER cc_start: 0.8706 (t) cc_final: 0.8203 (p) REVERT: A 566 MET cc_start: 0.7720 (tpp) cc_final: 0.7489 (tpp) REVERT: A 702 ASP cc_start: 0.8159 (OUTLIER) cc_final: 0.7793 (t0) REVERT: A 722 MET cc_start: 0.7375 (mtm) cc_final: 0.7131 (ptt) REVERT: A 968 ARG cc_start: 0.9271 (OUTLIER) cc_final: 0.8955 (ppt170) REVERT: A 1120 LEU cc_start: 0.9367 (OUTLIER) cc_final: 0.9127 (pp) REVERT: A 1200 MET cc_start: 0.8916 (mmm) cc_final: 0.8483 (mmm) REVERT: A 1238 ASN cc_start: 0.8752 (p0) cc_final: 0.8550 (p0) REVERT: A 1303 ILE cc_start: 0.9346 (mm) cc_final: 0.9069 (mt) REVERT: A 1339 MET cc_start: 0.7379 (mmp) cc_final: 0.7014 (mmp) REVERT: A 1372 MET cc_start: 0.8788 (tmm) cc_final: 0.8041 (mmt) REVERT: A 1378 ASP cc_start: 0.8387 (p0) cc_final: 0.8045 (p0) REVERT: A 1456 GLU cc_start: 0.8798 (tm-30) cc_final: 0.8382 (tm-30) REVERT: B 391 ILE cc_start: 0.9161 (tp) cc_final: 0.8424 (tt) REVERT: B 395 PHE cc_start: 0.8001 (m-80) cc_final: 0.7342 (m-80) outliers start: 46 outliers final: 31 residues processed: 189 average time/residue: 0.0977 time to fit residues: 29.0418 Evaluate side-chains 182 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 148 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 520 HIS Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 702 ASP Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 771 MET Chi-restraints excluded: chain A residue 968 ARG Chi-restraints excluded: chain A residue 1099 GLU Chi-restraints excluded: chain A residue 1116 ASP Chi-restraints excluded: chain A residue 1120 LEU Chi-restraints excluded: chain A residue 1293 MET Chi-restraints excluded: chain A residue 1298 LEU Chi-restraints excluded: chain A residue 1309 ASN Chi-restraints excluded: chain A residue 1336 HIS Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain A residue 1361 ILE Chi-restraints excluded: chain A residue 1387 LEU Chi-restraints excluded: chain A residue 1391 VAL Chi-restraints excluded: chain A residue 1434 LEU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 407 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 45 optimal weight: 10.0000 chunk 36 optimal weight: 4.9990 chunk 3 optimal weight: 6.9990 chunk 92 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 108 optimal weight: 9.9990 chunk 101 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 chunk 2 optimal weight: 0.0980 chunk 22 optimal weight: 10.0000 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 719 GLN A1011 GLN ** A1182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 301 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 = 0.4021 r_free = 0.4021 target = 0.089280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.071239 restraints weight = 57806.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.073048 restraints weight = 35303.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.074079 restraints weight = 24294.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.075066 restraints weight = 19280.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.075785 restraints weight = 15865.245| |-----------------------------------------------------------------------------| r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.3577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12773 Z= 0.122 Angle : 0.676 10.856 17356 Z= 0.331 Chirality : 0.046 0.281 1974 Planarity : 0.004 0.054 2177 Dihedral : 4.646 37.386 1686 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 2.90 % Allowed : 21.38 % Favored : 75.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.22), residues: 1520 helix: 0.45 (0.21), residues: 625 sheet: -0.33 (0.39), residues: 187 loop : -1.77 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1455 TYR 0.018 0.001 TYR A 229 PHE 0.031 0.002 PHE A1241 TRP 0.018 0.001 TRP B 142 HIS 0.002 0.001 HIS B 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (12761) covalent geometry : angle 0.66193 / 0.33 (17325) SS BOND : bond 0.00149 / 0.08 ( 2) SS BOND : angle 0.39212 / 0.36 ( 4) hydrogen bonds : bond 0.03393 / 2.25 ( 562) hydrogen bonds : angle 4.56160 / 3.18 ( 1611) Misc. bond : bond 0.00233 / 0.12 ( 1) link_ALPHA1-4 : bond 0.00708 / 0.36 ( 2) link_ALPHA1-4 : angle 1.72124 / 1.08 ( 6) link_BETA1-4 : bond 0.01154 / 0.58 ( 2) link_BETA1-4 : angle 1.79878 / 1.40 ( 6) link_NAG-ASN : bond 0.00741 / 0.38 ( 5) link_NAG-ASN : angle 4.51796 / 2.53 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 156 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 ARG cc_start: 0.8608 (ttt-90) cc_final: 0.8012 (tpt-90) REVERT: A 477 TYR cc_start: 0.9049 (m-80) cc_final: 0.8803 (m-10) REVERT: A 525 SER cc_start: 0.8698 (t) cc_final: 0.8200 (p) REVERT: A 566 MET cc_start: 0.7698 (tpp) cc_final: 0.7388 (tpp) REVERT: A 702 ASP cc_start: 0.8124 (OUTLIER) cc_final: 0.7755 (t0) REVERT: A 968 ARG cc_start: 0.9253 (OUTLIER) cc_final: 0.8947 (ppt170) REVERT: A 1012 ASP cc_start: 0.9118 (p0) cc_final: 0.8778 (p0) REVERT: A 1120 LEU cc_start: 0.9358 (OUTLIER) cc_final: 0.9119 (pp) REVERT: A 1200 MET cc_start: 0.8800 (mmm) cc_final: 0.8473 (mmm) REVERT: A 1238 ASN cc_start: 0.8683 (p0) cc_final: 0.8446 (p0) REVERT: A 1303 ILE cc_start: 0.9316 (mm) cc_final: 0.9044 (mt) REVERT: A 1339 MET cc_start: 0.7298 (mmp) cc_final: 0.6913 (mmp) REVERT: A 1372 MET cc_start: 0.8740 (tmm) cc_final: 0.8072 (mmt) REVERT: A 1378 ASP cc_start: 0.8362 (p0) cc_final: 0.8012 (p0) REVERT: A 1446 PHE cc_start: 0.7139 (t80) cc_final: 0.6888 (t80) REVERT: A 1456 GLU cc_start: 0.8758 (tm-30) cc_final: 0.8369 (tm-30) REVERT: B 176 ASN cc_start: 0.8260 (t0) cc_final: 0.7964 (t0) REVERT: B 391 ILE cc_start: 0.9171 (tp) cc_final: 0.8773 (tt) REVERT: B 395 PHE cc_start: 0.7971 (m-80) cc_final: 0.7354 (m-80) outliers start: 39 outliers final: 34 residues processed: 178 average time/residue: 0.0917 time to fit residues: 25.8355 Evaluate side-chains 190 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 153 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 520 HIS Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 702 ASP Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 771 MET Chi-restraints excluded: chain A residue 968 ARG Chi-restraints excluded: chain A residue 1097 LEU Chi-restraints excluded: chain A residue 1099 GLU Chi-restraints excluded: chain A residue 1116 ASP Chi-restraints excluded: chain A residue 1120 LEU Chi-restraints excluded: chain A residue 1206 ILE Chi-restraints excluded: chain A residue 1227 LEU Chi-restraints excluded: chain A residue 1264 TYR Chi-restraints excluded: chain A residue 1293 MET Chi-restraints excluded: chain A residue 1298 LEU Chi-restraints excluded: chain A residue 1309 ASN Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain A residue 1361 ILE Chi-restraints excluded: chain A residue 1387 LEU Chi-restraints excluded: chain A residue 1391 VAL Chi-restraints excluded: chain A residue 1434 LEU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 407 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 30 optimal weight: 9.9990 chunk 107 optimal weight: 9.9990 chunk 101 optimal weight: 1.9990 chunk 134 optimal weight: 7.9990 chunk 70 optimal weight: 0.0010 chunk 116 optimal weight: 6.9990 chunk 100 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 147 optimal weight: 9.9990 chunk 1 optimal weight: 0.3980 chunk 87 optimal weight: 0.5980 overall best weight: 0.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.090310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.072204 restraints weight = 57033.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.074065 restraints weight = 34302.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.075185 restraints weight = 23546.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.076303 restraints weight = 18393.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.076854 restraints weight = 14825.731| |-----------------------------------------------------------------------------| r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.3597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12773 Z= 0.120 Angle : 0.676 13.972 17356 Z= 0.329 Chirality : 0.045 0.315 1974 Planarity : 0.004 0.053 2177 Dihedral : 4.580 36.647 1686 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 2.97 % Allowed : 21.31 % Favored : 75.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.22), residues: 1520 helix: 0.48 (0.21), residues: 619 sheet: -0.22 (0.39), residues: 187 loop : -1.75 (0.24), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1009 TYR 0.018 0.001 TYR A 229 PHE 0.049 0.002 PHE A1241 TRP 0.017 0.001 TRP B 142 HIS 0.003 0.001 HIS B 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (12761) covalent geometry : angle 0.66251 / 0.33 (17325) SS BOND : bond 0.00270 / 0.14 ( 2) SS BOND : angle 0.37897 / 0.34 ( 4) hydrogen bonds : bond 0.03411 / 2.30 ( 562) hydrogen bonds : angle 4.50130 / 3.14 ( 1611) Misc. bond : bond 0.00202 / 0.11 ( 1) link_ALPHA1-4 : bond 0.00751 / 0.38 ( 2) link_ALPHA1-4 : angle 1.73209 / 1.08 ( 6) link_BETA1-4 : bond 0.01095 / 0.55 ( 2) link_BETA1-4 : angle 1.65152 / 1.29 ( 6) link_NAG-ASN : bond 0.00715 / 0.37 ( 5) link_NAG-ASN : angle 4.38029 / 2.47 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 153 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 ARG cc_start: 0.8664 (ttt-90) cc_final: 0.8000 (tpt-90) REVERT: A 464 MET cc_start: 0.7625 (tpp) cc_final: 0.7171 (mmm) REVERT: A 477 TYR cc_start: 0.9119 (m-80) cc_final: 0.8863 (m-10) REVERT: A 525 SER cc_start: 0.8723 (t) cc_final: 0.8207 (p) REVERT: A 566 MET cc_start: 0.7800 (tpp) cc_final: 0.7595 (tpp) REVERT: A 702 ASP cc_start: 0.8263 (OUTLIER) cc_final: 0.7886 (t0) REVERT: A 968 ARG cc_start: 0.9264 (OUTLIER) cc_final: 0.8958 (ppt170) REVERT: A 1053 MET cc_start: 0.8436 (mtp) cc_final: 0.7965 (tpt) REVERT: A 1200 MET cc_start: 0.8751 (mmm) cc_final: 0.8425 (mmm) REVERT: A 1238 ASN cc_start: 0.8726 (p0) cc_final: 0.8507 (p0) REVERT: A 1303 ILE cc_start: 0.9341 (mm) cc_final: 0.9059 (mt) REVERT: A 1339 MET cc_start: 0.7427 (mmp) cc_final: 0.7045 (mmp) REVERT: A 1372 MET cc_start: 0.8855 (tmm) cc_final: 0.8091 (mmt) REVERT: A 1378 ASP cc_start: 0.8483 (p0) cc_final: 0.8067 (p0) REVERT: A 1387 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8523 (mm) REVERT: A 1456 GLU cc_start: 0.8870 (tm-30) cc_final: 0.8444 (tm-30) REVERT: B 176 ASN cc_start: 0.8506 (t0) cc_final: 0.8194 (t0) REVERT: B 391 ILE cc_start: 0.9131 (tp) cc_final: 0.8729 (tt) REVERT: B 395 PHE cc_start: 0.8036 (m-80) cc_final: 0.7423 (m-80) outliers start: 40 outliers final: 30 residues processed: 177 average time/residue: 0.0914 time to fit residues: 25.8536 Evaluate side-chains 187 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 154 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 520 HIS Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 702 ASP Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 771 MET Chi-restraints excluded: chain A residue 968 ARG Chi-restraints excluded: chain A residue 1097 LEU Chi-restraints excluded: chain A residue 1099 GLU Chi-restraints excluded: chain A residue 1206 ILE Chi-restraints excluded: chain A residue 1227 LEU Chi-restraints excluded: chain A residue 1264 TYR Chi-restraints excluded: chain A residue 1309 ASN Chi-restraints excluded: chain A residue 1330 PHE Chi-restraints excluded: chain A residue 1336 HIS Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain A residue 1361 ILE Chi-restraints excluded: chain A residue 1387 LEU Chi-restraints excluded: chain A residue 1391 VAL Chi-restraints excluded: chain A residue 1434 LEU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 407 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 18 optimal weight: 10.0000 chunk 61 optimal weight: 10.0000 chunk 140 optimal weight: 0.0050 chunk 27 optimal weight: 8.9990 chunk 125 optimal weight: 10.0000 chunk 98 optimal weight: 0.9990 chunk 118 optimal weight: 8.9990 chunk 134 optimal weight: 0.7980 chunk 89 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 39 optimal weight: 8.9990 overall best weight: 2.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.087762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.069842 restraints weight = 58388.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.071569 restraints weight = 34715.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.072784 restraints weight = 23835.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.073808 restraints weight = 18230.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.074366 restraints weight = 14923.311| |-----------------------------------------------------------------------------| r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.3806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 12773 Z= 0.160 Angle : 0.691 14.347 17356 Z= 0.341 Chirality : 0.046 0.300 1974 Planarity : 0.004 0.052 2177 Dihedral : 4.643 41.898 1686 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 17.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 2.60 % Allowed : 21.90 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.22), residues: 1520 helix: 0.40 (0.21), residues: 624 sheet: -0.36 (0.38), residues: 187 loop : -1.79 (0.23), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1009 TYR 0.020 0.001 TYR A 619 PHE 0.048 0.002 PHE A1241 TRP 0.018 0.001 TRP A1395 HIS 0.002 0.001 HIS B 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 (12761) covalent geometry : angle 0.67829 / 0.34 (17325) SS BOND : bond 0.00102 / 0.05 ( 2) SS BOND : angle 0.43420 / 0.41 ( 4) hydrogen bonds : bond 0.03492 / 2.35 ( 562) hydrogen bonds : angle 4.66347 / 3.25 ( 1611) Misc. bond : bond 0.00241 / 0.13 ( 1) link_ALPHA1-4 : bond 0.00538 / 0.27 ( 2) link_ALPHA1-4 : angle 1.80038 / 1.12 ( 6) link_BETA1-4 : bond 0.01100 / 0.54 ( 2) link_BETA1-4 : angle 1.78666 / 1.47 ( 6) link_NAG-ASN : bond 0.00574 / 0.29 ( 5) link_NAG-ASN : angle 4.25312 / 2.41 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2048.87 seconds wall clock time: 36 minutes 26.06 seconds (2186.06 seconds total)