Starting phenix.real_space_refine on Wed Mar 4 10:30:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ky5_23068/03_2026/7ky5_23068.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ky5_23068/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7ky5_23068/03_2026/7ky5_23068.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ky5_23068/03_2026/7ky5_23068.map" model { file = "/net/cci-nas-00/data/ceres_data/7ky5_23068/03_2026/7ky5_23068.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ky5_23068/03_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-5986/lib/python3.9/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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 2.64, per 1000 atoms: 0.21 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: 1.09 Conformation dependent library (CDL) restraints added in 431.3 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: 0.56 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: 2.04 Time building geometry restraints manager: 1.39 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 - 21.41: 7317 21.41 - 42.82: 455 42.82 - 64.23: 42 64.23 - 85.63: 11 85.63 - 107.04: 9 Dihedral angle restraints: 7834 sinusoidal: 3355 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 7831 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: 1.450 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: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.210 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: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 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 : 13.512 107.042 4946 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 covalent geometry : bond 0.00362 (12761) covalent geometry : angle 1.08589 (17325) SS BOND : bond 0.00150 ( 2) SS BOND : angle 0.56534 ( 4) hydrogen bonds : bond 0.12136 ( 562) hydrogen bonds : angle 5.23141 ( 1611) Misc. bond : bond 0.00201 ( 1) link_ALPHA1-4 : bond 0.00560 ( 2) link_ALPHA1-4 : angle 1.96025 ( 6) link_BETA1-4 : bond 0.00488 ( 2) link_BETA1-4 : angle 0.95317 ( 6) link_NAG-ASN : bond 0.09268 ( 5) link_NAG-ASN : angle 6.48871 ( 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 : 0.294 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: 0.0876 time to fit residues: 29.2560 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 : 0.481 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.096087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.077449 restraints weight = 56973.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.079323 restraints weight = 34872.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.080863 restraints weight = 24814.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.081827 restraints weight = 18908.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.082769 restraints weight = 15486.340| |-----------------------------------------------------------------------------| r_work (final): 0.3899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.1291 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= 0.132 Angle : 0.668 11.076 17356 Z= 0.328 Chirality : 0.044 0.219 1974 Planarity : 0.004 0.050 2177 Dihedral : 8.761 95.019 2031 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 1.86 % Allowed : 9.80 % Favored : 88.34 % 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: -0.51 (0.37), residues: 196 loop : -1.93 (0.23), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 625 TYR 0.022 0.001 TYR A 260 PHE 0.030 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 covalent geometry : bond 0.00290 (12761) covalent geometry : angle 0.65557 (17325) SS BOND : bond 0.00100 ( 2) SS BOND : angle 0.41851 ( 4) hydrogen bonds : bond 0.03872 ( 562) hydrogen bonds : angle 4.64985 ( 1611) Misc. bond : bond 0.00122 ( 1) link_ALPHA1-4 : bond 0.00631 ( 2) link_ALPHA1-4 : angle 1.91824 ( 6) link_BETA1-4 : bond 0.00531 ( 2) link_BETA1-4 : angle 2.20434 ( 6) link_NAG-ASN : bond 0.00586 ( 5) link_NAG-ASN : angle 4.06310 ( 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 207 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 182 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 229 TYR cc_start: 0.7965 (m-10) cc_final: 0.7604 (m-10) REVERT: A 260 TYR cc_start: 0.6189 (m-10) cc_final: 0.5411 (m-10) REVERT: A 566 MET cc_start: 0.7517 (tpp) cc_final: 0.7185 (tpp) REVERT: A 756 GLU cc_start: 0.8183 (mp0) cc_final: 0.7886 (pm20) REVERT: A 778 MET cc_start: 0.6825 (ppp) cc_final: 0.6589 (ppp) REVERT: A 835 LYS cc_start: 0.8962 (mppt) cc_final: 0.8590 (tptt) REVERT: A 1120 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8971 (pp) REVERT: A 1238 ASN cc_start: 0.8663 (p0) cc_final: 0.8378 (p0) REVERT: A 1372 MET cc_start: 0.8490 (tmm) cc_final: 0.7691 (mmt) REVERT: A 1446 PHE cc_start: 0.7193 (t80) cc_final: 0.6938 (t80) REVERT: B 391 ILE cc_start: 0.9030 (tp) cc_final: 0.8504 (tp) REVERT: B 395 PHE cc_start: 0.7897 (m-80) cc_final: 0.7093 (m-80) outliers start: 25 outliers final: 17 residues processed: 190 average time/residue: 0.0840 time to fit residues: 25.0358 Evaluate side-chains 179 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 161 time to evaluate : 0.510 ------------------------------------------------------------------------------- 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: 10.0000 chunk 106 optimal weight: 8.9990 chunk 79 optimal weight: 10.0000 chunk 43 optimal weight: 7.9990 chunk 21 optimal weight: 5.9990 chunk 25 optimal weight: 20.0000 chunk 116 optimal weight: 9.9990 chunk 4 optimal weight: 7.9990 chunk 74 optimal weight: 4.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN ** A 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 809 GLN A 814 HIS ** A1208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** B 412 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.082362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.063415 restraints weight = 61130.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.065365 restraints weight = 35181.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.066740 restraints weight = 23846.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.067755 restraints weight = 17962.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.068496 restraints weight = 14634.743| |-----------------------------------------------------------------------------| r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.094 12773 Z= 0.362 Angle : 0.897 12.542 17356 Z= 0.462 Chirality : 0.051 0.257 1974 Planarity : 0.006 0.066 2177 Dihedral : 9.167 96.435 2031 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 24.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.22 % Favored : 91.78 % Rotamer: Outliers : 4.38 % Allowed : 13.96 % Favored : 81.66 % 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: -1.81 (0.21), residues: 1520 helix: -0.31 (0.20), residues: 630 sheet: -0.85 (0.35), residues: 219 loop : -2.20 (0.23), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 625 TYR 0.039 0.003 TYR A 260 PHE 0.025 0.003 PHE A1384 TRP 0.027 0.003 TRP B 348 HIS 0.007 0.002 HIS A 254 Details of bonding type rmsd covalent geometry : bond 0.00771 (12761) covalent geometry : angle 0.88758 (17325) SS BOND : bond 0.00698 ( 2) SS BOND : angle 0.95811 ( 4) hydrogen bonds : bond 0.04824 ( 562) hydrogen bonds : angle 5.58363 ( 1611) Misc. bond : bond 0.00444 ( 1) link_ALPHA1-4 : bond 0.00174 ( 2) link_ALPHA1-4 : angle 2.31003 ( 6) link_BETA1-4 : bond 0.01195 ( 2) link_BETA1-4 : angle 3.31200 ( 6) link_NAG-ASN : bond 0.00744 ( 5) link_NAG-ASN : angle 3.87018 ( 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 215 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 156 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 ARG cc_start: 0.8724 (ttt-90) cc_final: 0.8036 (tpt-90) REVERT: A 458 ASP cc_start: 0.8471 (t0) cc_final: 0.8157 (t0) REVERT: A 566 MET cc_start: 0.7495 (tpp) cc_final: 0.7161 (tpp) REVERT: A 1120 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.9089 (pp) REVERT: A 1200 MET cc_start: 0.9072 (mmm) cc_final: 0.8767 (mmm) REVERT: A 1237 LYS cc_start: 0.8802 (OUTLIER) cc_final: 0.8534 (ptmt) REVERT: A 1378 ASP cc_start: 0.8671 (p0) cc_final: 0.8367 (p0) REVERT: B 102 GLU cc_start: 0.8514 (pp20) cc_final: 0.7859 (pp20) REVERT: B 238 MET cc_start: 0.7803 (tpt) cc_final: 0.7588 (tpp) REVERT: B 292 MET cc_start: 0.8710 (mpp) cc_final: 0.8468 (mpp) REVERT: B 391 ILE cc_start: 0.9100 (tp) cc_final: 0.8478 (tt) REVERT: B 395 PHE cc_start: 0.8033 (m-80) cc_final: 0.7373 (m-80) outliers start: 59 outliers final: 47 residues processed: 187 average time/residue: 0.0879 time to fit residues: 25.6072 Evaluate side-chains 188 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 139 time to evaluate : 0.334 ------------------------------------------------------------------------------- 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 324 GLU Chi-restraints excluded: chain A residue 446 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 604 LEU Chi-restraints excluded: chain A residue 625 ARG Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 771 MET Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 953 THR Chi-restraints excluded: chain A residue 1028 LEU Chi-restraints excluded: chain A residue 1097 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 1213 THR Chi-restraints excluded: chain A residue 1227 LEU Chi-restraints excluded: chain A residue 1237 LYS Chi-restraints excluded: chain A residue 1278 ILE Chi-restraints excluded: chain A residue 1279 LEU 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 1349 ASP 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 A residue 1453 ILE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 176 ASN Chi-restraints excluded: chain B residue 210 ASP 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 342 LEU Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 361 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: 3.9990 chunk 123 optimal weight: 6.9990 chunk 70 optimal weight: 2.9990 chunk 41 optimal weight: 10.0000 chunk 76 optimal weight: 5.9990 chunk 121 optimal weight: 9.9990 chunk 34 optimal weight: 0.9990 chunk 145 optimal weight: 7.9990 chunk 19 optimal weight: 8.9990 chunk 29 optimal weight: 6.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1208 GLN ** A1252 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 = 0.3984 r_free = 0.3984 target = 0.087210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.068965 restraints weight = 58699.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.070746 restraints weight = 35334.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.071727 restraints weight = 24513.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.072834 restraints weight = 19660.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.073510 restraints weight = 16082.726| |-----------------------------------------------------------------------------| r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.3150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12773 Z= 0.171 Angle : 0.685 11.787 17356 Z= 0.345 Chirality : 0.046 0.235 1974 Planarity : 0.004 0.056 2177 Dihedral : 8.417 87.014 2031 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 17.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 3.56 % Allowed : 16.70 % 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: -1.41 (0.21), residues: 1520 helix: 0.11 (0.20), residues: 625 sheet: -0.64 (0.37), residues: 205 loop : -2.03 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 625 TYR 0.016 0.002 TYR A 229 PHE 0.029 0.002 PHE A 647 TRP 0.015 0.001 TRP B 126 HIS 0.003 0.001 HIS A 942 Details of bonding type rmsd covalent geometry : bond 0.00375 (12761) covalent geometry : angle 0.67413 (17325) SS BOND : bond 0.00180 ( 2) SS BOND : angle 0.64985 ( 4) hydrogen bonds : bond 0.03893 ( 562) hydrogen bonds : angle 5.00688 ( 1611) Misc. bond : bond 0.00179 ( 1) link_ALPHA1-4 : bond 0.00719 ( 2) link_ALPHA1-4 : angle 1.72912 ( 6) link_BETA1-4 : bond 0.00826 ( 2) link_BETA1-4 : angle 2.62877 ( 6) link_NAG-ASN : bond 0.00605 ( 5) link_NAG-ASN : angle 3.83338 ( 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 203 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 155 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 ARG cc_start: 0.8649 (ttt-90) cc_final: 0.7948 (tpt90) REVERT: A 566 MET cc_start: 0.7580 (tpp) cc_final: 0.7310 (tpp) REVERT: A 756 GLU cc_start: 0.8231 (mp0) cc_final: 0.7865 (pm20) REVERT: A 1011 GLN cc_start: 0.8612 (OUTLIER) cc_final: 0.8245 (mp10) REVERT: A 1120 LEU cc_start: 0.9359 (OUTLIER) cc_final: 0.9108 (pp) REVERT: A 1173 ASP cc_start: 0.7612 (OUTLIER) cc_final: 0.7061 (t0) REVERT: A 1208 GLN cc_start: 0.7912 (OUTLIER) cc_final: 0.7364 (pm20) REVERT: A 1237 LYS cc_start: 0.8685 (ptmt) cc_final: 0.8439 (ptmt) REVERT: A 1241 PHE cc_start: 0.8745 (t80) cc_final: 0.8482 (t80) REVERT: A 1280 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8267 (tp) REVERT: A 1339 MET cc_start: 0.7443 (mmp) cc_final: 0.6726 (mmp) REVERT: A 1372 MET cc_start: 0.8546 (tmm) cc_final: 0.7880 (mmt) REVERT: A 1378 ASP cc_start: 0.8561 (p0) cc_final: 0.8183 (p0) REVERT: A 1446 PHE cc_start: 0.7136 (t80) cc_final: 0.6900 (t80) REVERT: B 238 MET cc_start: 0.7403 (tpt) cc_final: 0.7194 (tpp) REVERT: B 388 MET cc_start: 0.8844 (tpp) cc_final: 0.8604 (tpp) REVERT: B 391 ILE cc_start: 0.9110 (tp) cc_final: 0.8537 (tt) REVERT: B 395 PHE cc_start: 0.7856 (m-80) cc_final: 0.7211 (m-80) outliers start: 48 outliers final: 35 residues processed: 182 average time/residue: 0.0870 time to fit residues: 24.8969 Evaluate side-chains 185 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 145 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 VAL 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 611 THR 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 1011 GLN Chi-restraints excluded: chain A residue 1028 LEU Chi-restraints excluded: chain A residue 1097 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 1173 ASP Chi-restraints excluded: chain A residue 1201 CYS Chi-restraints excluded: chain A residue 1208 GLN Chi-restraints excluded: chain A residue 1243 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 1321 VAL Chi-restraints excluded: chain A residue 1326 ILE 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 1384 PHE Chi-restraints excluded: chain A residue 1387 LEU Chi-restraints excluded: chain A residue 1434 LEU Chi-restraints excluded: chain B residue 63 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 359 ILE Chi-restraints excluded: chain B residue 407 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 81 optimal weight: 10.0000 chunk 117 optimal weight: 8.9990 chunk 21 optimal weight: 9.9990 chunk 55 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 chunk 51 optimal weight: 8.9990 chunk 1 optimal weight: 10.0000 chunk 148 optimal weight: 0.9990 chunk 89 optimal weight: 9.9990 chunk 53 optimal weight: 0.8980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 412 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.089288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.071200 restraints weight = 57777.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.072840 restraints weight = 35414.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.074064 restraints weight = 24575.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.075131 restraints weight = 18830.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.075620 restraints weight = 15444.238| |-----------------------------------------------------------------------------| r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12773 Z= 0.119 Angle : 0.645 11.872 17356 Z= 0.319 Chirality : 0.044 0.271 1974 Planarity : 0.004 0.055 2177 Dihedral : 7.925 83.276 2031 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 2.97 % Allowed : 18.63 % Favored : 78.40 % 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 (0.22), residues: 1520 helix: 0.27 (0.21), residues: 625 sheet: -0.39 (0.38), residues: 194 loop : -1.92 (0.23), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 625 TYR 0.022 0.001 TYR A 229 PHE 0.021 0.001 PHE A 647 TRP 0.012 0.001 TRP A 532 HIS 0.003 0.001 HIS A 455 Details of bonding type rmsd covalent geometry : bond 0.00258 (12761) covalent geometry : angle 0.63228 (17325) SS BOND : bond 0.00051 ( 2) SS BOND : angle 0.53003 ( 4) hydrogen bonds : bond 0.03571 ( 562) hydrogen bonds : angle 4.67883 ( 1611) Misc. bond : bond 0.00162 ( 1) link_ALPHA1-4 : bond 0.00631 ( 2) link_ALPHA1-4 : angle 1.72409 ( 6) link_BETA1-4 : bond 0.00719 ( 2) link_BETA1-4 : angle 2.51610 ( 6) link_NAG-ASN : bond 0.00717 ( 5) link_NAG-ASN : angle 3.97050 ( 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 203 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 163 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 566 MET cc_start: 0.7642 (tpp) cc_final: 0.7360 (tpp) REVERT: A 1120 LEU cc_start: 0.9349 (OUTLIER) cc_final: 0.9111 (pp) REVERT: A 1237 LYS cc_start: 0.8756 (ptmt) cc_final: 0.8488 (ptmt) REVERT: A 1241 PHE cc_start: 0.8680 (t80) cc_final: 0.8476 (t80) REVERT: A 1303 ILE cc_start: 0.9340 (mm) cc_final: 0.9033 (mt) REVERT: A 1339 MET cc_start: 0.7383 (mmp) cc_final: 0.6847 (mmp) REVERT: A 1372 MET cc_start: 0.8571 (tmm) cc_final: 0.7886 (mmt) REVERT: A 1378 ASP cc_start: 0.8427 (p0) cc_final: 0.8110 (p0) REVERT: A 1386 CYS cc_start: 0.8540 (m) cc_final: 0.8171 (p) REVERT: A 1446 PHE cc_start: 0.7147 (t80) cc_final: 0.6885 (t80) REVERT: B 391 ILE cc_start: 0.9148 (tp) cc_final: 0.8379 (tt) REVERT: B 395 PHE cc_start: 0.7890 (m-80) cc_final: 0.7233 (m-80) outliers start: 40 outliers final: 32 residues processed: 184 average time/residue: 0.0838 time to fit residues: 24.4152 Evaluate side-chains 186 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 153 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 308 LEU 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 791 PHE Chi-restraints excluded: chain A residue 1097 LEU Chi-restraints excluded: chain A residue 1116 ASP Chi-restraints excluded: chain A residue 1120 LEU Chi-restraints excluded: chain A residue 1201 CYS Chi-restraints excluded: chain A residue 1243 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 1321 VAL 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 1384 PHE Chi-restraints excluded: chain A residue 1387 LEU Chi-restraints excluded: chain A residue 1434 LEU 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 53 optimal weight: 6.9990 chunk 30 optimal weight: 9.9990 chunk 9 optimal weight: 7.9990 chunk 89 optimal weight: 3.9990 chunk 139 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 31 optimal weight: 6.9990 chunk 50 optimal weight: 20.0000 chunk 143 optimal weight: 10.0000 chunk 145 optimal weight: 5.9990 chunk 105 optimal weight: 3.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3980 r_free = 0.3980 target = 0.087188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.068963 restraints weight = 59298.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.070757 restraints weight = 36160.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.071990 restraints weight = 25013.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.072918 restraints weight = 19215.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.073709 restraints weight = 15840.002| |-----------------------------------------------------------------------------| r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 12773 Z= 0.176 Angle : 0.670 9.386 17356 Z= 0.335 Chirality : 0.045 0.264 1974 Planarity : 0.004 0.057 2177 Dihedral : 7.889 82.733 2031 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 17.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 4.53 % Allowed : 19.08 % Favored : 76.39 % 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: -1.17 (0.22), residues: 1520 helix: 0.30 (0.21), residues: 627 sheet: -0.51 (0.38), residues: 197 loop : -1.88 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 625 TYR 0.017 0.001 TYR A 619 PHE 0.027 0.002 PHE A1313 TRP 0.011 0.001 TRP A 969 HIS 0.003 0.001 HIS B 186 Details of bonding type rmsd covalent geometry : bond 0.00385 (12761) covalent geometry : angle 0.65215 (17325) SS BOND : bond 0.00208 ( 2) SS BOND : angle 0.69440 ( 4) hydrogen bonds : bond 0.03625 ( 562) hydrogen bonds : angle 4.75357 ( 1611) Misc. bond : bond 0.00231 ( 1) link_ALPHA1-4 : bond 0.00615 ( 2) link_ALPHA1-4 : angle 1.75173 ( 6) link_BETA1-4 : bond 0.00798 ( 2) link_BETA1-4 : angle 2.68659 ( 6) link_NAG-ASN : bond 0.00467 ( 5) link_NAG-ASN : angle 4.92825 ( 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 211 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 150 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 ARG cc_start: 0.8657 (ttt-90) cc_final: 0.7997 (tpt170) REVERT: A 525 SER cc_start: 0.8673 (t) cc_final: 0.8134 (p) REVERT: A 566 MET cc_start: 0.7619 (tpp) cc_final: 0.7351 (tpp) REVERT: A 968 ARG cc_start: 0.9284 (OUTLIER) cc_final: 0.8939 (ppt170) REVERT: A 1011 GLN cc_start: 0.8638 (OUTLIER) cc_final: 0.8421 (mp10) REVERT: A 1120 LEU cc_start: 0.9370 (OUTLIER) cc_final: 0.9137 (pp) REVERT: A 1167 MET cc_start: 0.7255 (mmm) cc_final: 0.6533 (mmm) REVERT: A 1237 LYS cc_start: 0.8801 (OUTLIER) cc_final: 0.8455 (ptmt) REVERT: A 1241 PHE cc_start: 0.8726 (t80) cc_final: 0.8505 (t80) REVERT: A 1303 ILE cc_start: 0.9390 (mm) cc_final: 0.9146 (mt) REVERT: A 1339 MET cc_start: 0.7444 (mmp) cc_final: 0.6823 (mmp) REVERT: A 1369 TYR cc_start: 0.8722 (t80) cc_final: 0.8494 (t80) REVERT: A 1372 MET cc_start: 0.8653 (tmm) cc_final: 0.7958 (mmt) REVERT: A 1378 ASP cc_start: 0.8415 (p0) cc_final: 0.8113 (p0) REVERT: A 1446 PHE cc_start: 0.7109 (t80) cc_final: 0.6862 (t80) REVERT: B 391 ILE cc_start: 0.9128 (tp) cc_final: 0.8767 (tt) REVERT: B 395 PHE cc_start: 0.7955 (m-80) cc_final: 0.7372 (m-80) outliers start: 61 outliers final: 44 residues processed: 187 average time/residue: 0.0900 time to fit residues: 26.0666 Evaluate side-chains 193 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 145 time to evaluate : 0.382 ------------------------------------------------------------------------------- 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 598 VAL Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 625 ARG Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 771 MET Chi-restraints excluded: chain A residue 791 PHE 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 1116 ASP Chi-restraints excluded: chain A residue 1120 LEU Chi-restraints excluded: chain A residue 1201 CYS Chi-restraints excluded: chain A residue 1213 THR Chi-restraints excluded: chain A residue 1237 LYS Chi-restraints excluded: chain A residue 1243 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 1321 VAL 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 1384 PHE Chi-restraints excluded: chain A residue 1387 LEU 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 103 VAL Chi-restraints excluded: chain B residue 121 ILE 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 10.0000 chunk 80 optimal weight: 0.9980 chunk 114 optimal weight: 9.9990 chunk 34 optimal weight: 7.9990 chunk 42 optimal weight: 0.0970 chunk 60 optimal weight: 10.0000 chunk 142 optimal weight: 10.0000 chunk 143 optimal weight: 4.9990 chunk 64 optimal weight: 8.9990 chunk 30 optimal weight: 1.9990 chunk 71 optimal weight: 8.9990 overall best weight: 3.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 522 ASN ** 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 = 0.3968 r_free = 0.3968 target = 0.086320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.068307 restraints weight = 59275.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.069940 restraints weight = 36006.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.070926 restraints weight = 24894.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.071954 restraints weight = 19777.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.072701 restraints weight = 16221.718| |-----------------------------------------------------------------------------| r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.3622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 12773 Z= 0.175 Angle : 0.688 13.240 17356 Z= 0.341 Chirality : 0.045 0.282 1974 Planarity : 0.004 0.053 2177 Dihedral : 7.711 79.613 2031 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 17.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 4.83 % Allowed : 18.86 % Favored : 76.32 % 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 (0.22), residues: 1520 helix: 0.38 (0.21), residues: 612 sheet: -0.52 (0.38), residues: 197 loop : -1.83 (0.24), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 625 TYR 0.018 0.001 TYR A 619 PHE 0.031 0.002 PHE A1330 TRP 0.011 0.001 TRP A 969 HIS 0.003 0.001 HIS B 186 Details of bonding type rmsd covalent geometry : bond 0.00384 (12761) covalent geometry : angle 0.67414 (17325) SS BOND : bond 0.00197 ( 2) SS BOND : angle 0.47345 ( 4) hydrogen bonds : bond 0.03638 ( 562) hydrogen bonds : angle 4.79077 ( 1611) Misc. bond : bond 0.00184 ( 1) link_ALPHA1-4 : bond 0.00756 ( 2) link_ALPHA1-4 : angle 1.64069 ( 6) link_BETA1-4 : bond 0.01196 ( 2) link_BETA1-4 : angle 2.83171 ( 6) link_NAG-ASN : bond 0.00597 ( 5) link_NAG-ASN : angle 4.27134 ( 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 214 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 149 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 464 MET cc_start: 0.7854 (tpp) cc_final: 0.7642 (tpp) REVERT: A 477 TYR cc_start: 0.9079 (m-80) cc_final: 0.8834 (m-10) REVERT: A 525 SER cc_start: 0.8700 (t) cc_final: 0.8179 (p) REVERT: A 566 MET cc_start: 0.7677 (tpp) cc_final: 0.7375 (tpp) REVERT: A 968 ARG cc_start: 0.9277 (OUTLIER) cc_final: 0.8941 (ppt170) REVERT: A 1120 LEU cc_start: 0.9384 (OUTLIER) cc_final: 0.9148 (pp) REVERT: A 1237 LYS cc_start: 0.8803 (OUTLIER) cc_final: 0.8450 (ptmt) REVERT: A 1339 MET cc_start: 0.7442 (mmp) cc_final: 0.6918 (mmp) REVERT: A 1369 TYR cc_start: 0.8829 (t80) cc_final: 0.8541 (t80) REVERT: A 1372 MET cc_start: 0.8698 (tmm) cc_final: 0.7981 (mmt) REVERT: A 1378 ASP cc_start: 0.8365 (p0) cc_final: 0.8045 (p0) REVERT: A 1386 CYS cc_start: 0.8560 (m) cc_final: 0.8196 (p) REVERT: A 1446 PHE cc_start: 0.7104 (t80) cc_final: 0.6874 (t80) REVERT: B 391 ILE cc_start: 0.9161 (tp) cc_final: 0.8783 (tt) REVERT: B 395 PHE cc_start: 0.8013 (m-80) cc_final: 0.7403 (m-80) outliers start: 65 outliers final: 49 residues processed: 189 average time/residue: 0.0928 time to fit residues: 27.0573 Evaluate side-chains 197 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 145 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 LEU 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 520 HIS Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 625 ARG Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 771 MET Chi-restraints excluded: chain A residue 791 PHE Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 968 ARG Chi-restraints excluded: chain A residue 1116 ASP Chi-restraints excluded: chain A residue 1120 LEU Chi-restraints excluded: chain A residue 1201 CYS Chi-restraints excluded: chain A residue 1213 THR Chi-restraints excluded: chain A residue 1237 LYS Chi-restraints excluded: chain A residue 1243 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 1321 VAL 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 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 93 ILE 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 247 LEU 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: 0.8980 chunk 62 optimal weight: 0.9990 chunk 104 optimal weight: 0.7980 chunk 135 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 138 optimal weight: 5.9990 chunk 50 optimal weight: 20.0000 chunk 86 optimal weight: 7.9990 chunk 69 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 323 ASN A 719 GLN A1011 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.087741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.069669 restraints weight = 57790.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.071491 restraints weight = 34984.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.072759 restraints weight = 24025.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.073487 restraints weight = 18480.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.074305 restraints weight = 15570.200| |-----------------------------------------------------------------------------| r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.3671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 12773 Z= 0.130 Angle : 0.665 11.739 17356 Z= 0.326 Chirality : 0.045 0.292 1974 Planarity : 0.004 0.056 2177 Dihedral : 7.341 75.094 2031 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 15.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 3.56 % Allowed : 20.42 % Favored : 76.02 % 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: -1.05 (0.22), residues: 1520 helix: 0.40 (0.21), residues: 619 sheet: -0.46 (0.38), residues: 197 loop : -1.79 (0.24), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 625 TYR 0.014 0.001 TYR A 619 PHE 0.028 0.002 PHE A1241 TRP 0.012 0.001 TRP A 532 HIS 0.003 0.001 HIS A 455 Details of bonding type rmsd covalent geometry : bond 0.00290 (12761) covalent geometry : angle 0.65112 (17325) SS BOND : bond 0.00027 ( 2) SS BOND : angle 0.52652 ( 4) hydrogen bonds : bond 0.03465 ( 562) hydrogen bonds : angle 4.64860 ( 1611) Misc. bond : bond 0.00122 ( 1) link_ALPHA1-4 : bond 0.00767 ( 2) link_ALPHA1-4 : angle 1.64399 ( 6) link_BETA1-4 : bond 0.01099 ( 2) link_BETA1-4 : angle 2.73678 ( 6) link_NAG-ASN : bond 0.00650 ( 5) link_NAG-ASN : angle 4.23539 ( 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: 48 poor density : 160 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 477 TYR cc_start: 0.9036 (m-80) cc_final: 0.8815 (m-10) REVERT: A 525 SER cc_start: 0.8660 (t) cc_final: 0.8150 (p) REVERT: A 566 MET cc_start: 0.7708 (tpp) cc_final: 0.7412 (tpp) REVERT: A 968 ARG cc_start: 0.9253 (OUTLIER) cc_final: 0.8922 (ppt170) REVERT: A 1120 LEU cc_start: 0.9383 (OUTLIER) cc_final: 0.9149 (pp) REVERT: A 1237 LYS cc_start: 0.8800 (OUTLIER) cc_final: 0.8479 (ptmt) REVERT: A 1339 MET cc_start: 0.7295 (mmp) cc_final: 0.6836 (mmp) REVERT: A 1369 TYR cc_start: 0.8781 (t80) cc_final: 0.8496 (t80) REVERT: A 1372 MET cc_start: 0.8661 (tmm) cc_final: 0.7978 (mmt) REVERT: A 1378 ASP cc_start: 0.8329 (p0) cc_final: 0.8000 (p0) REVERT: A 1386 CYS cc_start: 0.8500 (m) cc_final: 0.8191 (p) REVERT: A 1446 PHE cc_start: 0.7067 (t80) cc_final: 0.6867 (t80) REVERT: A 1456 GLU cc_start: 0.8780 (tm-30) cc_final: 0.8213 (tm-30) REVERT: B 391 ILE cc_start: 0.9153 (tp) cc_final: 0.8776 (tt) REVERT: B 395 PHE cc_start: 0.7972 (m-80) cc_final: 0.7359 (m-80) outliers start: 48 outliers final: 40 residues processed: 185 average time/residue: 0.0896 time to fit residues: 26.1273 Evaluate side-chains 195 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 152 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 LEU 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 703 LEU Chi-restraints excluded: chain A residue 791 PHE Chi-restraints excluded: chain A residue 968 ARG Chi-restraints excluded: chain A residue 1097 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 1237 LYS Chi-restraints excluded: chain A residue 1243 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 1321 VAL 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 93 ILE 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 247 LEU 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 367 LEU 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: 1.9990 chunk 3 optimal weight: 8.9990 chunk 92 optimal weight: 4.9990 chunk 118 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 108 optimal weight: 9.9990 chunk 101 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 22 optimal weight: 4.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.088078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.069829 restraints weight = 58340.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.071781 restraints weight = 35330.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.073222 restraints weight = 24411.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.074182 restraints weight = 18640.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.074736 restraints weight = 15299.609| |-----------------------------------------------------------------------------| r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.3760 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= 0.126 Angle : 0.670 13.884 17356 Z= 0.325 Chirality : 0.045 0.282 1974 Planarity : 0.004 0.055 2177 Dihedral : 7.120 72.690 2031 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 15.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 3.86 % Allowed : 20.56 % Favored : 75.58 % 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: -0.97 (0.22), residues: 1520 helix: 0.44 (0.21), residues: 619 sheet: -0.40 (0.38), residues: 197 loop : -1.72 (0.24), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1009 TYR 0.014 0.001 TYR A 619 PHE 0.053 0.002 PHE A1241 TRP 0.012 0.001 TRP A 513 HIS 0.003 0.001 HIS A 455 Details of bonding type rmsd covalent geometry : bond 0.00283 (12761) covalent geometry : angle 0.65653 (17325) SS BOND : bond 0.00015 ( 2) SS BOND : angle 0.51097 ( 4) hydrogen bonds : bond 0.03446 ( 562) hydrogen bonds : angle 4.57951 ( 1611) Misc. bond : bond 0.00144 ( 1) link_ALPHA1-4 : bond 0.00754 ( 2) link_ALPHA1-4 : angle 1.61995 ( 6) link_BETA1-4 : bond 0.01057 ( 2) link_BETA1-4 : angle 2.73632 ( 6) link_NAG-ASN : bond 0.00668 ( 5) link_NAG-ASN : angle 4.24794 ( 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 200 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 148 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 ARG cc_start: 0.8649 (ttt-90) cc_final: 0.8042 (tpt90) REVERT: A 477 TYR cc_start: 0.9105 (m-80) cc_final: 0.8888 (m-10) REVERT: A 525 SER cc_start: 0.8695 (t) cc_final: 0.8194 (p) REVERT: A 566 MET cc_start: 0.7773 (tpp) cc_final: 0.7475 (tpp) REVERT: A 968 ARG cc_start: 0.9268 (OUTLIER) cc_final: 0.8951 (ppt170) REVERT: A 1120 LEU cc_start: 0.9375 (OUTLIER) cc_final: 0.9141 (pp) REVERT: A 1200 MET cc_start: 0.8871 (mmm) cc_final: 0.8331 (mmt) REVERT: A 1237 LYS cc_start: 0.8840 (OUTLIER) cc_final: 0.8543 (ptmt) REVERT: A 1339 MET cc_start: 0.7423 (mmp) cc_final: 0.6979 (mmp) REVERT: A 1369 TYR cc_start: 0.8787 (t80) cc_final: 0.8505 (t80) REVERT: A 1372 MET cc_start: 0.8708 (tmm) cc_final: 0.8016 (mmt) REVERT: A 1378 ASP cc_start: 0.8328 (p0) cc_final: 0.7990 (p0) REVERT: A 1386 CYS cc_start: 0.8557 (m) cc_final: 0.8194 (p) REVERT: A 1456 GLU cc_start: 0.8815 (tm-30) cc_final: 0.8242 (tm-30) REVERT: B 391 ILE cc_start: 0.9157 (tp) cc_final: 0.8774 (tt) REVERT: B 395 PHE cc_start: 0.7979 (m-80) cc_final: 0.7376 (m-80) outliers start: 52 outliers final: 42 residues processed: 178 average time/residue: 0.0825 time to fit residues: 23.2216 Evaluate side-chains 190 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 145 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 LEU 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 598 VAL 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 791 PHE Chi-restraints excluded: chain A residue 968 ARG Chi-restraints excluded: chain A residue 1097 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 1213 THR Chi-restraints excluded: chain A residue 1227 LEU Chi-restraints excluded: chain A residue 1237 LYS Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1264 TYR 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 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 93 ILE Chi-restraints excluded: chain B residue 121 ILE 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 247 LEU 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 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: 8.9990 chunk 101 optimal weight: 0.9990 chunk 134 optimal weight: 7.9990 chunk 70 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 20 optimal weight: 0.0060 chunk 147 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 chunk 87 optimal weight: 0.7980 overall best weight: 0.9602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4021 r_free = 0.4021 target = 0.089310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.071283 restraints weight = 58150.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.073122 restraints weight = 34929.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.074149 restraints weight = 24197.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.075326 restraints weight = 19238.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.075860 restraints weight = 15633.518| |-----------------------------------------------------------------------------| r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.3773 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= 0.118 Angle : 0.669 10.963 17356 Z= 0.325 Chirality : 0.045 0.311 1974 Planarity : 0.004 0.049 2177 Dihedral : 6.860 69.412 2031 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 3.04 % Allowed : 21.53 % Favored : 75.43 % 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: 0.44 (0.21), residues: 620 sheet: -0.31 (0.38), residues: 197 loop : -1.70 (0.24), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1009 TYR 0.013 0.001 TYR A 619 PHE 0.055 0.002 PHE A1241 TRP 0.015 0.001 TRP A1395 HIS 0.003 0.001 HIS A 455 Details of bonding type rmsd covalent geometry : bond 0.00263 (12761) covalent geometry : angle 0.65459 (17325) SS BOND : bond 0.00038 ( 2) SS BOND : angle 0.54998 ( 4) hydrogen bonds : bond 0.03358 ( 562) hydrogen bonds : angle 4.48070 ( 1611) Misc. bond : bond 0.00098 ( 1) link_ALPHA1-4 : bond 0.00804 ( 2) link_ALPHA1-4 : angle 1.59906 ( 6) link_BETA1-4 : bond 0.01199 ( 2) link_BETA1-4 : angle 2.72293 ( 6) link_NAG-ASN : bond 0.00699 ( 5) link_NAG-ASN : angle 4.30996 ( 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 194 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 153 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 477 TYR cc_start: 0.9097 (m-80) cc_final: 0.8889 (m-10) REVERT: A 525 SER cc_start: 0.8687 (t) cc_final: 0.8177 (p) REVERT: A 566 MET cc_start: 0.7782 (tpp) cc_final: 0.7577 (tpp) REVERT: A 968 ARG cc_start: 0.9268 (OUTLIER) cc_final: 0.8954 (ppt170) REVERT: A 1120 LEU cc_start: 0.9364 (OUTLIER) cc_final: 0.9131 (pp) REVERT: A 1237 LYS cc_start: 0.8833 (OUTLIER) cc_final: 0.8547 (ptmt) REVERT: A 1369 TYR cc_start: 0.8739 (t80) cc_final: 0.8452 (t80) REVERT: A 1372 MET cc_start: 0.8739 (tmm) cc_final: 0.8030 (mmt) REVERT: A 1378 ASP cc_start: 0.8321 (p0) cc_final: 0.7538 (p0) REVERT: A 1386 CYS cc_start: 0.8559 (m) cc_final: 0.8163 (p) REVERT: A 1456 GLU cc_start: 0.8810 (tm-30) cc_final: 0.8229 (tm-30) REVERT: B 391 ILE cc_start: 0.9151 (tp) cc_final: 0.8768 (tt) REVERT: B 395 PHE cc_start: 0.7984 (m-80) cc_final: 0.7388 (m-80) outliers start: 41 outliers final: 36 residues processed: 175 average time/residue: 0.0881 time to fit residues: 24.4225 Evaluate side-chains 188 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 149 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 283 VAL 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 703 LEU Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 791 PHE Chi-restraints excluded: chain A residue 968 ARG Chi-restraints excluded: chain A residue 1097 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 1213 THR Chi-restraints excluded: chain A residue 1227 LEU Chi-restraints excluded: chain A residue 1237 LYS Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1279 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 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 1384 PHE 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 71 THR Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 176 ASN 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: 6.9990 chunk 61 optimal weight: 5.9990 chunk 140 optimal weight: 0.4980 chunk 27 optimal weight: 4.9990 chunk 125 optimal weight: 9.9990 chunk 98 optimal weight: 5.9990 chunk 118 optimal weight: 6.9990 chunk 134 optimal weight: 0.9990 chunk 89 optimal weight: 9.9990 chunk 2 optimal weight: 0.5980 chunk 39 optimal weight: 7.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN ** A 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.087049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.069034 restraints weight = 58677.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.070643 restraints weight = 35438.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.072254 restraints weight = 24838.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.073087 restraints weight = 18885.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.073904 restraints weight = 15657.957| |-----------------------------------------------------------------------------| r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.3962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12773 Z= 0.156 Angle : 0.689 11.009 17356 Z= 0.336 Chirality : 0.045 0.281 1974 Planarity : 0.004 0.050 2177 Dihedral : 6.881 67.761 2031 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 16.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 3.64 % Allowed : 21.01 % Favored : 75.35 % 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: -0.97 (0.22), residues: 1520 helix: 0.42 (0.21), residues: 625 sheet: -0.26 (0.39), residues: 187 loop : -1.75 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 625 TYR 0.018 0.001 TYR A 619 PHE 0.046 0.002 PHE A1241 TRP 0.017 0.001 TRP A1395 HIS 0.003 0.001 HIS A 455 Details of bonding type rmsd covalent geometry : bond 0.00346 (12761) covalent geometry : angle 0.67527 (17325) SS BOND : bond 0.00159 ( 2) SS BOND : angle 0.51313 ( 4) hydrogen bonds : bond 0.03482 ( 562) hydrogen bonds : angle 4.58881 ( 1611) Misc. bond : bond 0.00137 ( 1) link_ALPHA1-4 : bond 0.00692 ( 2) link_ALPHA1-4 : angle 1.65789 ( 6) link_BETA1-4 : bond 0.01053 ( 2) link_BETA1-4 : angle 2.83557 ( 6) link_NAG-ASN : bond 0.00623 ( 5) link_NAG-ASN : angle 4.33541 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2177.13 seconds wall clock time: 38 minutes 30.22 seconds (2310.22 seconds total)