Starting phenix.real_space_refine on Thu Sep 26 10:52:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ky5_23068/09_2024/7ky5_23068.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ky5_23068/09_2024/7ky5_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ky5_23068/09_2024/7ky5_23068.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ky5_23068/09_2024/7ky5_23068.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ky5_23068/09_2024/7ky5_23068.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ky5_23068/09_2024/7ky5_23068.cif" } resolution = 3.98 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: {'GLU:plan': 1, 'HIS:plan': 1, 'ASP: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: 7.08, per 1000 atoms: 0.57 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: 3.48 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.50 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: 4.88 Time building geometry restraints manager: 4.03 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: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.510 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 30.820 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.860 ------------------------------------------------------------------------------- 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 0.101 12761 Z= 0.242 Angle : 1.086 71.235 17325 Z= 0.477 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 : 16.72 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (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 TRP 0.048 0.001 TRP B 142 HIS 0.003 0.001 HIS A1350 PHE 0.039 0.002 PHE A1328 TYR 0.021 0.001 TYR A 260 ARG 0.011 0.001 ARG A1131 *********************** 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 fitting. rotamer outliers: 1 poor density : 213 time to evaluate : 1.453 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: 0.2122 time to fit residues: 69.2924 Evaluate side-chains 162 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 5.9990 chunk 115 optimal weight: 0.0040 chunk 63 optimal weight: 9.9990 chunk 39 optimal weight: 0.5980 chunk 77 optimal weight: 2.9990 chunk 61 optimal weight: 20.0000 chunk 119 optimal weight: 8.9990 chunk 46 optimal weight: 0.8980 chunk 72 optimal weight: 9.9990 chunk 88 optimal weight: 5.9990 chunk 138 optimal weight: 5.9990 overall best weight: 2.0996 ------------------------------------------------------------------------------- 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 ** A1252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 GLN ** B 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12761 Z= 0.207 Angle : 0.659 11.032 17325 Z= 0.329 Chirality : 0.044 0.211 1974 Planarity : 0.004 0.050 2177 Dihedral : 8.816 95.501 2031 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 1.93 % Allowed : 9.95 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.21), residues: 1520 helix: 0.44 (0.21), residues: 623 sheet: -0.53 (0.37), residues: 196 loop : -1.95 (0.23), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 142 HIS 0.004 0.001 HIS A 942 PHE 0.030 0.002 PHE A 602 TYR 0.021 0.001 TYR A 260 ARG 0.004 0.000 ARG A 625 *********************** 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 202 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 176 time to evaluate : 1.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 TYR cc_start: 0.7969 (m-10) cc_final: 0.7628 (m-10) REVERT: A 260 TYR cc_start: 0.6324 (m-10) cc_final: 0.6012 (m-10) REVERT: A 566 MET cc_start: 0.7553 (tpp) cc_final: 0.7213 (tpp) REVERT: A 756 GLU cc_start: 0.8206 (mp0) cc_final: 0.7933 (pm20) REVERT: A 778 MET cc_start: 0.7158 (ppp) cc_final: 0.6902 (ppp) REVERT: A 835 LYS cc_start: 0.9016 (mppt) cc_final: 0.8610 (tptt) REVERT: A 1120 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.8994 (pp) REVERT: A 1238 ASN cc_start: 0.8767 (p0) cc_final: 0.8481 (p0) REVERT: A 1372 MET cc_start: 0.8573 (tmm) cc_final: 0.7684 (mmt) REVERT: A 1446 PHE cc_start: 0.7361 (t80) cc_final: 0.7032 (t80) REVERT: B 102 GLU cc_start: 0.7730 (pp20) cc_final: 0.6924 (pp20) REVERT: B 391 ILE cc_start: 0.9026 (tp) cc_final: 0.8553 (tp) REVERT: B 395 PHE cc_start: 0.8068 (m-80) cc_final: 0.7277 (m-80) outliers start: 26 outliers final: 18 residues processed: 184 average time/residue: 0.1951 time to fit residues: 56.1048 Evaluate side-chains 178 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 159 time to evaluate : 1.333 ------------------------------------------------------------------------------- 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 1278 ILE 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 76 optimal weight: 7.9990 chunk 42 optimal weight: 8.9990 chunk 114 optimal weight: 8.9990 chunk 93 optimal weight: 5.9990 chunk 38 optimal weight: 10.0000 chunk 138 optimal weight: 3.9990 chunk 149 optimal weight: 5.9990 chunk 123 optimal weight: 6.9990 chunk 137 optimal weight: 8.9990 chunk 47 optimal weight: 2.9990 chunk 110 optimal weight: 0.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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** A 809 GLN A 814 HIS ** A1208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 12761 Z= 0.311 Angle : 0.701 8.811 17325 Z= 0.360 Chirality : 0.046 0.228 1974 Planarity : 0.005 0.053 2177 Dihedral : 8.493 91.845 2031 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 18.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 3.12 % Allowed : 13.21 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.21), residues: 1520 helix: 0.22 (0.21), residues: 618 sheet: -0.64 (0.36), residues: 209 loop : -1.95 (0.23), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 348 HIS 0.005 0.001 HIS A 254 PHE 0.020 0.002 PHE A1234 TYR 0.019 0.002 TYR A 260 ARG 0.009 0.001 ARG A 625 *********************** 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 210 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 168 time to evaluate : 1.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 TYR cc_start: 0.8023 (m-10) cc_final: 0.7758 (m-10) REVERT: A 314 ARG cc_start: 0.8664 (ttt-90) cc_final: 0.7896 (mtp180) REVERT: A 458 ASP cc_start: 0.8260 (t0) cc_final: 0.8037 (t0) REVERT: A 566 MET cc_start: 0.7502 (tpp) cc_final: 0.7239 (tpp) REVERT: A 835 LYS cc_start: 0.9038 (mppt) cc_final: 0.8476 (tptt) REVERT: A 1120 LEU cc_start: 0.9310 (OUTLIER) cc_final: 0.9088 (pp) REVERT: A 1303 ILE cc_start: 0.9380 (mm) cc_final: 0.9175 (mt) REVERT: A 1378 ASP cc_start: 0.8545 (p0) cc_final: 0.8190 (p0) REVERT: A 1446 PHE cc_start: 0.7347 (t80) cc_final: 0.7004 (t80) REVERT: B 238 MET cc_start: 0.7567 (tpt) cc_final: 0.7350 (tpp) REVERT: B 292 MET cc_start: 0.8690 (mpp) cc_final: 0.8464 (mpp) REVERT: B 391 ILE cc_start: 0.9065 (tp) cc_final: 0.8513 (tt) REVERT: B 395 PHE cc_start: 0.7992 (m-80) cc_final: 0.7303 (m-80) outliers start: 42 outliers final: 31 residues processed: 187 average time/residue: 0.2361 time to fit residues: 68.3948 Evaluate side-chains 179 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 147 time to evaluate : 1.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 771 MET Chi-restraints excluded: chain A residue 1028 LEU Chi-restraints excluded: chain A residue 1097 LEU Chi-restraints excluded: chain A residue 1106 LEU Chi-restraints excluded: chain A residue 1116 ASP Chi-restraints excluded: chain A residue 1120 LEU Chi-restraints excluded: chain A residue 1145 CYS Chi-restraints excluded: chain A residue 1201 CYS Chi-restraints excluded: chain A residue 1278 ILE Chi-restraints excluded: chain A residue 1280 LEU Chi-restraints excluded: chain A residue 1298 LEU Chi-restraints excluded: chain A residue 1309 ASN Chi-restraints excluded: chain A residue 1321 VAL Chi-restraints excluded: chain A residue 1361 ILE Chi-restraints excluded: chain A residue 1370 VAL Chi-restraints excluded: chain A residue 1387 LEU Chi-restraints excluded: chain A residue 1391 VAL Chi-restraints excluded: chain A residue 1406 ASN Chi-restraints excluded: chain A residue 1434 LEU Chi-restraints excluded: chain A residue 1453 ILE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 407 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 136 optimal weight: 8.9990 chunk 103 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 15 optimal weight: 8.9990 chunk 65 optimal weight: 20.0000 chunk 92 optimal weight: 0.9980 chunk 138 optimal weight: 0.8980 chunk 146 optimal weight: 6.9990 chunk 72 optimal weight: 9.9990 chunk 131 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- 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 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12761 Z= 0.197 Angle : 0.629 12.102 17325 Z= 0.318 Chirality : 0.044 0.249 1974 Planarity : 0.004 0.054 2177 Dihedral : 8.094 85.642 2031 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 16.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 3.56 % Allowed : 14.85 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.22), residues: 1520 helix: 0.31 (0.21), residues: 623 sheet: -0.51 (0.38), residues: 198 loop : -1.83 (0.23), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 562 HIS 0.002 0.001 HIS B 186 PHE 0.027 0.002 PHE A 647 TYR 0.018 0.001 TYR A1322 ARG 0.004 0.000 ARG A 625 *********************** 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 215 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 167 time to evaluate : 1.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 ARG cc_start: 0.8640 (ttt-90) cc_final: 0.7887 (mtp180) REVERT: A 525 SER cc_start: 0.8645 (t) cc_final: 0.8314 (m) REVERT: A 564 MET cc_start: 0.6608 (mpp) cc_final: 0.6398 (mpp) REVERT: A 566 MET cc_start: 0.7785 (tpp) cc_final: 0.7350 (tpp) REVERT: A 756 GLU cc_start: 0.8243 (mp0) cc_final: 0.7988 (pm20) REVERT: A 835 LYS cc_start: 0.9014 (mppt) cc_final: 0.8406 (tptt) REVERT: A 1120 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.9102 (pp) REVERT: A 1208 GLN cc_start: 0.8069 (OUTLIER) cc_final: 0.7761 (pm20) REVERT: A 1339 MET cc_start: 0.7748 (mmp) cc_final: 0.7085 (mmp) REVERT: A 1372 MET cc_start: 0.8634 (tmm) cc_final: 0.7859 (mmt) REVERT: A 1378 ASP cc_start: 0.8576 (p0) cc_final: 0.8216 (p0) REVERT: A 1446 PHE cc_start: 0.7306 (t80) cc_final: 0.6981 (t80) REVERT: B 176 ASN cc_start: 0.8482 (OUTLIER) cc_final: 0.8173 (t0) REVERT: B 391 ILE cc_start: 0.9086 (tp) cc_final: 0.8491 (tt) REVERT: B 395 PHE cc_start: 0.7991 (m-80) cc_final: 0.7307 (m-80) outliers start: 48 outliers final: 32 residues processed: 195 average time/residue: 0.1956 time to fit residues: 59.5587 Evaluate side-chains 187 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 152 time to evaluate : 1.457 ------------------------------------------------------------------------------- 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 953 THR Chi-restraints excluded: chain A residue 1097 LEU Chi-restraints excluded: chain A residue 1106 LEU Chi-restraints excluded: chain A residue 1116 ASP Chi-restraints excluded: chain A residue 1120 LEU Chi-restraints excluded: chain A residue 1206 ILE Chi-restraints excluded: chain A residue 1208 GLN Chi-restraints excluded: chain A residue 1227 LEU Chi-restraints excluded: chain A residue 1280 LEU Chi-restraints excluded: chain A residue 1293 MET Chi-restraints excluded: chain A residue 1298 LEU Chi-restraints excluded: chain A residue 1309 ASN Chi-restraints excluded: chain A residue 1336 HIS Chi-restraints excluded: chain A residue 1361 ILE Chi-restraints excluded: chain A residue 1370 VAL Chi-restraints excluded: chain A residue 1384 PHE Chi-restraints excluded: chain A residue 1387 LEU Chi-restraints excluded: chain A residue 1406 ASN Chi-restraints excluded: chain A residue 1434 LEU Chi-restraints excluded: chain A residue 1442 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 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 122 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 2 optimal weight: 0.0050 chunk 109 optimal weight: 10.0000 chunk 60 optimal weight: 8.9990 chunk 125 optimal weight: 5.9990 chunk 101 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 75 optimal weight: 5.9990 chunk 131 optimal weight: 8.9990 chunk 37 optimal weight: 8.9990 overall best weight: 3.2000 ------------------------------------------------------------------------------- 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** ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12761 Z= 0.246 Angle : 0.641 10.316 17325 Z= 0.325 Chirality : 0.044 0.251 1974 Planarity : 0.004 0.056 2177 Dihedral : 7.994 84.767 2031 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 17.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 4.01 % Allowed : 16.41 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.22), residues: 1520 helix: 0.29 (0.21), residues: 627 sheet: -0.39 (0.38), residues: 191 loop : -1.80 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 969 HIS 0.003 0.001 HIS B 186 PHE 0.021 0.002 PHE A 647 TYR 0.020 0.002 TYR A 229 ARG 0.006 0.000 ARG A 625 *********************** 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 207 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 153 time to evaluate : 1.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 TYR cc_start: 0.8425 (m-10) cc_final: 0.8221 (m-10) REVERT: A 314 ARG cc_start: 0.8658 (ttt-90) cc_final: 0.7882 (tpt90) REVERT: A 525 SER cc_start: 0.8657 (t) cc_final: 0.8128 (p) REVERT: A 566 MET cc_start: 0.7779 (tpp) cc_final: 0.7390 (tpp) REVERT: A 756 GLU cc_start: 0.8268 (mp0) cc_final: 0.7967 (pm20) REVERT: A 968 ARG cc_start: 0.9278 (OUTLIER) cc_final: 0.8951 (ppt170) REVERT: A 1011 GLN cc_start: 0.8647 (OUTLIER) cc_final: 0.8280 (mp10) REVERT: A 1120 LEU cc_start: 0.9356 (OUTLIER) cc_final: 0.9129 (pp) REVERT: A 1339 MET cc_start: 0.7781 (mmp) cc_final: 0.7172 (mmp) REVERT: A 1372 MET cc_start: 0.8717 (tmm) cc_final: 0.7878 (mmt) REVERT: A 1378 ASP cc_start: 0.8585 (p0) cc_final: 0.8236 (p0) REVERT: A 1446 PHE cc_start: 0.7336 (t80) cc_final: 0.7004 (t80) REVERT: B 391 ILE cc_start: 0.9109 (tp) cc_final: 0.8493 (tt) REVERT: B 395 PHE cc_start: 0.8053 (m-80) cc_final: 0.7351 (m-80) outliers start: 54 outliers final: 41 residues processed: 184 average time/residue: 0.2178 time to fit residues: 61.0676 Evaluate side-chains 192 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 148 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 599 ILE 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 953 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 1099 GLU Chi-restraints excluded: chain A residue 1106 LEU Chi-restraints excluded: chain A residue 1116 ASP Chi-restraints excluded: chain A residue 1120 LEU Chi-restraints excluded: chain A residue 1145 CYS Chi-restraints excluded: chain A residue 1201 CYS Chi-restraints excluded: chain A residue 1227 LEU Chi-restraints excluded: chain A residue 1264 TYR Chi-restraints excluded: chain A residue 1280 LEU Chi-restraints excluded: chain A residue 1293 MET Chi-restraints excluded: chain A residue 1298 LEU Chi-restraints excluded: chain A residue 1309 ASN Chi-restraints excluded: chain A residue 1336 HIS Chi-restraints excluded: chain A residue 1361 ILE Chi-restraints excluded: chain A residue 1370 VAL Chi-restraints excluded: chain A residue 1384 PHE Chi-restraints excluded: chain A residue 1387 LEU Chi-restraints excluded: chain A residue 1406 ASN Chi-restraints excluded: chain A residue 1434 LEU Chi-restraints excluded: chain A residue 1442 ILE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 145 VAL 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 346 LEU Chi-restraints excluded: chain B residue 359 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 49 optimal weight: 10.0000 chunk 132 optimal weight: 4.9990 chunk 29 optimal weight: 8.9990 chunk 86 optimal weight: 9.9990 chunk 36 optimal weight: 1.9990 chunk 147 optimal weight: 9.9990 chunk 122 optimal weight: 0.7980 chunk 68 optimal weight: 30.0000 chunk 12 optimal weight: 20.0000 chunk 48 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1208 GLN ** A1252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 GLN ** B 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12761 Z= 0.224 Angle : 0.646 12.643 17325 Z= 0.324 Chirality : 0.045 0.268 1974 Planarity : 0.004 0.057 2177 Dihedral : 7.735 81.229 2031 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 16.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 4.38 % Allowed : 17.22 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.22), residues: 1520 helix: 0.36 (0.21), residues: 624 sheet: -0.30 (0.39), residues: 187 loop : -1.81 (0.23), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 562 HIS 0.003 0.001 HIS B 186 PHE 0.022 0.002 PHE A1234 TYR 0.015 0.001 TYR A 229 ARG 0.003 0.000 ARG A1009 *********************** 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 223 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 164 time to evaluate : 1.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 TYR cc_start: 0.8452 (m-10) cc_final: 0.8137 (m-10) REVERT: A 314 ARG cc_start: 0.8735 (ttt-90) cc_final: 0.8025 (tpt-90) REVERT: A 525 SER cc_start: 0.8690 (t) cc_final: 0.8162 (p) REVERT: A 566 MET cc_start: 0.7789 (tpp) cc_final: 0.7371 (tpp) REVERT: A 968 ARG cc_start: 0.9272 (OUTLIER) cc_final: 0.8941 (ppt170) REVERT: A 1011 GLN cc_start: 0.8632 (OUTLIER) cc_final: 0.8310 (mp10) REVERT: A 1120 LEU cc_start: 0.9369 (OUTLIER) cc_final: 0.9144 (pp) REVERT: A 1200 MET cc_start: 0.8946 (mmt) cc_final: 0.8399 (mmt) REVERT: A 1339 MET cc_start: 0.7765 (mmp) cc_final: 0.7002 (mmp) REVERT: A 1372 MET cc_start: 0.8749 (tmm) cc_final: 0.7894 (mmt) REVERT: A 1378 ASP cc_start: 0.8582 (p0) cc_final: 0.8221 (p0) REVERT: A 1386 CYS cc_start: 0.8794 (m) cc_final: 0.8379 (p) REVERT: A 1446 PHE cc_start: 0.7325 (t80) cc_final: 0.7005 (t80) REVERT: A 1456 GLU cc_start: 0.9058 (tm-30) cc_final: 0.8460 (tm-30) REVERT: B 102 GLU cc_start: 0.8147 (pp20) cc_final: 0.7099 (tm-30) REVERT: B 176 ASN cc_start: 0.8349 (t0) cc_final: 0.7912 (m-40) REVERT: B 391 ILE cc_start: 0.9142 (tp) cc_final: 0.8517 (tt) REVERT: B 395 PHE cc_start: 0.8088 (m-80) cc_final: 0.7388 (m-80) outliers start: 59 outliers final: 45 residues processed: 201 average time/residue: 0.2185 time to fit residues: 67.5861 Evaluate side-chains 202 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 154 time to evaluate : 1.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 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 929 THR Chi-restraints excluded: chain A residue 953 THR Chi-restraints excluded: chain A residue 968 ARG Chi-restraints excluded: chain A residue 1011 GLN Chi-restraints excluded: chain A residue 1028 LEU Chi-restraints excluded: chain A residue 1097 LEU Chi-restraints excluded: chain A residue 1099 GLU Chi-restraints excluded: chain A residue 1106 LEU Chi-restraints excluded: chain A residue 1116 ASP Chi-restraints excluded: chain A residue 1120 LEU Chi-restraints excluded: chain A residue 1145 CYS Chi-restraints excluded: chain A residue 1227 LEU Chi-restraints excluded: chain A residue 1293 MET Chi-restraints excluded: chain A residue 1298 LEU Chi-restraints excluded: chain A residue 1309 ASN Chi-restraints excluded: chain A residue 1336 HIS Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain A residue 1361 ILE Chi-restraints excluded: chain A residue 1370 VAL Chi-restraints excluded: chain A residue 1384 PHE Chi-restraints excluded: chain A residue 1387 LEU Chi-restraints excluded: chain A residue 1391 VAL Chi-restraints excluded: chain A residue 1406 ASN Chi-restraints excluded: chain A residue 1434 LEU Chi-restraints excluded: chain A residue 1442 ILE Chi-restraints excluded: chain A residue 1451 ILE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 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 141 optimal weight: 1.9990 chunk 16 optimal weight: 0.4980 chunk 83 optimal weight: 0.0570 chunk 107 optimal weight: 7.9990 chunk 123 optimal weight: 0.8980 chunk 82 optimal weight: 8.9990 chunk 146 optimal weight: 9.9990 chunk 91 optimal weight: 0.9990 chunk 89 optimal weight: 10.0000 chunk 67 optimal weight: 20.0000 chunk 90 optimal weight: 0.9980 overall best weight: 0.6900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 323 ASN 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12761 Z= 0.157 Angle : 0.634 11.165 17325 Z= 0.314 Chirality : 0.045 0.294 1974 Planarity : 0.004 0.058 2177 Dihedral : 7.411 76.999 2031 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 3.27 % Allowed : 19.82 % Favored : 76.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.22), residues: 1520 helix: 0.40 (0.21), residues: 624 sheet: -0.22 (0.39), residues: 187 loop : -1.73 (0.24), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 532 HIS 0.002 0.001 HIS A 455 PHE 0.024 0.001 PHE A1234 TYR 0.016 0.001 TYR A1322 ARG 0.003 0.000 ARG A1009 *********************** 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 222 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 178 time to evaluate : 1.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 TYR cc_start: 0.8458 (m-10) cc_final: 0.8218 (m-10) REVERT: A 314 ARG cc_start: 0.8670 (ttt-90) cc_final: 0.7958 (tpt-90) REVERT: A 525 SER cc_start: 0.8646 (t) cc_final: 0.8126 (p) REVERT: A 702 ASP cc_start: 0.8215 (OUTLIER) cc_final: 0.7848 (t0) REVERT: A 722 MET cc_start: 0.7452 (mtm) cc_final: 0.7137 (ptt) REVERT: A 756 GLU cc_start: 0.8128 (mp0) cc_final: 0.7909 (pm20) REVERT: A 968 ARG cc_start: 0.9267 (OUTLIER) cc_final: 0.8959 (ppt170) REVERT: A 1011 GLN cc_start: 0.8554 (OUTLIER) cc_final: 0.8306 (mp10) REVERT: A 1012 ASP cc_start: 0.9057 (p0) cc_final: 0.8812 (p0) REVERT: A 1120 LEU cc_start: 0.9351 (OUTLIER) cc_final: 0.9117 (pp) REVERT: A 1200 MET cc_start: 0.8815 (mmt) cc_final: 0.8576 (mmm) REVERT: A 1339 MET cc_start: 0.7626 (mmp) cc_final: 0.6994 (mmp) REVERT: A 1372 MET cc_start: 0.8805 (tmm) cc_final: 0.7940 (mmt) REVERT: A 1378 ASP cc_start: 0.8537 (p0) cc_final: 0.8168 (p0) REVERT: A 1386 CYS cc_start: 0.8797 (m) cc_final: 0.8389 (p) REVERT: A 1446 PHE cc_start: 0.7329 (t80) cc_final: 0.7000 (t80) REVERT: A 1456 GLU cc_start: 0.9026 (tm-30) cc_final: 0.8588 (tm-30) REVERT: B 176 ASN cc_start: 0.8279 (t0) cc_final: 0.7775 (m-40) REVERT: B 391 ILE cc_start: 0.9140 (tp) cc_final: 0.8511 (tt) REVERT: B 395 PHE cc_start: 0.8137 (m-80) cc_final: 0.7470 (m-80) outliers start: 44 outliers final: 33 residues processed: 207 average time/residue: 0.2114 time to fit residues: 66.6519 Evaluate side-chains 197 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 160 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 702 ASP Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 771 MET Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 953 THR Chi-restraints excluded: chain A residue 968 ARG Chi-restraints excluded: chain A residue 1011 GLN Chi-restraints excluded: chain A residue 1099 GLU Chi-restraints excluded: chain A residue 1106 LEU Chi-restraints excluded: chain A residue 1116 ASP Chi-restraints excluded: chain A residue 1120 LEU Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1293 MET Chi-restraints excluded: chain A residue 1309 ASN Chi-restraints excluded: chain A residue 1336 HIS Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain A residue 1357 PHE 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 1406 ASN 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 103 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 346 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 58 optimal weight: 8.9990 chunk 87 optimal weight: 10.0000 chunk 44 optimal weight: 8.9990 chunk 28 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 72 optimal weight: 10.0000 chunk 13 optimal weight: 0.0170 chunk 115 optimal weight: 0.4980 chunk 133 optimal weight: 7.9990 chunk 140 optimal weight: 4.9990 overall best weight: 2.1024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.3253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12761 Z= 0.198 Angle : 0.663 13.040 17325 Z= 0.328 Chirality : 0.045 0.291 1974 Planarity : 0.004 0.059 2177 Dihedral : 7.320 75.799 2031 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 3.41 % Allowed : 20.79 % Favored : 75.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.22), residues: 1520 helix: 0.38 (0.21), residues: 626 sheet: -0.37 (0.39), residues: 192 loop : -1.72 (0.24), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1395 HIS 0.003 0.001 HIS B 131 PHE 0.023 0.002 PHE A1241 TYR 0.016 0.001 TYR A 239 ARG 0.005 0.000 ARG A1009 *********************** 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 213 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 167 time to evaluate : 1.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 TYR cc_start: 0.8443 (m-10) cc_final: 0.8240 (m-10) REVERT: A 314 ARG cc_start: 0.8707 (ttt-90) cc_final: 0.7997 (tpt-90) REVERT: A 525 SER cc_start: 0.8666 (t) cc_final: 0.8163 (p) REVERT: A 566 MET cc_start: 0.7896 (tpp) cc_final: 0.7475 (tpp) REVERT: A 702 ASP cc_start: 0.8283 (OUTLIER) cc_final: 0.7932 (t0) REVERT: A 722 MET cc_start: 0.7440 (mtm) cc_final: 0.7059 (ptt) REVERT: A 968 ARG cc_start: 0.9272 (OUTLIER) cc_final: 0.8967 (ppt170) REVERT: A 1011 GLN cc_start: 0.8615 (OUTLIER) cc_final: 0.8327 (mp10) REVERT: A 1120 LEU cc_start: 0.9368 (OUTLIER) cc_final: 0.9146 (pp) REVERT: A 1200 MET cc_start: 0.8802 (mmt) cc_final: 0.8233 (mmt) REVERT: A 1241 PHE cc_start: 0.8667 (t80) cc_final: 0.8391 (t80) REVERT: A 1372 MET cc_start: 0.8809 (tmm) cc_final: 0.7989 (mmt) REVERT: A 1378 ASP cc_start: 0.8531 (p0) cc_final: 0.7904 (t70) REVERT: A 1446 PHE cc_start: 0.7312 (t80) cc_final: 0.6980 (t80) REVERT: B 176 ASN cc_start: 0.8291 (t0) cc_final: 0.7764 (m-40) REVERT: B 391 ILE cc_start: 0.9146 (tp) cc_final: 0.8787 (tt) REVERT: B 395 PHE cc_start: 0.8177 (m-80) cc_final: 0.7537 (m-80) outliers start: 46 outliers final: 37 residues processed: 196 average time/residue: 0.2030 time to fit residues: 61.9081 Evaluate side-chains 200 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 159 time to evaluate : 1.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 520 HIS Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 702 ASP Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 771 MET Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 968 ARG Chi-restraints excluded: chain A residue 1011 GLN Chi-restraints excluded: chain A residue 1097 LEU Chi-restraints excluded: chain A residue 1099 GLU Chi-restraints excluded: chain A residue 1106 LEU Chi-restraints excluded: chain A residue 1116 ASP Chi-restraints excluded: chain A residue 1120 LEU Chi-restraints excluded: chain A residue 1227 LEU Chi-restraints excluded: chain A residue 1293 MET Chi-restraints excluded: chain A residue 1309 ASN Chi-restraints excluded: chain A residue 1336 HIS Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain A residue 1357 PHE 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 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 103 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 359 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 5.9990 chunk 136 optimal weight: 9.9990 chunk 140 optimal weight: 0.8980 chunk 82 optimal weight: 10.0000 chunk 59 optimal weight: 9.9990 chunk 107 optimal weight: 8.9990 chunk 41 optimal weight: 10.0000 chunk 123 optimal weight: 5.9990 chunk 129 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.3480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12761 Z= 0.229 Angle : 0.676 10.016 17325 Z= 0.334 Chirality : 0.046 0.266 1974 Planarity : 0.004 0.061 2177 Dihedral : 7.189 72.394 2031 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 16.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 3.56 % Allowed : 20.64 % Favored : 75.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.22), residues: 1520 helix: 0.40 (0.21), residues: 620 sheet: -0.62 (0.38), residues: 199 loop : -1.71 (0.24), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1395 HIS 0.002 0.001 HIS B 186 PHE 0.023 0.002 PHE A1234 TYR 0.016 0.001 TYR A 619 ARG 0.002 0.000 ARG A1226 *********************** 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 205 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 157 time to evaluate : 1.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 TYR cc_start: 0.8358 (m-10) cc_final: 0.8080 (m-10) REVERT: A 314 ARG cc_start: 0.8751 (ttt-90) cc_final: 0.8074 (tpt-90) REVERT: A 477 TYR cc_start: 0.9087 (m-80) cc_final: 0.8841 (m-10) REVERT: A 525 SER cc_start: 0.8679 (t) cc_final: 0.8169 (p) REVERT: A 566 MET cc_start: 0.7937 (tpp) cc_final: 0.7497 (tpp) REVERT: A 607 ILE cc_start: 0.9080 (tp) cc_final: 0.8869 (tp) REVERT: A 722 MET cc_start: 0.7436 (mtm) cc_final: 0.7052 (ptt) REVERT: A 968 ARG cc_start: 0.9290 (OUTLIER) cc_final: 0.8958 (ppt170) REVERT: A 1011 GLN cc_start: 0.8698 (OUTLIER) cc_final: 0.8341 (mp10) REVERT: A 1012 ASP cc_start: 0.9082 (p0) cc_final: 0.8862 (p0) REVERT: A 1026 ILE cc_start: 0.9168 (mp) cc_final: 0.8904 (mm) REVERT: A 1120 LEU cc_start: 0.9372 (OUTLIER) cc_final: 0.9145 (pp) REVERT: A 1167 MET cc_start: 0.7082 (mmm) cc_final: 0.6508 (mmm) REVERT: A 1200 MET cc_start: 0.8764 (mmt) cc_final: 0.8207 (mmt) REVERT: A 1241 PHE cc_start: 0.8707 (t80) cc_final: 0.8348 (t80) REVERT: A 1339 MET cc_start: 0.7729 (mmp) cc_final: 0.7055 (mmp) REVERT: A 1378 ASP cc_start: 0.8542 (p0) cc_final: 0.8190 (p0) REVERT: A 1386 CYS cc_start: 0.8792 (m) cc_final: 0.8367 (p) REVERT: A 1446 PHE cc_start: 0.7305 (t80) cc_final: 0.6978 (t80) REVERT: A 1456 GLU cc_start: 0.9034 (tm-30) cc_final: 0.8578 (tm-30) REVERT: B 102 GLU cc_start: 0.8407 (pp20) cc_final: 0.7664 (pp20) REVERT: B 176 ASN cc_start: 0.8356 (t0) cc_final: 0.7844 (m-40) REVERT: B 391 ILE cc_start: 0.9133 (tp) cc_final: 0.8783 (tt) REVERT: B 395 PHE cc_start: 0.8207 (m-80) cc_final: 0.7554 (m-80) outliers start: 48 outliers final: 37 residues processed: 189 average time/residue: 0.2082 time to fit residues: 61.6237 Evaluate side-chains 193 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 153 time to evaluate : 1.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 520 HIS Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 771 MET Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 968 ARG Chi-restraints excluded: chain A residue 1011 GLN Chi-restraints excluded: chain A residue 1097 LEU Chi-restraints excluded: chain A residue 1099 GLU Chi-restraints excluded: chain A residue 1106 LEU Chi-restraints excluded: chain A residue 1116 ASP Chi-restraints excluded: chain A residue 1120 LEU Chi-restraints excluded: chain A residue 1227 LEU Chi-restraints excluded: chain A residue 1293 MET Chi-restraints excluded: chain A residue 1298 LEU Chi-restraints excluded: chain A residue 1309 ASN Chi-restraints excluded: chain A residue 1336 HIS Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain A residue 1361 ILE Chi-restraints excluded: chain A residue 1370 VAL Chi-restraints excluded: chain A residue 1387 LEU Chi-restraints excluded: chain A residue 1391 VAL Chi-restraints excluded: chain A residue 1434 LEU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 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 367 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 88 optimal weight: 0.7980 chunk 68 optimal weight: 7.9990 chunk 100 optimal weight: 2.9990 chunk 151 optimal weight: 20.0000 chunk 139 optimal weight: 7.9990 chunk 120 optimal weight: 5.9990 chunk 12 optimal weight: 20.0000 chunk 93 optimal weight: 2.9990 chunk 73 optimal weight: 10.0000 chunk 95 optimal weight: 0.8980 chunk 128 optimal weight: 5.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.3700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12761 Z= 0.224 Angle : 0.683 14.491 17325 Z= 0.337 Chirality : 0.046 0.316 1974 Planarity : 0.004 0.061 2177 Dihedral : 7.019 69.202 2031 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 17.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 3.12 % Allowed : 21.23 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.22), residues: 1520 helix: 0.31 (0.21), residues: 630 sheet: -0.61 (0.38), residues: 198 loop : -1.82 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1395 HIS 0.002 0.001 HIS A 455 PHE 0.024 0.002 PHE A1234 TYR 0.015 0.001 TYR A 619 ARG 0.002 0.000 ARG A1009 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 151 time to evaluate : 1.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 TYR cc_start: 0.8353 (m-10) cc_final: 0.8149 (m-10) REVERT: A 314 ARG cc_start: 0.8756 (ttt-90) cc_final: 0.8101 (tpt-90) REVERT: A 477 TYR cc_start: 0.9084 (m-80) cc_final: 0.8843 (m-10) REVERT: A 525 SER cc_start: 0.8699 (t) cc_final: 0.8206 (p) REVERT: A 566 MET cc_start: 0.7907 (tpp) cc_final: 0.7481 (tpp) REVERT: A 607 ILE cc_start: 0.9122 (tp) cc_final: 0.8907 (tp) REVERT: A 722 MET cc_start: 0.7336 (mtm) cc_final: 0.6973 (ptt) REVERT: A 968 ARG cc_start: 0.9289 (OUTLIER) cc_final: 0.8953 (ppt170) REVERT: A 1011 GLN cc_start: 0.8723 (OUTLIER) cc_final: 0.8378 (mp10) REVERT: A 1012 ASP cc_start: 0.9035 (p0) cc_final: 0.8809 (p0) REVERT: A 1026 ILE cc_start: 0.9182 (mp) cc_final: 0.8914 (mm) REVERT: A 1120 LEU cc_start: 0.9371 (OUTLIER) cc_final: 0.9143 (pp) REVERT: A 1200 MET cc_start: 0.8767 (mmt) cc_final: 0.8194 (mmt) REVERT: A 1241 PHE cc_start: 0.8717 (t80) cc_final: 0.8432 (t80) REVERT: A 1339 MET cc_start: 0.7812 (mmp) cc_final: 0.7149 (mmp) REVERT: A 1372 MET cc_start: 0.8704 (ppp) cc_final: 0.8064 (mmt) REVERT: A 1378 ASP cc_start: 0.8503 (p0) cc_final: 0.8146 (p0) REVERT: A 1446 PHE cc_start: 0.7333 (t80) cc_final: 0.6985 (t80) REVERT: A 1456 GLU cc_start: 0.9048 (tm-30) cc_final: 0.8580 (tm-30) REVERT: B 102 GLU cc_start: 0.8431 (pp20) cc_final: 0.7970 (pp20) REVERT: B 176 ASN cc_start: 0.8386 (t0) cc_final: 0.7890 (m-40) REVERT: B 391 ILE cc_start: 0.9144 (tp) cc_final: 0.8802 (tt) REVERT: B 395 PHE cc_start: 0.8213 (m-80) cc_final: 0.7587 (m-80) outliers start: 42 outliers final: 35 residues processed: 180 average time/residue: 0.2093 time to fit residues: 58.0979 Evaluate side-chains 188 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 150 time to evaluate : 1.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 520 HIS Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 771 MET Chi-restraints excluded: chain A residue 968 ARG Chi-restraints excluded: chain A residue 1011 GLN Chi-restraints excluded: chain A residue 1097 LEU Chi-restraints excluded: chain A residue 1099 GLU Chi-restraints excluded: chain A residue 1106 LEU Chi-restraints excluded: chain A residue 1116 ASP Chi-restraints excluded: chain A residue 1120 LEU Chi-restraints excluded: chain A residue 1227 LEU Chi-restraints excluded: chain A residue 1293 MET Chi-restraints excluded: chain A residue 1309 ASN Chi-restraints excluded: chain A residue 1336 HIS Chi-restraints excluded: chain A residue 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 B residue 71 THR Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 407 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 36 optimal weight: 5.9990 chunk 111 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 33 optimal weight: 10.0000 chunk 120 optimal weight: 5.9990 chunk 50 optimal weight: 7.9990 chunk 124 optimal weight: 3.9990 chunk 15 optimal weight: 0.4980 chunk 22 optimal weight: 9.9990 chunk 106 optimal weight: 0.6980 chunk 6 optimal weight: 7.9990 overall best weight: 2.6386 ------------------------------------------------------------------------------- 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** ** A1208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 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 = 0.3985 r_free = 0.3985 target = 0.087158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.069196 restraints weight = 57931.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.071015 restraints weight = 34643.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.072211 restraints weight = 23671.967| |-----------------------------------------------------------------------------| r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.3838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12761 Z= 0.227 Angle : 0.691 14.308 17325 Z= 0.340 Chirality : 0.046 0.314 1974 Planarity : 0.004 0.059 2177 Dihedral : 6.899 66.168 2031 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 17.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 3.04 % Allowed : 21.16 % Favored : 75.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.22), residues: 1520 helix: 0.34 (0.21), residues: 624 sheet: -0.68 (0.37), residues: 200 loop : -1.78 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1395 HIS 0.003 0.001 HIS A 455 PHE 0.024 0.002 PHE A1234 TYR 0.016 0.001 TYR A 619 ARG 0.002 0.000 ARG A1226 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2593.76 seconds wall clock time: 47 minutes 24.75 seconds (2844.75 seconds total)