Starting phenix.real_space_refine on Thu Jun 12 21:37:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jsl_36622/06_2025/8jsl_36622.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jsl_36622/06_2025/8jsl_36622.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jsl_36622/06_2025/8jsl_36622.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jsl_36622/06_2025/8jsl_36622.map" model { file = "/net/cci-nas-00/data/ceres_data/8jsl_36622/06_2025/8jsl_36622.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jsl_36622/06_2025/8jsl_36622.cif" } resolution = 2.95 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 10 5.49 5 S 76 5.16 5 C 8953 2.51 5 N 2385 2.21 5 O 2644 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 14069 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 10897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1362, 10897 Classifications: {'peptide': 1362} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 2, 'PTRANS': 70, 'TRANS': 1289} Chain breaks: 3 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "B" Number of atoms: 1799 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 235, 1793 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 17, 'TRANS': 217} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 235, 1793 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 17, 'TRANS': 217} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 1823 Chain: "C" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 533 Classifications: {'peptide': 72} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 66} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 303 Classifications: {'peptide': 40} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} 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: "E" Number of atoms: 324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 324 Classifications: {'peptide': 42} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "G" Number of atoms: 212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 212 Classifications: {'RNA': 10} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 3, 'rna3p_pur': 2, 'rna3p_pyr': 3} Link IDs: {'rna2p': 5, 'rna3p': 4} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 9157 SG CYS A1150 47.347 43.269 98.527 1.00 95.98 S ATOM 9179 SG CYS A1153 50.110 40.569 98.102 1.00 97.97 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ASER B 266 " occ=0.67 ... (10 atoms not shown) pdb=" OG BSER B 266 " occ=0.33 Time building chain proxies: 9.79, per 1000 atoms: 0.70 Number of scatterers: 14069 At special positions: 0 Unit cell: (144.42, 133.63, 114.54, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 76 16.00 P 10 15.00 O 2644 8.00 N 2385 7.00 C 8953 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.99 Conformation dependent library (CDL) restraints added in 2.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2301 " pdb="ZN ZN A2301 " - pdb=" ND1 HIS A1345 " pdb="ZN ZN A2301 " - pdb=" NE2 HIS A1347 " pdb="ZN ZN A2301 " - pdb=" SG CYS A1153 " pdb="ZN ZN A2301 " - pdb=" SG CYS A1150 " Number of angles added : 2 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3336 Finding SS restraints... Secondary structure from input PDB file: 89 helices and 8 sheets defined 56.8% alpha, 4.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.81 Creating SS restraints... Processing helix chain 'A' and resid 21 through 30 removed outlier: 3.613A pdb=" N VAL A 25 " --> pdb=" O GLN A 21 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG A 27 " --> pdb=" O ASP A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 43 Processing helix chain 'A' and resid 51 through 55 removed outlier: 3.676A pdb=" N LYS A 54 " --> pdb=" O TYR A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 63 Processing helix chain 'A' and resid 72 through 75 removed outlier: 3.727A pdb=" N PHE A 75 " --> pdb=" O PRO A 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 72 through 75' Processing helix chain 'A' and resid 76 through 83 Processing helix chain 'A' and resid 100 through 122 Processing helix chain 'A' and resid 132 through 142 Processing helix chain 'A' and resid 145 through 163 removed outlier: 3.510A pdb=" N MET A 149 " --> pdb=" O PHE A 145 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N PHE A 150 " --> pdb=" O LEU A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 210 removed outlier: 3.534A pdb=" N MET A 210 " --> pdb=" O HIS A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 223 removed outlier: 4.023A pdb=" N LYS A 219 " --> pdb=" O THR A 215 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU A 220 " --> pdb=" O SER A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 261 removed outlier: 3.549A pdb=" N ILE A 238 " --> pdb=" O ALA A 234 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU A 258 " --> pdb=" O SER A 254 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N VAL A 259 " --> pdb=" O LYS A 255 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU A 260 " --> pdb=" O ILE A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 288 Processing helix chain 'A' and resid 291 through 296 Processing helix chain 'A' and resid 297 through 308 Processing helix chain 'A' and resid 317 through 334 Processing helix chain 'A' and resid 341 through 348 Processing helix chain 'A' and resid 349 through 357 Processing helix chain 'A' and resid 361 through 369 Processing helix chain 'A' and resid 381 through 391 Processing helix chain 'A' and resid 400 through 422 removed outlier: 3.503A pdb=" N ILE A 404 " --> pdb=" O ARG A 400 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER A 422 " --> pdb=" O HIS A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 436 Processing helix chain 'A' and resid 438 through 446 removed outlier: 4.390A pdb=" N TYR A 442 " --> pdb=" O GLY A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 463 Processing helix chain 'A' and resid 477 through 482 removed outlier: 3.864A pdb=" N ILE A 480 " --> pdb=" O ASP A 477 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE A 482 " --> pdb=" O SER A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 498 removed outlier: 3.530A pdb=" N TRP A 494 " --> pdb=" O ARG A 491 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N ASP A 495 " --> pdb=" O THR A 492 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N VAL A 497 " --> pdb=" O TRP A 494 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N PHE A 498 " --> pdb=" O ASP A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 504 Processing helix chain 'A' and resid 516 through 521 removed outlier: 3.599A pdb=" N LEU A 521 " --> pdb=" O PRO A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 537 Processing helix chain 'A' and resid 538 through 542 Processing helix chain 'A' and resid 567 through 584 removed outlier: 3.582A pdb=" N ASP A 583 " --> pdb=" O ALA A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 600 Processing helix chain 'A' and resid 601 through 610 Processing helix chain 'A' and resid 634 through 640 removed outlier: 4.156A pdb=" N ASN A 637 " --> pdb=" O GLU A 634 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N PHE A 640 " --> pdb=" O ASN A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 656 Proline residue: A 647 - end of helix removed outlier: 3.655A pdb=" N TYR A 656 " --> pdb=" O CYS A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 669 Processing helix chain 'A' and resid 688 through 692 removed outlier: 4.071A pdb=" N ARG A 691 " --> pdb=" O LEU A 688 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ASN A 692 " --> pdb=" O GLU A 689 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 688 through 692' Processing helix chain 'A' and resid 712 through 731 removed outlier: 3.527A pdb=" N TRP A 716 " --> pdb=" O GLN A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 783 removed outlier: 4.232A pdb=" N GLN A 763 " --> pdb=" O ASP A 759 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N CYS A 783 " --> pdb=" O VAL A 779 " (cutoff:3.500A) Processing helix chain 'A' and resid 815 through 820 Processing helix chain 'A' and resid 832 through 850 removed outlier: 3.877A pdb=" N GLU A 850 " --> pdb=" O ARG A 846 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 875 removed outlier: 3.728A pdb=" N PHE A 866 " --> pdb=" O ALA A 862 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE A 867 " --> pdb=" O PHE A 863 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 889 removed outlier: 3.732A pdb=" N LEU A 888 " --> pdb=" O ASP A 884 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR A 889 " --> pdb=" O LEU A 885 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 884 through 889' Processing helix chain 'A' and resid 895 through 903 Processing helix chain 'A' and resid 906 through 910 Processing helix chain 'A' and resid 916 through 921 Processing helix chain 'A' and resid 927 through 943 Processing helix chain 'A' and resid 948 through 955 removed outlier: 4.277A pdb=" N LYS A 955 " --> pdb=" O PRO A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 961 through 968 Processing helix chain 'A' and resid 974 through 978 removed outlier: 3.648A pdb=" N GLN A 978 " --> pdb=" O PRO A 975 " (cutoff:3.500A) Processing helix chain 'A' and resid 980 through 994 Processing helix chain 'A' and resid 1000 through 1005 Processing helix chain 'A' and resid 1008 through 1021 Processing helix chain 'A' and resid 1027 through 1036 removed outlier: 3.827A pdb=" N ALA A1031 " --> pdb=" O MET A1027 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER A1036 " --> pdb=" O ALA A1032 " (cutoff:3.500A) Processing helix chain 'A' and resid 1038 through 1048 removed outlier: 3.509A pdb=" N GLY A1048 " --> pdb=" O LEU A1044 " (cutoff:3.500A) Processing helix chain 'A' and resid 1052 through 1059 removed outlier: 3.530A pdb=" N LEU A1056 " --> pdb=" O GLY A1052 " (cutoff:3.500A) Processing helix chain 'A' and resid 1059 through 1064 Processing helix chain 'A' and resid 1069 through 1085 removed outlier: 3.578A pdb=" N ARG A1073 " --> pdb=" O PRO A1069 " (cutoff:3.500A) Processing helix chain 'A' and resid 1105 through 1117 Processing helix chain 'A' and resid 1134 through 1137 Processing helix chain 'A' and resid 1150 through 1155 Processing helix chain 'A' and resid 1182 through 1184 No H-bonds generated for 'chain 'A' and resid 1182 through 1184' Processing helix chain 'A' and resid 1213 through 1230 Processing helix chain 'A' and resid 1235 through 1245 removed outlier: 4.062A pdb=" N ILE A1240 " --> pdb=" O SER A1236 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LYS A1241 " --> pdb=" O ASP A1237 " (cutoff:3.500A) Proline residue: A1242 - end of helix Processing helix chain 'A' and resid 1254 through 1259 removed outlier: 3.912A pdb=" N MET A1258 " --> pdb=" O GLU A1254 " (cutoff:3.500A) Processing helix chain 'A' and resid 1266 through 1274 Processing helix chain 'A' and resid 1287 through 1290 removed outlier: 3.551A pdb=" N THR A1290 " --> pdb=" O ASN A1287 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1287 through 1290' Processing helix chain 'A' and resid 1296 through 1300 Processing helix chain 'A' and resid 1315 through 1331 Processing helix chain 'A' and resid 1335 through 1339 Processing helix chain 'B' and resid 107 through 119 Processing helix chain 'B' and resid 120 through 122 No H-bonds generated for 'chain 'B' and resid 120 through 122' Processing helix chain 'B' and resid 123 through 149 removed outlier: 4.025A pdb=" N THR B 127 " --> pdb=" O ASP B 123 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N SER B 130 " --> pdb=" O LYS B 126 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU B 131 " --> pdb=" O THR B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 165 removed outlier: 3.683A pdb=" N ALA B 164 " --> pdb=" O GLU B 160 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLU B 165 " --> pdb=" O ALA B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 187 Processing helix chain 'B' and resid 193 through 205 Processing helix chain 'B' and resid 220 through 232 removed outlier: 3.544A pdb=" N HIS B 231 " --> pdb=" O ILE B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 254 removed outlier: 3.835A pdb=" N GLN B 241 " --> pdb=" O THR B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 270 removed outlier: 3.546A pdb=" N GLY B 270 " --> pdb=" O ASER B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 284 Processing helix chain 'B' and resid 285 through 288 Processing helix chain 'B' and resid 304 through 309 removed outlier: 4.342A pdb=" N LYS B 309 " --> pdb=" O ALA B 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 119 Processing helix chain 'C' and resid 120 through 143 removed outlier: 3.589A pdb=" N SER C 129 " --> pdb=" O ALA C 125 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER C 130 " --> pdb=" O LYS C 126 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASP C 143 " --> pdb=" O VAL C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 164 Processing helix chain 'D' and resid 111 through 116 removed outlier: 3.603A pdb=" N GLU D 115 " --> pdb=" O THR D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 146 removed outlier: 3.600A pdb=" N TYR D 122 " --> pdb=" O LEU D 118 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASP D 123 " --> pdb=" O LYS D 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 117 Processing helix chain 'E' and resid 118 through 144 removed outlier: 3.813A pdb=" N LEU E 144 " --> pdb=" O ALA E 140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 173 through 177 Processing sheet with id=AA2, first strand: chain 'A' and resid 398 through 399 removed outlier: 3.859A pdb=" N SER B 174 " --> pdb=" O THR C 148 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 549 through 552 Processing sheet with id=AA4, first strand: chain 'A' and resid 734 through 740 removed outlier: 3.837A pdb=" N LYS A 734 " --> pdb=" O LEU A 749 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 798 through 801 Processing sheet with id=AA6, first strand: chain 'A' and resid 1139 through 1141 Processing sheet with id=AA7, first strand: chain 'A' and resid 1175 through 1176 removed outlier: 3.805A pdb=" N SER A1175 " --> pdb=" O ILE A1187 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 294 through 296 659 hydrogen bonds defined for protein. 1852 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: 4.79 Time building geometry restraints manager: 4.62 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: 4310 1.34 - 1.45: 2098 1.45 - 1.57: 7877 1.57 - 1.69: 19 1.69 - 1.81: 111 Bond restraints: 14415 Sorted by residual: bond pdb=" N TYR A1088 " pdb=" CA TYR A1088 " ideal model delta sigma weight residual 1.457 1.495 -0.037 1.29e-02 6.01e+03 8.42e+00 bond pdb=" N LEU A1089 " pdb=" CA LEU A1089 " ideal model delta sigma weight residual 1.460 1.495 -0.035 1.54e-02 4.22e+03 5.18e+00 bond pdb=" N ASP A1090 " pdb=" CA ASP A1090 " ideal model delta sigma weight residual 1.457 1.486 -0.029 1.29e-02 6.01e+03 4.96e+00 bond pdb=" N GLU C 178 " pdb=" CA GLU C 178 " ideal model delta sigma weight residual 1.459 1.487 -0.027 1.23e-02 6.61e+03 4.95e+00 bond pdb=" CA TYR A1088 " pdb=" C TYR A1088 " ideal model delta sigma weight residual 1.523 1.546 -0.023 1.34e-02 5.57e+03 2.92e+00 ... (remaining 14410 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 19305 1.88 - 3.76: 281 3.76 - 5.65: 33 5.65 - 7.53: 10 7.53 - 9.41: 2 Bond angle restraints: 19631 Sorted by residual: angle pdb=" N TYR A 51 " pdb=" CA TYR A 51 " pdb=" C TYR A 51 " ideal model delta sigma weight residual 114.56 107.58 6.98 1.27e+00 6.20e-01 3.02e+01 angle pdb=" CA LEU A1089 " pdb=" C LEU A1089 " pdb=" O LEU A1089 " ideal model delta sigma weight residual 122.03 118.02 4.01 1.17e+00 7.31e-01 1.17e+01 angle pdb=" C SER A 750 " pdb=" N VAL A 751 " pdb=" CA VAL A 751 " ideal model delta sigma weight residual 121.97 127.82 -5.85 1.80e+00 3.09e-01 1.06e+01 angle pdb=" C GLU B 212 " pdb=" N ASN B 213 " pdb=" CA ASN B 213 " ideal model delta sigma weight residual 121.54 127.36 -5.82 1.91e+00 2.74e-01 9.30e+00 angle pdb=" CA TYR A 51 " pdb=" C TYR A 51 " pdb=" N ARG A 52 " ideal model delta sigma weight residual 119.26 115.86 3.40 1.14e+00 7.69e-01 8.88e+00 ... (remaining 19626 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.06: 8512 34.06 - 68.12: 189 68.12 - 102.19: 18 102.19 - 136.25: 0 136.25 - 170.31: 1 Dihedral angle restraints: 8720 sinusoidal: 3572 harmonic: 5148 Sorted by residual: dihedral pdb=" O4' C G 7 " pdb=" C1' C G 7 " pdb=" N1 C G 7 " pdb=" C2 C G 7 " ideal model delta sinusoidal sigma weight residual 232.00 61.69 170.31 1 1.70e+01 3.46e-03 6.60e+01 dihedral pdb=" CA SER A 431 " pdb=" C SER A 431 " pdb=" N ASP A 432 " pdb=" CA ASP A 432 " ideal model delta harmonic sigma weight residual 180.00 157.20 22.80 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CG ARG A 870 " pdb=" CD ARG A 870 " pdb=" NE ARG A 870 " pdb=" CZ ARG A 870 " ideal model delta sinusoidal sigma weight residual 180.00 -136.01 -43.99 2 1.50e+01 4.44e-03 1.03e+01 ... (remaining 8717 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1541 0.035 - 0.069: 501 0.069 - 0.104: 150 0.104 - 0.139: 41 0.139 - 0.173: 3 Chirality restraints: 2236 Sorted by residual: chirality pdb=" CB ILE A 482 " pdb=" CA ILE A 482 " pdb=" CG1 ILE A 482 " pdb=" CG2 ILE A 482 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.49e-01 chirality pdb=" CA ASN A 681 " pdb=" N ASN A 681 " pdb=" C ASN A 681 " pdb=" CB ASN A 681 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.03e-01 chirality pdb=" CA LEU A 633 " pdb=" N LEU A 633 " pdb=" C LEU A 633 " pdb=" CB LEU A 633 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.72e-01 ... (remaining 2233 not shown) Planarity restraints: 2476 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A1085 " 0.011 2.00e-02 2.50e+03 1.34e-02 4.47e+00 pdb=" CG TRP A1085 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 TRP A1085 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP A1085 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A1085 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A1085 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A1085 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1085 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1085 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A1085 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A1145 " -0.025 5.00e-02 4.00e+02 3.75e-02 2.25e+00 pdb=" N PRO A1146 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO A1146 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A1146 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 550 " 0.012 2.00e-02 2.50e+03 1.09e-02 2.08e+00 pdb=" CG PHE A 550 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE A 550 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE A 550 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE A 550 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 550 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A 550 " 0.002 2.00e-02 2.50e+03 ... (remaining 2473 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1248 2.74 - 3.28: 13515 3.28 - 3.82: 21991 3.82 - 4.36: 25536 4.36 - 4.90: 46230 Nonbonded interactions: 108520 Sorted by model distance: nonbonded pdb=" OE2 GLU A 918 " pdb=" OH TYR A 922 " model vdw 2.203 3.040 nonbonded pdb=" ND2 ASN A1249 " pdb=" OH TYR A1381 " model vdw 2.255 3.120 nonbonded pdb=" O ARG D 110 " pdb=" OG SER D 113 " model vdw 2.259 3.040 nonbonded pdb=" O CYS B 275 " pdb=" NE2 GLN B 279 " model vdw 2.266 3.120 nonbonded pdb=" O GLU A 643 " pdb=" OG1 THR B 148 " model vdw 2.270 3.040 ... (remaining 108515 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 'D' and (resid 110 through 118 or (resid 119 and (name N or name CA or na \ me C or name O or name CB )) or resid 120 through 146)) selection = (chain 'E' and (resid 110 through 132 or (resid 133 and (name N or name CA or na \ me C or name O or name CB )) or resid 134 through 146)) } 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=0.33 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.640 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 39.060 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.070 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:11.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 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 : 0.003 0.037 14419 Z= 0.123 Angle : 0.570 20.030 19633 Z= 0.291 Chirality : 0.039 0.173 2236 Planarity : 0.004 0.037 2476 Dihedral : 14.700 170.311 5384 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.46 % Allowed : 6.17 % Favored : 93.37 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.78 (0.21), residues: 1738 helix: 1.99 (0.19), residues: 850 sheet: 1.43 (0.60), residues: 81 loop : -1.27 (0.22), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A1085 HIS 0.005 0.001 HIS A 5 PHE 0.025 0.001 PHE A 550 TYR 0.019 0.001 TYR A 636 ARG 0.004 0.000 ARG A 433 Details of bonding type rmsd hydrogen bonds : bond 0.16684 ( 659) hydrogen bonds : angle 4.53574 ( 1852) metal coordination : bond 0.00494 ( 4) metal coordination : angle 14.18950 ( 2) covalent geometry : bond 0.00252 (14415) covalent geometry : angle 0.55146 (19631) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 233 time to evaluate : 1.620 Fit side-chains revert: symmetry clash REVERT: A 154 ASP cc_start: 0.7731 (m-30) cc_final: 0.7455 (m-30) REVERT: A 238 ILE cc_start: 0.8657 (mm) cc_final: 0.8194 (mm) REVERT: A 242 ASP cc_start: 0.8049 (m-30) cc_final: 0.7818 (m-30) REVERT: A 990 ARG cc_start: 0.7810 (tpt170) cc_final: 0.7485 (tpm-80) REVERT: A 1064 ASN cc_start: 0.7785 (m-40) cc_final: 0.7401 (p0) REVERT: A 1340 GLN cc_start: 0.7924 (pm20) cc_final: 0.7617 (pm20) REVERT: B 165 GLU cc_start: 0.8024 (pm20) cc_final: 0.7777 (pm20) outliers start: 0 outliers final: 1 residues processed: 233 average time/residue: 1.4407 time to fit residues: 365.0153 Evaluate side-chains 175 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 174 time to evaluate : 1.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 2.9990 chunk 132 optimal weight: 8.9990 chunk 73 optimal weight: 0.5980 chunk 45 optimal weight: 0.4980 chunk 89 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 137 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 83 optimal weight: 0.5980 chunk 102 optimal weight: 3.9990 chunk 158 optimal weight: 9.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 HIS A 97 GLN A 743 ASN A 978 GLN A1120 HIS A1253 GLN ** A1269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1333 ASN A1342 ASN B 279 GLN E 132 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.136037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.095584 restraints weight = 24753.754| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 2.86 r_work: 0.2793 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2798 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2798 r_free = 0.2798 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2798 r_free = 0.2798 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2798 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.1056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 14419 Z= 0.159 Angle : 0.600 12.182 19633 Z= 0.306 Chirality : 0.041 0.151 2236 Planarity : 0.004 0.041 2476 Dihedral : 9.639 169.404 2061 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.63 % Favored : 93.03 % Rotamer: Outliers : 1.37 % Allowed : 9.52 % Favored : 89.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.76 (0.21), residues: 1738 helix: 1.90 (0.19), residues: 863 sheet: 1.45 (0.59), residues: 86 loop : -1.27 (0.22), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1085 HIS 0.005 0.001 HIS A 352 PHE 0.023 0.002 PHE A 550 TYR 0.016 0.001 TYR A 636 ARG 0.004 0.000 ARG A 491 Details of bonding type rmsd hydrogen bonds : bond 0.05657 ( 659) hydrogen bonds : angle 3.86007 ( 1852) metal coordination : bond 0.00949 ( 4) metal coordination : angle 5.67720 ( 2) covalent geometry : bond 0.00379 (14415) covalent geometry : angle 0.59705 (19631) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 196 time to evaluate : 1.508 Fit side-chains revert: symmetry clash REVERT: A 154 ASP cc_start: 0.8565 (m-30) cc_final: 0.8284 (m-30) REVERT: A 203 GLN cc_start: 0.8728 (OUTLIER) cc_final: 0.7682 (mp10) REVERT: A 242 ASP cc_start: 0.8786 (m-30) cc_final: 0.8553 (m-30) REVERT: A 518 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.7377 (mp0) REVERT: A 814 GLN cc_start: 0.8435 (OUTLIER) cc_final: 0.8053 (pt0) REVERT: A 990 ARG cc_start: 0.8408 (tpt170) cc_final: 0.8013 (tpm-80) REVERT: A 1064 ASN cc_start: 0.7520 (m-40) cc_final: 0.7032 (p0) REVERT: A 1340 GLN cc_start: 0.8219 (pm20) cc_final: 0.7575 (pm20) REVERT: B 165 GLU cc_start: 0.8120 (pm20) cc_final: 0.7837 (pm20) REVERT: C 168 GLN cc_start: 0.8628 (pt0) cc_final: 0.8424 (pt0) REVERT: E 132 ASN cc_start: 0.8624 (t0) cc_final: 0.8398 (t0) outliers start: 21 outliers final: 11 residues processed: 207 average time/residue: 1.4208 time to fit residues: 319.6360 Evaluate side-chains 192 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 178 time to evaluate : 1.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 203 GLN Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain A residue 518 GLU Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 814 GLN Chi-restraints excluded: chain A residue 963 ILE Chi-restraints excluded: chain A residue 1172 HIS Chi-restraints excluded: chain A residue 1229 VAL Chi-restraints excluded: chain A residue 1351 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 144 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 39 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 90 optimal weight: 0.0770 chunk 99 optimal weight: 4.9990 chunk 108 optimal weight: 5.9990 chunk 54 optimal weight: 0.6980 chunk 129 optimal weight: 0.5980 chunk 37 optimal weight: 0.0870 chunk 85 optimal weight: 0.5980 chunk 155 optimal weight: 5.9990 chunk 45 optimal weight: 0.6980 overall best weight: 0.4116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 HIS A 97 GLN A1120 HIS A1266 ASN A1269 HIS A1342 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.138537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.098357 restraints weight = 28235.138| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 3.20 r_work: 0.2825 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2819 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2819 r_free = 0.2819 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2819 r_free = 0.2819 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2819 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.1242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 14419 Z= 0.108 Angle : 0.545 11.243 19633 Z= 0.277 Chirality : 0.039 0.153 2236 Planarity : 0.004 0.038 2476 Dihedral : 9.262 170.228 2059 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.82 % Favored : 93.83 % Rotamer: Outliers : 1.37 % Allowed : 11.73 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.90 (0.21), residues: 1738 helix: 2.08 (0.19), residues: 858 sheet: 1.33 (0.58), residues: 86 loop : -1.23 (0.22), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1085 HIS 0.007 0.001 HIS A1269 PHE 0.016 0.001 PHE A 270 TYR 0.013 0.001 TYR A1381 ARG 0.007 0.000 ARG B 312 Details of bonding type rmsd hydrogen bonds : bond 0.04159 ( 659) hydrogen bonds : angle 3.69025 ( 1852) metal coordination : bond 0.00800 ( 4) metal coordination : angle 4.17887 ( 2) covalent geometry : bond 0.00229 (14415) covalent geometry : angle 0.54375 (19631) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 201 time to evaluate : 1.533 Fit side-chains revert: symmetry clash REVERT: A 154 ASP cc_start: 0.8551 (m-30) cc_final: 0.8257 (m-30) REVERT: A 203 GLN cc_start: 0.8697 (OUTLIER) cc_final: 0.7582 (mp10) REVERT: A 242 ASP cc_start: 0.8800 (m-30) cc_final: 0.8565 (m-30) REVERT: A 556 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.8248 (mt-10) REVERT: A 990 ARG cc_start: 0.8378 (tpt170) cc_final: 0.7954 (tpm-80) REVERT: A 1064 ASN cc_start: 0.7516 (m-40) cc_final: 0.6947 (p0) REVERT: A 1245 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7924 (tm-30) REVERT: A 1338 ASP cc_start: 0.8278 (t0) cc_final: 0.8029 (t0) REVERT: A 1340 GLN cc_start: 0.8173 (pm20) cc_final: 0.7613 (pm20) REVERT: B 339 LYS cc_start: 0.6967 (tppt) cc_final: 0.6380 (tppt) REVERT: E 132 ASN cc_start: 0.8577 (t0) cc_final: 0.8370 (t0) outliers start: 21 outliers final: 9 residues processed: 212 average time/residue: 1.2962 time to fit residues: 300.3683 Evaluate side-chains 201 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 190 time to evaluate : 1.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 203 GLN Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 963 ILE Chi-restraints excluded: chain A residue 1172 HIS Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain E residue 144 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 125 optimal weight: 10.0000 chunk 156 optimal weight: 8.9990 chunk 121 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 144 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 129 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 HIS A 97 GLN A 743 ASN A1091 HIS A1120 HIS A1253 GLN A1266 ASN A1269 HIS A1342 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.131279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.091138 restraints weight = 25057.001| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 2.79 r_work: 0.2706 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2722 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2722 r_free = 0.2722 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2722 r_free = 0.2722 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2722 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 14419 Z= 0.272 Angle : 0.684 11.046 19633 Z= 0.351 Chirality : 0.046 0.191 2236 Planarity : 0.005 0.046 2476 Dihedral : 9.591 167.902 2059 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.40 % Allowed : 7.32 % Favored : 92.28 % Rotamer: Outliers : 2.54 % Allowed : 12.91 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.54 (0.21), residues: 1738 helix: 1.73 (0.19), residues: 865 sheet: 1.27 (0.59), residues: 86 loop : -1.40 (0.22), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 664 HIS 0.007 0.002 HIS A 352 PHE 0.026 0.002 PHE A 548 TYR 0.029 0.002 TYR A 427 ARG 0.008 0.001 ARG B 312 Details of bonding type rmsd hydrogen bonds : bond 0.07269 ( 659) hydrogen bonds : angle 3.93555 ( 1852) metal coordination : bond 0.01362 ( 4) metal coordination : angle 7.38581 ( 2) covalent geometry : bond 0.00680 (14415) covalent geometry : angle 0.68038 (19631) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 191 time to evaluate : 1.747 Fit side-chains revert: symmetry clash REVERT: A 154 ASP cc_start: 0.8647 (m-30) cc_final: 0.8397 (m-30) REVERT: A 203 GLN cc_start: 0.8699 (OUTLIER) cc_final: 0.7549 (mp10) REVERT: A 242 ASP cc_start: 0.8819 (m-30) cc_final: 0.8562 (m-30) REVERT: A 406 GLU cc_start: 0.8866 (mm-30) cc_final: 0.8554 (mm-30) REVERT: A 518 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.7381 (mp0) REVERT: A 578 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7679 (tp30) REVERT: A 709 GLU cc_start: 0.7338 (OUTLIER) cc_final: 0.6682 (pm20) REVERT: A 990 ARG cc_start: 0.8529 (tpt170) cc_final: 0.8075 (tpm-80) REVERT: A 1013 ASP cc_start: 0.7897 (m-30) cc_final: 0.7358 (m-30) REVERT: A 1064 ASN cc_start: 0.7676 (m-40) cc_final: 0.7194 (p0) REVERT: A 1089 LEU cc_start: 0.8307 (mt) cc_final: 0.7714 (pt) REVERT: A 1245 GLU cc_start: 0.8133 (mm-30) cc_final: 0.7615 (tm-30) REVERT: A 1338 ASP cc_start: 0.8388 (t0) cc_final: 0.8012 (t0) REVERT: A 1340 GLN cc_start: 0.8246 (pm20) cc_final: 0.7760 (pm20) REVERT: B 165 GLU cc_start: 0.8082 (pm20) cc_final: 0.7800 (pm20) outliers start: 39 outliers final: 20 residues processed: 213 average time/residue: 1.8460 time to fit residues: 432.0801 Evaluate side-chains 205 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 181 time to evaluate : 2.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 203 GLN Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 444 LYS Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain A residue 518 GLU Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 578 GLU Chi-restraints excluded: chain A residue 628 SER Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 799 ILE Chi-restraints excluded: chain A residue 963 ILE Chi-restraints excluded: chain A residue 1172 HIS Chi-restraints excluded: chain A residue 1229 VAL Chi-restraints excluded: chain A residue 1334 THR Chi-restraints excluded: chain A residue 1351 CYS Chi-restraints excluded: chain A residue 1364 THR Chi-restraints excluded: chain B residue 126 LYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 141 LYS Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain E residue 144 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 172 optimal weight: 0.6980 chunk 84 optimal weight: 0.6980 chunk 135 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 151 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 86 optimal weight: 0.2980 chunk 127 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 HIS A 97 GLN A1091 HIS A1120 HIS A1266 ASN A1269 HIS A1342 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.135326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.092731 restraints weight = 33806.405| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 3.72 r_work: 0.2764 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2768 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2768 r_free = 0.2768 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2768 r_free = 0.2768 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2768 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14419 Z= 0.126 Angle : 0.577 10.252 19633 Z= 0.293 Chirality : 0.040 0.156 2236 Planarity : 0.004 0.038 2476 Dihedral : 9.450 168.554 2059 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.40 % Allowed : 5.59 % Favored : 94.01 % Rotamer: Outliers : 2.22 % Allowed : 14.34 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.81 (0.21), residues: 1738 helix: 2.02 (0.19), residues: 851 sheet: 1.20 (0.58), residues: 86 loop : -1.26 (0.22), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1019 HIS 0.004 0.001 HIS A 5 PHE 0.016 0.001 PHE A 548 TYR 0.013 0.001 TYR A 153 ARG 0.006 0.000 ARG B 312 Details of bonding type rmsd hydrogen bonds : bond 0.04790 ( 659) hydrogen bonds : angle 3.76343 ( 1852) metal coordination : bond 0.00928 ( 4) metal coordination : angle 4.86759 ( 2) covalent geometry : bond 0.00285 (14415) covalent geometry : angle 0.57447 (19631) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 191 time to evaluate : 1.471 Fit side-chains REVERT: A 154 ASP cc_start: 0.8631 (m-30) cc_final: 0.8385 (m-30) REVERT: A 203 GLN cc_start: 0.8701 (OUTLIER) cc_final: 0.7506 (mp10) REVERT: A 242 ASP cc_start: 0.8810 (m-30) cc_final: 0.8572 (m-30) REVERT: A 578 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7646 (tp30) REVERT: A 711 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7525 (mt) REVERT: A 990 ARG cc_start: 0.8501 (tpt170) cc_final: 0.8074 (tpm-80) REVERT: A 1013 ASP cc_start: 0.7845 (m-30) cc_final: 0.7308 (m-30) REVERT: A 1064 ASN cc_start: 0.7544 (m-40) cc_final: 0.7086 (p0) REVERT: A 1245 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7689 (tm-30) REVERT: A 1338 ASP cc_start: 0.8387 (t0) cc_final: 0.8046 (t0) REVERT: A 1340 GLN cc_start: 0.8265 (pm20) cc_final: 0.7744 (pm20) REVERT: B 118 LEU cc_start: 0.7314 (tt) cc_final: 0.7081 (tp) REVERT: B 339 LYS cc_start: 0.6933 (tppt) cc_final: 0.6209 (tppt) outliers start: 34 outliers final: 11 residues processed: 210 average time/residue: 1.4167 time to fit residues: 325.5601 Evaluate side-chains 199 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 185 time to evaluate : 1.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 203 GLN Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 578 GLU Chi-restraints excluded: chain A residue 637 ASN Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 963 ILE Chi-restraints excluded: chain A residue 1172 HIS Chi-restraints excluded: chain A residue 1229 VAL Chi-restraints excluded: chain A residue 1364 THR Chi-restraints excluded: chain C residue 141 LYS Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain E residue 139 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 4 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 120 optimal weight: 4.9990 chunk 72 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 chunk 138 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 89 optimal weight: 0.7980 chunk 141 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 HIS A 97 GLN ** A 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 743 ASN A1120 HIS ** A1266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1342 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.135773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.093611 restraints weight = 33878.718| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 3.64 r_work: 0.2775 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2781 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2781 r_free = 0.2781 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2781 r_free = 0.2781 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2781 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14419 Z= 0.123 Angle : 0.566 9.619 19633 Z= 0.285 Chirality : 0.040 0.171 2236 Planarity : 0.004 0.051 2476 Dihedral : 9.377 169.449 2059 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.40 % Allowed : 6.28 % Favored : 93.31 % Rotamer: Outliers : 2.15 % Allowed : 15.06 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.90 (0.21), residues: 1738 helix: 2.09 (0.19), residues: 853 sheet: 1.16 (0.58), residues: 86 loop : -1.21 (0.22), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1019 HIS 0.005 0.001 HIS B 166 PHE 0.016 0.001 PHE A 548 TYR 0.012 0.001 TYR A 153 ARG 0.011 0.000 ARG B 312 Details of bonding type rmsd hydrogen bonds : bond 0.04550 ( 659) hydrogen bonds : angle 3.67122 ( 1852) metal coordination : bond 0.00925 ( 4) metal coordination : angle 4.55364 ( 2) covalent geometry : bond 0.00282 (14415) covalent geometry : angle 0.56402 (19631) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 189 time to evaluate : 1.695 Fit side-chains REVERT: A 154 ASP cc_start: 0.8612 (m-30) cc_final: 0.8361 (m-30) REVERT: A 242 ASP cc_start: 0.8791 (m-30) cc_final: 0.8556 (m-30) REVERT: A 578 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7633 (tp30) REVERT: A 711 LEU cc_start: 0.8024 (OUTLIER) cc_final: 0.7543 (mt) REVERT: A 990 ARG cc_start: 0.8504 (tpt170) cc_final: 0.8062 (tpm-80) REVERT: A 1013 ASP cc_start: 0.7827 (m-30) cc_final: 0.7241 (m-30) REVERT: A 1064 ASN cc_start: 0.7527 (m-40) cc_final: 0.7064 (p0) REVERT: A 1338 ASP cc_start: 0.8415 (t0) cc_final: 0.8014 (t0) REVERT: A 1340 GLN cc_start: 0.8274 (pm20) cc_final: 0.7706 (pm20) REVERT: B 118 LEU cc_start: 0.7313 (tt) cc_final: 0.7100 (tp) REVERT: B 165 GLU cc_start: 0.8045 (pm20) cc_final: 0.7805 (pm20) REVERT: B 339 LYS cc_start: 0.7076 (tppt) cc_final: 0.6459 (tppt) REVERT: C 124 MET cc_start: 0.6452 (mmp) cc_final: 0.6241 (mmp) outliers start: 33 outliers final: 18 residues processed: 207 average time/residue: 1.4203 time to fit residues: 319.5448 Evaluate side-chains 197 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 177 time to evaluate : 1.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 578 GLU Chi-restraints excluded: chain A residue 628 SER Chi-restraints excluded: chain A residue 637 ASN Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 1172 HIS Chi-restraints excluded: chain A residue 1179 ASN Chi-restraints excluded: chain A residue 1229 VAL Chi-restraints excluded: chain A residue 1351 CYS Chi-restraints excluded: chain A residue 1364 THR Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain E residue 139 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 141 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 101 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 chunk 132 optimal weight: 0.0870 chunk 107 optimal weight: 0.0070 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 HIS A 97 GLN ** A 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1120 HIS A1266 ASN A1269 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.136091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.093677 restraints weight = 37760.153| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 4.15 r_work: 0.2758 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2759 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2759 r_free = 0.2759 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2759 r_free = 0.2759 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2759 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14419 Z= 0.121 Angle : 0.563 9.117 19633 Z= 0.285 Chirality : 0.039 0.191 2236 Planarity : 0.004 0.037 2476 Dihedral : 9.347 169.663 2059 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.46 % Allowed : 5.88 % Favored : 93.66 % Rotamer: Outliers : 2.09 % Allowed : 15.51 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.96 (0.21), residues: 1738 helix: 2.17 (0.19), residues: 847 sheet: 1.20 (0.58), residues: 86 loop : -1.20 (0.22), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1019 HIS 0.004 0.001 HIS B 166 PHE 0.016 0.001 PHE A 548 TYR 0.012 0.001 TYR A 153 ARG 0.006 0.000 ARG B 312 Details of bonding type rmsd hydrogen bonds : bond 0.04388 ( 659) hydrogen bonds : angle 3.64031 ( 1852) metal coordination : bond 0.00955 ( 4) metal coordination : angle 4.42519 ( 2) covalent geometry : bond 0.00275 (14415) covalent geometry : angle 0.56079 (19631) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 184 time to evaluate : 1.723 Fit side-chains REVERT: A 154 ASP cc_start: 0.8652 (m-30) cc_final: 0.8377 (m-30) REVERT: A 203 GLN cc_start: 0.8754 (OUTLIER) cc_final: 0.7522 (mp10) REVERT: A 242 ASP cc_start: 0.8833 (m-30) cc_final: 0.8596 (m-30) REVERT: A 578 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7645 (tp30) REVERT: A 628 SER cc_start: 0.9115 (OUTLIER) cc_final: 0.8875 (t) REVERT: A 711 LEU cc_start: 0.8006 (OUTLIER) cc_final: 0.7521 (mt) REVERT: A 1013 ASP cc_start: 0.7835 (m-30) cc_final: 0.7241 (m-30) REVERT: A 1064 ASN cc_start: 0.7531 (m-40) cc_final: 0.7019 (p0) REVERT: A 1338 ASP cc_start: 0.8402 (t0) cc_final: 0.8027 (t0) REVERT: A 1340 GLN cc_start: 0.8303 (pm20) cc_final: 0.7876 (pm20) REVERT: B 339 LYS cc_start: 0.6985 (tppt) cc_final: 0.6583 (tppt) outliers start: 32 outliers final: 18 residues processed: 202 average time/residue: 1.3812 time to fit residues: 305.4812 Evaluate side-chains 209 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 187 time to evaluate : 1.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 203 GLN Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain A residue 578 GLU Chi-restraints excluded: chain A residue 628 SER Chi-restraints excluded: chain A residue 637 ASN Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 1172 HIS Chi-restraints excluded: chain A residue 1229 VAL Chi-restraints excluded: chain A residue 1351 CYS Chi-restraints excluded: chain A residue 1364 THR Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 141 LYS Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain E residue 139 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 133 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 105 optimal weight: 0.5980 chunk 102 optimal weight: 4.9990 chunk 106 optimal weight: 0.7980 chunk 114 optimal weight: 7.9990 chunk 109 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 chunk 121 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 HIS A 97 GLN A 392 HIS A 608 GLN A 743 ASN A1120 HIS ** A1266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1342 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.135793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.093659 restraints weight = 32139.864| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 3.49 r_work: 0.2784 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2787 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2787 r_free = 0.2787 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2787 r_free = 0.2787 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2787 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14419 Z= 0.128 Angle : 0.579 10.332 19633 Z= 0.291 Chirality : 0.040 0.206 2236 Planarity : 0.004 0.039 2476 Dihedral : 9.339 169.722 2059 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.46 % Allowed : 5.94 % Favored : 93.60 % Rotamer: Outliers : 1.89 % Allowed : 15.97 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.94 (0.21), residues: 1738 helix: 2.16 (0.19), residues: 847 sheet: 1.16 (0.58), residues: 86 loop : -1.20 (0.22), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1019 HIS 0.005 0.001 HIS B 166 PHE 0.017 0.001 PHE A 548 TYR 0.013 0.001 TYR A 153 ARG 0.007 0.000 ARG B 312 Details of bonding type rmsd hydrogen bonds : bond 0.04523 ( 659) hydrogen bonds : angle 3.62883 ( 1852) metal coordination : bond 0.00925 ( 4) metal coordination : angle 4.46655 ( 2) covalent geometry : bond 0.00299 (14415) covalent geometry : angle 0.57738 (19631) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 194 time to evaluate : 1.657 Fit side-chains revert: symmetry clash REVERT: A 154 ASP cc_start: 0.8602 (m-30) cc_final: 0.8326 (m-30) REVERT: A 203 GLN cc_start: 0.8735 (OUTLIER) cc_final: 0.7503 (mp10) REVERT: A 242 ASP cc_start: 0.8773 (m-30) cc_final: 0.8539 (m-30) REVERT: A 578 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7597 (tp30) REVERT: A 711 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7535 (mt) REVERT: A 1013 ASP cc_start: 0.7830 (m-30) cc_final: 0.7241 (m-30) REVERT: A 1064 ASN cc_start: 0.7516 (m-40) cc_final: 0.7044 (p0) REVERT: A 1338 ASP cc_start: 0.8405 (t0) cc_final: 0.8040 (t0) REVERT: A 1340 GLN cc_start: 0.8262 (pm20) cc_final: 0.7786 (pm20) REVERT: B 165 GLU cc_start: 0.8013 (pm20) cc_final: 0.7787 (pm20) REVERT: D 124 MET cc_start: 0.7061 (ttp) cc_final: 0.6686 (ttt) outliers start: 29 outliers final: 17 residues processed: 214 average time/residue: 1.3978 time to fit residues: 325.7586 Evaluate side-chains 207 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 187 time to evaluate : 1.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 203 GLN Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain A residue 578 GLU Chi-restraints excluded: chain A residue 628 SER Chi-restraints excluded: chain A residue 637 ASN Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 1172 HIS Chi-restraints excluded: chain A residue 1229 VAL Chi-restraints excluded: chain A residue 1252 VAL Chi-restraints excluded: chain A residue 1351 CYS Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 141 LYS Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain E residue 139 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 145 optimal weight: 0.9980 chunk 112 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 104 optimal weight: 0.0870 chunk 88 optimal weight: 0.8980 chunk 166 optimal weight: 10.0000 chunk 156 optimal weight: 9.9990 chunk 55 optimal weight: 0.3980 chunk 15 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 142 optimal weight: 0.0040 overall best weight: 0.4370 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 HIS A 97 GLN A1120 HIS ** A1266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.137840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.095848 restraints weight = 38993.730| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 4.09 r_work: 0.2800 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2800 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2800 r_free = 0.2800 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2800 r_free = 0.2800 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2800 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 14419 Z= 0.110 Angle : 0.571 9.994 19633 Z= 0.285 Chirality : 0.039 0.219 2236 Planarity : 0.004 0.037 2476 Dihedral : 9.258 170.355 2059 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.46 % Allowed : 5.48 % Favored : 94.06 % Rotamer: Outliers : 1.50 % Allowed : 16.49 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.02 (0.21), residues: 1738 helix: 2.24 (0.19), residues: 847 sheet: 1.13 (0.57), residues: 86 loop : -1.16 (0.22), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 173 HIS 0.004 0.001 HIS A 5 PHE 0.013 0.001 PHE A 548 TYR 0.013 0.001 TYR A1381 ARG 0.004 0.000 ARG B 312 Details of bonding type rmsd hydrogen bonds : bond 0.03804 ( 659) hydrogen bonds : angle 3.55870 ( 1852) metal coordination : bond 0.00938 ( 4) metal coordination : angle 3.66051 ( 2) covalent geometry : bond 0.00243 (14415) covalent geometry : angle 0.56934 (19631) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 197 time to evaluate : 1.705 Fit side-chains revert: symmetry clash REVERT: A 154 ASP cc_start: 0.8621 (m-30) cc_final: 0.8328 (m-30) REVERT: A 203 GLN cc_start: 0.8741 (OUTLIER) cc_final: 0.7519 (mp10) REVERT: A 242 ASP cc_start: 0.8778 (m-30) cc_final: 0.8545 (m-30) REVERT: A 578 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7632 (tp30) REVERT: A 711 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7490 (mt) REVERT: A 1013 ASP cc_start: 0.7804 (m-30) cc_final: 0.7186 (m-30) REVERT: A 1064 ASN cc_start: 0.7528 (m-40) cc_final: 0.7009 (p0) REVERT: A 1338 ASP cc_start: 0.8401 (t0) cc_final: 0.8079 (t0) REVERT: A 1340 GLN cc_start: 0.8237 (pm20) cc_final: 0.7760 (pm20) REVERT: B 165 GLU cc_start: 0.8035 (pm20) cc_final: 0.7811 (pm20) outliers start: 23 outliers final: 15 residues processed: 210 average time/residue: 1.3780 time to fit residues: 315.7594 Evaluate side-chains 203 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 185 time to evaluate : 1.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 203 GLN Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain A residue 578 GLU Chi-restraints excluded: chain A residue 637 ASN Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 1172 HIS Chi-restraints excluded: chain A residue 1175 SER Chi-restraints excluded: chain A residue 1229 VAL Chi-restraints excluded: chain A residue 1252 VAL Chi-restraints excluded: chain A residue 1334 THR Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain C residue 141 LYS Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain D residue 134 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 38 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 139 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 156 optimal weight: 10.0000 chunk 166 optimal weight: 10.0000 chunk 60 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 HIS A 97 GLN A 743 ASN A1091 HIS A1120 HIS ** A1266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.134857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.094635 restraints weight = 29735.029| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 3.41 r_work: 0.2747 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2755 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2755 r_free = 0.2755 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2755 r_free = 0.2755 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2755 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14419 Z= 0.156 Angle : 0.615 12.703 19633 Z= 0.307 Chirality : 0.041 0.257 2236 Planarity : 0.004 0.038 2476 Dihedral : 9.348 169.685 2059 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.46 % Allowed : 5.99 % Favored : 93.54 % Rotamer: Outliers : 1.63 % Allowed : 16.43 % Favored : 81.94 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 3.12 % 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: 0.94 (0.21), residues: 1738 helix: 2.16 (0.19), residues: 842 sheet: 1.09 (0.58), residues: 86 loop : -1.16 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 664 HIS 0.005 0.001 HIS A 5 PHE 0.019 0.002 PHE A 548 TYR 0.015 0.001 TYR A 427 ARG 0.008 0.000 ARG B 312 Details of bonding type rmsd hydrogen bonds : bond 0.05012 ( 659) hydrogen bonds : angle 3.63590 ( 1852) metal coordination : bond 0.00990 ( 4) metal coordination : angle 4.86644 ( 2) covalent geometry : bond 0.00376 (14415) covalent geometry : angle 0.61337 (19631) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 192 time to evaluate : 1.671 Fit side-chains REVERT: A 154 ASP cc_start: 0.8614 (m-30) cc_final: 0.8308 (m-30) REVERT: A 203 GLN cc_start: 0.8741 (OUTLIER) cc_final: 0.7482 (mp10) REVERT: A 242 ASP cc_start: 0.8796 (m-30) cc_final: 0.8544 (m-30) REVERT: A 578 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7604 (tp30) REVERT: A 711 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7488 (mt) REVERT: A 1013 ASP cc_start: 0.7796 (m-30) cc_final: 0.7209 (m-30) REVERT: A 1064 ASN cc_start: 0.7524 (m-40) cc_final: 0.7002 (p0) REVERT: A 1338 ASP cc_start: 0.8394 (t0) cc_final: 0.8007 (t0) REVERT: A 1340 GLN cc_start: 0.8264 (pm20) cc_final: 0.7758 (pm20) REVERT: B 165 GLU cc_start: 0.7999 (pm20) cc_final: 0.7744 (pm20) REVERT: B 339 LYS cc_start: 0.7093 (tppt) cc_final: 0.6260 (tppt) outliers start: 25 outliers final: 20 residues processed: 209 average time/residue: 1.4377 time to fit residues: 327.3361 Evaluate side-chains 209 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 186 time to evaluate : 1.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 203 GLN Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 578 GLU Chi-restraints excluded: chain A residue 637 ASN Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 799 ILE Chi-restraints excluded: chain A residue 1172 HIS Chi-restraints excluded: chain A residue 1229 VAL Chi-restraints excluded: chain A residue 1252 VAL Chi-restraints excluded: chain A residue 1334 THR Chi-restraints excluded: chain A residue 1351 CYS Chi-restraints excluded: chain A residue 1364 THR Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 141 LYS Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain E residue 139 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 68 optimal weight: 2.9990 chunk 155 optimal weight: 9.9990 chunk 94 optimal weight: 0.9980 chunk 75 optimal weight: 4.9990 chunk 121 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 83 optimal weight: 0.9980 chunk 55 optimal weight: 0.5980 chunk 84 optimal weight: 0.9990 chunk 125 optimal weight: 0.0060 chunk 67 optimal weight: 0.9980 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 HIS A 97 GLN A1120 HIS ** A1266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1342 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.136253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.096331 restraints weight = 25081.868| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 2.74 r_work: 0.2812 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2816 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2816 r_free = 0.2816 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2816 r_free = 0.2816 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2816 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14419 Z= 0.127 Angle : 0.602 10.261 19633 Z= 0.301 Chirality : 0.040 0.231 2236 Planarity : 0.004 0.037 2476 Dihedral : 9.316 169.721 2059 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.46 % Allowed : 5.82 % Favored : 93.72 % Rotamer: Outliers : 1.63 % Allowed : 16.75 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.98 (0.21), residues: 1738 helix: 2.21 (0.19), residues: 841 sheet: 1.05 (0.58), residues: 86 loop : -1.16 (0.22), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 191 HIS 0.005 0.001 HIS A 5 PHE 0.017 0.001 PHE A 548 TYR 0.013 0.001 TYR A1381 ARG 0.005 0.000 ARG B 312 Details of bonding type rmsd hydrogen bonds : bond 0.04383 ( 659) hydrogen bonds : angle 3.60264 ( 1852) metal coordination : bond 0.00984 ( 4) metal coordination : angle 4.30409 ( 2) covalent geometry : bond 0.00292 (14415) covalent geometry : angle 0.60043 (19631) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11903.30 seconds wall clock time: 207 minutes 58.23 seconds (12478.23 seconds total)