Starting phenix.real_space_refine on Sun Jul 21 12:23:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jsl_36622/07_2024/8jsl_36622_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jsl_36622/07_2024/8jsl_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jsl_36622/07_2024/8jsl_36622.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jsl_36622/07_2024/8jsl_36622.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jsl_36622/07_2024/8jsl_36622_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jsl_36622/07_2024/8jsl_36622_neut.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 Residue "A PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 9.69, per 1000 atoms: 0.69 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 - 3.50 Amino acid : False - 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: 6.08 Conformation dependent library (CDL) restraints added in 3.1 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: 1.58 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: 5.16 Time building geometry restraints manager: 6.68 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: 99.26 - 106.20: 483 106.20 - 113.15: 7807 113.15 - 120.09: 5013 120.09 - 127.04: 6130 127.04 - 133.99: 198 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 2.440 nonbonded pdb=" ND2 ASN A1249 " pdb=" OH TYR A1381 " model vdw 2.255 2.520 nonbonded pdb=" O ARG D 110 " pdb=" OG SER D 113 " model vdw 2.259 2.440 nonbonded pdb=" O CYS B 275 " pdb=" NE2 GLN B 279 " model vdw 2.266 2.520 nonbonded pdb=" O GLU A 643 " pdb=" OG1 THR B 148 " model vdw 2.270 2.440 ... (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 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: 2.010 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: 0.530 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 46.460 Find NCS groups from input model: 0.260 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:12.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.860 ------------------------------------------------------------------------------- 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 14415 Z= 0.169 Angle : 0.551 9.410 19631 Z= 0.289 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 233 time to evaluate : 1.663 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: 1.3316 time to fit residues: 338.3499 Evaluate side-chains 175 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 174 time to evaluate : 1.577 ------------------------------------------------------------------------------- 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: 0.9990 chunk 132 optimal weight: 8.9990 chunk 73 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 137 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 chunk 102 optimal weight: 3.9990 chunk 158 optimal weight: 10.0000 overall best weight: 1.3588 ------------------------------------------------------------------------------- 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 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 671 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 ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.1130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 14415 Z= 0.277 Angle : 0.604 12.082 19631 Z= 0.310 Chirality : 0.042 0.161 2236 Planarity : 0.004 0.041 2476 Dihedral : 9.754 168.644 2061 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.40 % Allowed : 6.80 % Favored : 92.80 % Rotamer: Outliers : 1.63 % Allowed : 9.00 % Favored : 89.37 % 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: 0.75 (0.21), residues: 1738 helix: 1.90 (0.19), residues: 857 sheet: 1.45 (0.58), residues: 87 loop : -1.26 (0.22), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1085 HIS 0.006 0.001 HIS A 352 PHE 0.026 0.002 PHE A 550 TYR 0.019 0.002 TYR A 427 ARG 0.004 0.000 ARG A 491 *********************** 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 213 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 188 time to evaluate : 1.422 Fit side-chains revert: symmetry clash REVERT: A 154 ASP cc_start: 0.7797 (m-30) cc_final: 0.7547 (m-30) REVERT: A 242 ASP cc_start: 0.8048 (m-30) cc_final: 0.7821 (m-30) REVERT: A 578 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.6947 (tp30) REVERT: A 990 ARG cc_start: 0.7838 (tpt170) cc_final: 0.7556 (tpm-80) REVERT: A 1064 ASN cc_start: 0.7564 (m-40) cc_final: 0.7256 (p0) REVERT: A 1340 GLN cc_start: 0.8037 (pm20) cc_final: 0.7603 (pm20) REVERT: E 132 ASN cc_start: 0.8577 (t0) cc_final: 0.8344 (t0) outliers start: 25 outliers final: 15 residues processed: 200 average time/residue: 1.3113 time to fit residues: 286.0780 Evaluate side-chains 196 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 180 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 578 GLU Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 947 ASP 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 B residue 257 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 148 THR 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 88 optimal weight: 0.4980 chunk 49 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 159 optimal weight: 0.0770 chunk 171 optimal weight: 6.9990 chunk 141 optimal weight: 2.9990 chunk 157 optimal weight: 5.9990 chunk 54 optimal weight: 0.8980 chunk 127 optimal weight: 2.9990 overall best weight: 1.2942 ------------------------------------------------------------------------------- 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 434 ASN ** A 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 671 GLN A 743 ASN A1120 HIS A1266 ASN A1269 HIS A1342 ASN ** B 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 14415 Z= 0.264 Angle : 0.588 11.241 19631 Z= 0.301 Chirality : 0.041 0.163 2236 Planarity : 0.004 0.041 2476 Dihedral : 9.440 168.002 2059 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.46 % Allowed : 6.22 % Favored : 93.31 % Rotamer: Outliers : 2.35 % Allowed : 11.99 % Favored : 85.66 % 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: 0.74 (0.21), residues: 1738 helix: 1.94 (0.19), residues: 859 sheet: 1.36 (0.57), residues: 87 loop : -1.32 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1085 HIS 0.005 0.001 HIS A 352 PHE 0.020 0.002 PHE A 550 TYR 0.019 0.002 TYR A 427 ARG 0.007 0.000 ARG B 312 *********************** 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 227 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 191 time to evaluate : 1.636 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 154 ASP cc_start: 0.7826 (m-30) cc_final: 0.7594 (m-30) REVERT: A 242 ASP cc_start: 0.8021 (m-30) cc_final: 0.7788 (m-30) REVERT: A 556 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7950 (mt-10) REVERT: A 578 GLU cc_start: 0.7445 (OUTLIER) cc_final: 0.6965 (tp30) REVERT: A 734 LYS cc_start: 0.8332 (OUTLIER) cc_final: 0.8050 (tmtt) REVERT: A 990 ARG cc_start: 0.7843 (tpt170) cc_final: 0.7556 (tpm-80) REVERT: A 1064 ASN cc_start: 0.7636 (m-40) cc_final: 0.7338 (p0) REVERT: A 1266 ASN cc_start: 0.6900 (t0) cc_final: 0.6551 (t0) REVERT: A 1340 GLN cc_start: 0.8002 (pm20) cc_final: 0.7666 (pm20) REVERT: B 165 GLU cc_start: 0.7973 (pm20) cc_final: 0.7753 (pm20) REVERT: E 132 ASN cc_start: 0.8597 (t0) cc_final: 0.8375 (t0) outliers start: 36 outliers final: 17 residues processed: 207 average time/residue: 1.3771 time to fit residues: 310.7657 Evaluate side-chains 193 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 173 time to evaluate : 1.593 ------------------------------------------------------------------------------- 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 149 MET Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 556 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 734 LYS 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 B residue 327 VAL Chi-restraints excluded: chain C residue 141 LYS Chi-restraints excluded: chain D residue 149 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 157 optimal weight: 4.9990 chunk 119 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 159 optimal weight: 0.9980 chunk 169 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 151 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 overall best weight: 1.7784 ------------------------------------------------------------------------------- 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 434 ASN ** A 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 671 GLN A 743 ASN A1120 HIS A1342 ASN B 279 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 14415 Z= 0.345 Angle : 0.633 10.930 19631 Z= 0.325 Chirality : 0.043 0.182 2236 Planarity : 0.005 0.045 2476 Dihedral : 9.585 167.037 2059 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.52 % Allowed : 7.03 % Favored : 92.45 % Rotamer: Outliers : 3.00 % Allowed : 13.17 % Favored : 83.83 % 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: 0.61 (0.21), residues: 1738 helix: 1.84 (0.19), residues: 859 sheet: 1.23 (0.58), residues: 87 loop : -1.40 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 191 HIS 0.006 0.001 HIS A 352 PHE 0.022 0.002 PHE A 548 TYR 0.024 0.002 TYR A 427 ARG 0.010 0.000 ARG B 312 *********************** 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 fitting. rotamer outliers: 46 poor density : 184 time to evaluate : 1.532 Fit side-chains revert: symmetry clash REVERT: A 137 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8656 (tt) REVERT: A 154 ASP cc_start: 0.7878 (m-30) cc_final: 0.7617 (m-30) REVERT: A 242 ASP cc_start: 0.8013 (m-30) cc_final: 0.7789 (m-30) REVERT: A 578 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.7010 (tp30) REVERT: A 711 LEU cc_start: 0.8023 (OUTLIER) cc_final: 0.7540 (mt) REVERT: A 734 LYS cc_start: 0.8379 (OUTLIER) cc_final: 0.8113 (tmtt) REVERT: A 736 ARG cc_start: 0.7049 (mtp180) cc_final: 0.6844 (mtp180) REVERT: A 990 ARG cc_start: 0.7884 (tpt170) cc_final: 0.7595 (tpm-80) REVERT: A 1013 ASP cc_start: 0.7649 (m-30) cc_final: 0.7133 (m-30) REVERT: A 1064 ASN cc_start: 0.7688 (m-40) cc_final: 0.7441 (p0) REVERT: A 1266 ASN cc_start: 0.7161 (t0) cc_final: 0.6240 (t0) REVERT: A 1269 HIS cc_start: 0.7339 (m90) cc_final: 0.7071 (m170) REVERT: A 1340 GLN cc_start: 0.7980 (pm20) cc_final: 0.7696 (pm20) outliers start: 46 outliers final: 22 residues processed: 208 average time/residue: 1.3555 time to fit residues: 307.9163 Evaluate side-chains 208 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 182 time to evaluate : 1.695 ------------------------------------------------------------------------------- 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 137 LEU Chi-restraints excluded: chain A residue 429 VAL 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 711 LEU Chi-restraints excluded: chain A residue 734 LYS Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 790 ASP Chi-restraints excluded: chain A residue 799 ILE Chi-restraints excluded: chain A residue 963 ILE Chi-restraints excluded: chain A residue 1033 ASP Chi-restraints excluded: chain A residue 1044 LEU 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 1334 THR Chi-restraints excluded: chain A residue 1351 CYS Chi-restraints excluded: chain A residue 1364 THR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 140 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 chunk 125 optimal weight: 10.0000 chunk 69 optimal weight: 4.9990 chunk 144 optimal weight: 3.9990 chunk 116 optimal weight: 0.2980 chunk 0 optimal weight: 4.9990 chunk 86 optimal weight: 0.6980 chunk 151 optimal weight: 4.9990 chunk 42 optimal weight: 0.3980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 671 GLN A 743 ASN A1120 HIS A1342 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14415 Z= 0.176 Angle : 0.563 10.855 19631 Z= 0.286 Chirality : 0.039 0.157 2236 Planarity : 0.004 0.039 2476 Dihedral : 9.442 167.932 2059 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.46 % Allowed : 5.99 % Favored : 93.54 % Rotamer: Outliers : 2.15 % Allowed : 15.32 % Favored : 82.53 % 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: 0.84 (0.21), residues: 1738 helix: 2.08 (0.19), residues: 855 sheet: 1.28 (0.57), residues: 86 loop : -1.31 (0.22), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1019 HIS 0.004 0.001 HIS A 5 PHE 0.015 0.001 PHE A 793 TYR 0.012 0.001 TYR B 142 ARG 0.006 0.000 ARG B 312 *********************** 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 226 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 193 time to evaluate : 1.649 Fit side-chains revert: symmetry clash REVERT: A 154 ASP cc_start: 0.7858 (m-30) cc_final: 0.7579 (m-30) REVERT: A 242 ASP cc_start: 0.7964 (m-30) cc_final: 0.7736 (m-30) REVERT: A 578 GLU cc_start: 0.7407 (OUTLIER) cc_final: 0.6934 (tp30) REVERT: A 1064 ASN cc_start: 0.7568 (m-40) cc_final: 0.7280 (p0) REVERT: A 1266 ASN cc_start: 0.7074 (OUTLIER) cc_final: 0.6031 (t0) REVERT: A 1269 HIS cc_start: 0.7276 (m90) cc_final: 0.6933 (m170) REVERT: B 118 LEU cc_start: 0.7634 (tt) cc_final: 0.7391 (tp) REVERT: B 165 GLU cc_start: 0.7933 (pm20) cc_final: 0.7711 (pm20) REVERT: B 339 LYS cc_start: 0.6979 (tppt) cc_final: 0.6210 (tppt) outliers start: 33 outliers final: 12 residues processed: 209 average time/residue: 1.3856 time to fit residues: 314.9098 Evaluate side-chains 192 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 178 time to evaluate : 1.689 ------------------------------------------------------------------------------- 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 429 VAL Chi-restraints excluded: chain A residue 578 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 A residue 1229 VAL Chi-restraints excluded: chain A residue 1266 ASN Chi-restraints excluded: chain A residue 1364 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 E residue 138 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 56 optimal weight: 0.0370 chunk 152 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 169 optimal weight: 3.9990 chunk 140 optimal weight: 0.8980 chunk 78 optimal weight: 5.9990 chunk 14 optimal weight: 0.6980 chunk 88 optimal weight: 0.7980 chunk 163 optimal weight: 2.9990 overall best weight: 0.8860 ------------------------------------------------------------------------------- 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 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 743 ASN A1120 HIS A1342 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14415 Z= 0.206 Angle : 0.562 10.106 19631 Z= 0.286 Chirality : 0.040 0.173 2236 Planarity : 0.004 0.050 2476 Dihedral : 9.406 168.398 2059 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.46 % Allowed : 6.46 % Favored : 93.08 % Rotamer: Outliers : 2.02 % Allowed : 16.04 % Favored : 81.94 % 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: 0.87 (0.21), residues: 1738 helix: 2.06 (0.19), residues: 862 sheet: 1.30 (0.58), residues: 86 loop : -1.27 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1019 HIS 0.004 0.001 HIS B 166 PHE 0.017 0.001 PHE A 548 TYR 0.017 0.001 TYR A1088 ARG 0.011 0.000 ARG B 312 *********************** 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 217 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 186 time to evaluate : 1.573 Fit side-chains REVERT: A 154 ASP cc_start: 0.7867 (m-30) cc_final: 0.7585 (m-30) REVERT: A 242 ASP cc_start: 0.7967 (m-30) cc_final: 0.7731 (m-30) REVERT: A 578 GLU cc_start: 0.7446 (OUTLIER) cc_final: 0.6972 (tp30) REVERT: A 711 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7437 (mt) REVERT: A 1013 ASP cc_start: 0.7558 (m-30) cc_final: 0.7092 (m-30) REVERT: A 1064 ASN cc_start: 0.7564 (m-40) cc_final: 0.7276 (p0) REVERT: B 118 LEU cc_start: 0.7619 (tt) cc_final: 0.7395 (tp) REVERT: B 339 LYS cc_start: 0.7123 (tppt) cc_final: 0.6535 (tppt) REVERT: D 124 MET cc_start: 0.7232 (ttp) cc_final: 0.6831 (ttt) outliers start: 31 outliers final: 17 residues processed: 202 average time/residue: 1.4026 time to fit residues: 308.8273 Evaluate side-chains 202 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 183 time to evaluate : 1.619 ------------------------------------------------------------------------------- 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 427 TYR 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 711 LEU Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 790 ASP Chi-restraints excluded: chain A residue 963 ILE 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 1334 THR 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 D residue 149 THR Chi-restraints excluded: chain E residue 138 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 19 optimal weight: 2.9990 chunk 96 optimal weight: 0.4980 chunk 123 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 142 optimal weight: 0.0170 chunk 94 optimal weight: 0.8980 chunk 168 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 104 optimal weight: 0.5980 overall best weight: 0.6018 ------------------------------------------------------------------------------- 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 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 671 GLN A 743 ASN A1120 HIS ** A1266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14415 Z= 0.169 Angle : 0.560 10.883 19631 Z= 0.280 Chirality : 0.039 0.188 2236 Planarity : 0.004 0.038 2476 Dihedral : 9.338 168.908 2059 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.46 % Allowed : 5.94 % Favored : 93.60 % Rotamer: Outliers : 1.83 % Allowed : 16.36 % Favored : 81.81 % 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: 2.18 (0.19), residues: 855 sheet: 1.32 (0.58), residues: 86 loop : -1.22 (0.22), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1019 HIS 0.004 0.001 HIS A 5 PHE 0.014 0.001 PHE A 548 TYR 0.015 0.001 TYR A1088 ARG 0.006 0.000 ARG B 312 *********************** 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 220 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 192 time to evaluate : 1.450 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 154 ASP cc_start: 0.7817 (m-30) cc_final: 0.7538 (m-30) REVERT: A 242 ASP cc_start: 0.7946 (m-30) cc_final: 0.7715 (m-30) REVERT: A 578 GLU cc_start: 0.7414 (OUTLIER) cc_final: 0.6936 (tp30) REVERT: A 628 SER cc_start: 0.8860 (OUTLIER) cc_final: 0.8612 (t) REVERT: A 711 LEU cc_start: 0.7860 (OUTLIER) cc_final: 0.7391 (mt) REVERT: A 1064 ASN cc_start: 0.7504 (m-40) cc_final: 0.7206 (p0) REVERT: B 118 LEU cc_start: 0.7663 (tt) cc_final: 0.7461 (tp) REVERT: B 165 GLU cc_start: 0.7904 (pm20) cc_final: 0.7697 (pm20) REVERT: C 124 MET cc_start: 0.6728 (mmp) cc_final: 0.6487 (mmp) outliers start: 28 outliers final: 14 residues processed: 207 average time/residue: 1.3714 time to fit residues: 310.9171 Evaluate side-chains 202 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 185 time to evaluate : 1.640 ------------------------------------------------------------------------------- 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 429 VAL Chi-restraints excluded: chain A residue 578 GLU Chi-restraints excluded: chain A residue 628 SER Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 790 ASP 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 1252 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 C residue 148 THR Chi-restraints excluded: chain D residue 149 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 67 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 50 optimal weight: 0.0040 chunk 33 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 107 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 132 optimal weight: 7.9990 chunk 153 optimal weight: 3.9990 overall best weight: 0.6392 ------------------------------------------------------------------------------- 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 637 ASN A 671 GLN A 743 ASN A1120 HIS ** A1266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14415 Z= 0.174 Angle : 0.560 9.331 19631 Z= 0.281 Chirality : 0.039 0.209 2236 Planarity : 0.004 0.041 2476 Dihedral : 9.293 169.205 2059 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.46 % Allowed : 5.88 % Favored : 93.66 % Rotamer: Outliers : 1.83 % Allowed : 17.14 % Favored : 81.03 % 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: 0.99 (0.21), residues: 1738 helix: 2.19 (0.19), residues: 855 sheet: 1.29 (0.57), residues: 88 loop : -1.22 (0.22), residues: 795 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 A1088 ARG 0.008 0.000 ARG B 312 *********************** 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 224 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 196 time to evaluate : 1.583 Fit side-chains revert: symmetry clash REVERT: A 154 ASP cc_start: 0.7802 (m-30) cc_final: 0.7490 (m-30) REVERT: A 578 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.6928 (tp30) REVERT: A 628 SER cc_start: 0.8866 (OUTLIER) cc_final: 0.8609 (t) REVERT: A 711 LEU cc_start: 0.7843 (OUTLIER) cc_final: 0.7367 (mt) REVERT: A 1064 ASN cc_start: 0.7498 (m-40) cc_final: 0.7195 (p0) REVERT: B 118 LEU cc_start: 0.7607 (tt) cc_final: 0.7372 (tp) REVERT: B 165 GLU cc_start: 0.7890 (pm20) cc_final: 0.7685 (pm20) REVERT: B 339 LYS cc_start: 0.7096 (tppt) cc_final: 0.6263 (tppt) REVERT: C 124 MET cc_start: 0.6663 (mmp) cc_final: 0.6398 (mmp) REVERT: D 124 MET cc_start: 0.7200 (ttp) cc_final: 0.6770 (ttt) outliers start: 28 outliers final: 16 residues processed: 211 average time/residue: 1.3454 time to fit residues: 309.7702 Evaluate side-chains 204 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 185 time to evaluate : 1.725 ------------------------------------------------------------------------------- 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 427 TYR 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 711 LEU Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 790 ASP 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 A residue 1364 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 161 optimal weight: 0.7980 chunk 147 optimal weight: 1.9990 chunk 157 optimal weight: 9.9990 chunk 94 optimal weight: 0.7980 chunk 68 optimal weight: 0.0270 chunk 123 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 142 optimal weight: 0.0870 chunk 148 optimal weight: 1.9990 chunk 156 optimal weight: 7.9990 chunk 103 optimal weight: 2.9990 overall best weight: 0.5216 ------------------------------------------------------------------------------- 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 A1120 HIS ** A1266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14415 Z= 0.164 Angle : 0.576 13.950 19631 Z= 0.285 Chirality : 0.039 0.230 2236 Planarity : 0.004 0.037 2476 Dihedral : 9.248 169.517 2059 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.46 % Allowed : 5.99 % Favored : 93.54 % Rotamer: Outliers : 1.89 % Allowed : 17.47 % Favored : 80.64 % 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: 1.06 (0.21), residues: 1738 helix: 2.27 (0.19), residues: 849 sheet: 1.29 (0.57), residues: 86 loop : -1.17 (0.22), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1019 HIS 0.005 0.001 HIS A 5 PHE 0.014 0.001 PHE A 548 TYR 0.012 0.001 TYR A1088 ARG 0.005 0.000 ARG B 312 *********************** 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 221 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 192 time to evaluate : 1.666 Fit side-chains REVERT: A 154 ASP cc_start: 0.7782 (m-30) cc_final: 0.7458 (m-30) REVERT: A 578 GLU cc_start: 0.7370 (OUTLIER) cc_final: 0.6910 (tp30) REVERT: A 628 SER cc_start: 0.8852 (OUTLIER) cc_final: 0.8601 (t) REVERT: A 711 LEU cc_start: 0.7796 (OUTLIER) cc_final: 0.7353 (mt) REVERT: A 1064 ASN cc_start: 0.7479 (m-40) cc_final: 0.7181 (p0) REVERT: B 118 LEU cc_start: 0.7617 (tt) cc_final: 0.7376 (tp) REVERT: B 165 GLU cc_start: 0.7886 (pm20) cc_final: 0.7682 (pm20) REVERT: B 339 LYS cc_start: 0.7016 (tppt) cc_final: 0.6396 (tppt) REVERT: D 124 MET cc_start: 0.7139 (ttp) cc_final: 0.6764 (ttt) outliers start: 29 outliers final: 20 residues processed: 211 average time/residue: 1.3936 time to fit residues: 321.5845 Evaluate side-chains 207 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 184 time to evaluate : 1.686 ------------------------------------------------------------------------------- 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 427 TYR 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 663 ASN Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 790 ASP 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 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 257 ASP 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 166 optimal weight: 10.0000 chunk 101 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 115 optimal weight: 2.9990 chunk 174 optimal weight: 5.9990 chunk 160 optimal weight: 6.9990 chunk 138 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 107 optimal weight: 0.2980 chunk 85 optimal weight: 0.6980 chunk 110 optimal weight: 0.0030 overall best weight: 0.7992 ------------------------------------------------------------------------------- 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 671 GLN A 743 ASN A1120 HIS A1266 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14415 Z= 0.197 Angle : 0.580 9.185 19631 Z= 0.291 Chirality : 0.040 0.250 2236 Planarity : 0.004 0.038 2476 Dihedral : 9.269 169.278 2059 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.46 % Allowed : 5.99 % Favored : 93.54 % Rotamer: Outliers : 1.56 % Allowed : 17.93 % Favored : 80.51 % 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: 1.03 (0.21), residues: 1738 helix: 2.24 (0.19), residues: 849 sheet: 1.34 (0.58), residues: 86 loop : -1.18 (0.22), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 191 HIS 0.005 0.001 HIS A 5 PHE 0.016 0.001 PHE A 548 TYR 0.012 0.001 TYR A 153 ARG 0.007 0.000 ARG B 312 ********************** 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 209 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 185 time to evaluate : 1.507 Fit side-chains REVERT: A 154 ASP cc_start: 0.7787 (m-30) cc_final: 0.7499 (m-30) REVERT: A 578 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.6934 (tp30) REVERT: A 628 SER cc_start: 0.8869 (OUTLIER) cc_final: 0.8604 (t) REVERT: A 711 LEU cc_start: 0.7855 (OUTLIER) cc_final: 0.7387 (mt) REVERT: A 1013 ASP cc_start: 0.7529 (m-30) cc_final: 0.7151 (m-30) REVERT: A 1064 ASN cc_start: 0.7497 (m-40) cc_final: 0.7195 (p0) REVERT: B 118 LEU cc_start: 0.7631 (tt) cc_final: 0.7403 (tp) REVERT: B 165 GLU cc_start: 0.7880 (pm20) cc_final: 0.7675 (pm20) REVERT: B 339 LYS cc_start: 0.7109 (tppt) cc_final: 0.6280 (tppt) REVERT: D 124 MET cc_start: 0.7097 (ttp) cc_final: 0.6718 (ttt) outliers start: 24 outliers final: 20 residues processed: 201 average time/residue: 1.3136 time to fit residues: 289.8593 Evaluate side-chains 208 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 185 time to evaluate : 1.745 ------------------------------------------------------------------------------- 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 427 TYR 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 663 ASN Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 790 ASP 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 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 257 ASP 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 147 optimal weight: 1.9990 chunk 42 optimal weight: 0.1980 chunk 128 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 139 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 122 optimal weight: 0.2980 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 671 GLN A 743 ASN A1120 HIS A1266 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.135453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.095612 restraints weight = 32489.223| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 3.76 r_work: 0.2752 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2756 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2756 r_free = 0.2756 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2756 r_free = 0.2756 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2756 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14415 Z= 0.206 Angle : 0.590 10.138 19631 Z= 0.296 Chirality : 0.040 0.231 2236 Planarity : 0.004 0.041 2476 Dihedral : 9.291 168.951 2059 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.46 % Allowed : 6.22 % Favored : 93.31 % Rotamer: Outliers : 1.83 % Allowed : 17.86 % Favored : 80.31 % 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: 849 sheet: 1.34 (0.58), residues: 86 loop : -1.20 (0.22), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 191 HIS 0.005 0.001 HIS A 5 PHE 0.018 0.001 PHE A 548 TYR 0.013 0.001 TYR A 153 ARG 0.005 0.000 ARG B 312 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5437.79 seconds wall clock time: 95 minutes 48.71 seconds (5748.71 seconds total)