Starting phenix.real_space_refine on Sun Sep 13 17:25:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6m32_30069/09_2026/6m32_30069.cif Found real_map, /net/cci-nas-00/data/ceres_data/6m32_30069/09_2026/6m32_30069.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6m32_30069/09_2026/6m32_30069.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6m32_30069/09_2026/6m32_30069.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6m32_30069/09_2026/6m32_30069.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6m32_30069/09_2026/6m32_30069.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6m32_30069/09_2026/6m32_30069.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6m32_30069/09_2026/6m32_30069.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.009 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: 8 Type Number sf(0) Gaussians Ca 2 9.91 5 Fe 12 7.16 5 P 2 5.49 5 Mg 54 5.21 5 S 98 5.16 5 C 15940 2.51 5 N 3557 2.21 5 O 3901 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 111 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23566 Number of models: 1 Model: "" Number of chains: 13 Chain: "E" Number of atoms: 2815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2815 Classifications: {'peptide': 362} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 342} Chain: "F" Number of atoms: 2789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2789 Classifications: {'peptide': 358} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 338} Chain: "G" Number of atoms: 2789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2789 Classifications: {'peptide': 358} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 338} Chain: "D" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 766 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain breaks: 1 Chain: "B" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 731 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 6, 'TRANS': 88} Chain: "A" Number of atoms: 5030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 628, 5030 Classifications: {'peptide': 628} Link IDs: {'PTRANS': 26, 'TRANS': 601} Chain breaks: 2 Chain: "a" Number of atoms: 5030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 628, 5030 Classifications: {'peptide': 628} Link IDs: {'PTRANS': 26, 'TRANS': 601} Chain breaks: 2 Chain: "E" Number of atoms: 508 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 8, 508 Unusual residues: {'BCL': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "F" Number of atoms: 508 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 8, 508 Unusual residues: {'BCL': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "G" Number of atoms: 508 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 8, 508 Unusual residues: {'BCL': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 1042 Unusual residues: {' CA': 1, 'BCL': 12, 'F26': 1, 'F39': 1, 'G2O': 2, 'GS0': 1, 'LHG': 1, 'LMG': 1, 'SF4': 1} Classifications: {'undetermined': 21} Link IDs: {None: 20} Unresolved non-hydrogen bonds: 164 Unresolved non-hydrogen angles: 194 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'BCL:plan_0002': 7} Unresolved non-hydrogen planarities: 42 Chain: "a" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 1034 Unusual residues: {' CA': 1, 'BCL': 12, 'F26': 1, 'F39': 1, 'G2O': 2, 'GS0': 1, 'LHG': 1, 'LMG': 1} Classifications: {'undetermined': 20} Link IDs: {None: 19} Unresolved non-hydrogen bonds: 164 Unresolved non-hydrogen angles: 194 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'BCL:plan_0002': 7} Unresolved non-hydrogen planarities: 42 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 9279 SG CYS B 143 44.274 39.891 105.154 1.00 44.11 S ATOM 9262 SG CYS B 140 46.570 33.715 105.366 1.00 48.17 S ATOM 9634 SG CYS B 191 45.535 37.332 99.786 1.00 47.04 S ATOM 9297 SG CYS B 146 40.885 35.226 104.004 1.00 43.66 S ATOM 9573 SG CYS B 182 29.771 32.699 98.086 1.00 49.69 S ATOM 9328 SG CYS B 150 32.285 32.025 102.866 1.00 48.27 S ATOM 9590 SG CYS B 185 36.264 33.445 97.398 1.00 49.08 S ATOM 9553 SG CYS B 179 34.055 28.234 97.841 1.00 48.90 S ATOM 18554 SG CYS a 536 43.375 46.399 117.831 1.00 33.07 S ATOM 13524 SG CYS A 536 48.364 48.208 114.962 1.00 38.86 S ATOM 13465 SG CYS A 527 44.939 45.508 111.654 1.00 38.44 S ATOM 18495 SG CYS a 527 46.559 42.172 116.430 1.00 35.21 S Time building chain proxies: 4.44, per 1000 atoms: 0.19 Number of scatterers: 23566 At special positions: 0 Unit cell: (101.946, 120.244, 189.515, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Fe 12 26.01 Ca 2 19.99 S 98 16.00 P 2 15.00 Mg 54 11.99 O 3901 8.00 N 3557 7.00 C 15940 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=53, symmetry=0 Number of additional bonds: simple=53, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.54 Conformation dependent library (CDL) restraints added in 974.2 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 A 821 " pdb="FE2 SF4 A 821 " - pdb=" SG CYS A 536 " pdb="FE4 SF4 A 821 " - pdb=" SG CYS a 527 " pdb="FE1 SF4 A 821 " - pdb=" SG CYS a 536 " pdb="FE3 SF4 A 821 " - pdb=" SG CYS A 527 " pdb=" SF4 B 301 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 191 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 143 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 146 " pdb="FE2 SF4 B 301 " - pdb=" SG CYS B 140 " pdb=" SF4 B 302 " pdb="FE3 SF4 B 302 " - pdb=" SG CYS B 185 " pdb="FE4 SF4 B 302 " - pdb=" SG CYS B 179 " pdb="FE1 SF4 B 302 " - pdb=" SG CYS B 182 " pdb="FE2 SF4 B 302 " - pdb=" SG CYS B 150 " Number of angles added : 36 4998 Ramachandran restraints generated. 2499 Oldfield, 0 Emsley, 2499 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4576 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 13 sheets defined 43.2% alpha, 20.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'E' and resid 128 through 134 removed outlier: 3.883A pdb=" N VAL E 134 " --> pdb=" O VAL E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 156 through 173 Processing helix chain 'E' and resid 175 through 185 removed outlier: 4.887A pdb=" N ARG E 181 " --> pdb=" O ASN E 177 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ASP E 182 " --> pdb=" O ASP E 178 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N PHE E 183 " --> pdb=" O TRP E 179 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE E 185 " --> pdb=" O ARG E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 196 removed outlier: 4.125A pdb=" N THR E 191 " --> pdb=" O GLY E 187 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASN E 194 " --> pdb=" O PHE E 190 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU E 195 " --> pdb=" O THR E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 238 Processing helix chain 'E' and resid 292 through 299 Processing helix chain 'E' and resid 342 through 353 Processing helix chain 'F' and resid 128 through 134 removed outlier: 3.854A pdb=" N VAL F 134 " --> pdb=" O VAL F 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 156 through 173 Processing helix chain 'F' and resid 175 through 185 removed outlier: 4.888A pdb=" N ARG F 181 " --> pdb=" O ASN F 177 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ASP F 182 " --> pdb=" O ASP F 178 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N PHE F 183 " --> pdb=" O TRP F 179 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE F 185 " --> pdb=" O ARG F 181 " (cutoff:3.500A) Processing helix chain 'F' and resid 187 through 196 removed outlier: 4.126A pdb=" N THR F 191 " --> pdb=" O GLY F 187 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASN F 194 " --> pdb=" O PHE F 190 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU F 195 " --> pdb=" O THR F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 238 Processing helix chain 'F' and resid 292 through 299 Processing helix chain 'F' and resid 342 through 353 Processing helix chain 'G' and resid 128 through 134 removed outlier: 3.860A pdb=" N VAL G 134 " --> pdb=" O VAL G 130 " (cutoff:3.500A) Processing helix chain 'G' and resid 156 through 173 Processing helix chain 'G' and resid 175 through 185 removed outlier: 4.888A pdb=" N ARG G 181 " --> pdb=" O ASN G 177 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ASP G 182 " --> pdb=" O ASP G 178 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N PHE G 183 " --> pdb=" O TRP G 179 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE G 185 " --> pdb=" O ARG G 181 " (cutoff:3.500A) Processing helix chain 'G' and resid 187 through 196 removed outlier: 4.126A pdb=" N THR G 191 " --> pdb=" O GLY G 187 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASN G 194 " --> pdb=" O PHE G 190 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU G 195 " --> pdb=" O THR G 191 " (cutoff:3.500A) Processing helix chain 'G' and resid 233 through 238 Processing helix chain 'G' and resid 292 through 299 Processing helix chain 'G' and resid 342 through 353 Processing helix chain 'D' and resid 63 through 72 removed outlier: 3.583A pdb=" N ASP D 72 " --> pdb=" O ARG D 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 150 removed outlier: 4.068A pdb=" N LYS B 149 " --> pdb=" O LEU B 145 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N CYS B 150 " --> pdb=" O CYS B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 188 removed outlier: 3.602A pdb=" N GLY B 188 " --> pdb=" O ALA B 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 70 Processing helix chain 'A' and resid 71 through 97 removed outlier: 4.002A pdb=" N VAL A 75 " --> pdb=" O ASP A 71 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL A 76 " --> pdb=" O ASP A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 124 removed outlier: 3.983A pdb=" N ILE A 117 " --> pdb=" O PHE A 113 " (cutoff:3.500A) Proline residue: A 119 - end of helix Processing helix chain 'A' and resid 133 through 166 Processing helix chain 'A' and resid 202 through 228 removed outlier: 3.980A pdb=" N GLY A 207 " --> pdb=" O LYS A 203 " (cutoff:3.500A) Proline residue: A 208 - end of helix Processing helix chain 'A' and resid 239 through 263 removed outlier: 3.658A pdb=" N THR A 243 " --> pdb=" O ILE A 239 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE A 247 " --> pdb=" O THR A 243 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N TYR A 259 " --> pdb=" O ALA A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 272 removed outlier: 3.749A pdb=" N ASN A 272 " --> pdb=" O ILE A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 301 removed outlier: 3.521A pdb=" N PHE A 298 " --> pdb=" O GLY A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 305 removed outlier: 6.635A pdb=" N SER A 305 " --> pdb=" O GLN A 302 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 302 through 305' Processing helix chain 'A' and resid 306 through 311 Processing helix chain 'A' and resid 363 through 402 removed outlier: 3.691A pdb=" N THR A 369 " --> pdb=" O ALA A 365 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N HIS A 376 " --> pdb=" O ILE A 372 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN A 399 " --> pdb=" O LEU A 395 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY A 402 " --> pdb=" O ILE A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 407 removed outlier: 4.045A pdb=" N ILE A 407 " --> pdb=" O TYR A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 414 Processing helix chain 'A' and resid 419 through 452 removed outlier: 3.571A pdb=" N LEU A 431 " --> pdb=" O THR A 427 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N MET A 436 " --> pdb=" O CYS A 432 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU A 437 " --> pdb=" O PHE A 433 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N SER A 438 " --> pdb=" O ALA A 434 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU A 451 " --> pdb=" O THR A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 461 Processing helix chain 'A' and resid 468 through 472 removed outlier: 3.554A pdb=" N GLN A 472 " --> pdb=" O PRO A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 505 removed outlier: 3.573A pdb=" N TRP A 483 " --> pdb=" O SER A 479 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N THR A 490 " --> pdb=" O ALA A 486 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ALA A 499 " --> pdb=" O PHE A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 516 Processing helix chain 'A' and resid 530 through 534 Processing helix chain 'A' and resid 539 through 563 removed outlier: 4.522A pdb=" N LYS A 553 " --> pdb=" O LEU A 549 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N GLY A 554 " --> pdb=" O TRP A 550 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL A 558 " --> pdb=" O GLY A 554 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N CYS A 559 " --> pdb=" O LEU A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 580 No H-bonds generated for 'chain 'A' and resid 578 through 580' Processing helix chain 'A' and resid 581 through 586 Processing helix chain 'A' and resid 597 through 602 removed outlier: 4.065A pdb=" N TRP A 601 " --> pdb=" O PHE A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 608 Processing helix chain 'A' and resid 610 through 626 removed outlier: 3.582A pdb=" N PHE A 625 " --> pdb=" O HIS A 621 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE A 626 " --> pdb=" O LEU A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 632 removed outlier: 3.974A pdb=" N VAL A 630 " --> pdb=" O ILE A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 656 removed outlier: 3.683A pdb=" N ASP A 643 " --> pdb=" O LEU A 639 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY A 653 " --> pdb=" O ILE A 649 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LYS A 654 " --> pdb=" O ARG A 650 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LYS A 655 " --> pdb=" O TRP A 651 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N PHE A 656 " --> pdb=" O LEU A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 694 removed outlier: 3.531A pdb=" N PHE A 686 " --> pdb=" O PHE A 682 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU A 688 " --> pdb=" O GLY A 684 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N LEU A 691 " --> pdb=" O MET A 687 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE A 692 " --> pdb=" O LEU A 688 " (cutoff:3.500A) Processing helix chain 'a' and resid 66 through 70 Processing helix chain 'a' and resid 71 through 97 removed outlier: 4.001A pdb=" N VAL a 75 " --> pdb=" O ASP a 71 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL a 76 " --> pdb=" O ASP a 72 " (cutoff:3.500A) Processing helix chain 'a' and resid 111 through 124 removed outlier: 3.983A pdb=" N ILE a 117 " --> pdb=" O PHE a 113 " (cutoff:3.500A) Proline residue: a 119 - end of helix Processing helix chain 'a' and resid 133 through 166 Processing helix chain 'a' and resid 202 through 228 removed outlier: 3.978A pdb=" N GLY a 207 " --> pdb=" O LYS a 203 " (cutoff:3.500A) Proline residue: a 208 - end of helix Processing helix chain 'a' and resid 239 through 263 removed outlier: 3.658A pdb=" N THR a 243 " --> pdb=" O ILE a 239 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE a 247 " --> pdb=" O THR a 243 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N TYR a 259 " --> pdb=" O ALA a 255 " (cutoff:3.500A) Processing helix chain 'a' and resid 267 through 272 removed outlier: 3.749A pdb=" N ASN a 272 " --> pdb=" O ILE a 269 " (cutoff:3.500A) Processing helix chain 'a' and resid 276 through 301 removed outlier: 3.521A pdb=" N PHE a 298 " --> pdb=" O GLY a 294 " (cutoff:3.500A) Processing helix chain 'a' and resid 302 through 305 removed outlier: 6.635A pdb=" N SER a 305 " --> pdb=" O GLN a 302 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 302 through 305' Processing helix chain 'a' and resid 306 through 311 Processing helix chain 'a' and resid 363 through 402 removed outlier: 3.692A pdb=" N THR a 369 " --> pdb=" O ALA a 365 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N HIS a 376 " --> pdb=" O ILE a 372 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN a 399 " --> pdb=" O LEU a 395 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY a 402 " --> pdb=" O ILE a 398 " (cutoff:3.500A) Processing helix chain 'a' and resid 403 through 407 removed outlier: 4.046A pdb=" N ILE a 407 " --> pdb=" O TYR a 404 " (cutoff:3.500A) Processing helix chain 'a' and resid 409 through 414 Processing helix chain 'a' and resid 419 through 452 removed outlier: 3.570A pdb=" N LEU a 431 " --> pdb=" O THR a 427 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N MET a 436 " --> pdb=" O CYS a 432 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU a 437 " --> pdb=" O PHE a 433 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N SER a 438 " --> pdb=" O ALA a 434 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU a 451 " --> pdb=" O THR a 447 " (cutoff:3.500A) Processing helix chain 'a' and resid 457 through 461 Processing helix chain 'a' and resid 468 through 472 removed outlier: 3.555A pdb=" N GLN a 472 " --> pdb=" O PRO a 469 " (cutoff:3.500A) Processing helix chain 'a' and resid 479 through 505 removed outlier: 3.573A pdb=" N TRP a 483 " --> pdb=" O SER a 479 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N THR a 490 " --> pdb=" O ALA a 486 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ALA a 499 " --> pdb=" O PHE a 495 " (cutoff:3.500A) Processing helix chain 'a' and resid 510 through 516 Processing helix chain 'a' and resid 530 through 534 Processing helix chain 'a' and resid 539 through 563 removed outlier: 4.521A pdb=" N LYS a 553 " --> pdb=" O LEU a 549 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N GLY a 554 " --> pdb=" O TRP a 550 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL a 558 " --> pdb=" O GLY a 554 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N CYS a 559 " --> pdb=" O LEU a 555 " (cutoff:3.500A) Processing helix chain 'a' and resid 582 through 587 Processing helix chain 'a' and resid 597 through 602 removed outlier: 4.065A pdb=" N TRP a 601 " --> pdb=" O PHE a 597 " (cutoff:3.500A) Processing helix chain 'a' and resid 603 through 608 Processing helix chain 'a' and resid 610 through 626 removed outlier: 3.582A pdb=" N PHE a 625 " --> pdb=" O HIS a 621 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE a 626 " --> pdb=" O LEU a 622 " (cutoff:3.500A) Processing helix chain 'a' and resid 626 through 632 removed outlier: 3.974A pdb=" N VAL a 630 " --> pdb=" O ILE a 626 " (cutoff:3.500A) Processing helix chain 'a' and resid 634 through 656 removed outlier: 3.683A pdb=" N ASP a 643 " --> pdb=" O LEU a 639 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY a 653 " --> pdb=" O ILE a 649 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LYS a 654 " --> pdb=" O ARG a 650 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LYS a 655 " --> pdb=" O TRP a 651 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N PHE a 656 " --> pdb=" O LEU a 652 " (cutoff:3.500A) Processing helix chain 'a' and resid 669 through 694 removed outlier: 3.532A pdb=" N PHE a 686 " --> pdb=" O PHE a 682 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU a 688 " --> pdb=" O GLY a 684 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N LEU a 691 " --> pdb=" O MET a 687 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N PHE a 692 " --> pdb=" O LEU a 688 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 198 through 200 removed outlier: 3.704A pdb=" N ARG E 222 " --> pdb=" O GLY E 207 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLY E 207 " --> pdb=" O ARG E 222 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N ARG E 224 " --> pdb=" O VAL E 205 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N VAL E 205 " --> pdb=" O ARG E 224 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 198 through 200 removed outlier: 5.915A pdb=" N THR E 112 " --> pdb=" O PRO E 153 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N PHE E 64 " --> pdb=" O LEU E 58 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASP E 261 " --> pdb=" O GLY E 264 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLY E 264 " --> pdb=" O ASP E 261 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N ALA E 12 " --> pdb=" O ASP E 310 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N GLN E 312 " --> pdb=" O ALA E 12 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N SER E 14 " --> pdb=" O GLN E 312 " (cutoff:3.500A) removed outlier: 8.640A pdb=" N LYS E 314 " --> pdb=" O SER E 14 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N TYR E 16 " --> pdb=" O LYS E 314 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N VAL E 316 " --> pdb=" O TYR E 16 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ILE E 18 " --> pdb=" O VAL E 316 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER E 332 " --> pdb=" O ARG E 339 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 277 through 279 removed outlier: 5.683A pdb=" N ILE E 362 " --> pdb=" O ILE E 287 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N GLU E 361 " --> pdb=" O ALA E 326 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ALA E 326 " --> pdb=" O GLU E 361 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU E 363 " --> pdb=" O ARG E 324 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 198 through 200 removed outlier: 3.704A pdb=" N ARG F 222 " --> pdb=" O GLY F 207 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLY F 207 " --> pdb=" O ARG F 222 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N ARG F 224 " --> pdb=" O VAL F 205 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N VAL F 205 " --> pdb=" O ARG F 224 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 198 through 200 removed outlier: 5.916A pdb=" N THR F 112 " --> pdb=" O PRO F 153 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N PHE F 64 " --> pdb=" O LEU F 58 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU F 266 " --> pdb=" O ARG F 259 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASP F 261 " --> pdb=" O GLY F 264 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLY F 264 " --> pdb=" O ASP F 261 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N ALA F 12 " --> pdb=" O ASP F 310 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N GLN F 312 " --> pdb=" O ALA F 12 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N SER F 14 " --> pdb=" O GLN F 312 " (cutoff:3.500A) removed outlier: 8.641A pdb=" N LYS F 314 " --> pdb=" O SER F 14 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N TYR F 16 " --> pdb=" O LYS F 314 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N VAL F 316 " --> pdb=" O TYR F 16 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ILE F 18 " --> pdb=" O VAL F 316 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER F 332 " --> pdb=" O ARG F 339 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 277 through 279 removed outlier: 5.684A pdb=" N ILE F 362 " --> pdb=" O ILE F 287 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N GLU F 361 " --> pdb=" O ALA F 326 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ALA F 326 " --> pdb=" O GLU F 361 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU F 363 " --> pdb=" O ARG F 324 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 198 through 200 removed outlier: 3.704A pdb=" N ARG G 222 " --> pdb=" O GLY G 207 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLY G 207 " --> pdb=" O ARG G 222 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ARG G 224 " --> pdb=" O VAL G 205 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N VAL G 205 " --> pdb=" O ARG G 224 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 198 through 200 removed outlier: 5.917A pdb=" N THR G 112 " --> pdb=" O PRO G 153 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N PHE G 64 " --> pdb=" O LEU G 58 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU G 266 " --> pdb=" O ARG G 259 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASP G 261 " --> pdb=" O GLY G 264 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLY G 264 " --> pdb=" O ASP G 261 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N ALA G 12 " --> pdb=" O ASP G 310 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N GLN G 312 " --> pdb=" O ALA G 12 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N SER G 14 " --> pdb=" O GLN G 312 " (cutoff:3.500A) removed outlier: 8.641A pdb=" N LYS G 314 " --> pdb=" O SER G 14 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N TYR G 16 " --> pdb=" O LYS G 314 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N VAL G 316 " --> pdb=" O TYR G 16 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ILE G 18 " --> pdb=" O VAL G 316 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER G 332 " --> pdb=" O ARG G 339 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 277 through 279 removed outlier: 5.685A pdb=" N ILE G 362 " --> pdb=" O ILE G 287 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N GLU G 361 " --> pdb=" O ALA G 326 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ALA G 326 " --> pdb=" O GLU G 361 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU G 363 " --> pdb=" O ARG G 324 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 51 through 53 removed outlier: 3.538A pdb=" N GLU D 76 " --> pdb=" O GLU D 32 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 157 through 159 Processing sheet with id=AB3, first strand: chain 'A' and resid 317 through 318 Processing sheet with id=AB4, first strand: chain 'a' and resid 317 through 318 1042 hydrogen bonds defined for protein. 2997 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: 3.88 Time building geometry restraints manager: 3.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.10 - 1.34: 6845 1.34 - 1.58: 17270 1.58 - 1.82: 235 1.82 - 2.06: 162 2.06 - 2.30: 90 Bond restraints: 24602 Sorted by residual: bond pdb=" C32 F39 A 817 " pdb=" C35 F39 A 817 " ideal model delta sigma weight residual 1.349 1.646 -0.297 2.00e-02 2.50e+03 2.20e+02 bond pdb=" C32 F39 a 817 " pdb=" C35 F39 a 817 " ideal model delta sigma weight residual 1.349 1.646 -0.297 2.00e-02 2.50e+03 2.20e+02 bond pdb=" C40 F39 A 817 " pdb=" C41 F39 A 817 " ideal model delta sigma weight residual 1.352 1.648 -0.296 2.00e-02 2.50e+03 2.19e+02 bond pdb=" C40 F39 a 817 " pdb=" C41 F39 a 817 " ideal model delta sigma weight residual 1.352 1.648 -0.296 2.00e-02 2.50e+03 2.19e+02 bond pdb=" C53 F39 A 817 " pdb=" C56 F39 A 817 " ideal model delta sigma weight residual 1.339 1.627 -0.288 2.00e-02 2.50e+03 2.07e+02 ... (remaining 24597 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.84: 31995 3.84 - 7.67: 1866 7.67 - 11.51: 281 11.51 - 15.35: 67 15.35 - 19.19: 19 Bond angle restraints: 34228 Sorted by residual: angle pdb=" C PHE a 101 " pdb=" N PRO a 102 " pdb=" CA PRO a 102 " ideal model delta sigma weight residual 119.84 132.97 -13.13 1.25e+00 6.40e-01 1.10e+02 angle pdb=" C PHE A 101 " pdb=" N PRO A 102 " pdb=" CA PRO A 102 " ideal model delta sigma weight residual 119.84 131.79 -11.95 1.25e+00 6.40e-01 9.14e+01 angle pdb=" N ASN a 266 " pdb=" CA ASN a 266 " pdb=" C ASN a 266 " ideal model delta sigma weight residual 107.37 126.56 -19.19 2.07e+00 2.33e-01 8.59e+01 angle pdb=" N ASN A 266 " pdb=" CA ASN A 266 " pdb=" C ASN A 266 " ideal model delta sigma weight residual 107.37 126.55 -19.18 2.07e+00 2.33e-01 8.58e+01 angle pdb=" N TRP A 103 " pdb=" CA TRP A 103 " pdb=" C TRP A 103 " ideal model delta sigma weight residual 113.23 102.77 10.46 1.24e+00 6.50e-01 7.12e+01 ... (remaining 34223 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.94: 12735 35.94 - 71.89: 464 71.89 - 107.83: 25 107.83 - 143.78: 0 143.78 - 179.72: 5 Dihedral angle restraints: 13229 sinusoidal: 6046 harmonic: 7183 Sorted by residual: dihedral pdb=" CBD BCL E 371 " pdb=" CGD BCL E 371 " pdb=" O2D BCL E 371 " pdb=" CED BCL E 371 " ideal model delta sinusoidal sigma weight residual 180.00 0.28 179.72 1 5.00e+00 4.00e-02 7.68e+02 dihedral pdb=" CBD BCL F 371 " pdb=" CGD BCL F 371 " pdb=" O2D BCL F 371 " pdb=" CED BCL F 371 " ideal model delta sinusoidal sigma weight residual 180.00 0.32 179.68 1 5.00e+00 4.00e-02 7.68e+02 dihedral pdb=" CBD BCL G 371 " pdb=" CGD BCL G 371 " pdb=" O2D BCL G 371 " pdb=" CED BCL G 371 " ideal model delta sinusoidal sigma weight residual 180.00 0.35 179.65 1 5.00e+00 4.00e-02 7.68e+02 ... (remaining 13226 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.164: 3072 0.164 - 0.328: 115 0.328 - 0.493: 115 0.493 - 0.657: 58 0.657 - 0.821: 10 Chirality restraints: 3370 Sorted by residual: chirality pdb=" CBD G2O A 802 " pdb=" CAD G2O A 802 " pdb=" CGD G2O A 802 " pdb=" CHA G2O A 802 " both_signs ideal model delta sigma weight residual False 2.80 1.98 0.82 2.00e-01 2.50e+01 1.69e+01 chirality pdb=" CBD G2O a 802 " pdb=" CAD G2O a 802 " pdb=" CGD G2O a 802 " pdb=" CHA G2O a 802 " both_signs ideal model delta sigma weight residual False 2.80 1.98 0.82 2.00e-01 2.50e+01 1.69e+01 chirality pdb=" C3A G2O a 802 " pdb=" C2A G2O a 802 " pdb=" C4A G2O a 802 " pdb=" CMA G2O a 802 " both_signs ideal model delta sigma weight residual False -2.77 -2.07 -0.70 2.00e-01 2.50e+01 1.23e+01 ... (remaining 3367 not shown) Planarity restraints: 4186 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C57 F39 a 817 " 0.563 2.00e-02 2.50e+03 5.00e-01 3.13e+03 pdb=" C59 F39 a 817 " -0.636 2.00e-02 2.50e+03 pdb=" C62 F39 a 817 " -0.511 2.00e-02 2.50e+03 pdb=" C64 F39 a 817 " 0.514 2.00e-02 2.50e+03 pdb=" C65 F39 a 817 " 0.070 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C57 F39 A 817 " -0.562 2.00e-02 2.50e+03 5.00e-01 3.12e+03 pdb=" C59 F39 A 817 " 0.636 2.00e-02 2.50e+03 pdb=" C62 F39 A 817 " 0.511 2.00e-02 2.50e+03 pdb=" C64 F39 A 817 " -0.513 2.00e-02 2.50e+03 pdb=" C65 F39 A 817 " -0.071 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BCL A 808 " 0.281 1.50e-02 4.44e+03 2.41e-01 1.29e+03 pdb=" C2 BCL A 808 " -0.432 1.50e-02 4.44e+03 pdb=" C3 BCL A 808 " -0.007 1.50e-02 4.44e+03 pdb=" C4 BCL A 808 " 0.001 1.50e-02 4.44e+03 pdb=" C5 BCL A 808 " 0.156 1.50e-02 4.44e+03 ... (remaining 4183 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.23: 22 2.23 - 2.90: 8720 2.90 - 3.56: 32061 3.56 - 4.23: 56391 4.23 - 4.90: 98131 Nonbonded interactions: 195325 Sorted by model distance: nonbonded pdb=" CZ TYR A 202 " pdb=" OD2 ASP A 274 " model vdw 1.562 3.260 nonbonded pdb=" CE2 TYR A 202 " pdb=" OD2 ASP A 274 " model vdw 1.750 3.340 nonbonded pdb=" NH2 ARG G 331 " pdb=" O LEU A 271 " model vdw 1.870 3.120 nonbonded pdb=" O PRO a 265 " pdb=" OD1 ASN a 266 " model vdw 1.997 3.040 nonbonded pdb=" OG SER G 341 " pdb=" NZ LYS A 200 " model vdw 2.013 3.120 ... (remaining 195320 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 'A' and (resid 59 through 708 or (resid 806 through 807 and (name NB or n \ ame ND or name C1A or name C1B or name C1C or name C1D or name C2A or name C2B o \ r name C2C or name C2D or name C3A or name C3B or name C3C or name C3D or name C \ 4A or name C4B or name C4C or name C4D or name CAA or name CAB or name CAC or na \ me CAD or name CBA or name CBB or name CBC or name CBD or name CED or name CGA o \ r name CGD or name CHA or name CHB or name CHC or name CHD or name CMA or name C \ MB or name CMC or name CMD or name NA or name NC or name O1A or name O1D or name \ O2A or name O2D or name OBB or name OBD or name MG )) or resid 808 through 810 \ or (resid 811 through 815 and (name NB or name ND or name C1A or name C1B or nam \ e C1C or name C1D or name C2A or name C2B or name C2C or name C2D or name C3A or \ name C3B or name C3C or name C3D or name C4A or name C4B or name C4C or name C4 \ D or name CAA or name CAB or name CAC or name CAD or name CBA or name CBB or nam \ e CBC or name CBD or name CED or name CGA or name CGD or name CHA or name CHB or \ name CHC or name CHD or name CMA or name CMB or name CMC or name CMD or name NA \ or name NC or name O1A or name O1D or name O2A or name O2D or name OBB or name \ OBD or name MG )))) selection = (chain 'a' and (resid 59 through 708 or (resid 804 through 805 and (name NB or n \ ame ND or name C1A or name C1B or name C1C or name C1D or name C2A or name C2B o \ r name C2C or name C2D or name C3A or name C3B or name C3C or name C3D or name C \ 4A or name C4B or name C4C or name C4D or name CAA or name CAB or name CAC or na \ me CAD or name CBA or name CBB or name CBC or name CBD or name CED or name CGA o \ r name CGD or name CHA or name CHB or name CHC or name CHD or name CMA or name C \ MB or name CMC or name CMD or name NA or name NC or name O1A or name O1D or name \ O2A or name O2D or name OBB or name OBD or name MG )) or resid 806 through 807 \ or (resid 808 through 813 and (name NB or name ND or name C1A or name C1B or nam \ e C1C or name C1D or name C2A or name C2B or name C2C or name C2D or name C3A or \ name C3B or name C3C or name C3D or name C4A or name C4B or name C4C or name C4 \ D or name CAA or name CAB or name CAC or name CAD or name CBA or name CBB or nam \ e CBC or name CBD or name CED or name CGA or name CGD or name CHA or name CHB or \ name CHC or name CHD or name CMA or name CMB or name CMC or name CMD or name NA \ or name NC or name O1A or name O1D or name O2A or name O2D or name OBB or name \ OBD or name MG )))) } ncs_group { reference = (chain 'E' and (resid 9 through 366 or (resid 371 and (name NB or name ND or nam \ e C1A or name C1B or name C1C or name C1D or name C2A or name C2B or name C2C or \ name C2D or name C3A or name C3B or name C3C or name C3D or name C4A or name C4 \ B or name C4C or name C4D or name CAA or name CAB or name CAC or name CAD or nam \ e CBA or name CBB or name CBC or name CBD or name CED or name CGA or name CGD or \ name CHA or name CHB or name CHC or name CHD or name CMA or name CMB or name CM \ C or name CMD or name NA or name NC or name O1A or name O1D or name O2A or name \ O2D or name OBB or name OBD or name MG )) or resid 373 through 378 or (resid 372 \ and (name NB or name ND or name C1A or name C1B or name C1C or name C1D or name \ C2A or name C2B or name C2C or name C2D or name C3A or name C3B or name C3C or \ name C3D or name C4A or name C4B or name C4C or name C4D or name CAA or name CAB \ or name CAC or name CAD or name CBA or name CBB or name CBC or name CBD or name \ CED or name CGA or name CGD or name CHA or name CHB or name CHC or name CHD or \ name CMA or name CMB or name CMC or name CMD or name NA or name NC or name O1A o \ r name O1D or name O2A or name O2D or name OBB or name OBD or name MG )))) selection = (chain 'F' and (resid 9 through 366 or (resid 372 and (name NB or name ND or nam \ e C1A or name C1B or name C1C or name C1D or name C2A or name C2B or name C2C or \ name C2D or name C3A or name C3B or name C3C or name C3D or name C4A or name C4 \ B or name C4C or name C4D or name CAA or name CAB or name CAC or name CAD or nam \ e CBA or name CBB or name CBC or name CBD or name CED or name CGA or name CGD or \ name CHA or name CHB or name CHC or name CHD or name CMA or name CMB or name CM \ C or name CMD or name NA or name NC or name O1A or name O1D or name O2A or name \ O2D or name OBB or name OBD or name MG )) or resid 371 through 376 or (resid 377 \ through 378 and (name NB or name ND or name C1A or name C1B or name C1C or name \ C1D or name C2A or name C2B or name C2C or name C2D or name C3A or name C3B or \ name C3C or name C3D or name C4A or name C4B or name C4C or name C4D or name CAA \ or name CAB or name CAC or name CAD or name CBA or name CBB or name CBC or name \ CBD or name CED or name CGA or name CGD or name CHA or name CHB or name CHC or \ name CHD or name CMA or name CMB or name CMC or name CMD or name NA or name NC o \ r name O1A or name O1D or name O2A or name O2D or name OBB or name OBD or name M \ G )))) selection = (chain 'G' and (resid 9 through 375 or (resid 376 through 377 and (name NB or na \ me ND or name C1A or name C1B or name C1C or name C1D or name C2A or name C2B or \ name C2C or name C2D or name C3A or name C3B or name C3C or name C3D or name C4 \ A or name C4B or name C4C or name C4D or name CAA or name CAB or name CAC or nam \ e CAD or name CBA or name CBB or name CBC or name CBD or name CED or name CGA or \ name CGD or name CHA or name CHB or name CHC or name CHD or name CMA or name CM \ B or name CMC or name CMD or name NA or name NC or name O1A or name O1D or name \ O2A or name O2D or name OBB or name OBD or name MG )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.230 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: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 23.360 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 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 : 0.033 0.934 24667 Z= 2.294 Angle : 2.049 47.947 34264 Z= 0.856 Chirality : 0.134 0.821 3370 Planarity : 0.029 0.500 4186 Dihedral : 16.689 179.723 8653 Min Nonbonded Distance : 1.562 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.40 % Allowed : 7.52 % Favored : 92.08 % Rotamer: Outliers : 0.52 % Allowed : 2.58 % Favored : 96.90 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 5.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.17), residues: 2499 helix: -0.08 (0.17), residues: 939 sheet: 0.39 (0.25), residues: 447 loop : -2.42 (0.17), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 33 TYR 0.028 0.002 TYR F 325 PHE 0.022 0.002 PHE A 346 TRP 0.043 0.001 TRP D 112 HIS 0.006 0.001 HIS a 270 Details of bonding type rmsd/Z covalent geometry : bond 0.02145 / 0.97 (24602) covalent geometry : angle 1.95973 / 0.86 (34228) hydrogen bonds : bond 0.21857 / 14.61 ( 1036) hydrogen bonds : angle 7.55755 / 5.28 ( 2997) metal coordination : bond 0.15716 / 13.22 ( 12) metal coordination : angle 18.55955 / 12.01 ( 36) Misc. bond : bond 0.54017 / 36.92 ( 53) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4998 Ramachandran restraints generated. 2499 Oldfield, 0 Emsley, 2499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4998 Ramachandran restraints generated. 2499 Oldfield, 0 Emsley, 2499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 386 time to evaluate : 0.970 Fit side-chains REVERT: F 325 TYR cc_start: 0.6875 (t80) cc_final: 0.6550 (t80) REVERT: A 90 MET cc_start: 0.7616 (mmm) cc_final: 0.7414 (mmm) REVERT: A 103 TRP cc_start: 0.5925 (OUTLIER) cc_final: 0.5706 (p90) REVERT: A 548 MET cc_start: 0.8331 (mtp) cc_final: 0.8129 (mtp) outliers start: 11 outliers final: 1 residues processed: 392 average time/residue: 0.7452 time to fit residues: 331.9917 Evaluate side-chains 212 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 210 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 331 ARG Chi-restraints excluded: chain A residue 103 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 216 optimal weight: 5.9990 chunk 98 optimal weight: 30.0000 chunk 194 optimal weight: 20.0000 chunk 227 optimal weight: 5.9990 chunk 107 optimal weight: 0.0050 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 chunk 247 optimal weight: 2.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 9.9990 overall best weight: 4.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 359 GLN ** F 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 312 GLN F 334 ASN G 206 ASN G 334 ASN A 266 ASN A 272 ASN ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 589 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.117815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.103188 restraints weight = 43319.907| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 1.77 r_work: 0.3400 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3292 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3292 r_free = 0.3292 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3292 r_free = 0.3292 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3292 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.374 24667 Z= 0.223 Angle : 0.981 34.841 34264 Z= 0.386 Chirality : 0.046 0.296 3370 Planarity : 0.005 0.079 4186 Dihedral : 14.745 179.204 4179 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.92 % Favored : 93.00 % Rotamer: Outliers : 2.86 % Allowed : 11.78 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.17), residues: 2499 helix: 0.43 (0.17), residues: 949 sheet: 0.90 (0.24), residues: 473 loop : -2.26 (0.18), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG a 163 TYR 0.021 0.002 TYR A 288 PHE 0.020 0.002 PHE a 495 TRP 0.016 0.002 TRP G 239 HIS 0.018 0.002 HIS A 589 Details of bonding type rmsd/Z covalent geometry : bond 0.00523 / 0.22 (24602) covalent geometry : angle 0.85641 / 0.38 (34228) hydrogen bonds : bond 0.06001 / 4.03 ( 1036) hydrogen bonds : angle 5.23722 / 3.66 ( 2997) metal coordination : bond 0.01945 / 1.40 ( 12) metal coordination : angle 14.77576 / 9.10 ( 36) Misc. bond : bond 0.08934 / 4.82 ( 53) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4998 Ramachandran restraints generated. 2499 Oldfield, 0 Emsley, 2499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4998 Ramachandran restraints generated. 2499 Oldfield, 0 Emsley, 2499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 244 time to evaluate : 0.876 Fit side-chains revert: symmetry clash REVERT: E 324 ARG cc_start: 0.7495 (OUTLIER) cc_final: 0.6401 (ptm160) REVERT: F 234 ASP cc_start: 0.7531 (m-30) cc_final: 0.7275 (m-30) REVERT: B 148 ASP cc_start: 0.7534 (OUTLIER) cc_final: 0.7279 (m-30) REVERT: B 216 LEU cc_start: 0.6546 (pp) cc_final: 0.6121 (pp) REVERT: A 73 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7718 (tt0) REVERT: A 311 LYS cc_start: 0.8349 (OUTLIER) cc_final: 0.8027 (ptmm) REVERT: A 364 MET cc_start: 0.7949 (tpt) cc_final: 0.7702 (tpt) REVERT: A 397 LYS cc_start: 0.8384 (OUTLIER) cc_final: 0.8140 (ttmt) REVERT: a 68 GLU cc_start: 0.7567 (pp20) cc_final: 0.7208 (pp20) REVERT: a 275 MET cc_start: 0.7567 (OUTLIER) cc_final: 0.7257 (ttm) REVERT: a 654 LYS cc_start: 0.7013 (OUTLIER) cc_final: 0.6702 (mmpt) outliers start: 60 outliers final: 23 residues processed: 279 average time/residue: 0.6813 time to fit residues: 218.7482 Evaluate side-chains 228 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 198 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 93 LYS Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 324 ARG Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 127 SER Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain G residue 11 THR Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 235 SER Chi-restraints excluded: chain G residue 253 GLN Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 166 GLN Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 397 LYS Chi-restraints excluded: chain A residue 513 TRP Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain a residue 67 THR Chi-restraints excluded: chain a residue 95 ILE Chi-restraints excluded: chain a residue 252 ILE Chi-restraints excluded: chain a residue 275 MET Chi-restraints excluded: chain a residue 381 VAL Chi-restraints excluded: chain a residue 654 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 64 optimal weight: 4.9990 chunk 27 optimal weight: 6.9990 chunk 15 optimal weight: 9.9990 chunk 150 optimal weight: 6.9990 chunk 45 optimal weight: 6.9990 chunk 158 optimal weight: 10.0000 chunk 196 optimal weight: 30.0000 chunk 30 optimal weight: 10.0000 chunk 215 optimal weight: 0.0470 chunk 94 optimal weight: 6.9990 chunk 83 optimal weight: 9.9990 overall best weight: 5.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 209 ASN E 263 GLN ** F 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 312 GLN ** G 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.115351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.100673 restraints weight = 43648.345| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 1.77 r_work: 0.3366 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3260 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3260 r_free = 0.3260 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3260 r_free = 0.3260 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3260 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.346 24667 Z= 0.227 Angle : 0.877 29.656 34264 Z= 0.367 Chirality : 0.046 0.189 3370 Planarity : 0.005 0.067 4186 Dihedral : 13.749 179.997 4173 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.48 % Favored : 93.44 % Rotamer: Outliers : 3.72 % Allowed : 13.31 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.17), residues: 2499 helix: 0.54 (0.16), residues: 966 sheet: 0.93 (0.24), residues: 465 loop : -2.30 (0.18), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 171 TYR 0.027 0.002 TYR A 288 PHE 0.031 0.002 PHE D 105 TRP 0.013 0.002 TRP A 560 HIS 0.010 0.002 HIS G 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00553 / 0.22 (24602) covalent geometry : angle 0.80805 / 0.37 (34228) hydrogen bonds : bond 0.05521 / 3.70 ( 1036) hydrogen bonds : angle 4.89958 / 3.43 ( 2997) metal coordination : bond 0.02114 / 1.53 ( 12) metal coordination : angle 10.54794 / 5.88 ( 36) Misc. bond : bond 0.08081 / 4.34 ( 53) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4998 Ramachandran restraints generated. 2499 Oldfield, 0 Emsley, 2499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4998 Ramachandran restraints generated. 2499 Oldfield, 0 Emsley, 2499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 204 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 234 ASP cc_start: 0.7632 (m-30) cc_final: 0.7342 (m-30) REVERT: G 325 TYR cc_start: 0.7408 (t80) cc_final: 0.7135 (t80) REVERT: D 68 ARG cc_start: 0.6952 (OUTLIER) cc_final: 0.6666 (ptt180) REVERT: A 73 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7692 (tt0) REVERT: A 162 TRP cc_start: 0.8463 (t-100) cc_final: 0.8194 (t60) REVERT: A 364 MET cc_start: 0.7937 (tpt) cc_final: 0.7629 (tpt) REVERT: A 397 LYS cc_start: 0.8246 (OUTLIER) cc_final: 0.7830 (ttmt) REVERT: A 401 ASN cc_start: 0.7637 (OUTLIER) cc_final: 0.7395 (p0) REVERT: A 460 MET cc_start: 0.8380 (mtp) cc_final: 0.7948 (mtp) REVERT: a 275 MET cc_start: 0.7301 (OUTLIER) cc_final: 0.7050 (ttm) REVERT: a 311 LYS cc_start: 0.7987 (pptt) cc_final: 0.7682 (ptpp) REVERT: a 346 PHE cc_start: 0.5955 (OUTLIER) cc_final: 0.5510 (m-80) REVERT: a 519 LYS cc_start: 0.6993 (mmtt) cc_final: 0.6736 (mptp) outliers start: 78 outliers final: 32 residues processed: 250 average time/residue: 0.6530 time to fit residues: 188.3794 Evaluate side-chains 219 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 181 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 31 LYS Chi-restraints excluded: chain E residue 93 LYS Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 260 SER Chi-restraints excluded: chain E residue 324 ARG Chi-restraints excluded: chain E residue 353 CYS Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 127 SER Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain G residue 11 THR Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 235 SER Chi-restraints excluded: chain G residue 253 GLN Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 68 ARG Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 177 CYS Chi-restraints excluded: chain A residue 397 LYS Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 590 HIS Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain a residue 67 THR Chi-restraints excluded: chain a residue 206 LEU Chi-restraints excluded: chain a residue 275 MET Chi-restraints excluded: chain a residue 346 PHE Chi-restraints excluded: chain a residue 381 VAL Chi-restraints excluded: chain a residue 403 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 219 optimal weight: 9.9990 chunk 73 optimal weight: 10.0000 chunk 19 optimal weight: 9.9990 chunk 220 optimal weight: 6.9990 chunk 54 optimal weight: 9.9990 chunk 2 optimal weight: 7.9990 chunk 172 optimal weight: 7.9990 chunk 156 optimal weight: 7.9990 chunk 47 optimal weight: 0.4980 chunk 126 optimal weight: 9.9990 chunk 66 optimal weight: 9.9990 overall best weight: 6.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 263 GLN ** F 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 312 GLN D 29 HIS A 272 ASN ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 331 ASN a 658 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.113687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.099443 restraints weight = 43680.323| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 1.73 r_work: 0.3349 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3238 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3238 r_free = 0.3238 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3238 r_free = 0.3238 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3238 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.356 24667 Z= 0.257 Angle : 0.888 29.056 34264 Z= 0.374 Chirality : 0.047 0.236 3370 Planarity : 0.005 0.061 4186 Dihedral : 13.772 179.903 4173 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.08 % Favored : 92.88 % Rotamer: Outliers : 4.29 % Allowed : 14.36 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.16), residues: 2499 helix: 0.53 (0.16), residues: 956 sheet: 0.84 (0.23), residues: 476 loop : -2.32 (0.18), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG a 163 TYR 0.030 0.002 TYR G 125 PHE 0.021 0.002 PHE D 105 TRP 0.016 0.002 TRP a 162 HIS 0.009 0.002 HIS E 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00630 / 0.25 (24602) covalent geometry : angle 0.82901 / 0.37 (34228) hydrogen bonds : bond 0.05593 / 3.76 ( 1036) hydrogen bonds : angle 4.88821 / 3.41 ( 2997) metal coordination : bond 0.02056 / 1.47 ( 12) metal coordination : angle 9.82326 / 5.49 ( 36) Misc. bond : bond 0.08423 / 4.70 ( 53) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4998 Ramachandran restraints generated. 2499 Oldfield, 0 Emsley, 2499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4998 Ramachandran restraints generated. 2499 Oldfield, 0 Emsley, 2499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 196 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 195 GLU cc_start: 0.7857 (pp20) cc_final: 0.7498 (pp20) REVERT: E 300 MET cc_start: 0.8966 (mtp) cc_final: 0.8730 (mtp) REVERT: E 324 ARG cc_start: 0.7534 (OUTLIER) cc_final: 0.6127 (ptm160) REVERT: F 104 VAL cc_start: 0.8595 (OUTLIER) cc_final: 0.8387 (p) REVERT: G 94 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.8036 (mt-10) REVERT: G 224 ARG cc_start: 0.8658 (OUTLIER) cc_final: 0.7963 (mtp180) REVERT: D 68 ARG cc_start: 0.6924 (OUTLIER) cc_final: 0.6638 (ptt180) REVERT: D 96 ASP cc_start: 0.7215 (OUTLIER) cc_final: 0.6813 (t0) REVERT: D 101 TYR cc_start: 0.7545 (OUTLIER) cc_final: 0.7264 (m-10) REVERT: B 148 ASP cc_start: 0.7575 (OUTLIER) cc_final: 0.7267 (m-30) REVERT: A 73 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7666 (tt0) REVERT: A 162 TRP cc_start: 0.8535 (t-100) cc_final: 0.8300 (t-100) REVERT: A 202 TYR cc_start: 0.8154 (m-80) cc_final: 0.7948 (m-10) REVERT: A 224 MET cc_start: 0.7931 (mmm) cc_final: 0.7690 (mmm) REVERT: A 311 LYS cc_start: 0.8709 (OUTLIER) cc_final: 0.8324 (ttmm) REVERT: A 364 MET cc_start: 0.7970 (tpt) cc_final: 0.7706 (tpt) REVERT: A 397 LYS cc_start: 0.8322 (OUTLIER) cc_final: 0.7892 (ttmt) REVERT: A 401 ASN cc_start: 0.7862 (OUTLIER) cc_final: 0.7578 (p0) REVERT: A 460 MET cc_start: 0.8364 (mtp) cc_final: 0.7987 (mtp) REVERT: A 650 ARG cc_start: 0.7920 (tmm160) cc_final: 0.7719 (ttp80) REVERT: a 163 ARG cc_start: 0.7369 (ttt-90) cc_final: 0.6902 (ttm110) REVERT: a 270 HIS cc_start: 0.7916 (OUTLIER) cc_final: 0.7680 (m-70) REVERT: a 275 MET cc_start: 0.7322 (OUTLIER) cc_final: 0.7065 (ttm) REVERT: a 311 LYS cc_start: 0.8120 (pptt) cc_final: 0.7893 (ptmm) REVERT: a 316 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8669 (mt) outliers start: 90 outliers final: 45 residues processed: 258 average time/residue: 0.6556 time to fit residues: 194.9457 Evaluate side-chains 232 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 172 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 31 LYS Chi-restraints excluded: chain E residue 93 LYS Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 260 SER Chi-restraints excluded: chain E residue 315 VAL Chi-restraints excluded: chain E residue 324 ARG Chi-restraints excluded: chain E residue 353 CYS Chi-restraints excluded: chain E residue 361 GLU Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 127 SER Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 158 ASP Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 94 GLU Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain G residue 224 ARG Chi-restraints excluded: chain G residue 235 SER Chi-restraints excluded: chain G residue 253 GLN Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 68 ARG Chi-restraints excluded: chain D residue 96 ASP Chi-restraints excluded: chain D residue 101 TYR Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 177 CYS Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 397 LYS Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain A residue 414 LYS Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 590 HIS Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain a residue 67 THR Chi-restraints excluded: chain a residue 95 ILE Chi-restraints excluded: chain a residue 131 THR Chi-restraints excluded: chain a residue 206 LEU Chi-restraints excluded: chain a residue 270 HIS Chi-restraints excluded: chain a residue 275 MET Chi-restraints excluded: chain a residue 295 CYS Chi-restraints excluded: chain a residue 316 LEU Chi-restraints excluded: chain a residue 328 VAL Chi-restraints excluded: chain a residue 381 VAL Chi-restraints excluded: chain a residue 436 MET Chi-restraints excluded: chain a residue 488 VAL Chi-restraints excluded: chain a residue 589 HIS Chi-restraints excluded: chain a residue 664 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 151 optimal weight: 8.9990 chunk 25 optimal weight: 5.9990 chunk 162 optimal weight: 0.9990 chunk 230 optimal weight: 7.9990 chunk 26 optimal weight: 5.9990 chunk 114 optimal weight: 10.0000 chunk 235 optimal weight: 0.9990 chunk 46 optimal weight: 8.9990 chunk 10 optimal weight: 9.9990 chunk 129 optimal weight: 0.9990 chunk 91 optimal weight: 7.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 263 GLN ** F 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 312 GLN D 29 HIS A 272 ASN ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 658 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.115852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.101397 restraints weight = 43279.034| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 1.76 r_work: 0.3376 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3270 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3270 r_free = 0.3270 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3270 r_free = 0.3270 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3270 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.286 24667 Z= 0.159 Angle : 0.771 27.543 34264 Z= 0.323 Chirality : 0.043 0.193 3370 Planarity : 0.004 0.056 4186 Dihedral : 13.384 179.979 4173 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.40 % Favored : 93.56 % Rotamer: Outliers : 3.39 % Allowed : 16.32 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.17), residues: 2499 helix: 0.73 (0.17), residues: 964 sheet: 0.94 (0.23), residues: 472 loop : -2.17 (0.18), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 171 TYR 0.025 0.002 TYR G 125 PHE 0.036 0.001 PHE D 105 TRP 0.013 0.001 TRP G 239 HIS 0.007 0.001 HIS F 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 (24602) covalent geometry : angle 0.71268 / 0.32 (34228) hydrogen bonds : bond 0.04701 / 3.14 ( 1036) hydrogen bonds : angle 4.66248 / 3.25 ( 2997) metal coordination : bond 0.01317 / 0.96 ( 12) metal coordination : angle 9.12810 / 5.30 ( 36) Misc. bond : bond 0.06646 / 3.62 ( 53) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4998 Ramachandran restraints generated. 2499 Oldfield, 0 Emsley, 2499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4998 Ramachandran restraints generated. 2499 Oldfield, 0 Emsley, 2499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 200 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 300 MET cc_start: 0.8837 (mtp) cc_final: 0.8577 (mtp) REVERT: E 324 ARG cc_start: 0.7443 (OUTLIER) cc_final: 0.6028 (ptm160) REVERT: G 94 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.8035 (mt-10) REVERT: G 325 TYR cc_start: 0.7870 (t80) cc_final: 0.7662 (t80) REVERT: D 96 ASP cc_start: 0.7177 (OUTLIER) cc_final: 0.6754 (t0) REVERT: B 148 ASP cc_start: 0.7456 (OUTLIER) cc_final: 0.7150 (m-30) REVERT: B 198 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.7352 (tt0) REVERT: A 162 TRP cc_start: 0.8577 (t-100) cc_final: 0.8367 (t-100) REVERT: A 311 LYS cc_start: 0.8669 (OUTLIER) cc_final: 0.8380 (ttmm) REVERT: A 364 MET cc_start: 0.7886 (tpt) cc_final: 0.7624 (tpt) REVERT: A 397 LYS cc_start: 0.8221 (OUTLIER) cc_final: 0.7839 (ttmt) REVERT: A 403 MET cc_start: 0.8593 (mtp) cc_final: 0.8379 (mmm) REVERT: A 460 MET cc_start: 0.8358 (mtp) cc_final: 0.7913 (mtp) REVERT: a 162 TRP cc_start: 0.6957 (t-100) cc_final: 0.6640 (t60) REVERT: a 163 ARG cc_start: 0.7346 (ttt-90) cc_final: 0.7052 (ttp80) REVERT: a 316 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8646 (mt) REVERT: a 395 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8992 (tp) outliers start: 71 outliers final: 30 residues processed: 245 average time/residue: 0.6507 time to fit residues: 184.1108 Evaluate side-chains 219 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 180 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 260 SER Chi-restraints excluded: chain E residue 324 ARG Chi-restraints excluded: chain E residue 353 CYS Chi-restraints excluded: chain F residue 127 SER Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain G residue 11 THR Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 94 GLU Chi-restraints excluded: chain G residue 235 SER Chi-restraints excluded: chain D residue 96 ASP Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 397 LYS Chi-restraints excluded: chain A residue 414 LYS Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 590 HIS Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain a residue 67 THR Chi-restraints excluded: chain a residue 131 THR Chi-restraints excluded: chain a residue 206 LEU Chi-restraints excluded: chain a residue 295 CYS Chi-restraints excluded: chain a residue 316 LEU Chi-restraints excluded: chain a residue 346 PHE Chi-restraints excluded: chain a residue 395 LEU Chi-restraints excluded: chain a residue 488 VAL Chi-restraints excluded: chain a residue 515 ASP Chi-restraints excluded: chain a residue 664 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 69 optimal weight: 9.9990 chunk 65 optimal weight: 10.0000 chunk 239 optimal weight: 9.9990 chunk 229 optimal weight: 0.5980 chunk 42 optimal weight: 0.2980 chunk 225 optimal weight: 8.9990 chunk 21 optimal weight: 3.9990 chunk 93 optimal weight: 10.0000 chunk 38 optimal weight: 6.9990 chunk 136 optimal weight: 20.0000 chunk 207 optimal weight: 10.0000 overall best weight: 4.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 263 GLN ** F 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 312 GLN ** D 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 272 ASN a 74 GLN a 658 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.114943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.100828 restraints weight = 43327.868| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 1.72 r_work: 0.3367 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3260 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3260 r_free = 0.3260 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3260 r_free = 0.3260 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3260 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.302 24667 Z= 0.191 Angle : 0.795 27.459 34264 Z= 0.334 Chirality : 0.044 0.220 3370 Planarity : 0.004 0.081 4186 Dihedral : 13.323 179.972 4173 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.76 % Favored : 93.20 % Rotamer: Outliers : 3.72 % Allowed : 16.75 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.17), residues: 2499 helix: 0.71 (0.17), residues: 964 sheet: 0.92 (0.23), residues: 473 loop : -2.10 (0.18), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 171 TYR 0.027 0.002 TYR A 202 PHE 0.017 0.002 PHE a 686 TRP 0.014 0.001 TRP G 239 HIS 0.007 0.001 HIS E 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.19 (24602) covalent geometry : angle 0.73860 / 0.33 (34228) hydrogen bonds : bond 0.04843 / 3.26 ( 1036) hydrogen bonds : angle 4.64806 / 3.24 ( 2997) metal coordination : bond 0.01478 / 1.04 ( 12) metal coordination : angle 9.13094 / 5.26 ( 36) Misc. bond : bond 0.07164 / 3.94 ( 53) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4998 Ramachandran restraints generated. 2499 Oldfield, 0 Emsley, 2499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4998 Ramachandran restraints generated. 2499 Oldfield, 0 Emsley, 2499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 184 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 300 MET cc_start: 0.8876 (mtp) cc_final: 0.8592 (mtp) REVERT: E 324 ARG cc_start: 0.7467 (OUTLIER) cc_final: 0.6205 (ptm160) REVERT: G 94 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.8039 (mt-10) REVERT: D 96 ASP cc_start: 0.7002 (OUTLIER) cc_final: 0.6674 (t0) REVERT: A 311 LYS cc_start: 0.8687 (OUTLIER) cc_final: 0.8378 (ttmm) REVERT: A 460 MET cc_start: 0.8336 (mtp) cc_final: 0.7879 (mtp) REVERT: A 618 MET cc_start: 0.8312 (mtm) cc_final: 0.8061 (mtm) REVERT: a 162 TRP cc_start: 0.6962 (t-100) cc_final: 0.6640 (t60) REVERT: a 163 ARG cc_start: 0.7358 (ttt-90) cc_final: 0.7108 (ttp80) REVERT: a 316 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8624 (mt) REVERT: a 395 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8985 (tp) REVERT: a 485 MET cc_start: 0.8332 (tpt) cc_final: 0.8060 (tpt) outliers start: 78 outliers final: 39 residues processed: 239 average time/residue: 0.6273 time to fit residues: 173.4314 Evaluate side-chains 219 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 174 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 324 ARG Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 353 CYS Chi-restraints excluded: chain F residue 127 SER Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 337 GLU Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 94 GLU Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain G residue 235 SER Chi-restraints excluded: chain G residue 319 LYS Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 96 ASP Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 414 LYS Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 590 HIS Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain a residue 67 THR Chi-restraints excluded: chain a residue 131 THR Chi-restraints excluded: chain a residue 206 LEU Chi-restraints excluded: chain a residue 295 CYS Chi-restraints excluded: chain a residue 316 LEU Chi-restraints excluded: chain a residue 346 PHE Chi-restraints excluded: chain a residue 381 VAL Chi-restraints excluded: chain a residue 395 LEU Chi-restraints excluded: chain a residue 488 VAL Chi-restraints excluded: chain a residue 515 ASP Chi-restraints excluded: chain a residue 589 HIS Chi-restraints excluded: chain a residue 659 ARG Chi-restraints excluded: chain a residue 664 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 105 optimal weight: 0.9990 chunk 200 optimal weight: 10.0000 chunk 191 optimal weight: 1.9990 chunk 247 optimal weight: 10.0000 chunk 82 optimal weight: 30.0000 chunk 157 optimal weight: 9.9990 chunk 208 optimal weight: 9.9990 chunk 189 optimal weight: 8.9990 chunk 62 optimal weight: 8.9990 chunk 17 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 263 GLN ** F 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 312 GLN A 272 ASN a 658 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.116416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.101980 restraints weight = 43241.065| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 1.76 r_work: 0.3385 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3280 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3280 r_free = 0.3280 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3280 r_free = 0.3280 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3280 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.3580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.267 24667 Z= 0.154 Angle : 0.752 26.579 34264 Z= 0.316 Chirality : 0.043 0.195 3370 Planarity : 0.004 0.065 4186 Dihedral : 13.123 179.987 4173 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.56 % Favored : 93.40 % Rotamer: Outliers : 2.96 % Allowed : 17.75 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.17), residues: 2499 helix: 0.86 (0.17), residues: 964 sheet: 0.98 (0.23), residues: 473 loop : -2.05 (0.18), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 171 TYR 0.025 0.001 TYR G 125 PHE 0.029 0.001 PHE D 105 TRP 0.013 0.001 TRP G 239 HIS 0.006 0.001 HIS G 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.15 (24602) covalent geometry : angle 0.69561 / 0.31 (34228) hydrogen bonds : bond 0.04425 / 2.97 ( 1036) hydrogen bonds : angle 4.52856 / 3.16 ( 2997) metal coordination : bond 0.01141 / 0.79 ( 12) metal coordination : angle 8.88248 / 5.24 ( 36) Misc. bond : bond 0.06324 / 3.44 ( 53) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4998 Ramachandran restraints generated. 2499 Oldfield, 0 Emsley, 2499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4998 Ramachandran restraints generated. 2499 Oldfield, 0 Emsley, 2499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 182 time to evaluate : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 284 LEU cc_start: 0.8489 (mp) cc_final: 0.8157 (mp) REVERT: E 300 MET cc_start: 0.8862 (mtp) cc_final: 0.8548 (mtp) REVERT: E 324 ARG cc_start: 0.7548 (OUTLIER) cc_final: 0.6380 (ptm160) REVERT: F 62 LYS cc_start: 0.7601 (OUTLIER) cc_final: 0.6387 (mmtp) REVERT: G 94 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.8123 (mt-10) REVERT: G 325 TYR cc_start: 0.7941 (t80) cc_final: 0.7728 (t80) REVERT: D 96 ASP cc_start: 0.6934 (OUTLIER) cc_final: 0.6720 (t0) REVERT: B 148 ASP cc_start: 0.7492 (OUTLIER) cc_final: 0.7182 (m-30) REVERT: A 654 LYS cc_start: 0.7509 (tppt) cc_final: 0.7070 (mmmt) REVERT: a 163 ARG cc_start: 0.7341 (ttt-90) cc_final: 0.7070 (ttp80) REVERT: a 316 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8631 (mt) outliers start: 62 outliers final: 34 residues processed: 227 average time/residue: 0.5969 time to fit residues: 158.0751 Evaluate side-chains 216 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 176 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 324 ARG Chi-restraints excluded: chain E residue 353 CYS Chi-restraints excluded: chain F residue 62 LYS Chi-restraints excluded: chain F residue 127 SER Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain G residue 11 THR Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 94 GLU Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain G residue 235 SER Chi-restraints excluded: chain G residue 267 VAL Chi-restraints excluded: chain D residue 96 ASP Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 414 LYS Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 590 HIS Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain a residue 67 THR Chi-restraints excluded: chain a residue 131 THR Chi-restraints excluded: chain a residue 206 LEU Chi-restraints excluded: chain a residue 295 CYS Chi-restraints excluded: chain a residue 316 LEU Chi-restraints excluded: chain a residue 346 PHE Chi-restraints excluded: chain a residue 488 VAL Chi-restraints excluded: chain a residue 515 ASP Chi-restraints excluded: chain a residue 659 ARG Chi-restraints excluded: chain a residue 664 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 88 optimal weight: 6.9990 chunk 187 optimal weight: 9.9990 chunk 49 optimal weight: 5.9990 chunk 120 optimal weight: 0.0970 chunk 110 optimal weight: 8.9990 chunk 71 optimal weight: 10.0000 chunk 212 optimal weight: 30.0000 chunk 98 optimal weight: 9.9990 chunk 38 optimal weight: 20.0000 chunk 114 optimal weight: 9.9990 chunk 30 optimal weight: 10.0000 overall best weight: 6.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 263 GLN ** F 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 312 GLN A 272 ASN a 390 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.114256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.099812 restraints weight = 43669.827| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 1.76 r_work: 0.3350 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3244 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3244 r_free = 0.3244 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3244 r_free = 0.3244 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (23 function evaluations) r_final: 0.3244 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.3626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.324 24667 Z= 0.259 Angle : 0.844 27.840 34264 Z= 0.356 Chirality : 0.047 0.236 3370 Planarity : 0.005 0.062 4186 Dihedral : 13.299 179.992 4173 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.88 % Favored : 93.08 % Rotamer: Outliers : 3.20 % Allowed : 17.70 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.17), residues: 2499 helix: 0.71 (0.17), residues: 958 sheet: 0.89 (0.23), residues: 479 loop : -2.10 (0.18), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 650 TYR 0.030 0.002 TYR G 125 PHE 0.023 0.002 PHE a 625 TRP 0.016 0.002 TRP G 239 HIS 0.008 0.002 HIS E 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00637 / 0.26 (24602) covalent geometry : angle 0.78975 / 0.36 (34228) hydrogen bonds : bond 0.05098 / 3.43 ( 1036) hydrogen bonds : angle 4.66755 / 3.26 ( 2997) metal coordination : bond 0.01953 / 1.39 ( 12) metal coordination : angle 9.25216 / 5.27 ( 36) Misc. bond : bond 0.07702 / 4.31 ( 53) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4998 Ramachandran restraints generated. 2499 Oldfield, 0 Emsley, 2499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4998 Ramachandran restraints generated. 2499 Oldfield, 0 Emsley, 2499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 179 time to evaluate : 0.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 288 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.7872 (pt) REVERT: E 300 MET cc_start: 0.8928 (mtp) cc_final: 0.8647 (mtp) REVERT: E 324 ARG cc_start: 0.7567 (OUTLIER) cc_final: 0.6391 (ptm160) REVERT: D 96 ASP cc_start: 0.6994 (OUTLIER) cc_final: 0.6649 (t0) REVERT: B 148 ASP cc_start: 0.7511 (OUTLIER) cc_final: 0.7187 (m-30) REVERT: B 196 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8367 (mp) REVERT: B 198 GLU cc_start: 0.7844 (tt0) cc_final: 0.7540 (tt0) REVERT: A 618 MET cc_start: 0.8276 (mtm) cc_final: 0.8001 (mtm) REVERT: a 163 ARG cc_start: 0.7378 (ttt-90) cc_final: 0.7070 (ttp80) REVERT: a 316 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8650 (mt) outliers start: 67 outliers final: 41 residues processed: 228 average time/residue: 0.5967 time to fit residues: 158.1452 Evaluate side-chains 221 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 174 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 288 LEU Chi-restraints excluded: chain E residue 315 VAL Chi-restraints excluded: chain E residue 324 ARG Chi-restraints excluded: chain E residue 353 CYS Chi-restraints excluded: chain E residue 361 GLU Chi-restraints excluded: chain F residue 62 LYS Chi-restraints excluded: chain F residue 127 SER Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain G residue 235 SER Chi-restraints excluded: chain G residue 267 VAL Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 96 ASP Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 414 LYS Chi-restraints excluded: chain A residue 450 GLU Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 590 HIS Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain a residue 67 THR Chi-restraints excluded: chain a residue 131 THR Chi-restraints excluded: chain a residue 206 LEU Chi-restraints excluded: chain a residue 295 CYS Chi-restraints excluded: chain a residue 316 LEU Chi-restraints excluded: chain a residue 346 PHE Chi-restraints excluded: chain a residue 381 VAL Chi-restraints excluded: chain a residue 488 VAL Chi-restraints excluded: chain a residue 515 ASP Chi-restraints excluded: chain a residue 664 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 222 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 215 optimal weight: 20.0000 chunk 21 optimal weight: 8.9990 chunk 227 optimal weight: 10.0000 chunk 173 optimal weight: 0.0970 chunk 92 optimal weight: 10.0000 chunk 32 optimal weight: 4.9990 chunk 198 optimal weight: 4.9990 chunk 7 optimal weight: 10.0000 chunk 171 optimal weight: 6.9990 overall best weight: 5.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 334 ASN ** F 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 312 GLN A 272 ASN a 662 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.114264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.099862 restraints weight = 43737.548| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 1.75 r_work: 0.3352 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3244 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3245 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3245 r_free = 0.3245 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3245 r_free = 0.3245 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3245 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.3631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.324 24667 Z= 0.265 Angle : 0.845 27.840 34264 Z= 0.356 Chirality : 0.047 0.236 3370 Planarity : 0.005 0.062 4186 Dihedral : 13.299 179.992 4173 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.88 % Favored : 93.08 % Rotamer: Outliers : 2.39 % Allowed : 18.80 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.17), residues: 2499 helix: 0.71 (0.17), residues: 958 sheet: 0.89 (0.23), residues: 479 loop : -2.10 (0.18), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 650 TYR 0.030 0.002 TYR G 125 PHE 0.023 0.002 PHE a 625 TRP 0.016 0.002 TRP G 239 HIS 0.008 0.002 HIS E 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00637 / 0.26 (24602) covalent geometry : angle 0.78975 / 0.36 (34228) hydrogen bonds : bond 0.05098 / 3.43 ( 1036) hydrogen bonds : angle 4.66755 / 3.26 ( 2997) metal coordination : bond 0.08928 / 6.95 ( 12) metal coordination : angle 9.31655 / 5.36 ( 36) Misc. bond : bond 0.07702 / 4.31 ( 53) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4998 Ramachandran restraints generated. 2499 Oldfield, 0 Emsley, 2499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4998 Ramachandran restraints generated. 2499 Oldfield, 0 Emsley, 2499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 174 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 288 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.7871 (pt) REVERT: E 300 MET cc_start: 0.8926 (mtp) cc_final: 0.8642 (mtp) REVERT: E 324 ARG cc_start: 0.7568 (OUTLIER) cc_final: 0.6389 (ptm160) REVERT: D 96 ASP cc_start: 0.6922 (OUTLIER) cc_final: 0.6658 (t0) REVERT: B 148 ASP cc_start: 0.7497 (OUTLIER) cc_final: 0.7176 (m-30) REVERT: B 196 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8362 (mp) REVERT: B 198 GLU cc_start: 0.7841 (tt0) cc_final: 0.7539 (tt0) REVERT: A 618 MET cc_start: 0.8280 (mtm) cc_final: 0.8000 (mtm) REVERT: a 163 ARG cc_start: 0.7370 (ttt-90) cc_final: 0.7087 (ttp80) REVERT: a 316 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8654 (mt) outliers start: 50 outliers final: 41 residues processed: 209 average time/residue: 0.6134 time to fit residues: 149.6630 Evaluate side-chains 221 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 174 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 288 LEU Chi-restraints excluded: chain E residue 315 VAL Chi-restraints excluded: chain E residue 324 ARG Chi-restraints excluded: chain E residue 353 CYS Chi-restraints excluded: chain E residue 361 GLU Chi-restraints excluded: chain F residue 62 LYS Chi-restraints excluded: chain F residue 127 SER Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain G residue 235 SER Chi-restraints excluded: chain G residue 267 VAL Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 96 ASP Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 414 LYS Chi-restraints excluded: chain A residue 450 GLU Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 590 HIS Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain a residue 67 THR Chi-restraints excluded: chain a residue 131 THR Chi-restraints excluded: chain a residue 206 LEU Chi-restraints excluded: chain a residue 295 CYS Chi-restraints excluded: chain a residue 316 LEU Chi-restraints excluded: chain a residue 346 PHE Chi-restraints excluded: chain a residue 381 VAL Chi-restraints excluded: chain a residue 488 VAL Chi-restraints excluded: chain a residue 515 ASP Chi-restraints excluded: chain a residue 664 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 55 optimal weight: 7.9990 chunk 51 optimal weight: 7.9990 chunk 33 optimal weight: 9.9990 chunk 127 optimal weight: 1.9990 chunk 180 optimal weight: 7.9990 chunk 118 optimal weight: 10.0000 chunk 60 optimal weight: 0.9980 chunk 106 optimal weight: 0.0170 chunk 189 optimal weight: 0.2980 chunk 94 optimal weight: 2.9990 chunk 107 optimal weight: 0.0370 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 334 ASN ** F 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 312 GLN F 333 GLN ** A 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.119660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.105348 restraints weight = 42994.185| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 1.77 r_work: 0.3439 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3332 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3333 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3333 r_free = 0.3333 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3333 r_free = 0.3333 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3333 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.3798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.191 24667 Z= 0.120 Angle : 0.720 24.312 34264 Z= 0.303 Chirality : 0.042 0.197 3370 Planarity : 0.004 0.049 4186 Dihedral : 12.844 179.990 4173 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.08 % Favored : 93.88 % Rotamer: Outliers : 1.67 % Allowed : 19.56 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.17), residues: 2499 helix: 1.00 (0.17), residues: 968 sheet: 1.08 (0.23), residues: 483 loop : -1.90 (0.19), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG a 659 TYR 0.020 0.001 TYR G 125 PHE 0.032 0.001 PHE D 105 TRP 0.017 0.001 TRP A 566 HIS 0.005 0.001 HIS A 282 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (24602) covalent geometry : angle 0.66397 / 0.30 (34228) hydrogen bonds : bond 0.03694 / 2.47 ( 1036) hydrogen bonds : angle 4.41175 / 3.08 ( 2997) metal coordination : bond 0.01012 / 0.83 ( 12) metal coordination : angle 8.64126 / 5.45 ( 36) Misc. bond : bond 0.04389 / 2.37 ( 53) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4998 Ramachandran restraints generated. 2499 Oldfield, 0 Emsley, 2499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4998 Ramachandran restraints generated. 2499 Oldfield, 0 Emsley, 2499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 209 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 324 ARG cc_start: 0.7482 (OUTLIER) cc_final: 0.6471 (ptm160) REVERT: F 15 ASP cc_start: 0.7215 (t70) cc_final: 0.6662 (t0) REVERT: B 148 ASP cc_start: 0.7459 (OUTLIER) cc_final: 0.7110 (m-30) REVERT: B 198 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7454 (tt0) REVERT: A 414 LYS cc_start: 0.8191 (OUTLIER) cc_final: 0.7924 (tppt) REVERT: A 548 MET cc_start: 0.8948 (mtp) cc_final: 0.8557 (mtp) REVERT: a 163 ARG cc_start: 0.7181 (ttt-90) cc_final: 0.6951 (ttp80) REVERT: a 316 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8638 (mt) outliers start: 35 outliers final: 21 residues processed: 234 average time/residue: 0.5754 time to fit residues: 157.4774 Evaluate side-chains 201 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 175 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 324 ARG Chi-restraints excluded: chain E residue 361 GLU Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain G residue 11 THR Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain G residue 267 VAL Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 414 LYS Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain a residue 67 THR Chi-restraints excluded: chain a residue 131 THR Chi-restraints excluded: chain a residue 206 LEU Chi-restraints excluded: chain a residue 316 LEU Chi-restraints excluded: chain a residue 346 PHE Chi-restraints excluded: chain a residue 355 LEU Chi-restraints excluded: chain a residue 488 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 110 optimal weight: 3.9990 chunk 84 optimal weight: 9.9990 chunk 41 optimal weight: 8.9990 chunk 60 optimal weight: 20.0000 chunk 118 optimal weight: 8.9990 chunk 101 optimal weight: 4.9990 chunk 192 optimal weight: 8.9990 chunk 72 optimal weight: 0.8980 chunk 156 optimal weight: 10.0000 chunk 54 optimal weight: 8.9990 chunk 160 optimal weight: 6.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 334 ASN ** F 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 312 GLN A 272 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.114950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.100524 restraints weight = 43815.376| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 1.76 r_work: 0.3362 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3256 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3256 r_free = 0.3256 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3256 r_free = 0.3256 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3256 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.3792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.313 24667 Z= 0.220 Angle : 0.812 27.702 34264 Z= 0.344 Chirality : 0.045 0.218 3370 Planarity : 0.004 0.051 4186 Dihedral : 13.090 179.941 4173 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.52 % Favored : 93.44 % Rotamer: Outliers : 1.86 % Allowed : 19.70 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.17), residues: 2499 helix: 0.83 (0.17), residues: 969 sheet: 1.02 (0.23), residues: 479 loop : -1.99 (0.18), residues: 1051 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 115 TYR 0.017 0.002 TYR a 202 PHE 0.020 0.002 PHE A 686 TRP 0.016 0.002 TRP G 239 HIS 0.007 0.002 HIS F 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00541 / 0.22 (24602) covalent geometry : angle 0.75905 / 0.34 (34228) hydrogen bonds : bond 0.04812 / 3.24 ( 1036) hydrogen bonds : angle 4.52886 / 3.17 ( 2997) metal coordination : bond 0.01846 / 1.30 ( 12) metal coordination : angle 8.94547 / 5.20 ( 36) Misc. bond : bond 0.07500 / 4.14 ( 53) =============================================================================== Job complete usr+sys time: 7825.28 seconds wall clock time: 133 minutes 57.71 seconds (8037.71 seconds total)