Starting phenix.real_space_refine on Fri Mar 15 05:43:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e1n_8958/03_2024/6e1n_8958_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e1n_8958/03_2024/6e1n_8958.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e1n_8958/03_2024/6e1n_8958.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e1n_8958/03_2024/6e1n_8958.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e1n_8958/03_2024/6e1n_8958_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e1n_8958/03_2024/6e1n_8958_neut_updated.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 36 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 6 9.91 5 P 8 5.49 5 S 46 5.16 5 C 7164 2.51 5 N 1576 2.21 5 O 1882 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 62": "NH1" <-> "NH2" Residue "A TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 191": "NH1" <-> "NH2" Residue "A PHE 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 498": "NH1" <-> "NH2" Residue "A ARG 537": "NH1" <-> "NH2" Residue "B ARG 62": "NH1" <-> "NH2" Residue "B TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 191": "NH1" <-> "NH2" Residue "B PHE 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 498": "NH1" <-> "NH2" Residue "B ARG 537": "NH1" <-> "NH2" Residue "B PHE 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10682 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 639, 5145 Classifications: {'peptide': 639} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 18, 'TRANS': 620} Chain breaks: 3 Unresolved non-hydrogen bonds: 137 Unresolved non-hydrogen angles: 173 Unresolved non-hydrogen dihedrals: 115 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 4, 'TPO:plan-1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 3, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 84 Chain: "B" Number of atoms: 5145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 639, 5145 Classifications: {'peptide': 639} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 18, 'TRANS': 620} Chain breaks: 3 Unresolved non-hydrogen bonds: 137 Unresolved non-hydrogen angles: 173 Unresolved non-hydrogen dihedrals: 115 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 4, 'TPO:plan-1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 3, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 84 Chain: "A" Number of atoms: 195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 195 Unusual residues: {' CA': 3, '3PH': 1, 'PLM': 8} Classifications: {'undetermined': 12} Link IDs: {None: 11} Chain: "B" Number of atoms: 195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 195 Unusual residues: {' CA': 3, '3PH': 1, 'PLM': 8} Classifications: {'undetermined': 12} Link IDs: {None: 11} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 6.19, per 1000 atoms: 0.58 Number of scatterers: 10682 At special positions: 0 Unit cell: (137.363, 91.17, 106.973, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 6 19.99 S 46 16.00 P 8 15.00 O 1882 8.00 N 1576 7.00 C 7164 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=18, symmetry=0 Number of additional bonds: simple=18, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.70 Conformation dependent library (CDL) restraints added in 1.8 seconds 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2440 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 65 helices and 0 sheets defined 67.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.15 Creating SS restraints... Processing helix chain 'A' and resid 37 through 44 removed outlier: 3.884A pdb=" N GLY A 44 " --> pdb=" O LEU A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 73 removed outlier: 3.626A pdb=" N PHE A 67 " --> pdb=" O TYR A 63 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU A 72 " --> pdb=" O THR A 68 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE A 73 " --> pdb=" O ARG A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 86 removed outlier: 3.791A pdb=" N ALA A 80 " --> pdb=" O LEU A 76 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU A 81 " --> pdb=" O ASN A 77 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N LEU A 84 " --> pdb=" O ALA A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 91 No H-bonds generated for 'chain 'A' and resid 89 through 91' Processing helix chain 'A' and resid 117 through 140 removed outlier: 3.830A pdb=" N ILE A 121 " --> pdb=" O ASN A 117 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE A 122 " --> pdb=" O ALA A 118 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N TYR A 123 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLU A 124 " --> pdb=" O SER A 120 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ILE A 126 " --> pdb=" O ILE A 122 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR A 127 " --> pdb=" O TYR A 123 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE A 130 " --> pdb=" O ILE A 126 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU A 132 " --> pdb=" O LEU A 128 " (cutoff:3.500A) Proline residue: A 138 - end of helix Processing helix chain 'A' and resid 144 through 147 No H-bonds generated for 'chain 'A' and resid 144 through 147' Processing helix chain 'A' and resid 151 through 172 removed outlier: 3.512A pdb=" N VAL A 155 " --> pdb=" O ARG A 151 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU A 163 " --> pdb=" O CYS A 159 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU A 168 " --> pdb=" O PHE A 164 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU A 172 " --> pdb=" O LEU A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 198 removed outlier: 4.067A pdb=" N VAL A 192 " --> pdb=" O PRO A 188 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE A 193 " --> pdb=" O TYR A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 211 removed outlier: 3.923A pdb=" N LEU A 208 " --> pdb=" O ASP A 204 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU A 209 " --> pdb=" O THR A 205 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER A 210 " --> pdb=" O LEU A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 237 removed outlier: 4.161A pdb=" N ASN A 218 " --> pdb=" O GLY A 214 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU A 222 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE A 226 " --> pdb=" O LEU A 222 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ALA A 234 " --> pdb=" O ALA A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 246 Processing helix chain 'A' and resid 252 through 263 removed outlier: 3.967A pdb=" N GLN A 257 " --> pdb=" O ALA A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 275 removed outlier: 4.412A pdb=" N TRP A 271 " --> pdb=" O ASN A 267 " (cutoff:3.500A) Proline residue: A 273 - end of helix Processing helix chain 'A' and resid 279 through 294 removed outlier: 3.858A pdb=" N VAL A 283 " --> pdb=" O TRP A 280 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N VAL A 286 " --> pdb=" O VAL A 283 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR A 288 " --> pdb=" O PHE A 285 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N VAL A 289 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL A 293 " --> pdb=" O LEU A 290 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N TYR A 294 " --> pdb=" O ILE A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 332 removed outlier: 3.630A pdb=" N LEU A 301 " --> pdb=" O THR A 297 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL A 303 " --> pdb=" O LEU A 299 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N MET A 322 " --> pdb=" O GLY A 318 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N LYS A 329 " --> pdb=" O ARG A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 352 removed outlier: 3.896A pdb=" N LEU A 350 " --> pdb=" O GLN A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 370 removed outlier: 5.370A pdb=" N GLY A 369 " --> pdb=" O LYS A 365 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LEU A 370 " --> pdb=" O GLU A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 397 removed outlier: 4.122A pdb=" N LEU A 391 " --> pdb=" O GLU A 387 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLN A 393 " --> pdb=" O ALA A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 428 removed outlier: 3.690A pdb=" N LEU A 419 " --> pdb=" O TYR A 415 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLN A 421 " --> pdb=" O SER A 417 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLN A 422 " --> pdb=" O ALA A 418 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA A 425 " --> pdb=" O GLN A 421 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N PHE A 426 " --> pdb=" O GLN A 422 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL A 427 " --> pdb=" O LEU A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 455 removed outlier: 3.622A pdb=" N LEU A 440 " --> pdb=" O ILE A 436 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE A 441 " --> pdb=" O SER A 437 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE A 442 " --> pdb=" O PHE A 438 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N PHE A 444 " --> pdb=" O LEU A 440 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ILE A 445 " --> pdb=" O ILE A 441 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ALA A 446 " --> pdb=" O ILE A 442 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N VAL A 447 " --> pdb=" O ASN A 443 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N VAL A 448 " --> pdb=" O PHE A 444 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N VAL A 449 " --> pdb=" O ILE A 445 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N THR A 452 " --> pdb=" O VAL A 448 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ILE A 455 " --> pdb=" O THR A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 486 removed outlier: 3.727A pdb=" N PHE A 471 " --> pdb=" O GLU A 468 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE A 474 " --> pdb=" O PHE A 471 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL A 476 " --> pdb=" O TRP A 473 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU A 477 " --> pdb=" O ILE A 474 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLU A 478 " --> pdb=" O TYR A 475 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU A 481 " --> pdb=" O GLU A 478 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LYS A 482 " --> pdb=" O MET A 479 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ILE A 483 " --> pdb=" O ALA A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 492 Processing helix chain 'A' and resid 497 through 512 removed outlier: 3.616A pdb=" N LEU A 502 " --> pdb=" O ARG A 498 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N VAL A 506 " --> pdb=" O LEU A 502 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR A 512 " --> pdb=" O VAL A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 540 removed outlier: 4.700A pdb=" N LEU A 535 " --> pdb=" O ARG A 531 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N ALA A 536 " --> pdb=" O TYR A 532 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N ARG A 537 " --> pdb=" O LEU A 533 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N MET A 538 " --> pdb=" O LEU A 534 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG A 540 " --> pdb=" O ALA A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 564 removed outlier: 3.922A pdb=" N ILE A 562 " --> pdb=" O PHE A 558 " (cutoff:3.500A) Proline residue: A 563 - end of helix Processing helix chain 'A' and resid 567 through 586 removed outlier: 4.028A pdb=" N ILE A 572 " --> pdb=" O TYR A 568 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N SER A 581 " --> pdb=" O CYS A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 605 No H-bonds generated for 'chain 'A' and resid 602 through 605' Processing helix chain 'A' and resid 617 through 628 removed outlier: 3.668A pdb=" N PHE A 624 " --> pdb=" O MET A 620 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU A 626 " --> pdb=" O THR A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 642 removed outlier: 3.938A pdb=" N ASP A 641 " --> pdb=" O GLU A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 665 removed outlier: 3.607A pdb=" N ILE A 658 " --> pdb=" O SER A 654 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N LEU A 664 " --> pdb=" O ILE A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 687 removed outlier: 3.545A pdb=" N LEU A 672 " --> pdb=" O VAL A 668 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N PHE A 676 " --> pdb=" O LEU A 672 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU A 685 " --> pdb=" O LEU A 681 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 44 removed outlier: 3.731A pdb=" N GLY B 44 " --> pdb=" O LEU B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 56 Processing helix chain 'B' and resid 63 through 73 removed outlier: 3.719A pdb=" N PHE B 67 " --> pdb=" O TYR B 63 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU B 72 " --> pdb=" O THR B 68 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE B 73 " --> pdb=" O ARG B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 86 removed outlier: 4.705A pdb=" N LEU B 84 " --> pdb=" O ALA B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 91 No H-bonds generated for 'chain 'B' and resid 89 through 91' Processing helix chain 'B' and resid 117 through 140 removed outlier: 3.823A pdb=" N ILE B 121 " --> pdb=" O ASN B 117 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE B 122 " --> pdb=" O ALA B 118 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TYR B 123 " --> pdb=" O GLU B 119 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLU B 124 " --> pdb=" O SER B 120 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ILE B 126 " --> pdb=" O ILE B 122 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR B 127 " --> pdb=" O TYR B 123 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE B 130 " --> pdb=" O ILE B 126 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU B 132 " --> pdb=" O LEU B 128 " (cutoff:3.500A) Proline residue: B 138 - end of helix Processing helix chain 'B' and resid 144 through 147 No H-bonds generated for 'chain 'B' and resid 144 through 147' Processing helix chain 'B' and resid 151 through 172 removed outlier: 3.959A pdb=" N LYS B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE B 162 " --> pdb=" O ALA B 158 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU B 163 " --> pdb=" O CYS B 159 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU B 168 " --> pdb=" O PHE B 164 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP B 170 " --> pdb=" O ASP B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 198 removed outlier: 4.044A pdb=" N VAL B 192 " --> pdb=" O PRO B 188 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE B 193 " --> pdb=" O TYR B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 211 removed outlier: 3.927A pdb=" N LEU B 208 " --> pdb=" O ASP B 204 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU B 209 " --> pdb=" O THR B 205 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER B 210 " --> pdb=" O LEU B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 237 removed outlier: 4.205A pdb=" N ASN B 218 " --> pdb=" O GLY B 214 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU B 222 " --> pdb=" O ASN B 218 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE B 226 " --> pdb=" O LEU B 222 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ALA B 234 " --> pdb=" O ALA B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 246 Processing helix chain 'B' and resid 252 through 263 removed outlier: 3.981A pdb=" N GLN B 257 " --> pdb=" O ALA B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 275 removed outlier: 4.389A pdb=" N TRP B 271 " --> pdb=" O ASN B 267 " (cutoff:3.500A) Proline residue: B 273 - end of helix Processing helix chain 'B' and resid 279 through 294 removed outlier: 3.790A pdb=" N VAL B 283 " --> pdb=" O TRP B 280 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE B 284 " --> pdb=" O SER B 281 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N VAL B 286 " --> pdb=" O VAL B 283 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N VAL B 289 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL B 293 " --> pdb=" O LEU B 290 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N TYR B 294 " --> pdb=" O ILE B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 332 removed outlier: 3.654A pdb=" N LEU B 301 " --> pdb=" O THR B 297 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL B 303 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N MET B 322 " --> pdb=" O GLY B 318 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LYS B 329 " --> pdb=" O ARG B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 354 removed outlier: 4.060A pdb=" N LEU B 350 " --> pdb=" O GLN B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 370 removed outlier: 5.159A pdb=" N GLY B 369 " --> pdb=" O LYS B 365 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LEU B 370 " --> pdb=" O GLU B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 397 removed outlier: 4.151A pdb=" N LEU B 391 " --> pdb=" O GLU B 387 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLN B 393 " --> pdb=" O ALA B 389 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA B 396 " --> pdb=" O CYS B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 427 removed outlier: 3.714A pdb=" N LEU B 419 " --> pdb=" O TYR B 415 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLN B 421 " --> pdb=" O SER B 417 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLN B 422 " --> pdb=" O ALA B 418 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA B 425 " --> pdb=" O GLN B 421 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N PHE B 426 " --> pdb=" O GLN B 422 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL B 427 " --> pdb=" O LEU B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 443 removed outlier: 3.596A pdb=" N LEU B 440 " --> pdb=" O ILE B 436 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE B 441 " --> pdb=" O SER B 437 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE B 442 " --> pdb=" O PHE B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 455 removed outlier: 3.780A pdb=" N VAL B 448 " --> pdb=" O ILE B 445 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL B 449 " --> pdb=" O ALA B 446 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU B 450 " --> pdb=" O VAL B 447 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASN B 454 " --> pdb=" O THR B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 486 removed outlier: 3.740A pdb=" N PHE B 471 " --> pdb=" O GLU B 468 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE B 474 " --> pdb=" O PHE B 471 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N VAL B 476 " --> pdb=" O TRP B 473 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU B 477 " --> pdb=" O ILE B 474 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU B 478 " --> pdb=" O TYR B 475 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU B 481 " --> pdb=" O GLU B 478 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS B 482 " --> pdb=" O MET B 479 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ILE B 483 " --> pdb=" O ALA B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 492 Processing helix chain 'B' and resid 497 through 512 removed outlier: 3.692A pdb=" N LEU B 502 " --> pdb=" O ARG B 498 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N VAL B 506 " --> pdb=" O LEU B 502 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THR B 512 " --> pdb=" O VAL B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 540 removed outlier: 4.727A pdb=" N LEU B 535 " --> pdb=" O ARG B 531 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N ALA B 536 " --> pdb=" O TYR B 532 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N ARG B 537 " --> pdb=" O LEU B 533 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N MET B 538 " --> pdb=" O LEU B 534 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARG B 540 " --> pdb=" O ALA B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 544 No H-bonds generated for 'chain 'B' and resid 542 through 544' Processing helix chain 'B' and resid 552 through 564 removed outlier: 3.934A pdb=" N ILE B 562 " --> pdb=" O PHE B 558 " (cutoff:3.500A) Proline residue: B 563 - end of helix Processing helix chain 'B' and resid 567 through 586 removed outlier: 4.095A pdb=" N ILE B 572 " --> pdb=" O TYR B 568 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N SER B 581 " --> pdb=" O CYS B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 605 No H-bonds generated for 'chain 'B' and resid 602 through 605' Processing helix chain 'B' and resid 617 through 628 removed outlier: 3.644A pdb=" N PHE B 624 " --> pdb=" O MET B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 642 removed outlier: 3.952A pdb=" N ASP B 641 " --> pdb=" O GLU B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 665 removed outlier: 3.510A pdb=" N ILE B 658 " --> pdb=" O SER B 654 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N LEU B 664 " --> pdb=" O ILE B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 687 removed outlier: 3.557A pdb=" N LEU B 672 " --> pdb=" O VAL B 668 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N PHE B 676 " --> pdb=" O LEU B 672 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU B 685 " --> pdb=" O LEU B 681 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS B 686 " --> pdb=" O GLU B 682 " (cutoff:3.500A) 419 hydrogen bonds defined for protein. 1155 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.65 Time building geometry restraints manager: 5.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1657 1.31 - 1.43: 3084 1.43 - 1.56: 6077 1.56 - 1.68: 32 1.68 - 1.81: 74 Bond restraints: 10924 Sorted by residual: bond pdb=" OG1 TPO B 26 " pdb=" P TPO B 26 " ideal model delta sigma weight residual 1.717 1.603 0.114 2.00e-02 2.50e+03 3.27e+01 bond pdb=" OG1 TPO A 26 " pdb=" P TPO A 26 " ideal model delta sigma weight residual 1.717 1.603 0.114 2.00e-02 2.50e+03 3.27e+01 bond pdb=" OG1 TPO A 29 " pdb=" P TPO A 29 " ideal model delta sigma weight residual 1.717 1.608 0.109 2.00e-02 2.50e+03 2.95e+01 bond pdb=" OG1 TPO B 29 " pdb=" P TPO B 29 " ideal model delta sigma weight residual 1.717 1.609 0.108 2.00e-02 2.50e+03 2.94e+01 bond pdb=" C31 3PH A 812 " pdb=" O31 3PH A 812 " ideal model delta sigma weight residual 1.325 1.409 -0.084 2.00e-02 2.50e+03 1.78e+01 ... (remaining 10919 not shown) Histogram of bond angle deviations from ideal: 93.10 - 101.42: 27 101.42 - 109.75: 1771 109.75 - 118.07: 6461 118.07 - 126.40: 6346 126.40 - 134.72: 159 Bond angle restraints: 14764 Sorted by residual: angle pdb=" C ILE A 371 " pdb=" N PHE A 372 " pdb=" CA PHE A 372 " ideal model delta sigma weight residual 121.19 130.14 -8.95 1.59e+00 3.96e-01 3.17e+01 angle pdb=" C ILE B 371 " pdb=" N PHE B 372 " pdb=" CA PHE B 372 " ideal model delta sigma weight residual 121.19 130.12 -8.93 1.59e+00 3.96e-01 3.15e+01 angle pdb=" C THR B 264 " pdb=" CA THR B 264 " pdb=" CB THR B 264 " ideal model delta sigma weight residual 111.80 104.25 7.55 1.46e+00 4.69e-01 2.67e+01 angle pdb=" C THR A 264 " pdb=" CA THR A 264 " pdb=" CB THR A 264 " ideal model delta sigma weight residual 111.80 104.38 7.42 1.46e+00 4.69e-01 2.58e+01 angle pdb=" C VAL A 628 " pdb=" N MET A 629 " pdb=" CA MET A 629 " ideal model delta sigma weight residual 122.35 129.25 -6.90 1.46e+00 4.69e-01 2.23e+01 ... (remaining 14759 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.40: 5733 17.40 - 34.80: 485 34.80 - 52.20: 118 52.20 - 69.61: 42 69.61 - 87.01: 6 Dihedral angle restraints: 6384 sinusoidal: 2608 harmonic: 3776 Sorted by residual: dihedral pdb=" CA THR B 378 " pdb=" C THR B 378 " pdb=" N ARG B 379 " pdb=" CA ARG B 379 " ideal model delta harmonic sigma weight residual -180.00 -133.46 -46.54 0 5.00e+00 4.00e-02 8.66e+01 dihedral pdb=" CA ILE B 660 " pdb=" C ILE B 660 " pdb=" N LEU B 661 " pdb=" CA LEU B 661 " ideal model delta harmonic sigma weight residual 180.00 135.77 44.23 0 5.00e+00 4.00e-02 7.82e+01 dihedral pdb=" CA ILE A 660 " pdb=" C ILE A 660 " pdb=" N LEU A 661 " pdb=" CA LEU A 661 " ideal model delta harmonic sigma weight residual 180.00 138.04 41.96 0 5.00e+00 4.00e-02 7.04e+01 ... (remaining 6381 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 1276 0.081 - 0.163: 322 0.163 - 0.244: 46 0.244 - 0.325: 2 0.325 - 0.407: 4 Chirality restraints: 1650 Sorted by residual: chirality pdb=" CB ILE A 186 " pdb=" CA ILE A 186 " pdb=" CG1 ILE A 186 " pdb=" CG2 ILE A 186 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.41 2.00e-01 2.50e+01 4.13e+00 chirality pdb=" CB ILE B 186 " pdb=" CA ILE B 186 " pdb=" CG1 ILE B 186 " pdb=" CG2 ILE B 186 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.40 2.00e-01 2.50e+01 4.02e+00 chirality pdb=" C2 3PH A 812 " pdb=" C1 3PH A 812 " pdb=" C3 3PH A 812 " pdb=" O21 3PH A 812 " both_signs ideal model delta sigma weight residual False -2.33 -2.67 0.35 2.00e-01 2.50e+01 3.02e+00 ... (remaining 1647 not shown) Planarity restraints: 1794 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 587 " -0.035 2.00e-02 2.50e+03 2.34e-02 9.55e+00 pdb=" CG PHE B 587 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 PHE B 587 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE B 587 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE B 587 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE B 587 " -0.008 2.00e-02 2.50e+03 pdb=" CZ PHE B 587 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 153 " -0.015 2.00e-02 2.50e+03 3.04e-02 9.26e+00 pdb=" CG ASN A 153 " 0.053 2.00e-02 2.50e+03 pdb=" OD1 ASN A 153 " -0.020 2.00e-02 2.50e+03 pdb=" ND2 ASN A 153 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A 89 " -0.047 5.00e-02 4.00e+02 7.08e-02 8.02e+00 pdb=" N PRO A 90 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO A 90 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 90 " -0.040 5.00e-02 4.00e+02 ... (remaining 1791 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 188 2.62 - 3.19: 9945 3.19 - 3.76: 16427 3.76 - 4.33: 23086 4.33 - 4.90: 35712 Nonbonded interactions: 85358 Sorted by model distance: nonbonded pdb=" O LEU B 197 " pdb=" NH1 ARG B 203 " model vdw 2.054 2.520 nonbonded pdb=" O LEU A 197 " pdb=" NH1 ARG A 203 " model vdw 2.058 2.520 nonbonded pdb=" OD2 ASP A 606 " pdb=" O HOH A 901 " model vdw 2.204 2.440 nonbonded pdb=" NZ LYS B 344 " pdb=" OG SER B 364 " model vdw 2.209 2.520 nonbonded pdb=" OD2 ASP B 606 " pdb=" O HOH B 901 " model vdw 2.236 2.440 ... (remaining 85353 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 4.260 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 31.310 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 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 : 0.015 0.124 10924 Z= 0.938 Angle : 1.548 12.441 14764 Z= 0.818 Chirality : 0.072 0.407 1650 Planarity : 0.008 0.071 1794 Dihedral : 14.921 87.007 3944 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.25 % Favored : 91.59 % Rotamer: Outliers : 0.37 % Allowed : 2.89 % Favored : 96.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.89 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.21 (0.17), residues: 1248 helix: -3.82 (0.11), residues: 732 sheet: None (None), residues: 0 loop : -2.65 (0.23), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.005 TRP A 529 HIS 0.004 0.002 HIS B 27 PHE 0.047 0.005 PHE B 587 TYR 0.034 0.005 TYR B 532 ARG 0.015 0.002 ARG A 537 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 1140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 409 time to evaluate : 1.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ASP cc_start: 0.8775 (m-30) cc_final: 0.8317 (m-30) REVERT: A 77 ASN cc_start: 0.8438 (m-40) cc_final: 0.8235 (t0) REVERT: A 95 LYS cc_start: 0.8537 (tttt) cc_final: 0.8118 (tppt) REVERT: A 96 ASN cc_start: 0.8646 (p0) cc_final: 0.8039 (p0) REVERT: A 121 ILE cc_start: 0.9204 (mm) cc_final: 0.8961 (mm) REVERT: A 141 TYR cc_start: 0.8677 (p90) cc_final: 0.8376 (p90) REVERT: A 194 ILE cc_start: 0.8466 (mt) cc_final: 0.8186 (mt) REVERT: A 200 ARG cc_start: 0.8041 (ttp80) cc_final: 0.7792 (ttt90) REVERT: A 210 SER cc_start: 0.8986 (m) cc_final: 0.8595 (p) REVERT: A 220 LEU cc_start: 0.9117 (tp) cc_final: 0.8605 (tt) REVERT: A 238 PHE cc_start: 0.8849 (m-10) cc_final: 0.8628 (m-10) REVERT: A 321 GLN cc_start: 0.8394 (mt0) cc_final: 0.8114 (pp30) REVERT: A 326 MET cc_start: 0.8644 (mmm) cc_final: 0.8439 (tpt) REVERT: A 438 PHE cc_start: 0.7520 (m-80) cc_final: 0.7276 (m-80) REVERT: A 491 TYR cc_start: 0.7373 (t80) cc_final: 0.7067 (t80) REVERT: A 499 PHE cc_start: 0.8788 (m-10) cc_final: 0.8543 (m-80) REVERT: A 602 GLU cc_start: 0.8378 (mt-10) cc_final: 0.7644 (mm-30) REVERT: A 637 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7153 (tm-30) REVERT: A 687 CYS cc_start: 0.5548 (m) cc_final: 0.4490 (t) REVERT: B 95 LYS cc_start: 0.8550 (tttt) cc_final: 0.8111 (tppt) REVERT: B 96 ASN cc_start: 0.8664 (p0) cc_final: 0.8115 (p0) REVERT: B 121 ILE cc_start: 0.9194 (mm) cc_final: 0.8964 (mm) REVERT: B 141 TYR cc_start: 0.8665 (p90) cc_final: 0.8351 (p90) REVERT: B 152 LEU cc_start: 0.8053 (tp) cc_final: 0.7800 (tt) REVERT: B 166 ASP cc_start: 0.8479 (t0) cc_final: 0.7838 (t70) REVERT: B 194 ILE cc_start: 0.8474 (mt) cc_final: 0.8176 (mt) REVERT: B 200 ARG cc_start: 0.8019 (ttp80) cc_final: 0.7786 (ttt90) REVERT: B 210 SER cc_start: 0.8966 (m) cc_final: 0.8617 (p) REVERT: B 220 LEU cc_start: 0.9105 (tp) cc_final: 0.8395 (tt) REVERT: B 497 ASN cc_start: 0.8190 (t0) cc_final: 0.7926 (t0) REVERT: B 499 PHE cc_start: 0.8829 (m-10) cc_final: 0.8553 (m-80) REVERT: B 544 LEU cc_start: 0.7830 (mt) cc_final: 0.7471 (tp) REVERT: B 602 GLU cc_start: 0.8331 (mt-10) cc_final: 0.7626 (mm-30) REVERT: B 606 ASP cc_start: 0.9083 (m-30) cc_final: 0.8403 (m-30) REVERT: B 637 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7156 (tm-30) REVERT: B 683 GLU cc_start: 0.8187 (mt-10) cc_final: 0.7760 (mt-10) outliers start: 4 outliers final: 1 residues processed: 413 average time/residue: 0.2058 time to fit residues: 120.7081 Evaluate side-chains 302 residues out of total 1140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 301 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 613 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 52 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 chunk 64 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 98 optimal weight: 9.9990 chunk 38 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 73 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN A 257 GLN A 454 ASN A 618 ASN B 89 GLN B 257 GLN B 454 ASN ** B 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 618 ASN B 665 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7124 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10924 Z= 0.218 Angle : 0.765 10.117 14764 Z= 0.391 Chirality : 0.044 0.217 1650 Planarity : 0.005 0.039 1794 Dihedral : 15.108 81.110 1704 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 2.61 % Allowed : 12.01 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.81 (0.19), residues: 1248 helix: -2.56 (0.14), residues: 792 sheet: None (None), residues: 0 loop : -2.13 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 223 HIS 0.001 0.000 HIS A 27 PHE 0.020 0.002 PHE B 613 TYR 0.018 0.002 TYR B 551 ARG 0.007 0.001 ARG A 69 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 1140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 350 time to evaluate : 1.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 ASN cc_start: 0.9237 (t0) cc_final: 0.8876 (t0) REVERT: A 95 LYS cc_start: 0.8498 (tttt) cc_final: 0.8146 (tttt) REVERT: A 96 ASN cc_start: 0.8479 (p0) cc_final: 0.7698 (p0) REVERT: A 121 ILE cc_start: 0.9102 (mm) cc_final: 0.8837 (mm) REVERT: A 166 ASP cc_start: 0.8242 (t70) cc_final: 0.7421 (t70) REVERT: A 326 MET cc_start: 0.8481 (mmm) cc_final: 0.8273 (tpt) REVERT: A 372 PHE cc_start: 0.7663 (m-10) cc_final: 0.7054 (t80) REVERT: A 602 GLU cc_start: 0.8311 (mt-10) cc_final: 0.7851 (mm-30) REVERT: A 637 GLU cc_start: 0.7902 (mt-10) cc_final: 0.6962 (tm-30) REVERT: B 95 LYS cc_start: 0.8516 (tttt) cc_final: 0.8223 (tttt) REVERT: B 96 ASN cc_start: 0.8501 (p0) cc_final: 0.7747 (p0) REVERT: B 121 ILE cc_start: 0.9135 (mm) cc_final: 0.8879 (mm) REVERT: B 170 ASP cc_start: 0.8271 (m-30) cc_final: 0.7989 (m-30) REVERT: B 212 MET cc_start: 0.8523 (mtp) cc_final: 0.8266 (ttm) REVERT: B 238 PHE cc_start: 0.8877 (m-10) cc_final: 0.8613 (m-10) REVERT: B 354 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8564 (tp) REVERT: B 438 PHE cc_start: 0.7546 (m-80) cc_final: 0.7281 (m-80) REVERT: B 544 LEU cc_start: 0.7740 (mt) cc_final: 0.7450 (tp) REVERT: B 602 GLU cc_start: 0.8309 (mt-10) cc_final: 0.7839 (mm-30) REVERT: B 637 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7017 (tm-30) REVERT: B 683 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7857 (mt-10) outliers start: 28 outliers final: 14 residues processed: 362 average time/residue: 0.2039 time to fit residues: 105.4627 Evaluate side-chains 305 residues out of total 1140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 290 time to evaluate : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 434 TYR Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 434 TYR Chi-restraints excluded: chain B residue 613 PHE Chi-restraints excluded: chain B residue 659 THR Chi-restraints excluded: chain B residue 679 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 10.0000 chunk 35 optimal weight: 5.9990 chunk 95 optimal weight: 0.7980 chunk 77 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 chunk 114 optimal weight: 0.0670 chunk 123 optimal weight: 0.6980 chunk 102 optimal weight: 8.9990 chunk 113 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN A 134 HIS A 585 GLN B 89 GLN B 134 HIS B 585 GLN ** B 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 moved from start: 0.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10924 Z= 0.195 Angle : 0.669 8.191 14764 Z= 0.337 Chirality : 0.042 0.207 1650 Planarity : 0.004 0.038 1794 Dihedral : 13.914 79.716 1704 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 2.23 % Allowed : 16.76 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.86 (0.21), residues: 1248 helix: -1.79 (0.16), residues: 790 sheet: None (None), residues: 0 loop : -1.79 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 271 HIS 0.001 0.001 HIS B 134 PHE 0.029 0.002 PHE A 438 TYR 0.018 0.002 TYR A 357 ARG 0.005 0.000 ARG B 543 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 308 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 LEU cc_start: 0.9195 (tp) cc_final: 0.8871 (tt) REVERT: A 95 LYS cc_start: 0.8467 (tttt) cc_final: 0.8196 (tttt) REVERT: A 96 ASN cc_start: 0.8427 (p0) cc_final: 0.7622 (p0) REVERT: A 119 GLU cc_start: 0.7760 (tp30) cc_final: 0.7538 (tm-30) REVERT: A 121 ILE cc_start: 0.9109 (mm) cc_final: 0.8810 (mm) REVERT: A 124 GLU cc_start: 0.9268 (mt-10) cc_final: 0.9050 (mt-10) REVERT: A 206 LEU cc_start: 0.9078 (tp) cc_final: 0.8814 (mp) REVERT: A 326 MET cc_start: 0.8520 (mmm) cc_final: 0.8192 (tpt) REVERT: A 372 PHE cc_start: 0.7716 (m-10) cc_final: 0.7081 (t80) REVERT: A 387 GLU cc_start: 0.9019 (mm-30) cc_final: 0.8686 (mm-30) REVERT: A 438 PHE cc_start: 0.7199 (m-80) cc_final: 0.6961 (m-80) REVERT: A 552 ARG cc_start: 0.8248 (tpt170) cc_final: 0.7839 (tpt-90) REVERT: A 602 GLU cc_start: 0.8282 (mt-10) cc_final: 0.7806 (mm-30) REVERT: A 637 GLU cc_start: 0.7818 (mt-10) cc_final: 0.6985 (tm-30) REVERT: B 95 LYS cc_start: 0.8520 (tttt) cc_final: 0.8258 (tttt) REVERT: B 96 ASN cc_start: 0.8412 (p0) cc_final: 0.7569 (p0) REVERT: B 121 ILE cc_start: 0.9120 (mm) cc_final: 0.8817 (mm) REVERT: B 127 THR cc_start: 0.8699 (m) cc_final: 0.8472 (p) REVERT: B 166 ASP cc_start: 0.8058 (t70) cc_final: 0.7286 (t0) REVERT: B 170 ASP cc_start: 0.8185 (m-30) cc_final: 0.7927 (m-30) REVERT: B 212 MET cc_start: 0.8687 (mtp) cc_final: 0.8112 (ttm) REVERT: B 354 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8447 (tp) REVERT: B 544 LEU cc_start: 0.8154 (mt) cc_final: 0.7929 (tp) REVERT: B 552 ARG cc_start: 0.8312 (tpt170) cc_final: 0.8101 (tpt-90) REVERT: B 637 GLU cc_start: 0.7834 (mt-10) cc_final: 0.7132 (tm-30) REVERT: B 683 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7779 (mt-10) outliers start: 24 outliers final: 12 residues processed: 320 average time/residue: 0.1999 time to fit residues: 92.5961 Evaluate side-chains 293 residues out of total 1140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 280 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 434 TYR Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 434 TYR Chi-restraints excluded: chain B residue 613 PHE Chi-restraints excluded: chain B residue 679 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 0.7980 chunk 86 optimal weight: 0.7980 chunk 59 optimal weight: 0.9980 chunk 12 optimal weight: 6.9990 chunk 54 optimal weight: 0.6980 chunk 76 optimal weight: 4.9990 chunk 115 optimal weight: 0.7980 chunk 121 optimal weight: 0.6980 chunk 60 optimal weight: 0.5980 chunk 109 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN A 585 GLN B 89 GLN B 528 GLN B 585 GLN ** B 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 665 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 moved from start: 0.3947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10924 Z= 0.188 Angle : 0.649 8.524 14764 Z= 0.325 Chirality : 0.041 0.198 1650 Planarity : 0.004 0.034 1794 Dihedral : 13.110 78.289 1704 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 2.61 % Allowed : 18.53 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (0.22), residues: 1248 helix: -1.42 (0.16), residues: 840 sheet: None (None), residues: 0 loop : -1.80 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 505 HIS 0.007 0.002 HIS A 134 PHE 0.026 0.002 PHE A 399 TYR 0.028 0.002 TYR A 491 ARG 0.002 0.000 ARG B 543 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 302 time to evaluate : 1.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 LEU cc_start: 0.9181 (tp) cc_final: 0.8841 (tt) REVERT: A 95 LYS cc_start: 0.8434 (tttt) cc_final: 0.8191 (tttt) REVERT: A 96 ASN cc_start: 0.8387 (p0) cc_final: 0.7554 (p0) REVERT: A 119 GLU cc_start: 0.7711 (tp30) cc_final: 0.7453 (tm-30) REVERT: A 121 ILE cc_start: 0.9149 (mm) cc_final: 0.8821 (mm) REVERT: A 194 ILE cc_start: 0.8107 (mt) cc_final: 0.7900 (mp) REVERT: A 206 LEU cc_start: 0.9041 (tp) cc_final: 0.8816 (mp) REVERT: A 387 GLU cc_start: 0.9109 (mm-30) cc_final: 0.8764 (mm-30) REVERT: A 543 ARG cc_start: 0.8109 (tmm160) cc_final: 0.7893 (tmm160) REVERT: A 544 LEU cc_start: 0.8524 (mt) cc_final: 0.8016 (tt) REVERT: A 602 GLU cc_start: 0.8285 (mt-10) cc_final: 0.7795 (mm-30) REVERT: A 637 GLU cc_start: 0.7729 (mt-10) cc_final: 0.7038 (tm-30) REVERT: B 76 LEU cc_start: 0.9171 (tp) cc_final: 0.8885 (tt) REVERT: B 95 LYS cc_start: 0.8458 (tttt) cc_final: 0.8207 (tttt) REVERT: B 96 ASN cc_start: 0.8406 (p0) cc_final: 0.7601 (p0) REVERT: B 119 GLU cc_start: 0.7721 (tp30) cc_final: 0.7445 (tm-30) REVERT: B 121 ILE cc_start: 0.9128 (mm) cc_final: 0.8813 (mm) REVERT: B 127 THR cc_start: 0.8679 (m) cc_final: 0.8464 (p) REVERT: B 141 TYR cc_start: 0.8698 (p90) cc_final: 0.8405 (p90) REVERT: B 194 ILE cc_start: 0.8094 (mt) cc_final: 0.7867 (mp) REVERT: B 212 MET cc_start: 0.8707 (mtp) cc_final: 0.8449 (ttm) REVERT: B 275 TYR cc_start: 0.8248 (t80) cc_final: 0.7988 (t80) REVERT: B 326 MET cc_start: 0.8519 (tpt) cc_final: 0.8270 (tpt) REVERT: B 354 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8381 (tp) REVERT: B 372 PHE cc_start: 0.7875 (m-10) cc_final: 0.7571 (m-10) REVERT: B 434 TYR cc_start: 0.5281 (OUTLIER) cc_final: 0.4854 (m-80) REVERT: B 438 PHE cc_start: 0.7501 (m-80) cc_final: 0.7191 (m-80) REVERT: B 637 GLU cc_start: 0.7772 (mt-10) cc_final: 0.7184 (tm-30) REVERT: B 683 GLU cc_start: 0.8150 (mt-10) cc_final: 0.7880 (mt-10) outliers start: 28 outliers final: 17 residues processed: 316 average time/residue: 0.2095 time to fit residues: 94.8980 Evaluate side-chains 299 residues out of total 1140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 280 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 434 TYR Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 434 TYR Chi-restraints excluded: chain B residue 613 PHE Chi-restraints excluded: chain B residue 677 THR Chi-restraints excluded: chain B residue 679 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 9.9990 chunk 69 optimal weight: 0.4980 chunk 1 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 chunk 103 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 62 optimal weight: 0.4980 chunk 109 optimal weight: 0.9990 chunk 30 optimal weight: 9.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 585 GLN B 585 GLN ** B 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.4256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10924 Z= 0.182 Angle : 0.637 8.907 14764 Z= 0.316 Chirality : 0.041 0.191 1650 Planarity : 0.003 0.032 1794 Dihedral : 12.484 77.299 1704 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 2.05 % Allowed : 20.20 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.22), residues: 1248 helix: -1.11 (0.16), residues: 860 sheet: None (None), residues: 0 loop : -1.83 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 271 HIS 0.006 0.002 HIS A 134 PHE 0.043 0.002 PHE A 438 TYR 0.014 0.001 TYR A 305 ARG 0.005 0.000 ARG B 69 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 303 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 LEU cc_start: 0.9140 (tp) cc_final: 0.8815 (tt) REVERT: A 95 LYS cc_start: 0.8404 (tttt) cc_final: 0.8171 (tttt) REVERT: A 96 ASN cc_start: 0.8396 (p0) cc_final: 0.7634 (p0) REVERT: A 119 GLU cc_start: 0.7590 (tp30) cc_final: 0.7356 (tm-30) REVERT: A 121 ILE cc_start: 0.9187 (mm) cc_final: 0.8839 (mm) REVERT: A 194 ILE cc_start: 0.8096 (mt) cc_final: 0.7845 (mp) REVERT: A 354 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.8054 (tp) REVERT: A 387 GLU cc_start: 0.9099 (mm-30) cc_final: 0.8790 (mm-30) REVERT: A 612 ASN cc_start: 0.6919 (OUTLIER) cc_final: 0.6541 (p0) REVERT: A 632 TRP cc_start: 0.8630 (p-90) cc_final: 0.8425 (p-90) REVERT: A 637 GLU cc_start: 0.7632 (mt-10) cc_final: 0.7117 (tm-30) REVERT: B 76 LEU cc_start: 0.9139 (tp) cc_final: 0.8861 (tt) REVERT: B 95 LYS cc_start: 0.8428 (tttt) cc_final: 0.8206 (tttt) REVERT: B 96 ASN cc_start: 0.8385 (p0) cc_final: 0.7633 (p0) REVERT: B 119 GLU cc_start: 0.7586 (tp30) cc_final: 0.7323 (tm-30) REVERT: B 121 ILE cc_start: 0.9129 (mm) cc_final: 0.8778 (mm) REVERT: B 124 GLU cc_start: 0.9289 (mt-10) cc_final: 0.9082 (mt-10) REVERT: B 127 THR cc_start: 0.8690 (m) cc_final: 0.8459 (p) REVERT: B 141 TYR cc_start: 0.8649 (p90) cc_final: 0.8411 (p90) REVERT: B 194 ILE cc_start: 0.8111 (mt) cc_final: 0.7845 (mp) REVERT: B 212 MET cc_start: 0.8716 (mtp) cc_final: 0.8106 (ttm) REVERT: B 275 TYR cc_start: 0.8312 (t80) cc_final: 0.7946 (t80) REVERT: B 326 MET cc_start: 0.8383 (tpt) cc_final: 0.8072 (tpt) REVERT: B 372 PHE cc_start: 0.7875 (m-10) cc_final: 0.7603 (m-10) REVERT: B 434 TYR cc_start: 0.4842 (OUTLIER) cc_final: 0.4372 (m-80) REVERT: B 544 LEU cc_start: 0.8441 (tp) cc_final: 0.8204 (tt) REVERT: B 560 THR cc_start: 0.8952 (p) cc_final: 0.8741 (t) REVERT: B 637 GLU cc_start: 0.7862 (mt-10) cc_final: 0.7146 (tm-30) REVERT: B 683 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7829 (mt-10) outliers start: 22 outliers final: 13 residues processed: 314 average time/residue: 0.1899 time to fit residues: 86.7324 Evaluate side-chains 295 residues out of total 1140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 279 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 612 ASN Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 434 TYR Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 613 PHE Chi-restraints excluded: chain B residue 679 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 6.9990 chunk 109 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 30 optimal weight: 8.9990 chunk 121 optimal weight: 0.8980 chunk 101 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 64 optimal weight: 0.7980 chunk 117 optimal weight: 4.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 549 GLN B 585 GLN ** B 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 625 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 0.4398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10924 Z= 0.229 Angle : 0.658 9.263 14764 Z= 0.325 Chirality : 0.041 0.135 1650 Planarity : 0.003 0.029 1794 Dihedral : 12.239 76.777 1704 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 3.35 % Allowed : 21.23 % Favored : 75.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.23), residues: 1248 helix: -0.88 (0.17), residues: 864 sheet: None (None), residues: 0 loop : -1.93 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 271 HIS 0.005 0.001 HIS A 134 PHE 0.022 0.002 PHE A 226 TYR 0.015 0.002 TYR A 305 ARG 0.005 0.000 ARG A 69 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 287 time to evaluate : 1.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 LEU cc_start: 0.9134 (tp) cc_final: 0.8934 (mt) REVERT: A 96 ASN cc_start: 0.8531 (p0) cc_final: 0.7771 (p0) REVERT: A 119 GLU cc_start: 0.7578 (tp30) cc_final: 0.7361 (tm-30) REVERT: A 121 ILE cc_start: 0.9160 (mm) cc_final: 0.8823 (mm) REVERT: A 194 ILE cc_start: 0.8161 (mt) cc_final: 0.7870 (mp) REVERT: A 387 GLU cc_start: 0.9095 (mm-30) cc_final: 0.8808 (mm-30) REVERT: A 632 TRP cc_start: 0.8717 (p-90) cc_final: 0.8464 (p-90) REVERT: A 637 GLU cc_start: 0.7712 (mt-10) cc_final: 0.7086 (tm-30) REVERT: B 96 ASN cc_start: 0.8491 (p0) cc_final: 0.7759 (p0) REVERT: B 119 GLU cc_start: 0.7570 (tp30) cc_final: 0.7310 (tm-30) REVERT: B 121 ILE cc_start: 0.9132 (mm) cc_final: 0.8792 (mm) REVERT: B 141 TYR cc_start: 0.8575 (p90) cc_final: 0.8364 (p90) REVERT: B 194 ILE cc_start: 0.8171 (mt) cc_final: 0.7888 (mp) REVERT: B 212 MET cc_start: 0.8796 (mtp) cc_final: 0.8111 (ttm) REVERT: B 434 TYR cc_start: 0.4728 (OUTLIER) cc_final: 0.4322 (m-80) REVERT: B 438 PHE cc_start: 0.7387 (m-80) cc_final: 0.7065 (m-80) REVERT: B 544 LEU cc_start: 0.8433 (tp) cc_final: 0.8189 (tp) REVERT: B 637 GLU cc_start: 0.7888 (mt-10) cc_final: 0.7161 (tm-30) REVERT: B 683 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7827 (mt-10) outliers start: 36 outliers final: 23 residues processed: 307 average time/residue: 0.1954 time to fit residues: 87.7201 Evaluate side-chains 295 residues out of total 1140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 271 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 347 CYS Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 434 TYR Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 491 TYR Chi-restraints excluded: chain A residue 499 PHE Chi-restraints excluded: chain A residue 648 SER Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 434 TYR Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 613 PHE Chi-restraints excluded: chain B residue 648 SER Chi-restraints excluded: chain B residue 679 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 0.9980 chunk 69 optimal weight: 0.1980 chunk 89 optimal weight: 0.5980 chunk 68 optimal weight: 0.8980 chunk 102 optimal weight: 6.9990 chunk 121 optimal weight: 0.8980 chunk 76 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 48 optimal weight: 0.4980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 618 ASN B 625 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.4671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10924 Z= 0.170 Angle : 0.641 10.586 14764 Z= 0.311 Chirality : 0.040 0.158 1650 Planarity : 0.003 0.033 1794 Dihedral : 11.876 76.929 1704 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 2.79 % Allowed : 22.16 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.23), residues: 1248 helix: -0.62 (0.17), residues: 866 sheet: None (None), residues: 0 loop : -1.98 (0.33), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 271 HIS 0.005 0.001 HIS B 134 PHE 0.023 0.001 PHE A 226 TYR 0.015 0.001 TYR A 475 ARG 0.007 0.000 ARG A 69 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 285 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 LEU cc_start: 0.9090 (tp) cc_final: 0.8731 (tt) REVERT: A 96 ASN cc_start: 0.8386 (p0) cc_final: 0.7715 (p0) REVERT: A 121 ILE cc_start: 0.9137 (mm) cc_final: 0.8783 (mm) REVERT: A 194 ILE cc_start: 0.8282 (mt) cc_final: 0.8004 (mp) REVERT: A 354 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.8021 (tp) REVERT: A 387 GLU cc_start: 0.9080 (mm-30) cc_final: 0.8814 (mm-30) REVERT: A 576 LEU cc_start: 0.9109 (tp) cc_final: 0.8888 (mp) REVERT: A 632 TRP cc_start: 0.8604 (p-90) cc_final: 0.8384 (p-90) REVERT: A 637 GLU cc_start: 0.7718 (mt-10) cc_final: 0.7068 (tm-30) REVERT: B 81 LEU cc_start: 0.8927 (tp) cc_final: 0.8613 (tt) REVERT: B 96 ASN cc_start: 0.8430 (p0) cc_final: 0.7749 (p0) REVERT: B 121 ILE cc_start: 0.9186 (mm) cc_final: 0.8839 (mm) REVERT: B 194 ILE cc_start: 0.8169 (mt) cc_final: 0.7895 (mp) REVERT: B 212 MET cc_start: 0.8820 (mtp) cc_final: 0.8567 (mtt) REVERT: B 434 TYR cc_start: 0.4723 (OUTLIER) cc_final: 0.4333 (m-80) REVERT: B 438 PHE cc_start: 0.7464 (m-80) cc_final: 0.7249 (m-80) REVERT: B 613 PHE cc_start: 0.8064 (OUTLIER) cc_final: 0.7825 (m-80) REVERT: B 637 GLU cc_start: 0.7804 (mt-10) cc_final: 0.7142 (tm-30) outliers start: 30 outliers final: 18 residues processed: 304 average time/residue: 0.1964 time to fit residues: 87.3766 Evaluate side-chains 287 residues out of total 1140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 266 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 434 TYR Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 491 TYR Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 434 TYR Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 499 PHE Chi-restraints excluded: chain B residue 613 PHE Chi-restraints excluded: chain B residue 648 SER Chi-restraints excluded: chain B residue 679 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 4.9990 chunk 36 optimal weight: 0.0770 chunk 23 optimal weight: 0.6980 chunk 77 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 chunk 60 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 95 optimal weight: 4.9990 chunk 110 optimal weight: 0.6980 chunk 116 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 585 GLN ** B 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 625 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7115 moved from start: 0.4869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10924 Z= 0.174 Angle : 0.651 10.578 14764 Z= 0.313 Chirality : 0.040 0.154 1650 Planarity : 0.003 0.031 1794 Dihedral : 11.587 76.770 1704 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 1.96 % Allowed : 24.12 % Favored : 73.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.23), residues: 1248 helix: -0.39 (0.17), residues: 854 sheet: None (None), residues: 0 loop : -2.04 (0.32), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 632 HIS 0.005 0.001 HIS A 134 PHE 0.026 0.001 PHE B 226 TYR 0.015 0.001 TYR A 551 ARG 0.006 0.000 ARG A 69 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 274 time to evaluate : 1.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 LEU cc_start: 0.9063 (tp) cc_final: 0.8682 (tt) REVERT: A 96 ASN cc_start: 0.8402 (p0) cc_final: 0.7752 (p0) REVERT: A 121 ILE cc_start: 0.9057 (mm) cc_final: 0.8678 (mm) REVERT: A 194 ILE cc_start: 0.8236 (mt) cc_final: 0.7917 (mp) REVERT: A 354 LEU cc_start: 0.8305 (tp) cc_final: 0.8019 (tp) REVERT: A 387 GLU cc_start: 0.9073 (mm-30) cc_final: 0.8822 (mm-30) REVERT: A 637 GLU cc_start: 0.7751 (mt-10) cc_final: 0.7060 (tm-30) REVERT: A 640 LYS cc_start: 0.7925 (tmmt) cc_final: 0.7676 (tmmt) REVERT: A 673 GLU cc_start: 0.8000 (tp30) cc_final: 0.7752 (tp30) REVERT: B 81 LEU cc_start: 0.8922 (tp) cc_final: 0.8635 (tt) REVERT: B 96 ASN cc_start: 0.8469 (p0) cc_final: 0.7828 (p0) REVERT: B 121 ILE cc_start: 0.9120 (mm) cc_final: 0.8784 (mm) REVERT: B 139 ILE cc_start: 0.8881 (mt) cc_final: 0.8504 (pt) REVERT: B 194 ILE cc_start: 0.8180 (mt) cc_final: 0.7885 (mp) REVERT: B 212 MET cc_start: 0.8813 (mtp) cc_final: 0.8580 (mtt) REVERT: B 434 TYR cc_start: 0.4672 (OUTLIER) cc_final: 0.4296 (m-80) REVERT: B 438 PHE cc_start: 0.7393 (m-80) cc_final: 0.7163 (m-80) REVERT: B 552 ARG cc_start: 0.8088 (tpt-90) cc_final: 0.7754 (tpp80) REVERT: B 632 TRP cc_start: 0.8553 (p-90) cc_final: 0.8304 (p-90) REVERT: B 637 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7220 (tm-30) outliers start: 21 outliers final: 16 residues processed: 289 average time/residue: 0.1988 time to fit residues: 83.6241 Evaluate side-chains 284 residues out of total 1140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 267 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 LYS Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 347 CYS Chi-restraints excluded: chain A residue 434 TYR Chi-restraints excluded: chain A residue 491 TYR Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 434 TYR Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 648 SER Chi-restraints excluded: chain B residue 650 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 0.8980 chunk 116 optimal weight: 3.9990 chunk 68 optimal weight: 0.0970 chunk 49 optimal weight: 3.9990 chunk 88 optimal weight: 0.4980 chunk 34 optimal weight: 3.9990 chunk 102 optimal weight: 0.0270 chunk 107 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 chunk 74 optimal weight: 0.9980 chunk 119 optimal weight: 0.9980 overall best weight: 0.5036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 585 GLN ** B 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 625 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.5068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10924 Z= 0.167 Angle : 0.648 10.888 14764 Z= 0.310 Chirality : 0.039 0.149 1650 Planarity : 0.003 0.038 1794 Dihedral : 11.337 76.887 1702 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 1.96 % Allowed : 24.86 % Favored : 73.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.23), residues: 1248 helix: -0.27 (0.17), residues: 854 sheet: None (None), residues: 0 loop : -2.11 (0.32), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 632 HIS 0.005 0.001 HIS B 134 PHE 0.027 0.001 PHE B 226 TYR 0.015 0.001 TYR A 551 ARG 0.004 0.000 ARG B 62 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 273 time to evaluate : 1.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 LEU cc_start: 0.8994 (tp) cc_final: 0.8590 (tt) REVERT: A 96 ASN cc_start: 0.8403 (p0) cc_final: 0.7789 (p0) REVERT: A 121 ILE cc_start: 0.9000 (mm) cc_final: 0.8611 (mm) REVERT: A 194 ILE cc_start: 0.8282 (mt) cc_final: 0.7972 (mp) REVERT: A 305 TYR cc_start: 0.8548 (t80) cc_final: 0.8268 (t80) REVERT: A 354 LEU cc_start: 0.8331 (tp) cc_final: 0.8056 (tp) REVERT: A 387 GLU cc_start: 0.9076 (mm-30) cc_final: 0.8821 (mm-30) REVERT: A 637 GLU cc_start: 0.7791 (mt-10) cc_final: 0.7085 (tm-30) REVERT: A 640 LYS cc_start: 0.7894 (tmmt) cc_final: 0.7646 (tmmt) REVERT: A 673 GLU cc_start: 0.7998 (tp30) cc_final: 0.7681 (tp30) REVERT: B 96 ASN cc_start: 0.8444 (p0) cc_final: 0.7814 (p0) REVERT: B 121 ILE cc_start: 0.9085 (mm) cc_final: 0.8731 (mm) REVERT: B 139 ILE cc_start: 0.8832 (mt) cc_final: 0.8442 (pt) REVERT: B 194 ILE cc_start: 0.8192 (mt) cc_final: 0.7884 (mp) REVERT: B 212 MET cc_start: 0.8750 (mtp) cc_final: 0.8510 (mtt) REVERT: B 305 TYR cc_start: 0.8525 (t80) cc_final: 0.8230 (t80) REVERT: B 434 TYR cc_start: 0.4624 (OUTLIER) cc_final: 0.4255 (m-80) REVERT: B 438 PHE cc_start: 0.7394 (m-80) cc_final: 0.7191 (m-80) REVERT: B 552 ARG cc_start: 0.8097 (tpt-90) cc_final: 0.7743 (tpp80) REVERT: B 637 GLU cc_start: 0.7827 (mt-10) cc_final: 0.7228 (tm-30) outliers start: 21 outliers final: 15 residues processed: 288 average time/residue: 0.2078 time to fit residues: 87.2016 Evaluate side-chains 277 residues out of total 1140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 261 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 347 CYS Chi-restraints excluded: chain A residue 434 TYR Chi-restraints excluded: chain A residue 491 TYR Chi-restraints excluded: chain A residue 648 SER Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 434 TYR Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 648 SER Chi-restraints excluded: chain B residue 650 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 83 optimal weight: 0.9990 chunk 125 optimal weight: 2.9990 chunk 115 optimal weight: 0.6980 chunk 99 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 61 optimal weight: 0.6980 chunk 79 optimal weight: 0.0980 chunk 106 optimal weight: 5.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 585 GLN ** B 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 618 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 moved from start: 0.5134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10924 Z= 0.177 Angle : 0.658 11.321 14764 Z= 0.315 Chirality : 0.040 0.150 1650 Planarity : 0.003 0.030 1794 Dihedral : 11.230 76.875 1702 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 1.58 % Allowed : 25.14 % Favored : 73.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.23), residues: 1248 helix: -0.16 (0.17), residues: 854 sheet: None (None), residues: 0 loop : -2.09 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 271 HIS 0.005 0.001 HIS B 134 PHE 0.029 0.001 PHE A 226 TYR 0.024 0.001 TYR B 63 ARG 0.004 0.000 ARG B 69 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 273 time to evaluate : 1.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 LEU cc_start: 0.8990 (tp) cc_final: 0.8587 (tt) REVERT: A 96 ASN cc_start: 0.8433 (p0) cc_final: 0.7826 (p0) REVERT: A 121 ILE cc_start: 0.9035 (mm) cc_final: 0.8655 (mm) REVERT: A 194 ILE cc_start: 0.8287 (mt) cc_final: 0.7974 (mp) REVERT: A 354 LEU cc_start: 0.8340 (tp) cc_final: 0.8073 (tp) REVERT: A 387 GLU cc_start: 0.9079 (mm-30) cc_final: 0.8827 (mm-30) REVERT: A 637 GLU cc_start: 0.7705 (mt-10) cc_final: 0.7053 (tm-30) REVERT: A 640 LYS cc_start: 0.7929 (tmmt) cc_final: 0.7686 (tmmt) REVERT: A 673 GLU cc_start: 0.8012 (tp30) cc_final: 0.7706 (tp30) REVERT: B 96 ASN cc_start: 0.8481 (p0) cc_final: 0.7865 (p0) REVERT: B 121 ILE cc_start: 0.9119 (mm) cc_final: 0.8767 (mm) REVERT: B 194 ILE cc_start: 0.8211 (mt) cc_final: 0.7867 (mp) REVERT: B 212 MET cc_start: 0.8720 (mtp) cc_final: 0.8474 (mtt) REVERT: B 300 ILE cc_start: 0.8987 (tt) cc_final: 0.8752 (mt) REVERT: B 305 TYR cc_start: 0.8538 (t80) cc_final: 0.8251 (t80) REVERT: B 434 TYR cc_start: 0.4680 (OUTLIER) cc_final: 0.4338 (m-80) REVERT: B 632 TRP cc_start: 0.8375 (p-90) cc_final: 0.8166 (p-90) REVERT: B 637 GLU cc_start: 0.7841 (mt-10) cc_final: 0.7218 (tm-30) outliers start: 17 outliers final: 15 residues processed: 284 average time/residue: 0.1936 time to fit residues: 80.4050 Evaluate side-chains 280 residues out of total 1140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 264 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 347 CYS Chi-restraints excluded: chain A residue 434 TYR Chi-restraints excluded: chain A residue 491 TYR Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 434 TYR Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 648 SER Chi-restraints excluded: chain B residue 650 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 100 optimal weight: 5.9990 chunk 41 optimal weight: 0.5980 chunk 102 optimal weight: 0.3980 chunk 12 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 625 ASN B 585 GLN ** B 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 625 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.205998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.165435 restraints weight = 16168.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.169535 restraints weight = 7510.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.172025 restraints weight = 4573.048| |-----------------------------------------------------------------------------| r_work (final): 0.4110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.5231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10924 Z= 0.186 Angle : 0.656 11.386 14764 Z= 0.317 Chirality : 0.040 0.154 1650 Planarity : 0.003 0.031 1794 Dihedral : 11.145 76.972 1702 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 1.68 % Allowed : 25.61 % Favored : 72.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.24), residues: 1248 helix: -0.06 (0.18), residues: 852 sheet: None (None), residues: 0 loop : -2.11 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 271 HIS 0.005 0.001 HIS A 134 PHE 0.029 0.001 PHE A 226 TYR 0.020 0.001 TYR B 63 ARG 0.007 0.000 ARG A 69 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2452.33 seconds wall clock time: 44 minutes 39.64 seconds (2679.64 seconds total)