Starting phenix.real_space_refine on Fri Jan 19 18:46:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e1p_8960/01_2024/6e1p_8960_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e1p_8960/01_2024/6e1p_8960.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/6e1p_8960/01_2024/6e1p_8960.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e1p_8960/01_2024/6e1p_8960.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e1p_8960/01_2024/6e1p_8960_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e1p_8960/01_2024/6e1p_8960_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 1632 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 5 9.91 5 P 6 5.49 5 S 46 5.16 5 C 7154 2.51 5 N 1588 2.21 5 O 1898 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 151": "NH1" <-> "NH2" Residue "A PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 358": "NH1" <-> "NH2" Residue "A ARG 379": "NH1" <-> "NH2" Residue "A ARG 493": "NH1" <-> "NH2" Residue "B ARG 151": "NH1" <-> "NH2" Residue "B PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 358": "NH1" <-> "NH2" Residue "B ARG 379": "NH1" <-> "NH2" Residue "B ARG 493": "NH1" <-> "NH2" Residue "B TYR 532": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 10697 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 646, 5201 Classifications: {'peptide': 646} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 20, 'TRANS': 625} Chain breaks: 3 Unresolved non-hydrogen bonds: 142 Unresolved non-hydrogen angles: 184 Unresolved non-hydrogen dihedrals: 130 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'TPO:plan-1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 3, 'ASP:plan': 3, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 100 Chain: "B" Number of atoms: 5201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 646, 5201 Classifications: {'peptide': 646} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 20, 'TRANS': 625} Chain breaks: 3 Unresolved non-hydrogen bonds: 142 Unresolved non-hydrogen angles: 184 Unresolved non-hydrogen dihedrals: 130 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'TPO:plan-1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 3, 'ASP:plan': 3, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 100 Chain: "A" Number of atoms: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 146 Unusual residues: {' CA': 2, 'PLM': 8} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "B" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 147 Unusual residues: {' CA': 3, 'PLM': 8} Classifications: {'undetermined': 11} Link IDs: {None: 10} 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: 5.74, per 1000 atoms: 0.54 Number of scatterers: 10697 At special positions: 0 Unit cell: (127.638, 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 5 19.99 S 46 16.00 P 6 15.00 O 1898 8.00 N 1588 7.00 C 7154 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=9, symmetry=0 Number of additional bonds: simple=9, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.43 Conformation dependent library (CDL) restraints added in 1.8 seconds 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2464 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 65 helices and 0 sheets defined 67.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.36 Creating SS restraints... Processing helix chain 'A' and resid 36 through 45 removed outlier: 3.606A pdb=" N LEU A 40 " --> pdb=" O ALA A 36 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE A 45 " --> pdb=" O ALA A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 56 Processing helix chain 'A' and resid 64 through 73 Processing helix chain 'A' and resid 75 through 91 removed outlier: 3.873A pdb=" N GLU A 88 " --> pdb=" O LEU A 84 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N GLN A 89 " --> pdb=" O ASN A 85 " (cutoff:3.500A) Proline residue: A 90 - end of helix Processing helix chain 'A' and resid 117 through 139 removed outlier: 3.730A pdb=" N ILE A 121 " --> pdb=" O ASN A 117 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ILE A 122 " --> pdb=" O ALA A 118 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TYR A 123 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR A 127 " --> pdb=" O TYR A 123 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE A 130 " --> pdb=" O ILE A 126 " (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 153 through 172 removed outlier: 3.759A pdb=" N ALA A 158 " --> pdb=" O LEU A 154 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU A 168 " --> pdb=" O PHE A 164 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASP A 170 " --> pdb=" O ASP A 166 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N PHE A 171 " --> pdb=" O VAL A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 198 removed outlier: 3.624A pdb=" N VAL A 192 " --> pdb=" O PRO A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 210 removed outlier: 3.912A pdb=" N LEU A 208 " --> pdb=" O ASP A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 237 removed outlier: 3.559A pdb=" N ASN A 218 " --> pdb=" O GLY A 214 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA A 221 " --> pdb=" O LEU A 217 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU A 222 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE A 226 " --> pdb=" O LEU A 222 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ALA A 230 " --> pdb=" O PHE A 226 " (cutoff:3.500A) removed outlier: 3.783A 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: 3.523A pdb=" N ILE A 260 " --> pdb=" O TYR A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 277 removed outlier: 4.309A pdb=" N TRP A 271 " --> pdb=" O ASN A 267 " (cutoff:3.500A) Proline residue: A 273 - end of helix removed outlier: 3.624A pdb=" N SER A 277 " --> pdb=" O PRO A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 292 removed outlier: 4.289A pdb=" N VAL A 286 " --> pdb=" O VAL A 283 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N VAL A 289 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU A 290 " --> pdb=" O LEU A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 334 removed outlier: 3.714A pdb=" N GLU A 310 " --> pdb=" O ASP A 306 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N MET A 322 " --> pdb=" O GLY A 318 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS A 329 " --> pdb=" O ARG A 325 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE A 334 " --> pdb=" O ALA A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 353 removed outlier: 4.377A pdb=" N LEU A 350 " --> pdb=" O GLN A 346 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N PHE A 351 " --> pdb=" O CYS A 347 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N GLU A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLN A 353 " --> pdb=" O LYS A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 370 Processing helix chain 'A' and resid 385 through 398 removed outlier: 3.572A pdb=" N ALA A 389 " --> pdb=" O LYS A 385 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLN A 393 " --> pdb=" O ALA A 389 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA A 394 " --> pdb=" O ASP A 390 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ALA A 396 " --> pdb=" O CYS A 392 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N LEU A 397 " --> pdb=" O GLN A 393 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG A 398 " --> pdb=" O ALA A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 452 removed outlier: 4.120A pdb=" N LEU A 440 " --> pdb=" O ILE A 436 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ILE A 441 " --> pdb=" O SER A 437 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL A 447 " --> pdb=" O ASN A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 477 removed outlier: 3.690A pdb=" N VAL A 466 " --> pdb=" O LYS A 462 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ALA A 467 " --> pdb=" O PRO A 463 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE A 469 " --> pdb=" O GLN A 465 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N VAL A 470 " --> pdb=" O VAL A 466 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N PHE A 471 " --> pdb=" O ALA A 467 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N GLY A 472 " --> pdb=" O GLU A 468 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N TRP A 473 " --> pdb=" O PHE A 469 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N TYR A 475 " --> pdb=" O PHE A 471 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N VAL A 476 " --> pdb=" O GLY A 472 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N LEU A 477 " --> pdb=" O TRP A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 485 removed outlier: 3.568A pdb=" N TYR A 484 " --> pdb=" O ALA A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 499 Processing helix chain 'A' and resid 501 through 512 removed outlier: 3.591A pdb=" N TRP A 505 " --> pdb=" O PHE A 501 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ILE A 507 " --> pdb=" O VAL A 503 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N VAL A 508 " --> pdb=" O THR A 504 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ILE A 509 " --> pdb=" O TRP A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 532 removed outlier: 3.675A pdb=" N TRP A 529 " --> pdb=" O SER A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 547 removed outlier: 3.811A pdb=" N ARG A 543 " --> pdb=" O LEU A 539 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N MET A 546 " --> pdb=" O ILE A 542 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ASN A 547 " --> pdb=" O ARG A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 586 removed outlier: 5.684A pdb=" N ALA A 553 " --> pdb=" O ARG A 550 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ILE A 555 " --> pdb=" O ARG A 552 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA A 556 " --> pdb=" O ALA A 553 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR A 557 " --> pdb=" O PHE A 554 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ILE A 559 " --> pdb=" O ALA A 556 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE A 562 " --> pdb=" O ILE A 559 " (cutoff:3.500A) Proline residue: A 563 - end of helix Proline residue: A 567 - end of helix removed outlier: 4.231A pdb=" N THR A 571 " --> pdb=" O TYR A 568 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU A 576 " --> pdb=" O PHE A 573 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N CYS A 580 " --> pdb=" O CYS A 577 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE A 582 " --> pdb=" O TYR A 579 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N VAL A 584 " --> pdb=" O SER A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 599 No H-bonds generated for 'chain 'A' and resid 596 through 599' 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 616 through 628 removed outlier: 3.525A pdb=" N VAL A 621 " --> pdb=" O PRO A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 642 removed outlier: 3.843A pdb=" N ASP A 641 " --> pdb=" O GLU A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 666 removed outlier: 3.573A pdb=" N ILE A 658 " --> pdb=" O SER A 654 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LEU A 664 " --> pdb=" O ILE A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 692 removed outlier: 3.584A pdb=" N LEU A 672 " --> pdb=" O VAL A 668 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE A 676 " --> pdb=" O LEU A 672 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP A 680 " --> pdb=" O PHE A 676 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU A 681 " --> pdb=" O THR A 677 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU A 682 " --> pdb=" O GLU A 678 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LYS A 686 " --> pdb=" O GLU A 682 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N CYS A 687 " --> pdb=" O GLU A 683 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLN A 690 " --> pdb=" O LYS A 686 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ASP A 691 " --> pdb=" O CYS A 687 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 45 removed outlier: 3.536A pdb=" N LEU B 40 " --> pdb=" O ALA B 36 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE B 45 " --> pdb=" O ALA B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 56 Processing helix chain 'B' and resid 65 through 73 removed outlier: 3.506A pdb=" N LEU B 72 " --> pdb=" O THR B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 91 removed outlier: 3.778A pdb=" N GLU B 88 " --> pdb=" O LEU B 84 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N GLN B 89 " --> pdb=" O ASN B 85 " (cutoff:3.500A) Proline residue: B 90 - end of helix Processing helix chain 'B' and resid 117 through 139 removed outlier: 3.720A pdb=" N ILE B 122 " --> pdb=" O ALA B 118 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR B 123 " --> pdb=" O GLU B 119 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU B 124 " --> pdb=" O SER B 120 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR B 127 " --> pdb=" O TYR B 123 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE B 130 " --> pdb=" O ILE B 126 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE B 136 " --> pdb=" O LEU B 132 " (cutoff:3.500A) Proline residue: B 138 - end of helix Processing helix chain 'B' and resid 144 through 149 removed outlier: 4.308A pdb=" N THR B 149 " --> pdb=" O ARG B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 172 removed outlier: 3.603A pdb=" N ALA B 158 " --> pdb=" O LEU B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 198 removed outlier: 3.631A pdb=" N VAL B 192 " --> pdb=" O PRO B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 210 removed outlier: 3.905A pdb=" N LEU B 208 " --> pdb=" O ASP B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 237 removed outlier: 3.701A pdb=" N ASN B 218 " --> pdb=" O GLY B 214 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA B 221 " --> pdb=" O LEU B 217 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU B 222 " --> pdb=" O ASN B 218 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ALA B 230 " --> pdb=" O PHE B 226 " (cutoff:3.500A) removed outlier: 3.818A 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: 3.523A pdb=" N ILE B 260 " --> pdb=" O TYR B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 277 removed outlier: 4.289A pdb=" N TRP B 271 " --> pdb=" O ASN B 267 " (cutoff:3.500A) Proline residue: B 273 - end of helix removed outlier: 3.581A pdb=" N SER B 277 " --> pdb=" O PRO B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 292 removed outlier: 3.511A pdb=" N VAL B 283 " --> pdb=" O TRP B 280 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N VAL B 286 " --> pdb=" O VAL B 283 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N VAL B 289 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU B 290 " --> pdb=" O LEU B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 334 removed outlier: 3.719A pdb=" N GLU B 310 " --> pdb=" O ASP B 306 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N MET B 322 " --> pdb=" O GLY B 318 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS B 329 " --> pdb=" O ARG B 325 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE B 334 " --> pdb=" O ALA B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 354 removed outlier: 4.409A pdb=" N LEU B 350 " --> pdb=" O GLN B 346 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N PHE B 351 " --> pdb=" O CYS B 347 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N GLU B 352 " --> pdb=" O ILE B 348 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLN B 353 " --> pdb=" O LYS B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 370 removed outlier: 3.568A pdb=" N PHE B 368 " --> pdb=" O SER B 364 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N GLY B 369 " --> pdb=" O LYS B 365 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU B 370 " --> pdb=" O GLU B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 398 removed outlier: 3.563A pdb=" N ALA B 389 " --> pdb=" O LYS B 385 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLN B 393 " --> pdb=" O ALA B 389 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ALA B 396 " --> pdb=" O CYS B 392 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N LEU B 397 " --> pdb=" O GLN B 393 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG B 398 " --> pdb=" O ALA B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 435 Processing helix chain 'B' and resid 439 through 454 removed outlier: 3.955A pdb=" N VAL B 447 " --> pdb=" O ASN B 443 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL B 448 " --> pdb=" O PHE B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 477 removed outlier: 3.728A pdb=" N VAL B 466 " --> pdb=" O LYS B 462 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ALA B 467 " --> pdb=" O PRO B 463 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N PHE B 469 " --> pdb=" O GLN B 465 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N VAL B 470 " --> pdb=" O VAL B 466 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N PHE B 471 " --> pdb=" O ALA B 467 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N GLY B 472 " --> pdb=" O GLU B 468 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N TRP B 473 " --> pdb=" O PHE B 469 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE B 474 " --> pdb=" O VAL B 470 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N TYR B 475 " --> pdb=" O PHE B 471 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N VAL B 476 " --> pdb=" O GLY B 472 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N LEU B 477 " --> pdb=" O TRP B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 485 removed outlier: 3.504A pdb=" N TYR B 484 " --> pdb=" O ALA B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 499 Processing helix chain 'B' and resid 501 through 512 removed outlier: 3.569A pdb=" N TRP B 505 " --> pdb=" O PHE B 501 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ILE B 507 " --> pdb=" O VAL B 503 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N VAL B 508 " --> pdb=" O THR B 504 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ILE B 509 " --> pdb=" O TRP B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 527 through 531 removed outlier: 3.827A pdb=" N ARG B 531 " --> pdb=" O GLY B 527 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 527 through 531' Processing helix chain 'B' and resid 537 through 547 removed outlier: 3.637A pdb=" N ARG B 543 " --> pdb=" O LEU B 539 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN B 547 " --> pdb=" O ARG B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 586 removed outlier: 5.671A pdb=" N ALA B 553 " --> pdb=" O ARG B 550 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA B 556 " --> pdb=" O ALA B 553 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N THR B 557 " --> pdb=" O PHE B 554 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE B 559 " --> pdb=" O ALA B 556 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU B 561 " --> pdb=" O PHE B 558 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE B 562 " --> pdb=" O ILE B 559 " (cutoff:3.500A) Proline residue: B 563 - end of helix Proline residue: B 567 - end of helix removed outlier: 4.217A pdb=" N THR B 571 " --> pdb=" O TYR B 568 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU B 576 " --> pdb=" O PHE B 573 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N CYS B 580 " --> pdb=" O CYS B 577 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE B 582 " --> pdb=" O TYR B 579 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N VAL B 584 " --> pdb=" O SER B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 599 No H-bonds generated for 'chain 'B' and resid 596 through 599' 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 616 through 628 removed outlier: 3.526A pdb=" N VAL B 621 " --> pdb=" O PRO B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 642 removed outlier: 3.863A pdb=" N ASP B 641 " --> pdb=" O GLU B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 665 removed outlier: 3.569A pdb=" N ILE B 658 " --> pdb=" O SER B 654 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N LEU B 664 " --> pdb=" O ILE B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 692 removed outlier: 3.624A pdb=" N LEU B 672 " --> pdb=" O VAL B 668 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE B 676 " --> pdb=" O LEU B 672 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP B 680 " --> pdb=" O PHE B 676 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU B 681 " --> pdb=" O THR B 677 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU B 682 " --> pdb=" O GLU B 678 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS B 686 " --> pdb=" O GLU B 682 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N CYS B 687 " --> pdb=" O GLU B 683 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASP B 691 " --> pdb=" O CYS B 687 " (cutoff:3.500A) 421 hydrogen bonds defined for protein. 1110 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: 2.90 Time building geometry restraints manager: 4.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3049 1.34 - 1.46: 2399 1.46 - 1.58: 5400 1.58 - 1.70: 20 1.70 - 1.82: 74 Bond restraints: 10942 Sorted by residual: bond pdb=" OG1 TPO B 29 " pdb=" P TPO B 29 " ideal model delta sigma weight residual 1.717 1.604 0.113 2.00e-02 2.50e+03 3.18e+01 bond pdb=" OG1 TPO A 29 " pdb=" P TPO A 29 " ideal model delta sigma weight residual 1.717 1.604 0.113 2.00e-02 2.50e+03 3.17e+01 bond pdb=" OG1 TPO A 26 " pdb=" P TPO A 26 " ideal model delta sigma weight residual 1.717 1.611 0.106 2.00e-02 2.50e+03 2.83e+01 bond pdb=" OG1 TPO B 26 " pdb=" P TPO B 26 " ideal model delta sigma weight residual 1.717 1.611 0.106 2.00e-02 2.50e+03 2.80e+01 bond pdb=" O1P TPO A 26 " pdb=" P TPO A 26 " ideal model delta sigma weight residual 1.525 1.610 -0.085 2.00e-02 2.50e+03 1.80e+01 ... (remaining 10937 not shown) Histogram of bond angle deviations from ideal: 97.84 - 105.28: 163 105.28 - 112.73: 5646 112.73 - 120.17: 4465 120.17 - 127.62: 4429 127.62 - 135.07: 105 Bond angle restraints: 14808 Sorted by residual: angle pdb=" N PHE B 611 " pdb=" CA PHE B 611 " pdb=" CB PHE B 611 " ideal model delta sigma weight residual 110.49 99.93 10.56 1.69e+00 3.50e-01 3.90e+01 angle pdb=" C LEU B 610 " pdb=" N PHE B 611 " pdb=" CA PHE B 611 " ideal model delta sigma weight residual 121.54 131.71 -10.17 1.91e+00 2.74e-01 2.84e+01 angle pdb=" C SER A 150 " pdb=" N ARG A 151 " pdb=" CA ARG A 151 " ideal model delta sigma weight residual 121.54 131.63 -10.09 1.91e+00 2.74e-01 2.79e+01 angle pdb=" N ASN B 612 " pdb=" CA ASN B 612 " pdb=" C ASN B 612 " ideal model delta sigma weight residual 110.80 121.78 -10.98 2.13e+00 2.20e-01 2.66e+01 angle pdb=" C ILE B 371 " pdb=" N PHE B 372 " pdb=" CA PHE B 372 " ideal model delta sigma weight residual 120.79 127.69 -6.90 1.39e+00 5.18e-01 2.46e+01 ... (remaining 14803 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.01: 5742 15.01 - 30.02: 425 30.02 - 45.03: 138 45.03 - 60.03: 75 60.03 - 75.04: 2 Dihedral angle restraints: 6382 sinusoidal: 2568 harmonic: 3814 Sorted by residual: dihedral pdb=" CA LEU B 610 " pdb=" C LEU B 610 " pdb=" N PHE B 611 " pdb=" CA PHE B 611 " ideal model delta harmonic sigma weight residual -180.00 -130.54 -49.46 0 5.00e+00 4.00e-02 9.79e+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 180.00 137.35 42.65 0 5.00e+00 4.00e-02 7.27e+01 dihedral pdb=" CA PHE A 611 " pdb=" C PHE A 611 " pdb=" N ASN A 612 " pdb=" CA ASN A 612 " ideal model delta harmonic sigma weight residual -180.00 -137.64 -42.36 0 5.00e+00 4.00e-02 7.18e+01 ... (remaining 6379 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 1469 0.085 - 0.171: 176 0.171 - 0.256: 19 0.256 - 0.342: 2 0.342 - 0.427: 2 Chirality restraints: 1668 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 2.22 0.43 2.00e-01 2.50e+01 4.57e+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 2.22 0.42 2.00e-01 2.50e+01 4.51e+00 chirality pdb=" CB TPO A 29 " pdb=" CA TPO A 29 " pdb=" OG1 TPO A 29 " pdb=" CG2 TPO A 29 " both_signs ideal model delta sigma weight residual False 2.48 2.77 -0.29 2.00e-01 2.50e+01 2.09e+00 ... (remaining 1665 not shown) Planarity restraints: 1810 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 613 " 0.027 2.00e-02 2.50e+03 2.10e-02 7.75e+00 pdb=" CG PHE A 613 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 PHE A 613 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE A 613 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 613 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 613 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 613 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN B 89 " -0.042 5.00e-02 4.00e+02 6.27e-02 6.29e+00 pdb=" N PRO B 90 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO B 90 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 90 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 613 " -0.023 2.00e-02 2.50e+03 1.85e-02 5.96e+00 pdb=" CG PHE B 613 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE B 613 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE B 613 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE B 613 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE B 613 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE B 613 " -0.005 2.00e-02 2.50e+03 ... (remaining 1807 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.24: 7 2.24 - 2.90: 4281 2.90 - 3.57: 15553 3.57 - 4.23: 25060 4.23 - 4.90: 40060 Nonbonded interactions: 84961 Sorted by model distance: nonbonded pdb=" CC PLM A 809 " pdb=" CA PLM B 804 " model vdw 1.571 3.072 nonbonded pdb=" C3 PLM A 810 " pdb=" C5 PLM B 803 " model vdw 1.742 3.072 nonbonded pdb=" O2P TPO A 26 " pdb=" O1P TPO A 29 " model vdw 2.090 3.040 nonbonded pdb=" OE2 GLU B 450 " pdb=" NH2 ARG B 531 " model vdw 2.179 2.520 nonbonded pdb=" OH TYR B 114 " pdb=" OD2 ASP B 615 " model vdw 2.183 2.440 ... (remaining 84956 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' and (resid 22 through 693 or resid 801 or resid 803 through 804 or re \ sid 807 through 810)) selection = (chain 'B' and (resid 22 through 693 or resid 801 or resid 803 through 804 or re \ sid 807 through 810)) } 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: 0.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.000 Extract box with map and model: 4.210 Check model and map are aligned: 0.170 Set scattering table: 0.100 Process input model: 30.480 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.060 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6932 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 : 0.010 0.113 10942 Z= 0.616 Angle : 1.296 12.140 14808 Z= 0.696 Chirality : 0.059 0.427 1668 Planarity : 0.007 0.063 1810 Dihedral : 14.000 75.042 3918 Min Nonbonded Distance : 1.571 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.89 % Favored : 92.95 % Rotamer: Outliers : 0.18 % Allowed : 2.28 % Favored : 97.54 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % 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: -5.32 (0.16), residues: 1262 helix: -3.67 (0.10), residues: 826 sheet: None (None), residues: 0 loop : -2.82 (0.26), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP A 280 HIS 0.002 0.001 HIS A 416 PHE 0.048 0.004 PHE A 613 TYR 0.029 0.004 TYR A 579 ARG 0.007 0.001 ARG A 540 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 489 time to evaluate : 1.091 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 27 HIS cc_start: 0.8048 (t70) cc_final: 0.7767 (t70) REVERT: A 71 ASP cc_start: 0.9382 (t0) cc_final: 0.8974 (t0) REVERT: A 77 ASN cc_start: 0.9363 (m-40) cc_final: 0.9119 (m110) REVERT: A 89 GLN cc_start: 0.8843 (mt0) cc_final: 0.8426 (mt0) REVERT: A 117 ASN cc_start: 0.9336 (m-40) cc_final: 0.8841 (t0) REVERT: A 137 PHE cc_start: 0.9127 (t80) cc_final: 0.8480 (t80) REVERT: A 195 PHE cc_start: 0.8901 (t80) cc_final: 0.8549 (t80) REVERT: A 204 ASP cc_start: 0.8801 (m-30) cc_final: 0.8529 (m-30) REVERT: A 212 MET cc_start: 0.9066 (ttp) cc_final: 0.8229 (ttp) REVERT: A 307 SER cc_start: 0.9323 (m) cc_final: 0.9099 (t) REVERT: A 320 ASP cc_start: 0.9270 (m-30) cc_final: 0.9037 (m-30) REVERT: A 322 MET cc_start: 0.8509 (tmm) cc_final: 0.8038 (tmm) REVERT: A 326 MET cc_start: 0.9053 (mmm) cc_final: 0.8456 (mmp) REVERT: A 333 LEU cc_start: 0.8218 (tp) cc_final: 0.7952 (tt) REVERT: A 450 GLU cc_start: 0.8209 (tm-30) cc_final: 0.7934 (tm-30) REVERT: A 497 ASN cc_start: 0.8911 (m110) cc_final: 0.8564 (m110) REVERT: A 562 ILE cc_start: 0.8974 (mt) cc_final: 0.8561 (mt) REVERT: A 602 GLU cc_start: 0.8549 (mt-10) cc_final: 0.7937 (mp0) REVERT: A 603 LEU cc_start: 0.8028 (mt) cc_final: 0.7788 (mt) REVERT: A 617 PRO cc_start: 0.8316 (Cg_endo) cc_final: 0.8113 (Cg_exo) REVERT: A 620 MET cc_start: 0.8744 (mmm) cc_final: 0.8536 (tpp) REVERT: A 632 TRP cc_start: 0.8810 (p-90) cc_final: 0.8400 (p-90) REVERT: A 637 GLU cc_start: 0.8132 (tp30) cc_final: 0.7313 (tp30) REVERT: A 641 ASP cc_start: 0.9028 (m-30) cc_final: 0.8591 (t0) REVERT: A 648 SER cc_start: 0.9020 (m) cc_final: 0.8521 (p) REVERT: A 673 GLU cc_start: 0.8946 (mm-30) cc_final: 0.8639 (mm-30) REVERT: A 675 PHE cc_start: 0.8181 (t80) cc_final: 0.7852 (t80) REVERT: A 678 GLU cc_start: 0.8268 (mm-30) cc_final: 0.7989 (mm-30) REVERT: B 27 HIS cc_start: 0.8270 (t70) cc_final: 0.7957 (t70) REVERT: B 71 ASP cc_start: 0.9372 (t0) cc_final: 0.8969 (t0) REVERT: B 77 ASN cc_start: 0.9384 (m-40) cc_final: 0.9144 (m110) REVERT: B 137 PHE cc_start: 0.9134 (t80) cc_final: 0.8509 (t80) REVERT: B 195 PHE cc_start: 0.8876 (t80) cc_final: 0.8585 (t80) REVERT: B 204 ASP cc_start: 0.8796 (m-30) cc_final: 0.8526 (m-30) REVERT: B 212 MET cc_start: 0.9053 (ttp) cc_final: 0.8246 (ttp) REVERT: B 232 TRP cc_start: 0.9084 (t60) cc_final: 0.8710 (t60) REVERT: B 307 SER cc_start: 0.9336 (m) cc_final: 0.9092 (t) REVERT: B 320 ASP cc_start: 0.9284 (m-30) cc_final: 0.9052 (m-30) REVERT: B 322 MET cc_start: 0.8503 (tmm) cc_final: 0.8028 (tmm) REVERT: B 326 MET cc_start: 0.9070 (mmm) cc_final: 0.8467 (mmp) REVERT: B 333 LEU cc_start: 0.8213 (tp) cc_final: 0.7916 (tt) REVERT: B 450 GLU cc_start: 0.8215 (tm-30) cc_final: 0.7961 (tm-30) REVERT: B 497 ASN cc_start: 0.8847 (m110) cc_final: 0.8268 (m110) REVERT: B 542 ILE cc_start: 0.8829 (mt) cc_final: 0.8605 (mt) REVERT: B 602 GLU cc_start: 0.8489 (mt-10) cc_final: 0.7820 (mp0) REVERT: B 635 TRP cc_start: 0.9050 (m-90) cc_final: 0.8743 (m-90) REVERT: B 637 GLU cc_start: 0.8091 (tp30) cc_final: 0.7509 (tp30) REVERT: B 641 ASP cc_start: 0.9030 (m-30) cc_final: 0.8592 (t0) REVERT: B 648 SER cc_start: 0.9037 (m) cc_final: 0.8538 (p) REVERT: B 673 GLU cc_start: 0.8969 (mm-30) cc_final: 0.8647 (mm-30) REVERT: B 675 PHE cc_start: 0.8187 (t80) cc_final: 0.7946 (t80) REVERT: B 681 LEU cc_start: 0.7767 (mt) cc_final: 0.7415 (mt) outliers start: 2 outliers final: 2 residues processed: 490 average time/residue: 0.2210 time to fit residues: 159.3275 Evaluate side-chains 348 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 346 time to evaluate : 1.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain B residue 440 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 1.9990 chunk 97 optimal weight: 0.0470 chunk 53 optimal weight: 0.7980 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 6.9990 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 0.0070 chunk 38 optimal weight: 0.0870 chunk 61 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 116 optimal weight: 0.9990 overall best weight: 0.3674 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN A 346 GLN A 549 GLN B 89 GLN B 346 GLN ** B 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 454 ASN B 549 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6865 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10942 Z= 0.171 Angle : 0.692 8.666 14808 Z= 0.343 Chirality : 0.041 0.154 1668 Planarity : 0.005 0.042 1810 Dihedral : 13.207 59.975 1628 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.60 % Favored : 95.25 % Rotamer: Outliers : 2.83 % Allowed : 17.15 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -3.14 (0.21), residues: 1262 helix: -1.98 (0.15), residues: 824 sheet: None (None), residues: 0 loop : -1.96 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 232 HIS 0.003 0.001 HIS B 27 PHE 0.021 0.002 PHE B 554 TYR 0.018 0.001 TYR A 305 ARG 0.006 0.001 ARG B 398 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 435 time to evaluate : 1.231 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 27 HIS cc_start: 0.8088 (t70) cc_final: 0.7499 (t70) REVERT: A 71 ASP cc_start: 0.9412 (t0) cc_final: 0.8782 (t0) REVERT: A 117 ASN cc_start: 0.9368 (m-40) cc_final: 0.9112 (t0) REVERT: A 137 PHE cc_start: 0.8993 (t80) cc_final: 0.8229 (t80) REVERT: A 199 ILE cc_start: 0.8532 (mt) cc_final: 0.8240 (mt) REVERT: A 203 ARG cc_start: 0.9086 (ttp-110) cc_final: 0.8796 (ttm110) REVERT: A 232 TRP cc_start: 0.9136 (t60) cc_final: 0.8735 (t60) REVERT: A 295 PHE cc_start: 0.8627 (m-10) cc_final: 0.8325 (m-10) REVERT: A 322 MET cc_start: 0.8640 (tmm) cc_final: 0.8131 (tmm) REVERT: A 324 ARG cc_start: 0.8005 (ttm-80) cc_final: 0.7501 (ttt180) REVERT: A 326 MET cc_start: 0.8966 (mmm) cc_final: 0.8508 (mmp) REVERT: A 387 GLU cc_start: 0.9466 (mp0) cc_final: 0.9264 (mp0) REVERT: A 400 GLN cc_start: 0.8165 (tp-100) cc_final: 0.7917 (tp40) REVERT: A 602 GLU cc_start: 0.8510 (mt-10) cc_final: 0.7899 (mp0) REVERT: A 618 ASN cc_start: 0.8472 (m-40) cc_final: 0.7728 (m110) REVERT: A 634 VAL cc_start: 0.9174 (t) cc_final: 0.8808 (p) REVERT: A 637 GLU cc_start: 0.7954 (tp30) cc_final: 0.7384 (tp30) REVERT: A 641 ASP cc_start: 0.8942 (m-30) cc_final: 0.8455 (t0) REVERT: A 648 SER cc_start: 0.8947 (m) cc_final: 0.8356 (p) REVERT: A 673 GLU cc_start: 0.8928 (mm-30) cc_final: 0.8525 (mm-30) REVERT: A 675 PHE cc_start: 0.8517 (t80) cc_final: 0.8234 (t80) REVERT: A 678 GLU cc_start: 0.8147 (mm-30) cc_final: 0.7933 (mm-30) REVERT: B 27 HIS cc_start: 0.8028 (t70) cc_final: 0.7522 (t70) REVERT: B 71 ASP cc_start: 0.9450 (t0) cc_final: 0.8965 (t0) REVERT: B 108 TYR cc_start: 0.8234 (m-80) cc_final: 0.8022 (m-80) REVERT: B 117 ASN cc_start: 0.9341 (OUTLIER) cc_final: 0.8677 (t0) REVERT: B 124 GLU cc_start: 0.9345 (mt-10) cc_final: 0.9028 (mp0) REVERT: B 137 PHE cc_start: 0.8996 (t80) cc_final: 0.8363 (t80) REVERT: B 170 ASP cc_start: 0.8863 (t0) cc_final: 0.8482 (t0) REVERT: B 199 ILE cc_start: 0.8544 (mt) cc_final: 0.8323 (mt) REVERT: B 203 ARG cc_start: 0.9072 (ttp-110) cc_final: 0.8808 (ttm110) REVERT: B 232 TRP cc_start: 0.9018 (t60) cc_final: 0.8585 (t60) REVERT: B 306 ASP cc_start: 0.8838 (t0) cc_final: 0.8591 (t0) REVERT: B 322 MET cc_start: 0.8650 (tmm) cc_final: 0.8144 (tmm) REVERT: B 324 ARG cc_start: 0.7935 (ttm-80) cc_final: 0.7477 (ttt180) REVERT: B 326 MET cc_start: 0.8980 (mmm) cc_final: 0.8522 (mmp) REVERT: B 387 GLU cc_start: 0.9430 (mp0) cc_final: 0.9208 (mp0) REVERT: B 561 LEU cc_start: 0.8957 (tp) cc_final: 0.8475 (tp) REVERT: B 598 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8872 (tp) REVERT: B 602 GLU cc_start: 0.8380 (mt-10) cc_final: 0.7788 (mp0) REVERT: B 620 MET cc_start: 0.8325 (tpp) cc_final: 0.8069 (tpp) REVERT: B 634 VAL cc_start: 0.9195 (t) cc_final: 0.8817 (p) REVERT: B 635 TRP cc_start: 0.9102 (m-90) cc_final: 0.8622 (m-90) REVERT: B 637 GLU cc_start: 0.8024 (tp30) cc_final: 0.7503 (tp30) REVERT: B 641 ASP cc_start: 0.8924 (m-30) cc_final: 0.8418 (t0) REVERT: B 648 SER cc_start: 0.8962 (m) cc_final: 0.8351 (p) REVERT: B 673 GLU cc_start: 0.9011 (mm-30) cc_final: 0.8541 (mm-30) outliers start: 31 outliers final: 17 residues processed: 451 average time/residue: 0.1982 time to fit residues: 128.4931 Evaluate side-chains 396 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 377 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 117 ASN Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 416 HIS Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 611 PHE Chi-restraints excluded: chain B residue 622 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 64 optimal weight: 10.0000 chunk 36 optimal weight: 3.9990 chunk 96 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 116 optimal weight: 0.8980 chunk 125 optimal weight: 0.8980 chunk 103 optimal weight: 0.0370 chunk 115 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 overall best weight: 0.7058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN A 311 GLN A 315 GLN A 346 GLN B 77 ASN B 311 GLN B 315 GLN B 443 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6876 moved from start: 0.3950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10942 Z= 0.171 Angle : 0.652 9.334 14808 Z= 0.321 Chirality : 0.041 0.164 1668 Planarity : 0.004 0.036 1810 Dihedral : 11.667 59.942 1626 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.99 % Favored : 94.85 % Rotamer: Outliers : 4.01 % Allowed : 20.62 % Favored : 75.36 % 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: -2.10 (0.22), residues: 1262 helix: -1.09 (0.16), residues: 826 sheet: None (None), residues: 0 loop : -1.74 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 271 HIS 0.001 0.000 HIS B 27 PHE 0.018 0.001 PHE B 171 TYR 0.021 0.001 TYR A 123 ARG 0.011 0.001 ARG A 493 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 395 time to evaluate : 1.194 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 27 HIS cc_start: 0.7750 (t70) cc_final: 0.7539 (t70) REVERT: A 71 ASP cc_start: 0.9371 (t0) cc_final: 0.8652 (t0) REVERT: A 91 LEU cc_start: 0.8684 (mt) cc_final: 0.8377 (mt) REVERT: A 109 LEU cc_start: 0.8560 (mp) cc_final: 0.8346 (mp) REVERT: A 137 PHE cc_start: 0.8868 (t80) cc_final: 0.8114 (t80) REVERT: A 151 ARG cc_start: 0.7771 (OUTLIER) cc_final: 0.7249 (pmt-80) REVERT: A 203 ARG cc_start: 0.9046 (ttp-110) cc_final: 0.8779 (ttm110) REVERT: A 212 MET cc_start: 0.9035 (ttp) cc_final: 0.8553 (tpp) REVERT: A 232 TRP cc_start: 0.9162 (t60) cc_final: 0.8768 (t60) REVERT: A 307 SER cc_start: 0.9530 (OUTLIER) cc_final: 0.9027 (p) REVERT: A 310 GLU cc_start: 0.8979 (tt0) cc_final: 0.8686 (tm-30) REVERT: A 322 MET cc_start: 0.8661 (tmm) cc_final: 0.8088 (tmm) REVERT: A 324 ARG cc_start: 0.8013 (ttm-80) cc_final: 0.7651 (ttt180) REVERT: A 326 MET cc_start: 0.8946 (mmm) cc_final: 0.8434 (mmp) REVERT: A 387 GLU cc_start: 0.9533 (mp0) cc_final: 0.9279 (mp0) REVERT: A 400 GLN cc_start: 0.8209 (tp-100) cc_final: 0.7811 (mp10) REVERT: A 497 ASN cc_start: 0.8826 (m110) cc_final: 0.8199 (t0) REVERT: A 554 PHE cc_start: 0.8533 (t80) cc_final: 0.8132 (t80) REVERT: A 602 GLU cc_start: 0.8572 (mt-10) cc_final: 0.7911 (mp0) REVERT: A 618 ASN cc_start: 0.8387 (m-40) cc_final: 0.7970 (m110) REVERT: A 634 VAL cc_start: 0.9219 (t) cc_final: 0.8940 (p) REVERT: A 637 GLU cc_start: 0.7815 (tp30) cc_final: 0.7286 (tp30) REVERT: A 641 ASP cc_start: 0.8941 (m-30) cc_final: 0.8430 (t0) REVERT: A 648 SER cc_start: 0.8859 (m) cc_final: 0.8341 (p) REVERT: A 673 GLU cc_start: 0.8948 (mm-30) cc_final: 0.8644 (mm-30) REVERT: A 675 PHE cc_start: 0.8479 (t80) cc_final: 0.8264 (t80) REVERT: B 71 ASP cc_start: 0.9394 (t0) cc_final: 0.8888 (t0) REVERT: B 109 LEU cc_start: 0.8665 (mp) cc_final: 0.8445 (mp) REVERT: B 117 ASN cc_start: 0.9299 (OUTLIER) cc_final: 0.8644 (t0) REVERT: B 137 PHE cc_start: 0.8983 (t80) cc_final: 0.8297 (t80) REVERT: B 203 ARG cc_start: 0.9053 (ttp-110) cc_final: 0.8779 (ttm110) REVERT: B 204 ASP cc_start: 0.8647 (m-30) cc_final: 0.8325 (m-30) REVERT: B 212 MET cc_start: 0.8985 (ttp) cc_final: 0.8561 (tpp) REVERT: B 232 TRP cc_start: 0.8942 (t60) cc_final: 0.8508 (t60) REVERT: B 306 ASP cc_start: 0.8926 (t70) cc_final: 0.8661 (t0) REVERT: B 307 SER cc_start: 0.9458 (OUTLIER) cc_final: 0.9020 (p) REVERT: B 310 GLU cc_start: 0.9039 (tt0) cc_final: 0.8736 (tm-30) REVERT: B 322 MET cc_start: 0.8671 (tmm) cc_final: 0.8102 (tmm) REVERT: B 324 ARG cc_start: 0.7997 (ttm-80) cc_final: 0.7637 (ttt180) REVERT: B 326 MET cc_start: 0.8956 (mmm) cc_final: 0.8443 (mmp) REVERT: B 387 GLU cc_start: 0.9500 (mp0) cc_final: 0.9235 (mp0) REVERT: B 531 ARG cc_start: 0.8747 (mtt180) cc_final: 0.8419 (mtt180) REVERT: B 538 MET cc_start: 0.8405 (mmp) cc_final: 0.8054 (mpp) REVERT: B 561 LEU cc_start: 0.8760 (tp) cc_final: 0.8546 (tp) REVERT: B 602 GLU cc_start: 0.8472 (mt-10) cc_final: 0.7916 (mm-30) REVERT: B 620 MET cc_start: 0.8575 (tpp) cc_final: 0.8240 (tpp) REVERT: B 634 VAL cc_start: 0.9223 (t) cc_final: 0.8848 (p) REVERT: B 641 ASP cc_start: 0.8903 (m-30) cc_final: 0.8451 (t0) REVERT: B 648 SER cc_start: 0.8857 (m) cc_final: 0.8353 (p) REVERT: B 673 GLU cc_start: 0.8944 (mm-30) cc_final: 0.8633 (mm-30) outliers start: 44 outliers final: 31 residues processed: 413 average time/residue: 0.1964 time to fit residues: 117.6036 Evaluate side-chains 413 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 378 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 551 TYR Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 117 ASN Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 280 TRP Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 307 SER Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 416 HIS Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 611 PHE Chi-restraints excluded: chain B residue 622 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 115 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 60 optimal weight: 0.5980 chunk 12 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 116 optimal weight: 0.5980 chunk 123 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 110 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 GLN ** B 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6888 moved from start: 0.4310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10942 Z= 0.170 Angle : 0.647 8.429 14808 Z= 0.313 Chirality : 0.041 0.156 1668 Planarity : 0.004 0.038 1810 Dihedral : 11.116 58.553 1626 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.44 % Favored : 95.40 % Rotamer: Outliers : 4.01 % Allowed : 22.17 % Favored : 73.81 % 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: -1.48 (0.23), residues: 1262 helix: -0.63 (0.17), residues: 820 sheet: None (None), residues: 0 loop : -1.44 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 271 HIS 0.008 0.001 HIS B 27 PHE 0.017 0.001 PHE B 171 TYR 0.022 0.001 TYR A 656 ARG 0.004 0.000 ARG B 398 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 396 time to evaluate : 1.176 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 27 HIS cc_start: 0.7524 (t70) cc_final: 0.7171 (t70) REVERT: A 39 ASP cc_start: 0.8958 (OUTLIER) cc_final: 0.8636 (m-30) REVERT: A 71 ASP cc_start: 0.9347 (t0) cc_final: 0.8499 (t0) REVERT: A 109 LEU cc_start: 0.8605 (mp) cc_final: 0.8389 (mp) REVERT: A 137 PHE cc_start: 0.8933 (t80) cc_final: 0.8094 (t80) REVERT: A 191 ARG cc_start: 0.8972 (mtt180) cc_final: 0.8672 (mtp85) REVERT: A 203 ARG cc_start: 0.9019 (ttp-110) cc_final: 0.8757 (ttm110) REVERT: A 212 MET cc_start: 0.8991 (ttp) cc_final: 0.8564 (tpp) REVERT: A 232 TRP cc_start: 0.9173 (t60) cc_final: 0.8840 (t60) REVERT: A 307 SER cc_start: 0.9513 (OUTLIER) cc_final: 0.9022 (p) REVERT: A 310 GLU cc_start: 0.9044 (tt0) cc_final: 0.8729 (tm-30) REVERT: A 322 MET cc_start: 0.8680 (tmm) cc_final: 0.8127 (tmm) REVERT: A 324 ARG cc_start: 0.7973 (ttm-80) cc_final: 0.7596 (ttt180) REVERT: A 326 MET cc_start: 0.8949 (mmm) cc_final: 0.8426 (mmp) REVERT: A 387 GLU cc_start: 0.9539 (mp0) cc_final: 0.9291 (mp0) REVERT: A 393 GLN cc_start: 0.9139 (tp40) cc_final: 0.8716 (mt0) REVERT: A 602 GLU cc_start: 0.8495 (mt-10) cc_final: 0.7930 (mp0) REVERT: A 634 VAL cc_start: 0.9224 (t) cc_final: 0.8965 (p) REVERT: A 637 GLU cc_start: 0.7819 (tp30) cc_final: 0.7292 (tp30) REVERT: A 641 ASP cc_start: 0.8870 (m-30) cc_final: 0.8385 (t0) REVERT: A 648 SER cc_start: 0.8872 (m) cc_final: 0.8330 (p) REVERT: A 673 GLU cc_start: 0.8876 (mm-30) cc_final: 0.8586 (mm-30) REVERT: B 27 HIS cc_start: 0.7846 (t70) cc_final: 0.7231 (t-90) REVERT: B 39 ASP cc_start: 0.8864 (t0) cc_final: 0.8540 (m-30) REVERT: B 71 ASP cc_start: 0.9406 (t0) cc_final: 0.8873 (t0) REVERT: B 89 GLN cc_start: 0.8673 (mt0) cc_final: 0.8467 (mt0) REVERT: B 109 LEU cc_start: 0.8655 (mp) cc_final: 0.8411 (mp) REVERT: B 117 ASN cc_start: 0.9250 (OUTLIER) cc_final: 0.8725 (t0) REVERT: B 137 PHE cc_start: 0.8972 (t80) cc_final: 0.8241 (t80) REVERT: B 170 ASP cc_start: 0.8732 (t70) cc_final: 0.8437 (t70) REVERT: B 191 ARG cc_start: 0.8842 (mtp85) cc_final: 0.8599 (ptp90) REVERT: B 203 ARG cc_start: 0.9035 (ttp-110) cc_final: 0.8756 (ttm110) REVERT: B 204 ASP cc_start: 0.8610 (m-30) cc_final: 0.8323 (m-30) REVERT: B 219 ILE cc_start: 0.8766 (OUTLIER) cc_final: 0.8552 (tp) REVERT: B 232 TRP cc_start: 0.9040 (t60) cc_final: 0.8582 (t60) REVERT: B 306 ASP cc_start: 0.8798 (t70) cc_final: 0.8489 (t0) REVERT: B 310 GLU cc_start: 0.9067 (tt0) cc_final: 0.8755 (tm-30) REVERT: B 322 MET cc_start: 0.8684 (tmm) cc_final: 0.8135 (tmm) REVERT: B 324 ARG cc_start: 0.7996 (ttm-80) cc_final: 0.7590 (ttt180) REVERT: B 326 MET cc_start: 0.8996 (mmm) cc_final: 0.8488 (mmp) REVERT: B 387 GLU cc_start: 0.9524 (mp0) cc_final: 0.9263 (mp0) REVERT: B 393 GLN cc_start: 0.9038 (tp40) cc_final: 0.8773 (mt0) REVERT: B 531 ARG cc_start: 0.8677 (mtt180) cc_final: 0.8450 (mtt180) REVERT: B 538 MET cc_start: 0.8278 (mmp) cc_final: 0.7989 (mpp) REVERT: B 561 LEU cc_start: 0.8700 (tp) cc_final: 0.8468 (tp) REVERT: B 577 CYS cc_start: 0.8929 (m) cc_final: 0.8654 (m) REVERT: B 602 GLU cc_start: 0.8353 (mt-10) cc_final: 0.7693 (tp30) REVERT: B 628 VAL cc_start: 0.8332 (t) cc_final: 0.8121 (m) REVERT: B 641 ASP cc_start: 0.8835 (m-30) cc_final: 0.8235 (t0) REVERT: B 648 SER cc_start: 0.8875 (m) cc_final: 0.8373 (p) REVERT: B 673 GLU cc_start: 0.8885 (mm-30) cc_final: 0.8572 (mm-30) outliers start: 44 outliers final: 33 residues processed: 415 average time/residue: 0.1988 time to fit residues: 119.7837 Evaluate side-chains 408 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 371 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 622 THR Chi-restraints excluded: chain A residue 636 MET Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 117 ASN Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 280 TRP Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 416 HIS Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 611 PHE Chi-restraints excluded: chain B residue 622 THR Chi-restraints excluded: chain B residue 645 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 103 optimal weight: 10.0000 chunk 70 optimal weight: 0.7980 chunk 1 optimal weight: 7.9990 chunk 92 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 105 optimal weight: 6.9990 chunk 85 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 63 optimal weight: 5.9990 chunk 111 optimal weight: 8.9990 chunk 31 optimal weight: 9.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 GLN ** A 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6997 moved from start: 0.4373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 10942 Z= 0.462 Angle : 0.806 9.281 14808 Z= 0.406 Chirality : 0.047 0.166 1668 Planarity : 0.005 0.049 1810 Dihedral : 12.503 59.998 1626 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 21.48 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.34 % Favored : 93.50 % Rotamer: Outliers : 8.58 % Allowed : 20.80 % Favored : 70.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.57 (0.23), residues: 1262 helix: -0.75 (0.17), residues: 844 sheet: None (None), residues: 0 loop : -1.37 (0.33), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 280 HIS 0.006 0.002 HIS B 27 PHE 0.023 0.002 PHE B 613 TYR 0.026 0.002 TYR B 651 ARG 0.011 0.001 ARG A 69 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 336 time to evaluate : 1.147 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 27 HIS cc_start: 0.7986 (t70) cc_final: 0.7543 (t70) REVERT: A 69 ARG cc_start: 0.9062 (mmp80) cc_final: 0.8718 (mmp80) REVERT: A 71 ASP cc_start: 0.9390 (t0) cc_final: 0.8612 (t0) REVERT: A 137 PHE cc_start: 0.8871 (t80) cc_final: 0.7942 (t80) REVERT: A 151 ARG cc_start: 0.8075 (OUTLIER) cc_final: 0.7605 (pmt-80) REVERT: A 203 ARG cc_start: 0.8970 (ttp-110) cc_final: 0.8663 (ttm110) REVERT: A 225 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8906 (mp) REVERT: A 232 TRP cc_start: 0.9219 (t60) cc_final: 0.8981 (t60) REVERT: A 261 LEU cc_start: 0.8029 (mt) cc_final: 0.7655 (tp) REVERT: A 310 GLU cc_start: 0.9132 (tt0) cc_final: 0.8915 (tm-30) REVERT: A 322 MET cc_start: 0.8627 (tmm) cc_final: 0.8083 (tmm) REVERT: A 324 ARG cc_start: 0.8171 (ttm-80) cc_final: 0.7590 (ttt180) REVERT: A 326 MET cc_start: 0.8998 (mmm) cc_final: 0.8402 (mmp) REVERT: A 387 GLU cc_start: 0.9539 (mp0) cc_final: 0.9280 (mp0) REVERT: A 481 LEU cc_start: 0.7718 (OUTLIER) cc_final: 0.6491 (mm) REVERT: A 590 LEU cc_start: 0.7487 (OUTLIER) cc_final: 0.5925 (mp) REVERT: A 598 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8505 (tp) REVERT: A 602 GLU cc_start: 0.8431 (mt-10) cc_final: 0.8053 (mp0) REVERT: A 637 GLU cc_start: 0.7832 (tp30) cc_final: 0.7412 (tp30) REVERT: A 641 ASP cc_start: 0.8890 (m-30) cc_final: 0.8551 (t0) REVERT: A 648 SER cc_start: 0.8941 (m) cc_final: 0.8657 (p) REVERT: A 673 GLU cc_start: 0.8864 (mm-30) cc_final: 0.8418 (mm-30) REVERT: B 27 HIS cc_start: 0.7912 (t70) cc_final: 0.7065 (t-90) REVERT: B 39 ASP cc_start: 0.8998 (OUTLIER) cc_final: 0.8674 (m-30) REVERT: B 71 ASP cc_start: 0.9491 (t0) cc_final: 0.8910 (t0) REVERT: B 117 ASN cc_start: 0.9294 (OUTLIER) cc_final: 0.8698 (t0) REVERT: B 137 PHE cc_start: 0.8882 (t80) cc_final: 0.8062 (t80) REVERT: B 141 TYR cc_start: 0.8732 (p90) cc_final: 0.8443 (p90) REVERT: B 170 ASP cc_start: 0.8825 (t70) cc_final: 0.8451 (t70) REVERT: B 203 ARG cc_start: 0.9000 (ttp-110) cc_final: 0.8665 (ttm110) REVERT: B 212 MET cc_start: 0.9039 (OUTLIER) cc_final: 0.8761 (tpp) REVERT: B 232 TRP cc_start: 0.9210 (t60) cc_final: 0.8707 (t60) REVERT: B 261 LEU cc_start: 0.8026 (mt) cc_final: 0.7698 (tp) REVERT: B 307 SER cc_start: 0.9383 (OUTLIER) cc_final: 0.9091 (p) REVERT: B 310 GLU cc_start: 0.9108 (OUTLIER) cc_final: 0.8898 (tm-30) REVERT: B 322 MET cc_start: 0.8597 (tmm) cc_final: 0.8036 (tmm) REVERT: B 324 ARG cc_start: 0.8167 (ttm-80) cc_final: 0.7589 (ttt180) REVERT: B 326 MET cc_start: 0.9007 (mmm) cc_final: 0.8450 (mmp) REVERT: B 387 GLU cc_start: 0.9523 (mp0) cc_final: 0.8958 (mp0) REVERT: B 481 LEU cc_start: 0.7104 (OUTLIER) cc_final: 0.6749 (tp) REVERT: B 546 MET cc_start: 0.4949 (mmm) cc_final: 0.4587 (mmm) REVERT: B 590 LEU cc_start: 0.7344 (OUTLIER) cc_final: 0.5878 (mp) REVERT: B 598 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8753 (tt) REVERT: B 602 GLU cc_start: 0.8519 (mt-10) cc_final: 0.8117 (tp30) REVERT: B 620 MET cc_start: 0.8633 (tpp) cc_final: 0.8361 (tpp) REVERT: B 641 ASP cc_start: 0.8825 (m-30) cc_final: 0.8376 (t0) REVERT: B 648 SER cc_start: 0.8936 (m) cc_final: 0.8658 (p) REVERT: B 673 GLU cc_start: 0.8786 (mm-30) cc_final: 0.8453 (mm-30) outliers start: 94 outliers final: 67 residues processed: 377 average time/residue: 0.2041 time to fit residues: 110.7918 Evaluate side-chains 394 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 314 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain A residue 538 MET Chi-restraints excluded: chain A residue 551 TYR Chi-restraints excluded: chain A residue 559 ILE Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 581 SER Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 622 THR Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 117 ASN Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 212 MET Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 280 TRP Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 307 SER Chi-restraints excluded: chain B residue 310 GLU Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 416 HIS Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 581 SER Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 611 PHE Chi-restraints excluded: chain B residue 622 THR Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 659 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 41 optimal weight: 9.9990 chunk 111 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 123 optimal weight: 0.9990 chunk 102 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 40 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 GLN A 315 GLN A 497 ASN B 311 GLN B 315 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6941 moved from start: 0.4599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10942 Z= 0.227 Angle : 0.682 8.405 14808 Z= 0.332 Chirality : 0.042 0.176 1668 Planarity : 0.004 0.053 1810 Dihedral : 11.504 59.307 1626 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 16.42 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.91 % Favored : 94.93 % Rotamer: Outliers : 6.30 % Allowed : 22.81 % Favored : 70.89 % 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: -1.06 (0.24), residues: 1262 helix: -0.35 (0.17), residues: 818 sheet: None (None), residues: 0 loop : -1.14 (0.32), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 271 HIS 0.005 0.001 HIS B 27 PHE 0.026 0.001 PHE A 554 TYR 0.020 0.002 TYR B 656 ARG 0.005 0.001 ARG A 69 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 366 time to evaluate : 1.137 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 71 ASP cc_start: 0.9343 (t0) cc_final: 0.8627 (t0) REVERT: A 124 GLU cc_start: 0.9169 (mt-10) cc_final: 0.8933 (mp0) REVERT: A 137 PHE cc_start: 0.8924 (t80) cc_final: 0.7935 (t80) REVERT: A 203 ARG cc_start: 0.8975 (ttp-110) cc_final: 0.8677 (ttm110) REVERT: A 225 LEU cc_start: 0.9225 (OUTLIER) cc_final: 0.8914 (mp) REVERT: A 232 TRP cc_start: 0.9225 (t60) cc_final: 0.9003 (t60) REVERT: A 310 GLU cc_start: 0.9146 (OUTLIER) cc_final: 0.8851 (tm-30) REVERT: A 322 MET cc_start: 0.8665 (tmm) cc_final: 0.8108 (tmm) REVERT: A 324 ARG cc_start: 0.7841 (ttm-80) cc_final: 0.7469 (ttt180) REVERT: A 326 MET cc_start: 0.9039 (mmm) cc_final: 0.8485 (mmp) REVERT: A 387 GLU cc_start: 0.9551 (mp0) cc_final: 0.9285 (mp0) REVERT: A 546 MET cc_start: 0.8872 (tpp) cc_final: 0.8476 (tmm) REVERT: A 602 GLU cc_start: 0.8519 (mt-10) cc_final: 0.8130 (mp0) REVERT: A 637 GLU cc_start: 0.7833 (tp30) cc_final: 0.7261 (tp30) REVERT: A 641 ASP cc_start: 0.8882 (m-30) cc_final: 0.8454 (t0) REVERT: A 648 SER cc_start: 0.8881 (m) cc_final: 0.8469 (p) REVERT: A 673 GLU cc_start: 0.8862 (mm-30) cc_final: 0.8447 (mm-30) REVERT: A 678 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7904 (mt-10) REVERT: B 27 HIS cc_start: 0.7823 (t70) cc_final: 0.7165 (t-90) REVERT: B 39 ASP cc_start: 0.9026 (t0) cc_final: 0.8718 (m-30) REVERT: B 71 ASP cc_start: 0.9431 (t0) cc_final: 0.8769 (t0) REVERT: B 117 ASN cc_start: 0.9285 (OUTLIER) cc_final: 0.8775 (t0) REVERT: B 137 PHE cc_start: 0.8929 (t80) cc_final: 0.8051 (t80) REVERT: B 141 TYR cc_start: 0.8706 (p90) cc_final: 0.8397 (p90) REVERT: B 170 ASP cc_start: 0.8718 (t70) cc_final: 0.8324 (t70) REVERT: B 199 ILE cc_start: 0.8474 (mt) cc_final: 0.8224 (mt) REVERT: B 203 ARG cc_start: 0.8979 (ttp-110) cc_final: 0.8683 (ttm110) REVERT: B 232 TRP cc_start: 0.9125 (t60) cc_final: 0.8621 (t60) REVERT: B 286 VAL cc_start: 0.9277 (m) cc_final: 0.9034 (m) REVERT: B 306 ASP cc_start: 0.8936 (t0) cc_final: 0.8705 (t0) REVERT: B 307 SER cc_start: 0.9365 (OUTLIER) cc_final: 0.9129 (p) REVERT: B 310 GLU cc_start: 0.9095 (tt0) cc_final: 0.8875 (tm-30) REVERT: B 322 MET cc_start: 0.8691 (tmm) cc_final: 0.8140 (tmm) REVERT: B 324 ARG cc_start: 0.7838 (ttm-80) cc_final: 0.7424 (ttt180) REVERT: B 326 MET cc_start: 0.9040 (mmm) cc_final: 0.8493 (mmp) REVERT: B 387 GLU cc_start: 0.9519 (mp0) cc_final: 0.8939 (mp0) REVERT: B 546 MET cc_start: 0.5105 (mmm) cc_final: 0.4688 (mmm) REVERT: B 577 CYS cc_start: 0.8960 (m) cc_final: 0.8650 (m) REVERT: B 602 GLU cc_start: 0.8571 (mt-10) cc_final: 0.8224 (tp30) REVERT: B 603 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7849 (tp) REVERT: B 620 MET cc_start: 0.8531 (tpp) cc_final: 0.8093 (tpp) REVERT: B 641 ASP cc_start: 0.8772 (m-30) cc_final: 0.8327 (t0) REVERT: B 648 SER cc_start: 0.8877 (m) cc_final: 0.8457 (p) REVERT: B 673 GLU cc_start: 0.8708 (mm-30) cc_final: 0.8453 (mm-30) outliers start: 69 outliers final: 52 residues processed: 395 average time/residue: 0.1937 time to fit residues: 110.9817 Evaluate side-chains 381 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 324 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 538 MET Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 622 THR Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 117 ASN Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 280 TRP Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 307 SER Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 416 HIS Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 611 PHE Chi-restraints excluded: chain B residue 622 THR Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 645 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 57.6907 > 50: distance: 10 - 37: 13.273 distance: 16 - 21: 3.200 distance: 21 - 22: 4.151 distance: 22 - 23: 3.828 distance: 22 - 25: 5.920 distance: 23 - 24: 10.362 distance: 25 - 26: 4.679 distance: 26 - 27: 7.286 distance: 26 - 28: 8.923 distance: 29 - 30: 5.168 distance: 30 - 31: 9.014 distance: 30 - 33: 8.613 distance: 31 - 37: 4.752 distance: 33 - 34: 6.763 distance: 34 - 35: 7.450 distance: 34 - 36: 10.023 distance: 37 - 38: 5.058 distance: 38 - 39: 5.180 distance: 38 - 41: 3.725 distance: 39 - 40: 4.247 distance: 39 - 45: 7.308 distance: 41 - 42: 8.458 distance: 41 - 43: 6.281 distance: 42 - 44: 12.746 distance: 45 - 46: 21.003 distance: 46 - 47: 12.800 distance: 46 - 49: 27.684 distance: 47 - 48: 13.077 distance: 47 - 50: 18.643 distance: 50 - 51: 20.506 distance: 51 - 52: 14.906 distance: 51 - 54: 29.463 distance: 52 - 53: 6.607 distance: 52 - 56: 11.385 distance: 53 - 84: 18.154 distance: 54 - 55: 13.020 distance: 56 - 57: 10.343 distance: 57 - 58: 8.122 distance: 57 - 60: 10.651 distance: 58 - 59: 6.384 distance: 58 - 64: 4.713 distance: 59 - 95: 4.043 distance: 60 - 61: 5.045 distance: 61 - 62: 9.876 distance: 61 - 63: 4.811 distance: 64 - 65: 4.300 distance: 65 - 66: 3.745 distance: 65 - 68: 4.741 distance: 66 - 72: 3.139 distance: 67 - 100: 10.470 distance: 68 - 69: 4.945 distance: 69 - 70: 8.030 distance: 69 - 71: 8.488 distance: 74 - 75: 7.477 distance: 74 - 84: 3.048 distance: 75 - 107: 3.443 distance: 76 - 77: 3.699 distance: 77 - 78: 4.421 distance: 77 - 79: 6.833 distance: 79 - 81: 4.567 distance: 80 - 82: 6.416 distance: 81 - 82: 4.633 distance: 82 - 83: 3.344 distance: 84 - 85: 4.206 distance: 85 - 86: 5.612 distance: 85 - 88: 9.280 distance: 86 - 95: 4.297 distance: 87 - 115: 8.287 distance: 88 - 89: 11.761 distance: 89 - 90: 9.900 distance: 89 - 91: 5.720 distance: 90 - 92: 5.995 distance: 91 - 93: 5.494 distance: 92 - 94: 5.276 distance: 93 - 94: 11.359 distance: 96 - 97: 3.577 distance: 97 - 98: 4.511 distance: 97 - 100: 3.029 distance: 98 - 121: 4.799