Starting phenix.real_space_refine on Fri Mar 15 23:26:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kso_23021/03_2024/7kso_23021.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kso_23021/03_2024/7kso_23021.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kso_23021/03_2024/7kso_23021.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kso_23021/03_2024/7kso_23021.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kso_23021/03_2024/7kso_23021.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kso_23021/03_2024/7kso_23021.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 8 6.06 5 S 92 5.16 5 C 8263 2.51 5 N 2322 2.21 5 O 2390 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 100": "NH1" <-> "NH2" Residue "A TYR 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 553": "OD1" <-> "OD2" Residue "A PHE 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 650": "OD1" <-> "OD2" Residue "A ARG 686": "NH1" <-> "NH2" Residue "A ASP 706": "OD1" <-> "OD2" Residue "B ASP 91": "OD1" <-> "OD2" Residue "B PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 109": "OD1" <-> "OD2" Residue "B PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 303": "OD1" <-> "OD2" Residue "B ASP 357": "OD1" <-> "OD2" Residue "B ARG 414": "NH1" <-> "NH2" Residue "C ASP 82": "OD1" <-> "OD2" Residue "C GLU 84": "OE1" <-> "OE2" Residue "C ARG 98": "NH1" <-> "NH2" Residue "C ARG 101": "NH1" <-> "NH2" Residue "C ARG 103": "NH1" <-> "NH2" Residue "C PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 204": "NH1" <-> "NH2" Residue "C ARG 307": "NH1" <-> "NH2" Residue "C ARG 360": "NH1" <-> "NH2" Residue "C ASP 447": "OD1" <-> "OD2" Residue "C PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 493": "OE1" <-> "OE2" Residue "C PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 516": "NH1" <-> "NH2" Residue "C ARG 522": "NH1" <-> "NH2" Residue "C ASP 582": "OD1" <-> "OD2" Residue "C PHE 666": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 131": "NH1" <-> "NH2" Residue "D TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 218": "OD1" <-> "OD2" Residue "D ARG 258": "NH1" <-> "NH2" Residue "D PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 404": "OD1" <-> "OD2" Residue "E ARG 409": "NH1" <-> "NH2" Residue "E PHE 430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 455": "OD1" <-> "OD2" Residue "E ARG 467": "NH1" <-> "NH2" Residue "F ASP 156": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 13075 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3098 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 19, 'TRANS': 375} Chain breaks: 4 Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 44 Chain: "B" Number of atoms: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2917 Classifications: {'peptide': 365} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 12, 'TRANS': 352} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 16 Chain: "C" Number of atoms: 3109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3109 Classifications: {'peptide': 420} Incomplete info: {'truncation_to_alanine': 108} Link IDs: {'PTRANS': 17, 'TRANS': 402} Chain breaks: 8 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 400 Unresolved non-hydrogen angles: 509 Unresolved non-hydrogen dihedrals: 332 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'GLN:plan1': 11, 'ASP:plan': 7, 'TYR:plan': 4, 'ASN:plan1': 5, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 7, 'GLU:plan': 7, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 232 Chain: "D" Number of atoms: 3054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3054 Classifications: {'peptide': 387} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 22, 'TRANS': 364} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 18 Chain: "E" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 724 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 5, 'TRANS': 94} Chain breaks: 2 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 117 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 44 Chain: "F" Number of atoms: 165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 165 Classifications: {'peptide': 23} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 19} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Unusual residues: {' ZN': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 939 SG CYS A 302 41.272 34.975 42.728 0.99112.68 S ATOM 985 SG CYS A 307 43.600 37.499 41.887 0.87109.30 S ATOM 1591 SG CYS A 531 53.781 18.105 32.983 1.00147.38 S ATOM 1684 SG CYS A 544 53.913 20.388 36.890 1.00127.17 S ATOM 1734 SG CYS A 550 50.230 18.725 34.098 1.00138.70 S ATOM 1591 SG CYS A 531 53.781 18.105 32.983 1.00147.38 S ATOM 1684 SG CYS A 544 53.913 20.388 36.890 1.00127.17 S ATOM 1534 SG CYS A 524 53.362 24.288 32.749 1.00139.61 S ATOM 1719 SG CYS A 548 50.506 22.685 34.072 1.00132.86 S ATOM 1819 SG CYS A 561 46.461 14.460 53.389 1.00122.99 S ATOM 1973 SG CYS A 581 46.466 18.162 54.594 1.00110.26 S ATOM 2031 SG CYS A 589 42.548 15.690 54.701 1.00123.10 S ATOM 1819 SG CYS A 561 46.461 14.460 53.389 1.00122.99 S ATOM 1867 SG CYS A 567 47.437 15.971 57.352 1.00120.66 S ATOM 1906 SG CYS A 572 50.553 14.459 55.048 1.00117.49 S ATOM 1867 SG CYS A 567 47.437 15.971 57.352 1.00120.66 S Time building chain proxies: 8.43, per 1000 atoms: 0.64 Number of scatterers: 13075 At special positions: 0 Unit cell: (97.5, 111.8, 158.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 8 29.99 S 92 16.00 O 2390 8.00 N 2322 7.00 C 8263 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.95 Conformation dependent library (CDL) restraints added in 2.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 801 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 302 " pdb="ZN ZN A 801 " - pdb=" ND1 HIS A 310 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 307 " pdb=" ZN A 803 " pdb="ZN ZN A 803 " - pdb=" SG CYS A 544 " pdb="ZN ZN A 803 " - pdb="ZN ZN A 804 " pdb="ZN ZN A 803 " - pdb=" SG CYS A 531 " pdb=" ZN A 804 " pdb="ZN ZN A 804 " - pdb=" SG CYS A 548 " pdb="ZN ZN A 804 " - pdb=" SG CYS A 524 " pdb=" ZN A 806 " pdb="ZN ZN A 806 " - pdb=" SG CYS A 567 " pdb="ZN ZN A 806 " - pdb=" SG CYS A 561 " pdb="ZN ZN A 806 " - pdb=" SG CYS A 572 " pdb=" ZN A 807 " pdb="ZN ZN A 807 " - pdb=" SG CYS A 567 " pdb=" ZN C 801 " pdb="ZN ZN C 801 " - pdb=" NE2 HIS C 471 " 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3238 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 23 sheets defined 22.0% alpha, 21.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.40 Creating SS restraints... Processing helix chain 'A' and resid 34 through 62 removed outlier: 3.943A pdb=" N LYS A 62 " --> pdb=" O GLU A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 291 Processing helix chain 'A' and resid 291 through 298 Processing helix chain 'A' and resid 315 through 319 removed outlier: 3.984A pdb=" N VAL A 318 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TYR A 319 " --> pdb=" O PRO A 316 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 315 through 319' Processing helix chain 'A' and resid 435 through 450 Processing helix chain 'A' and resid 452 through 461 Processing helix chain 'A' and resid 464 through 474 removed outlier: 3.722A pdb=" N LYS A 474 " --> pdb=" O GLN A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 540 removed outlier: 3.702A pdb=" N MET A 539 " --> pdb=" O CYS A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 577 removed outlier: 4.112A pdb=" N ALA A 577 " --> pdb=" O PRO A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 610 Processing helix chain 'A' and resid 648 through 663 removed outlier: 4.674A pdb=" N LYS A 661 " --> pdb=" O LYS A 657 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N TYR A 662 " --> pdb=" O VAL A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 688 removed outlier: 3.549A pdb=" N ALA A 688 " --> pdb=" O ILE A 685 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 279 Processing helix chain 'B' and resid 339 through 343 removed outlier: 3.612A pdb=" N LYS B 342 " --> pdb=" O ASP B 339 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ILE B 343 " --> pdb=" O ILE B 340 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 339 through 343' Processing helix chain 'B' and resid 395 through 399 Processing helix chain 'C' and resid 79 through 107 removed outlier: 3.523A pdb=" N HIS C 83 " --> pdb=" O VAL C 79 " (cutoff:3.500A) Proline residue: C 93 - end of helix removed outlier: 3.745A pdb=" N THR C 102 " --> pdb=" O ARG C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 115 Processing helix chain 'C' and resid 126 through 131 removed outlier: 3.919A pdb=" N LYS C 130 " --> pdb=" O ASN C 126 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N THR C 131 " --> pdb=" O ILE C 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 126 through 131' Processing helix chain 'C' and resid 136 through 145 removed outlier: 4.235A pdb=" N LYS C 140 " --> pdb=" O ASP C 136 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL C 141 " --> pdb=" O MET C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 470 removed outlier: 3.576A pdb=" N LEU C 463 " --> pdb=" O LYS C 459 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 506 removed outlier: 3.900A pdb=" N ASP C 505 " --> pdb=" O ASN C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 589 through 602 removed outlier: 3.941A pdb=" N ARG C 593 " --> pdb=" O PRO C 589 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE C 600 " --> pdb=" O THR C 596 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 624 Processing helix chain 'C' and resid 630 through 649 removed outlier: 4.001A pdb=" N HIS C 634 " --> pdb=" O ASN C 630 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N MET C 637 " --> pdb=" O ASN C 633 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU C 641 " --> pdb=" O MET C 637 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N GLN C 645 " --> pdb=" O GLU C 641 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N LYS C 646 " --> pdb=" O ASN C 642 " (cutoff:3.500A) Processing helix chain 'C' and resid 652 through 666 removed outlier: 3.705A pdb=" N PHE C 666 " --> pdb=" O SER C 662 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 686 removed outlier: 3.549A pdb=" N ILE C 674 " --> pdb=" O SER C 670 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N MET C 684 " --> pdb=" O LYS C 680 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 28 Processing helix chain 'D' and resid 355 through 362 removed outlier: 3.857A pdb=" N ASP D 361 " --> pdb=" O GLU D 357 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLY D 362 " --> pdb=" O ASP D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 410 removed outlier: 4.130A pdb=" N TYR D 409 " --> pdb=" O ALA D 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 399 through 418 removed outlier: 3.876A pdb=" N ALA E 405 " --> pdb=" O GLN E 401 " (cutoff:3.500A) Processing helix chain 'E' and resid 468 through 470 No H-bonds generated for 'chain 'E' and resid 468 through 470' Processing helix chain 'F' and resid 153 through 164 removed outlier: 3.680A pdb=" N PHE F 157 " --> pdb=" O LYS F 153 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 82 through 85 Processing sheet with id=AA2, first strand: chain 'A' and resid 100 through 101 removed outlier: 6.069A pdb=" N ARG A 100 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N LEU B 134 " --> pdb=" O GLU B 125 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N GLU B 125 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLN B 136 " --> pdb=" O LEU B 123 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA B 114 " --> pdb=" O GLN B 100 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN B 100 " --> pdb=" O ALA B 114 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL B 116 " --> pdb=" O GLY B 98 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLY B 98 " --> pdb=" O VAL B 116 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 115 through 116 removed outlier: 5.789A pdb=" N SER A 115 " --> pdb=" O GLY A 682 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 121 through 122 removed outlier: 6.537A pdb=" N PHE A 121 " --> pdb=" O LEU A 646 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 615 through 619 Processing sheet with id=AA6, first strand: chain 'A' and resid 638 through 640 removed outlier: 6.878A pdb=" N PHE A 638 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ALA A 713 " --> pdb=" O PHE A 638 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 83 through 89 removed outlier: 6.237A pdb=" N CYS B 84 " --> pdb=" O ASP B 438 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N ASP B 438 " --> pdb=" O CYS B 84 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ASN B 86 " --> pdb=" O ARG B 436 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N SER B 433 " --> pdb=" O CYS B 429 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N GLN B 415 " --> pdb=" O VAL B 428 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 149 through 154 removed outlier: 4.486A pdb=" N THR B 149 " --> pdb=" O ALA B 166 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA B 166 " --> pdb=" O THR B 149 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS B 184 " --> pdb=" O ILE B 174 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ASN B 176 " --> pdb=" O CYS B 182 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N CYS B 182 " --> pdb=" O ASN B 176 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 193 through 198 removed outlier: 4.001A pdb=" N GLU B 195 " --> pdb=" O VAL B 209 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LEU B 215 " --> pdb=" O ILE B 228 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N ILE B 228 " --> pdb=" O LEU B 215 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N LEU B 217 " --> pdb=" O VAL B 226 " (cutoff:3.500A) removed outlier: 10.783A pdb=" N GLN B 292 " --> pdb=" O THR B 224 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N VAL B 226 " --> pdb=" O GLN B 292 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 239 through 244 Processing sheet with id=AB2, first strand: chain 'B' and resid 312 through 315 removed outlier: 7.320A pdb=" N LYS B 332 " --> pdb=" O ILE B 352 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N ILE B 352 " --> pdb=" O LYS B 332 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 368 through 369 Processing sheet with id=AB4, first strand: chain 'C' and resid 230 through 234 removed outlier: 4.413A pdb=" N GLN C 356 " --> pdb=" O THR C 162 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N PHE C 164 " --> pdb=" O THR C 354 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N THR C 354 " --> pdb=" O PHE C 164 " (cutoff:3.500A) removed outlier: 8.295A pdb=" N ILE E 435 " --> pdb=" O ALA C 318 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 203 through 211 removed outlier: 7.012A pdb=" N VAL C 186 " --> pdb=" O THR C 208 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N LYS C 210 " --> pdb=" O LEU C 184 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N LEU C 184 " --> pdb=" O LYS C 210 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 429 through 431 removed outlier: 3.613A pdb=" N ARG C 486 " --> pdb=" O VAL C 479 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL C 479 " --> pdb=" O ARG C 486 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 557 through 560 removed outlier: 3.575A pdb=" N ILE C 525 " --> pdb=" O ALA D 39 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU D 34 " --> pdb=" O GLN D 403 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 47 through 49 removed outlier: 7.331A pdb=" N ASN D 77 " --> pdb=" O ASN D 122 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ASN D 122 " --> pdb=" O ASN D 77 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N LEU D 79 " --> pdb=" O LYS D 120 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N LYS D 120 " --> pdb=" O LEU D 79 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ILE D 81 " --> pdb=" O GLU D 118 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 130 through 132 Processing sheet with id=AC1, first strand: chain 'D' and resid 183 through 185 removed outlier: 3.557A pdb=" N SER D 197 " --> pdb=" O THR D 201 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N THR D 201 " --> pdb=" O SER D 197 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 230 through 235 removed outlier: 3.756A pdb=" N LYS D 251 " --> pdb=" O ALA D 247 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 276 through 281 removed outlier: 3.948A pdb=" N THR D 297 " --> pdb=" O SER D 293 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N HIS D 311 " --> pdb=" O LEU D 300 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 320 through 322 removed outlier: 7.021A pdb=" N SER D 336 " --> pdb=" O PHE D 321 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ASP D 346 " --> pdb=" O LEU D 366 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N LEU D 366 " --> pdb=" O ASP D 346 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 428 through 431 437 hydrogen bonds defined for protein. 1227 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.13 Time building geometry restraints manager: 5.43 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: 4261 1.34 - 1.46: 2910 1.46 - 1.58: 6076 1.58 - 1.70: 0 1.70 - 1.82: 127 Bond restraints: 13374 Sorted by residual: bond pdb=" C ARG A 529 " pdb=" N PRO A 530 " ideal model delta sigma weight residual 1.328 1.359 -0.031 1.26e-02 6.30e+03 6.08e+00 bond pdb=" C THR D 28 " pdb=" N PRO D 29 " ideal model delta sigma weight residual 1.334 1.389 -0.055 2.34e-02 1.83e+03 5.48e+00 bond pdb=" CA HIS C 561 " pdb=" C HIS C 561 " ideal model delta sigma weight residual 1.520 1.539 -0.018 1.21e-02 6.83e+03 2.23e+00 bond pdb=" C ASN D 282 " pdb=" N PRO D 283 " ideal model delta sigma weight residual 1.334 1.369 -0.035 2.34e-02 1.83e+03 2.21e+00 bond pdb=" CB PHE C 90 " pdb=" CG PHE C 90 " ideal model delta sigma weight residual 1.502 1.536 -0.034 2.30e-02 1.89e+03 2.16e+00 ... (remaining 13369 not shown) Histogram of bond angle deviations from ideal: 100.44 - 107.15: 475 107.15 - 113.86: 7352 113.86 - 120.56: 5020 120.56 - 127.27: 5084 127.27 - 133.98: 210 Bond angle restraints: 18141 Sorted by residual: angle pdb=" N ASN F 171 " pdb=" CA ASN F 171 " pdb=" C ASN F 171 " ideal model delta sigma weight residual 111.54 119.01 -7.47 1.36e+00 5.41e-01 3.02e+01 angle pdb=" N PHE F 160 " pdb=" CA PHE F 160 " pdb=" C PHE F 160 " ideal model delta sigma weight residual 111.28 107.36 3.92 1.09e+00 8.42e-01 1.29e+01 angle pdb=" CA MET A 663 " pdb=" CB MET A 663 " pdb=" CG MET A 663 " ideal model delta sigma weight residual 114.10 121.13 -7.03 2.00e+00 2.50e-01 1.23e+01 angle pdb=" N LEU F 161 " pdb=" CA LEU F 161 " pdb=" C LEU F 161 " ideal model delta sigma weight residual 111.28 114.94 -3.66 1.09e+00 8.42e-01 1.13e+01 angle pdb=" N PHE F 157 " pdb=" CA PHE F 157 " pdb=" C PHE F 157 " ideal model delta sigma weight residual 111.28 114.89 -3.61 1.09e+00 8.42e-01 1.09e+01 ... (remaining 18136 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.34: 7488 17.34 - 34.67: 414 34.67 - 52.01: 60 52.01 - 69.35: 17 69.35 - 86.69: 11 Dihedral angle restraints: 7990 sinusoidal: 3039 harmonic: 4951 Sorted by residual: dihedral pdb=" C ASN F 171 " pdb=" N ASN F 171 " pdb=" CA ASN F 171 " pdb=" CB ASN F 171 " ideal model delta harmonic sigma weight residual -122.60 -135.97 13.37 0 2.50e+00 1.60e-01 2.86e+01 dihedral pdb=" N ASN F 171 " pdb=" C ASN F 171 " pdb=" CA ASN F 171 " pdb=" CB ASN F 171 " ideal model delta harmonic sigma weight residual 122.80 136.08 -13.28 0 2.50e+00 1.60e-01 2.82e+01 dihedral pdb=" CA TYR B 244 " pdb=" C TYR B 244 " pdb=" N ASP B 245 " pdb=" CA ASP B 245 " ideal model delta harmonic sigma weight residual 180.00 159.69 20.31 0 5.00e+00 4.00e-02 1.65e+01 ... (remaining 7987 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 1906 0.109 - 0.217: 96 0.217 - 0.326: 0 0.326 - 0.435: 1 0.435 - 0.544: 1 Chirality restraints: 2004 Sorted by residual: chirality pdb=" CA ASN F 171 " pdb=" N ASN F 171 " pdb=" C ASN F 171 " pdb=" CB ASN F 171 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.39e+00 chirality pdb=" CA LEU E 447 " pdb=" N LEU E 447 " pdb=" C LEU E 447 " pdb=" CB LEU E 447 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.24e+00 chirality pdb=" CA VAL D 298 " pdb=" N VAL D 298 " pdb=" C VAL D 298 " pdb=" CB VAL D 298 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.86e-01 ... (remaining 2001 not shown) Planarity restraints: 2348 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER F 166 " -0.010 2.00e-02 2.50e+03 2.03e-02 4.12e+00 pdb=" C SER F 166 " 0.035 2.00e-02 2.50e+03 pdb=" O SER F 166 " -0.013 2.00e-02 2.50e+03 pdb=" N PRO F 167 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU F 155 " -0.010 2.00e-02 2.50e+03 2.00e-02 3.99e+00 pdb=" C GLU F 155 " 0.035 2.00e-02 2.50e+03 pdb=" O GLU F 155 " -0.013 2.00e-02 2.50e+03 pdb=" N ASP F 156 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 140 " -0.009 2.00e-02 2.50e+03 1.76e-02 3.11e+00 pdb=" C LYS C 140 " 0.030 2.00e-02 2.50e+03 pdb=" O LYS C 140 " -0.011 2.00e-02 2.50e+03 pdb=" N VAL C 141 " -0.010 2.00e-02 2.50e+03 ... (remaining 2345 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 382 2.70 - 3.25: 12628 3.25 - 3.80: 19065 3.80 - 4.35: 25310 4.35 - 4.90: 42757 Nonbonded interactions: 100142 Sorted by model distance: nonbonded pdb=" OG1 THR F 154 " pdb=" OE1 GLU F 155 " model vdw 2.151 2.440 nonbonded pdb=" OD1 ASP B 431 " pdb=" OG SER B 433 " model vdw 2.202 2.440 nonbonded pdb=" SG CYS A 561 " pdb="ZN ZN A 805 " model vdw 2.233 2.590 nonbonded pdb=" CE2 PHE F 157 " pdb=" CD1 LEU F 161 " model vdw 2.270 3.760 nonbonded pdb=" OG SER D 147 " pdb=" O HIS D 176 " model vdw 2.276 2.440 ... (remaining 100137 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.20 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: 0.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.070 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 39.800 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 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 : 0.004 0.055 13374 Z= 0.295 Angle : 0.728 8.854 18141 Z= 0.390 Chirality : 0.050 0.544 2004 Planarity : 0.004 0.043 2348 Dihedral : 11.733 86.686 4752 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 0.29 % Allowed : 1.84 % Favored : 97.86 % Cbeta Deviations : 0.06 % 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: -3.99 (0.17), residues: 1648 helix: -1.61 (0.23), residues: 308 sheet: -2.99 (0.23), residues: 343 loop : -2.99 (0.16), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 345 HIS 0.004 0.001 HIS B 397 PHE 0.023 0.001 PHE C 86 TYR 0.014 0.001 TYR B 244 ARG 0.002 0.000 ARG D 258 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 1534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 421 time to evaluate : 1.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "HIS C 449 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 71 MET cc_start: 0.6625 (tpt) cc_final: 0.6321 (tmm) REVERT: A 112 TYR cc_start: 0.7061 (m-80) cc_final: 0.6824 (m-80) REVERT: A 117 LEU cc_start: 0.8426 (mt) cc_final: 0.8202 (mt) REVERT: A 558 PHE cc_start: 0.8405 (t80) cc_final: 0.8172 (t80) REVERT: A 643 CYS cc_start: 0.8367 (m) cc_final: 0.8015 (t) REVERT: A 666 PHE cc_start: 0.7673 (m-80) cc_final: 0.7411 (m-80) REVERT: B 103 TRP cc_start: 0.8435 (m-10) cc_final: 0.8089 (m-10) REVERT: B 109 ASP cc_start: 0.7355 (p0) cc_final: 0.7143 (p0) REVERT: B 139 VAL cc_start: 0.8326 (t) cc_final: 0.7749 (t) REVERT: B 240 LEU cc_start: 0.9042 (mt) cc_final: 0.8713 (mm) REVERT: B 252 MET cc_start: 0.8467 (tpp) cc_final: 0.8132 (tpp) REVERT: B 265 ILE cc_start: 0.8741 (pt) cc_final: 0.8449 (mm) REVERT: B 375 LYS cc_start: 0.8029 (mttt) cc_final: 0.7700 (mttt) REVERT: C 85 LEU cc_start: 0.8219 (tt) cc_final: 0.7949 (tt) REVERT: C 91 GLU cc_start: 0.7625 (tm-30) cc_final: 0.7276 (tm-30) REVERT: C 561 HIS cc_start: 0.7300 (OUTLIER) cc_final: 0.7057 (p-80) REVERT: C 657 MET cc_start: 0.8355 (mtm) cc_final: 0.7654 (mpp) REVERT: D 13 GLU cc_start: 0.7564 (tt0) cc_final: 0.7176 (tt0) REVERT: D 44 SER cc_start: 0.9029 (t) cc_final: 0.8825 (p) REVERT: D 49 TRP cc_start: 0.8665 (m100) cc_final: 0.8305 (m100) REVERT: D 185 TRP cc_start: 0.8249 (m100) cc_final: 0.7829 (m100) REVERT: D 194 LEU cc_start: 0.9165 (mt) cc_final: 0.8907 (mt) REVERT: D 203 CYS cc_start: 0.7709 (m) cc_final: 0.7088 (m) REVERT: D 242 LEU cc_start: 0.7863 (pt) cc_final: 0.7572 (pp) REVERT: D 275 GLU cc_start: 0.7694 (mt-10) cc_final: 0.7093 (mp0) REVERT: D 306 LEU cc_start: 0.9256 (mt) cc_final: 0.8979 (mp) REVERT: D 331 THR cc_start: 0.8219 (p) cc_final: 0.7905 (t) REVERT: D 381 SER cc_start: 0.8871 (t) cc_final: 0.8281 (p) REVERT: E 420 GLU cc_start: 0.7300 (mp0) cc_final: 0.6807 (mp0) REVERT: E 430 PHE cc_start: 0.8316 (m-80) cc_final: 0.8082 (m-10) REVERT: E 476 HIS cc_start: 0.7336 (t-90) cc_final: 0.7046 (t70) REVERT: E 492 ILE cc_start: 0.7542 (mt) cc_final: 0.7323 (mt) outliers start: 4 outliers final: 2 residues processed: 425 average time/residue: 0.2486 time to fit residues: 154.4228 Evaluate side-chains 262 residues out of total 1534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 259 time to evaluate : 1.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 561 HIS Chi-restraints excluded: chain F residue 156 ASP Chi-restraints excluded: chain F residue 160 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 141 optimal weight: 6.9990 chunk 126 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 130 optimal weight: 10.0000 chunk 50 optimal weight: 4.9990 chunk 79 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 151 optimal weight: 0.3980 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 HIS ** A 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 160 HIS ** B 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 GLN ** B 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 440 GLN C 466 HIS D 128 ASN ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 370 HIS ** E 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 171 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13374 Z= 0.237 Angle : 0.598 8.197 18141 Z= 0.305 Chirality : 0.046 0.322 2004 Planarity : 0.004 0.064 2348 Dihedral : 4.454 35.999 1796 Min Nonbonded Distance : 1.567 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.21 % Allowed : 10.75 % Favored : 87.04 % 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: -2.93 (0.18), residues: 1648 helix: -0.48 (0.26), residues: 325 sheet: -2.30 (0.24), residues: 348 loop : -2.41 (0.17), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 345 HIS 0.009 0.001 HIS D 176 PHE 0.028 0.002 PHE C 656 TYR 0.023 0.002 TYR A 521 ARG 0.014 0.001 ARG A 529 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 276 time to evaluate : 1.491 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "HIS C 449 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 112 TYR cc_start: 0.7476 (m-80) cc_final: 0.7078 (m-80) REVERT: A 539 MET cc_start: 0.7953 (mtp) cc_final: 0.7264 (mmm) REVERT: A 558 PHE cc_start: 0.8688 (t80) cc_final: 0.8310 (t80) REVERT: A 643 CYS cc_start: 0.8827 (m) cc_final: 0.8487 (t) REVERT: A 666 PHE cc_start: 0.7731 (m-80) cc_final: 0.7520 (m-10) REVERT: B 119 ASN cc_start: 0.6818 (t0) cc_final: 0.6569 (t0) REVERT: B 240 LEU cc_start: 0.9185 (mt) cc_final: 0.8951 (mm) REVERT: B 252 MET cc_start: 0.8112 (tpp) cc_final: 0.7671 (tpp) REVERT: C 85 LEU cc_start: 0.8338 (tt) cc_final: 0.8080 (tt) REVERT: C 91 GLU cc_start: 0.8148 (tm-30) cc_final: 0.7817 (tm-30) REVERT: C 572 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8701 (mm) REVERT: C 643 TYR cc_start: 0.7071 (m-80) cc_final: 0.6834 (m-10) REVERT: C 657 MET cc_start: 0.8375 (mtm) cc_final: 0.7630 (mpp) REVERT: D 118 GLU cc_start: 0.8806 (mm-30) cc_final: 0.8587 (mt-10) REVERT: D 275 GLU cc_start: 0.7905 (mt-10) cc_final: 0.7519 (mp0) REVERT: D 295 ASP cc_start: 0.7904 (p0) cc_final: 0.7649 (p0) REVERT: D 306 LEU cc_start: 0.9392 (mt) cc_final: 0.9168 (mp) REVERT: D 346 ASP cc_start: 0.8180 (t0) cc_final: 0.7964 (t0) REVERT: D 380 PHE cc_start: 0.9306 (p90) cc_final: 0.9106 (p90) REVERT: D 381 SER cc_start: 0.9174 (t) cc_final: 0.8667 (p) REVERT: E 402 THR cc_start: 0.8571 (OUTLIER) cc_final: 0.8365 (t) REVERT: E 406 ILE cc_start: 0.9087 (tp) cc_final: 0.8395 (tt) REVERT: E 476 HIS cc_start: 0.7470 (t-90) cc_final: 0.6091 (t-90) REVERT: E 492 ILE cc_start: 0.7951 (mt) cc_final: 0.7658 (mt) outliers start: 30 outliers final: 13 residues processed: 293 average time/residue: 0.2123 time to fit residues: 93.6836 Evaluate side-chains 233 residues out of total 1534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 218 time to evaluate : 1.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 196 ARG Chi-restraints excluded: chain C residue 477 ASN Chi-restraints excluded: chain C residue 572 LEU Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain D residue 404 MET Chi-restraints excluded: chain E residue 402 THR Chi-restraints excluded: chain E residue 448 LEU Chi-restraints excluded: chain E residue 484 THR Chi-restraints excluded: chain F residue 156 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 84 optimal weight: 6.9990 chunk 47 optimal weight: 0.8980 chunk 126 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 151 optimal weight: 0.9990 chunk 164 optimal weight: 3.9990 chunk 135 optimal weight: 10.0000 chunk 150 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 121 optimal weight: 5.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 HIS ** B 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 219 ASN D 78 HIS ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13374 Z= 0.187 Angle : 0.543 7.581 18141 Z= 0.280 Chirality : 0.044 0.197 2004 Planarity : 0.004 0.048 2348 Dihedral : 4.185 26.878 1792 Min Nonbonded Distance : 1.415 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.28 % Allowed : 13.11 % Favored : 84.61 % 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: -2.36 (0.19), residues: 1648 helix: -0.02 (0.28), residues: 329 sheet: -1.88 (0.25), residues: 357 loop : -2.06 (0.18), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 434 HIS 0.011 0.001 HIS D 176 PHE 0.024 0.002 PHE A 46 TYR 0.017 0.002 TYR A 521 ARG 0.004 0.000 ARG B 216 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 241 time to evaluate : 1.432 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "HIS C 449 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 112 TYR cc_start: 0.7509 (m-80) cc_final: 0.7089 (m-80) REVERT: A 434 TRP cc_start: 0.7265 (m-10) cc_final: 0.7003 (m-10) REVERT: A 558 PHE cc_start: 0.8695 (t80) cc_final: 0.8359 (t80) REVERT: A 643 CYS cc_start: 0.8989 (m) cc_final: 0.8617 (t) REVERT: B 109 ASP cc_start: 0.7206 (p0) cc_final: 0.6718 (p0) REVERT: C 85 LEU cc_start: 0.8490 (tt) cc_final: 0.8146 (tt) REVERT: C 460 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8588 (tp) REVERT: C 572 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8686 (mm) REVERT: C 657 MET cc_start: 0.8389 (mtm) cc_final: 0.7670 (mpp) REVERT: D 118 GLU cc_start: 0.8870 (mm-30) cc_final: 0.8621 (mt-10) REVERT: D 250 GLN cc_start: 0.8039 (mp10) cc_final: 0.7700 (mp10) REVERT: D 302 ASP cc_start: 0.8026 (t0) cc_final: 0.7812 (t0) REVERT: D 306 LEU cc_start: 0.9399 (mt) cc_final: 0.9139 (mp) REVERT: D 345 TRP cc_start: 0.9122 (OUTLIER) cc_final: 0.8886 (m100) REVERT: D 381 SER cc_start: 0.9200 (t) cc_final: 0.8666 (p) REVERT: E 420 GLU cc_start: 0.7960 (mp0) cc_final: 0.7683 (mp0) REVERT: E 492 ILE cc_start: 0.8070 (mt) cc_final: 0.7765 (mt) outliers start: 31 outliers final: 19 residues processed: 260 average time/residue: 0.2172 time to fit residues: 84.1823 Evaluate side-chains 224 residues out of total 1534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 202 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 546 LYS Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 477 ASN Chi-restraints excluded: chain C residue 561 HIS Chi-restraints excluded: chain C residue 572 LEU Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 674 ILE Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 181 TYR Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain D residue 345 TRP Chi-restraints excluded: chain D residue 404 MET Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain F residue 156 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 150 optimal weight: 6.9990 chunk 114 optimal weight: 9.9990 chunk 78 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 72 optimal weight: 9.9990 chunk 102 optimal weight: 0.3980 chunk 152 optimal weight: 0.5980 chunk 161 optimal weight: 10.0000 chunk 79 optimal weight: 8.9990 chunk 144 optimal weight: 0.9980 chunk 43 optimal weight: 6.9990 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 194 ASN ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 235 HIS C 504 GLN D 48 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.4053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13374 Z= 0.258 Angle : 0.584 8.360 18141 Z= 0.300 Chirality : 0.046 0.312 2004 Planarity : 0.004 0.056 2348 Dihedral : 4.384 28.039 1792 Min Nonbonded Distance : 1.046 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 3.90 % Allowed : 13.48 % Favored : 82.62 % 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: -2.05 (0.19), residues: 1648 helix: 0.12 (0.28), residues: 330 sheet: -1.66 (0.25), residues: 377 loop : -1.81 (0.19), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP D 205 HIS 0.009 0.001 HIS D 176 PHE 0.017 0.002 PHE A 46 TYR 0.017 0.002 TYR B 244 ARG 0.009 0.001 ARG C 563 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 224 time to evaluate : 1.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 TYR cc_start: 0.8403 (t80) cc_final: 0.7659 (t80) REVERT: A 112 TYR cc_start: 0.7719 (m-80) cc_final: 0.7198 (m-80) REVERT: A 283 LYS cc_start: 0.7435 (mttt) cc_final: 0.7016 (pptt) REVERT: A 434 TRP cc_start: 0.6931 (m100) cc_final: 0.6650 (m-10) REVERT: A 558 PHE cc_start: 0.8690 (t80) cc_final: 0.8354 (t80) REVERT: A 643 CYS cc_start: 0.9153 (m) cc_final: 0.8764 (t) REVERT: B 252 MET cc_start: 0.8259 (tpp) cc_final: 0.7981 (tpp) REVERT: B 347 GLU cc_start: 0.8208 (tp30) cc_final: 0.7919 (tm-30) REVERT: B 389 TRP cc_start: 0.9071 (m-90) cc_final: 0.8818 (m-90) REVERT: C 85 LEU cc_start: 0.8624 (tt) cc_final: 0.8340 (tt) REVERT: C 460 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8686 (tp) REVERT: C 504 GLN cc_start: 0.8568 (OUTLIER) cc_final: 0.8364 (tm-30) REVERT: C 643 TYR cc_start: 0.7927 (m-10) cc_final: 0.7665 (m-10) REVERT: C 657 MET cc_start: 0.8479 (mtm) cc_final: 0.7647 (mpp) REVERT: D 13 GLU cc_start: 0.7951 (tt0) cc_final: 0.7367 (tt0) REVERT: D 27 ASN cc_start: 0.8909 (t0) cc_final: 0.8527 (t0) REVERT: D 85 GLN cc_start: 0.7643 (OUTLIER) cc_final: 0.7406 (mt0) REVERT: D 345 TRP cc_start: 0.9201 (OUTLIER) cc_final: 0.8976 (m100) REVERT: E 420 GLU cc_start: 0.8076 (mp0) cc_final: 0.7722 (mp0) REVERT: E 452 MET cc_start: 0.6312 (ppp) cc_final: 0.6096 (ppp) outliers start: 53 outliers final: 31 residues processed: 262 average time/residue: 0.2129 time to fit residues: 85.9653 Evaluate side-chains 228 residues out of total 1534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 193 time to evaluate : 1.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 546 LYS Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 452 TRP Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 464 LEU Chi-restraints excluded: chain C residue 475 ILE Chi-restraints excluded: chain C residue 477 ASN Chi-restraints excluded: chain C residue 504 GLN Chi-restraints excluded: chain C residue 525 ILE Chi-restraints excluded: chain C residue 561 HIS Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 653 CYS Chi-restraints excluded: chain C residue 671 ILE Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 85 GLN Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 181 TYR Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain D residue 203 CYS Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain D residue 345 TRP Chi-restraints excluded: chain D residue 404 MET Chi-restraints excluded: chain E residue 484 THR Chi-restraints excluded: chain F residue 156 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 134 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 120 optimal weight: 0.5980 chunk 66 optimal weight: 9.9990 chunk 137 optimal weight: 0.9990 chunk 111 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 82 optimal weight: 50.0000 chunk 144 optimal weight: 1.9990 chunk 40 optimal weight: 9.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 614 HIS C 634 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.4321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13374 Z= 0.217 Angle : 0.566 12.282 18141 Z= 0.288 Chirality : 0.044 0.166 2004 Planarity : 0.003 0.044 2348 Dihedral : 4.311 23.185 1792 Min Nonbonded Distance : 1.210 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 3.31 % Allowed : 15.46 % Favored : 81.22 % 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: -1.82 (0.20), residues: 1648 helix: 0.24 (0.28), residues: 327 sheet: -1.38 (0.26), residues: 383 loop : -1.69 (0.19), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 205 HIS 0.011 0.001 HIS E 476 PHE 0.018 0.002 PHE D 61 TYR 0.014 0.001 TYR B 154 ARG 0.005 0.000 ARG B 216 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 203 time to evaluate : 1.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 TYR cc_start: 0.8484 (t80) cc_final: 0.8160 (t80) REVERT: A 112 TYR cc_start: 0.7759 (m-80) cc_final: 0.7153 (m-80) REVERT: A 283 LYS cc_start: 0.7501 (mttt) cc_final: 0.7039 (pptt) REVERT: A 434 TRP cc_start: 0.6883 (m100) cc_final: 0.6614 (m-10) REVERT: B 196 LEU cc_start: 0.9341 (mt) cc_final: 0.8758 (tp) REVERT: B 252 MET cc_start: 0.8210 (tpp) cc_final: 0.7954 (tpp) REVERT: B 347 GLU cc_start: 0.8177 (tp30) cc_final: 0.7893 (tm-30) REVERT: B 389 TRP cc_start: 0.9050 (m-90) cc_final: 0.8784 (m-90) REVERT: C 85 LEU cc_start: 0.8686 (tt) cc_final: 0.8396 (tt) REVERT: C 460 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8544 (tp) REVERT: C 504 GLN cc_start: 0.8571 (OUTLIER) cc_final: 0.8292 (tm-30) REVERT: C 657 MET cc_start: 0.8531 (mtm) cc_final: 0.7676 (mpp) REVERT: C 663 MET cc_start: 0.8795 (mtm) cc_final: 0.8593 (ttm) REVERT: D 13 GLU cc_start: 0.7889 (tt0) cc_final: 0.7421 (tt0) REVERT: D 27 ASN cc_start: 0.8860 (t0) cc_final: 0.8578 (t0) REVERT: D 85 GLN cc_start: 0.7758 (OUTLIER) cc_final: 0.7397 (mt0) REVERT: D 242 LEU cc_start: 0.8453 (pt) cc_final: 0.8155 (pp) REVERT: D 345 TRP cc_start: 0.9194 (OUTLIER) cc_final: 0.8980 (m100) REVERT: E 420 GLU cc_start: 0.8034 (mp0) cc_final: 0.7772 (mp0) REVERT: E 476 HIS cc_start: 0.7867 (t-90) cc_final: 0.7602 (t-90) outliers start: 45 outliers final: 31 residues processed: 238 average time/residue: 0.2065 time to fit residues: 76.0375 Evaluate side-chains 224 residues out of total 1534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 189 time to evaluate : 1.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 546 LYS Chi-restraints excluded: chain A residue 608 GLN Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 452 TRP Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 477 ASN Chi-restraints excluded: chain C residue 504 GLN Chi-restraints excluded: chain C residue 525 ILE Chi-restraints excluded: chain C residue 561 HIS Chi-restraints excluded: chain C residue 572 LEU Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 653 CYS Chi-restraints excluded: chain C residue 671 ILE Chi-restraints excluded: chain C residue 674 ILE Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 85 GLN Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 181 TYR Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain D residue 203 CYS Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain D residue 345 TRP Chi-restraints excluded: chain D residue 404 MET Chi-restraints excluded: chain E residue 402 THR Chi-restraints excluded: chain F residue 156 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 54 optimal weight: 6.9990 chunk 145 optimal weight: 0.0980 chunk 31 optimal weight: 1.9990 chunk 94 optimal weight: 10.0000 chunk 39 optimal weight: 0.4980 chunk 161 optimal weight: 10.0000 chunk 134 optimal weight: 6.9990 chunk 74 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 690 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.4510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13374 Z= 0.184 Angle : 0.549 7.848 18141 Z= 0.279 Chirality : 0.044 0.309 2004 Planarity : 0.003 0.048 2348 Dihedral : 4.222 23.904 1792 Min Nonbonded Distance : 1.209 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 3.68 % Allowed : 15.98 % Favored : 80.34 % 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: -1.60 (0.20), residues: 1648 helix: 0.37 (0.29), residues: 333 sheet: -1.21 (0.27), residues: 369 loop : -1.56 (0.19), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 205 HIS 0.007 0.001 HIS E 476 PHE 0.029 0.002 PHE A 312 TYR 0.014 0.001 TYR A 521 ARG 0.005 0.000 ARG B 216 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 210 time to evaluate : 1.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 TYR cc_start: 0.8498 (t80) cc_final: 0.8249 (t80) REVERT: A 112 TYR cc_start: 0.7804 (m-80) cc_final: 0.7264 (m-80) REVERT: A 283 LYS cc_start: 0.7523 (mttt) cc_final: 0.7061 (pptt) REVERT: A 434 TRP cc_start: 0.6819 (m100) cc_final: 0.6579 (m-10) REVERT: B 196 LEU cc_start: 0.9063 (mt) cc_final: 0.8690 (tp) REVERT: B 310 ASP cc_start: 0.8668 (m-30) cc_final: 0.7995 (t0) REVERT: B 347 GLU cc_start: 0.8100 (tp30) cc_final: 0.7819 (tm-30) REVERT: B 389 TRP cc_start: 0.9057 (m-90) cc_final: 0.8788 (m-90) REVERT: B 390 ASP cc_start: 0.7998 (m-30) cc_final: 0.7717 (m-30) REVERT: C 85 LEU cc_start: 0.8685 (tt) cc_final: 0.8380 (tt) REVERT: C 657 MET cc_start: 0.8525 (mtm) cc_final: 0.7696 (mpp) REVERT: C 684 MET cc_start: 0.6697 (ppp) cc_final: 0.6037 (ppp) REVERT: D 27 ASN cc_start: 0.8977 (t0) cc_final: 0.8634 (t0) REVERT: D 85 GLN cc_start: 0.7697 (OUTLIER) cc_final: 0.7374 (mt0) REVERT: D 345 TRP cc_start: 0.9197 (OUTLIER) cc_final: 0.8910 (m100) REVERT: E 476 HIS cc_start: 0.7730 (t-90) cc_final: 0.7478 (t-90) outliers start: 50 outliers final: 36 residues processed: 242 average time/residue: 0.2012 time to fit residues: 75.3529 Evaluate side-chains 233 residues out of total 1534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 195 time to evaluate : 1.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 546 LYS Chi-restraints excluded: chain A residue 608 GLN Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 452 TRP Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 475 ILE Chi-restraints excluded: chain C residue 477 ASN Chi-restraints excluded: chain C residue 525 ILE Chi-restraints excluded: chain C residue 561 HIS Chi-restraints excluded: chain C residue 572 LEU Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 653 CYS Chi-restraints excluded: chain C residue 671 ILE Chi-restraints excluded: chain C residue 674 ILE Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 85 GLN Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 181 TYR Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain D residue 203 CYS Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain D residue 345 TRP Chi-restraints excluded: chain D residue 404 MET Chi-restraints excluded: chain E residue 402 THR Chi-restraints excluded: chain E residue 484 THR Chi-restraints excluded: chain F residue 156 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 155 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 92 optimal weight: 50.0000 chunk 117 optimal weight: 0.8980 chunk 91 optimal weight: 30.0000 chunk 136 optimal weight: 0.7980 chunk 90 optimal weight: 8.9990 chunk 160 optimal weight: 8.9990 chunk 100 optimal weight: 6.9990 chunk 98 optimal weight: 0.0270 chunk 74 optimal weight: 10.0000 overall best weight: 1.9442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 634 HIS ** D 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.4753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13374 Z= 0.233 Angle : 0.573 7.967 18141 Z= 0.291 Chirality : 0.044 0.179 2004 Planarity : 0.003 0.046 2348 Dihedral : 4.305 19.399 1792 Min Nonbonded Distance : 1.176 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 3.46 % Allowed : 17.23 % Favored : 79.31 % 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: -1.52 (0.20), residues: 1648 helix: 0.40 (0.29), residues: 332 sheet: -1.09 (0.27), residues: 371 loop : -1.52 (0.19), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP D 205 HIS 0.008 0.001 HIS E 476 PHE 0.025 0.002 PHE A 312 TYR 0.014 0.001 TYR B 244 ARG 0.005 0.000 ARG B 216 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 205 time to evaluate : 1.526 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 112 TYR cc_start: 0.7822 (m-80) cc_final: 0.7546 (m-80) REVERT: A 283 LYS cc_start: 0.7556 (mttt) cc_final: 0.7093 (pptt) REVERT: A 434 TRP cc_start: 0.6839 (m100) cc_final: 0.6636 (m-10) REVERT: A 643 CYS cc_start: 0.9223 (m) cc_final: 0.8884 (t) REVERT: B 119 ASN cc_start: 0.6981 (t0) cc_final: 0.6484 (t0) REVERT: B 196 LEU cc_start: 0.8932 (mt) cc_final: 0.8722 (tp) REVERT: B 389 TRP cc_start: 0.9134 (m-90) cc_final: 0.8881 (m-90) REVERT: B 390 ASP cc_start: 0.8105 (m-30) cc_final: 0.7823 (m-30) REVERT: C 85 LEU cc_start: 0.8811 (tt) cc_final: 0.8482 (tt) REVERT: C 643 TYR cc_start: 0.7862 (m-10) cc_final: 0.7513 (m-10) REVERT: D 13 GLU cc_start: 0.7783 (tt0) cc_final: 0.7257 (tt0) REVERT: D 85 GLN cc_start: 0.7665 (OUTLIER) cc_final: 0.7360 (mt0) REVERT: D 345 TRP cc_start: 0.9225 (OUTLIER) cc_final: 0.8982 (m100) REVERT: E 420 GLU cc_start: 0.7653 (mp0) cc_final: 0.7444 (mp0) REVERT: E 493 TYR cc_start: 0.8411 (t80) cc_final: 0.8078 (t80) outliers start: 47 outliers final: 38 residues processed: 239 average time/residue: 0.2132 time to fit residues: 77.6617 Evaluate side-chains 233 residues out of total 1534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 193 time to evaluate : 1.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 546 LYS Chi-restraints excluded: chain A residue 608 GLN Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 452 TRP Chi-restraints excluded: chain C residue 453 CYS Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 464 LEU Chi-restraints excluded: chain C residue 475 ILE Chi-restraints excluded: chain C residue 477 ASN Chi-restraints excluded: chain C residue 525 ILE Chi-restraints excluded: chain C residue 561 HIS Chi-restraints excluded: chain C residue 572 LEU Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 653 CYS Chi-restraints excluded: chain C residue 671 ILE Chi-restraints excluded: chain C residue 674 ILE Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 85 GLN Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 181 TYR Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain D residue 203 CYS Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain D residue 345 TRP Chi-restraints excluded: chain D residue 399 MET Chi-restraints excluded: chain D residue 404 MET Chi-restraints excluded: chain E residue 402 THR Chi-restraints excluded: chain E residue 484 THR Chi-restraints excluded: chain F residue 156 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 99 optimal weight: 0.1980 chunk 64 optimal weight: 2.9990 chunk 96 optimal weight: 10.0000 chunk 48 optimal weight: 6.9990 chunk 31 optimal weight: 0.8980 chunk 102 optimal weight: 8.9990 chunk 109 optimal weight: 9.9990 chunk 79 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 126 optimal weight: 7.9990 chunk 146 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 690 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 498 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.4801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 13374 Z= 0.156 Angle : 0.561 9.360 18141 Z= 0.281 Chirality : 0.044 0.311 2004 Planarity : 0.003 0.050 2348 Dihedral : 4.178 19.804 1792 Min Nonbonded Distance : 1.255 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 3.02 % Allowed : 17.97 % Favored : 79.01 % 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: -1.43 (0.20), residues: 1648 helix: 0.41 (0.29), residues: 333 sheet: -0.91 (0.28), residues: 372 loop : -1.49 (0.19), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP D 205 HIS 0.007 0.001 HIS D 226 PHE 0.024 0.001 PHE D 152 TYR 0.015 0.001 TYR A 42 ARG 0.008 0.000 ARG B 120 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 219 time to evaluate : 1.516 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 283 LYS cc_start: 0.7534 (mttt) cc_final: 0.7074 (pptt) REVERT: A 695 ASN cc_start: 0.8847 (p0) cc_final: 0.8637 (p0) REVERT: B 310 ASP cc_start: 0.8637 (m-30) cc_final: 0.8032 (t0) REVERT: C 85 LEU cc_start: 0.8773 (tt) cc_final: 0.8448 (tt) REVERT: C 643 TYR cc_start: 0.7805 (m-10) cc_final: 0.7438 (m-10) REVERT: C 684 MET cc_start: 0.7377 (ppp) cc_final: 0.7090 (pmm) REVERT: D 13 GLU cc_start: 0.7793 (tt0) cc_final: 0.7257 (tt0) REVERT: D 85 GLN cc_start: 0.7572 (OUTLIER) cc_final: 0.7230 (mt0) REVERT: D 345 TRP cc_start: 0.9193 (OUTLIER) cc_final: 0.8926 (m100) REVERT: E 420 GLU cc_start: 0.7583 (mp0) cc_final: 0.7383 (mp0) REVERT: E 493 TYR cc_start: 0.8311 (t80) cc_final: 0.7978 (t80) outliers start: 41 outliers final: 29 residues processed: 246 average time/residue: 0.1998 time to fit residues: 76.5816 Evaluate side-chains 235 residues out of total 1534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 204 time to evaluate : 1.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 546 LYS Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 452 TRP Chi-restraints excluded: chain C residue 453 CYS Chi-restraints excluded: chain C residue 475 ILE Chi-restraints excluded: chain C residue 477 ASN Chi-restraints excluded: chain C residue 561 HIS Chi-restraints excluded: chain C residue 572 LEU Chi-restraints excluded: chain C residue 653 CYS Chi-restraints excluded: chain C residue 671 ILE Chi-restraints excluded: chain C residue 672 MET Chi-restraints excluded: chain C residue 674 ILE Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 85 GLN Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 181 TYR Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain D residue 203 CYS Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 345 TRP Chi-restraints excluded: chain E residue 402 THR Chi-restraints excluded: chain E residue 452 MET Chi-restraints excluded: chain F residue 156 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 154 optimal weight: 4.9990 chunk 140 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 chunk 90 optimal weight: 0.0020 chunk 65 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 135 optimal weight: 7.9990 chunk 141 optimal weight: 9.9990 chunk 98 optimal weight: 0.9980 chunk 158 optimal weight: 0.9990 overall best weight: 0.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 690 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.4878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 13374 Z= 0.158 Angle : 0.561 9.810 18141 Z= 0.281 Chirality : 0.044 0.186 2004 Planarity : 0.003 0.047 2348 Dihedral : 4.103 18.906 1792 Min Nonbonded Distance : 1.244 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.65 % Allowed : 18.92 % Favored : 78.42 % 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: -1.34 (0.20), residues: 1648 helix: 0.49 (0.29), residues: 333 sheet: -0.79 (0.28), residues: 369 loop : -1.46 (0.19), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP D 205 HIS 0.007 0.001 HIS D 226 PHE 0.023 0.001 PHE A 312 TYR 0.014 0.001 TYR B 244 ARG 0.006 0.000 ARG B 120 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 215 time to evaluate : 1.604 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 283 LYS cc_start: 0.7435 (mttt) cc_final: 0.7046 (pptt) REVERT: B 310 ASP cc_start: 0.8629 (m-30) cc_final: 0.8013 (t0) REVERT: B 364 TRP cc_start: 0.6263 (p-90) cc_final: 0.5838 (p-90) REVERT: C 85 LEU cc_start: 0.8774 (tt) cc_final: 0.8455 (tt) REVERT: C 684 MET cc_start: 0.7361 (ppp) cc_final: 0.7002 (pmm) REVERT: D 13 GLU cc_start: 0.7802 (tt0) cc_final: 0.7165 (tt0) REVERT: D 85 GLN cc_start: 0.7506 (OUTLIER) cc_final: 0.7218 (mt0) REVERT: D 345 TRP cc_start: 0.9225 (OUTLIER) cc_final: 0.8959 (m100) REVERT: F 159 THR cc_start: 0.7925 (p) cc_final: 0.7710 (p) outliers start: 36 outliers final: 33 residues processed: 242 average time/residue: 0.2022 time to fit residues: 76.1253 Evaluate side-chains 237 residues out of total 1534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 202 time to evaluate : 1.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 546 LYS Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 452 TRP Chi-restraints excluded: chain C residue 453 CYS Chi-restraints excluded: chain C residue 475 ILE Chi-restraints excluded: chain C residue 477 ASN Chi-restraints excluded: chain C residue 525 ILE Chi-restraints excluded: chain C residue 561 HIS Chi-restraints excluded: chain C residue 653 CYS Chi-restraints excluded: chain C residue 671 ILE Chi-restraints excluded: chain C residue 672 MET Chi-restraints excluded: chain C residue 674 ILE Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 85 GLN Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 181 TYR Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain D residue 203 CYS Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 345 TRP Chi-restraints excluded: chain D residue 404 MET Chi-restraints excluded: chain E residue 402 THR Chi-restraints excluded: chain E residue 452 MET Chi-restraints excluded: chain E residue 484 THR Chi-restraints excluded: chain E residue 492 ILE Chi-restraints excluded: chain F residue 156 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 96 optimal weight: 0.0010 chunk 75 optimal weight: 0.9980 chunk 110 optimal weight: 7.9990 chunk 166 optimal weight: 7.9990 chunk 153 optimal weight: 0.8980 chunk 132 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 chunk 102 optimal weight: 0.9980 chunk 81 optimal weight: 7.9990 chunk 105 optimal weight: 0.9980 chunk 141 optimal weight: 9.9990 overall best weight: 0.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 194 ASN ** D 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.4953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 13374 Z= 0.162 Angle : 0.563 9.450 18141 Z= 0.283 Chirality : 0.045 0.354 2004 Planarity : 0.003 0.049 2348 Dihedral : 4.055 18.879 1792 Min Nonbonded Distance : 1.257 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 2.72 % Allowed : 19.00 % Favored : 78.28 % 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: -1.27 (0.20), residues: 1648 helix: 0.55 (0.29), residues: 333 sheet: -0.79 (0.28), residues: 381 loop : -1.40 (0.19), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP D 205 HIS 0.013 0.001 HIS E 476 PHE 0.022 0.001 PHE A 312 TYR 0.015 0.001 TYR B 244 ARG 0.006 0.000 ARG B 120 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 215 time to evaluate : 1.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 LYS cc_start: 0.7437 (mttt) cc_final: 0.7046 (pptt) REVERT: B 124 TYR cc_start: 0.8025 (m-10) cc_final: 0.7708 (m-10) REVERT: B 310 ASP cc_start: 0.8617 (m-30) cc_final: 0.8003 (t0) REVERT: B 364 TRP cc_start: 0.6253 (p-90) cc_final: 0.5834 (p-90) REVERT: C 85 LEU cc_start: 0.8781 (tt) cc_final: 0.8455 (tt) REVERT: C 664 HIS cc_start: 0.7639 (t70) cc_final: 0.7335 (t70) REVERT: C 684 MET cc_start: 0.7322 (ppp) cc_final: 0.6915 (pmm) REVERT: D 13 GLU cc_start: 0.7729 (tt0) cc_final: 0.7167 (tt0) REVERT: D 85 GLN cc_start: 0.7489 (OUTLIER) cc_final: 0.7030 (mt0) REVERT: D 174 ARG cc_start: 0.7944 (ttm110) cc_final: 0.7655 (ttm-80) REVERT: D 345 TRP cc_start: 0.9230 (OUTLIER) cc_final: 0.8865 (m100) REVERT: F 159 THR cc_start: 0.7848 (p) cc_final: 0.7612 (p) outliers start: 37 outliers final: 32 residues processed: 240 average time/residue: 0.2121 time to fit residues: 79.7985 Evaluate side-chains 237 residues out of total 1534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 203 time to evaluate : 1.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 546 LYS Chi-restraints excluded: chain A residue 553 ASP Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 452 TRP Chi-restraints excluded: chain C residue 453 CYS Chi-restraints excluded: chain C residue 475 ILE Chi-restraints excluded: chain C residue 477 ASN Chi-restraints excluded: chain C residue 525 ILE Chi-restraints excluded: chain C residue 561 HIS Chi-restraints excluded: chain C residue 653 CYS Chi-restraints excluded: chain C residue 672 MET Chi-restraints excluded: chain C residue 674 ILE Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 85 GLN Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 181 TYR Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain D residue 203 CYS Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 345 TRP Chi-restraints excluded: chain D residue 404 MET Chi-restraints excluded: chain E residue 402 THR Chi-restraints excluded: chain E residue 452 MET Chi-restraints excluded: chain F residue 156 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 40 optimal weight: 8.9990 chunk 122 optimal weight: 4.9990 chunk 19 optimal weight: 20.0000 chunk 36 optimal weight: 4.9990 chunk 132 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 24 optimal weight: 0.5980 chunk 116 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.140620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.105896 restraints weight = 22779.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.108429 restraints weight = 15231.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.110077 restraints weight = 11841.048| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3416 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3416 r_free = 0.3416 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3408 r_free = 0.3408 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3408 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.5249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13374 Z= 0.280 Angle : 0.621 10.233 18141 Z= 0.316 Chirality : 0.045 0.175 2004 Planarity : 0.004 0.049 2348 Dihedral : 4.370 18.790 1792 Min Nonbonded Distance : 1.189 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 3.09 % Allowed : 18.70 % Favored : 78.20 % 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: -1.26 (0.21), residues: 1648 helix: 0.54 (0.29), residues: 331 sheet: -0.84 (0.28), residues: 381 loop : -1.35 (0.20), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP D 205 HIS 0.013 0.001 HIS E 476 PHE 0.022 0.002 PHE A 312 TYR 0.016 0.002 TYR B 244 ARG 0.006 0.001 ARG B 120 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2632.67 seconds wall clock time: 48 minutes 33.22 seconds (2913.22 seconds total)