Starting phenix.real_space_refine (version: dev) on Wed Feb 22 08:52:14 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gs2_34218/02_2023/8gs2_34218.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gs2_34218/02_2023/8gs2_34218.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gs2_34218/02_2023/8gs2_34218.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gs2_34218/02_2023/8gs2_34218.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gs2_34218/02_2023/8gs2_34218.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gs2_34218/02_2023/8gs2_34218.pdb" } resolution = 2.84 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.116 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 Process input model Symmetric amino acids flipped Residue "A TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 714": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 776": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1005": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 16935 Number of models: 1 Model: "" Number of chains: 7 Chain: "R" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 801 Classifications: {'RNA': 38} Modifications used: {'5*END': 1, 'rna2p_pur': 12, 'rna2p_pyr': 9, 'rna3p_pur': 5, 'rna3p_pyr': 12} Link IDs: {'rna2p': 21, 'rna3p': 16} Chain: "D" Number of atoms: 492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 492 Classifications: {'RNA': 23} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 1, 'rna3p_pur': 11, 'rna3p_pyr': 8} Link IDs: {'rna2p': 4, 'rna3p': 18} Chain: "A" Number of atoms: 11710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1452, 11710 Classifications: {'peptide': 1452} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 80, 'TRANS': 1371} Chain breaks: 7 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 3882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3882 Classifications: {'peptide': 464} Link IDs: {'PTRANS': 14, 'TRANS': 449} Chain breaks: 3 Chain: "D" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Classifications: {'RNA': 1} Modifications used: {'rna3p_pyr': 1} Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 26 Unusual residues: {' ZN': 4} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna3p_pur': 1} Link IDs: {None: 4} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Classifications: {'DNA': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' A:plan': 1, ' A:plan2': 1} Unresolved non-hydrogen planarities: 13 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2243 SG CYS A 115 45.047 28.429 148.341 1.00 63.96 S ATOM 2305 SG CYS A 123 42.617 29.327 146.049 1.00 59.07 S ATOM 2329 SG CYS A 126 44.820 28.539 144.988 1.00 60.95 S ATOM 4665 SG CYS A 463 51.199 52.747 121.519 1.00 42.09 S ATOM 4727 SG CYS A 472 51.640 51.598 125.129 1.00 40.41 S ATOM 4741 SG CYS A 474 48.970 54.158 124.274 1.00 38.93 S ATOM 4763 SG CYS A 477 48.520 50.629 123.073 1.00 34.23 S ATOM 6581 SG CYS A 706 60.281 66.198 97.314 1.00 45.83 S ATOM 6596 SG CYS A 708 57.163 68.056 96.317 1.00 31.25 S ATOM 6618 SG CYS A 711 56.849 64.419 97.465 1.00 38.02 S ATOM 8483 SG CYS A 965 54.750 62.166 59.402 1.00 18.00 S ATOM 10654 SG CYS A1312 57.498 61.890 61.968 1.00 20.46 S ATOM 10893 SG CYS A1342 55.962 65.288 61.009 1.00 28.15 S ATOM 10911 SG CYS A1345 54.036 62.938 63.168 1.00 30.70 S Time building chain proxies: 10.18, per 1000 atoms: 0.60 Number of scatterers: 16935 At special positions: 0 Unit cell: (111.22, 102.92, 170.98, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 73 16.00 P 63 15.00 O 3320 8.00 N 2988 7.00 C 10487 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: 7.35 Conformation dependent library (CDL) restraints added in 2.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1702 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 126 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 123 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 115 " pdb=" ZN A1703 " pdb="ZN ZN A1703 " - pdb=" SG CYS A 477 " pdb="ZN ZN A1703 " - pdb=" SG CYS A 463 " pdb="ZN ZN A1703 " - pdb=" SG CYS A 474 " pdb="ZN ZN A1703 " - pdb=" SG CYS A 472 " pdb=" ZN A1704 " pdb="ZN ZN A1704 " - pdb=" ND1 HIS A 703 " pdb="ZN ZN A1704 " - pdb=" SG CYS A 708 " pdb="ZN ZN A1704 " - pdb=" SG CYS A 706 " pdb="ZN ZN A1704 " - pdb=" SG CYS A 711 " pdb=" ZN A1705 " pdb="ZN ZN A1705 " - pdb=" SG CYS A1342 " pdb="ZN ZN A1705 " - pdb=" SG CYS A 965 " pdb="ZN ZN A1705 " - pdb=" SG CYS A1312 " pdb="ZN ZN A1705 " - pdb=" SG CYS A1345 " Number of angles added : 15 3784 Ramachandran restraints generated. 1892 Oldfield, 0 Emsley, 1892 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3584 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 22 sheets defined 40.4% alpha, 21.6% beta 18 base pairs and 23 stacking pairs defined. Time for finding SS restraints: 5.56 Creating SS restraints... Processing helix chain 'A' and resid 22 through 26 removed outlier: 3.581A pdb=" N ARG A 26 " --> pdb=" O SER A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 36 Processing helix chain 'A' and resid 37 through 39 No H-bonds generated for 'chain 'A' and resid 37 through 39' Processing helix chain 'A' and resid 57 through 76 removed outlier: 3.551A pdb=" N LEU A 61 " --> pdb=" O THR A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 98 Processing helix chain 'A' and resid 123 through 130 Processing helix chain 'A' and resid 163 through 166 Processing helix chain 'A' and resid 211 through 225 Processing helix chain 'A' and resid 262 through 276 Processing helix chain 'A' and resid 281 through 291 Processing helix chain 'A' and resid 292 through 299 removed outlier: 5.737A pdb=" N SER A 296 " --> pdb=" O ARG A 293 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N LYS A 297 " --> pdb=" O ARG A 294 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU A 298 " --> pdb=" O SER A 295 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL A 299 " --> pdb=" O SER A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 338 Processing helix chain 'A' and resid 340 through 343 Processing helix chain 'A' and resid 344 through 366 removed outlier: 3.536A pdb=" N MET A 366 " --> pdb=" O LYS A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 460 Processing helix chain 'A' and resid 474 through 481 Processing helix chain 'A' and resid 542 through 554 Processing helix chain 'A' and resid 562 through 566 Processing helix chain 'A' and resid 584 through 594 Processing helix chain 'A' and resid 595 through 598 Processing helix chain 'A' and resid 599 through 607 Processing helix chain 'A' and resid 608 through 610 No H-bonds generated for 'chain 'A' and resid 608 through 610' Processing helix chain 'A' and resid 643 through 648 removed outlier: 3.727A pdb=" N VAL A 648 " --> pdb=" O ILE A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 675 through 689 Processing helix chain 'A' and resid 699 through 701 No H-bonds generated for 'chain 'A' and resid 699 through 701' Processing helix chain 'A' and resid 708 through 714 Processing helix chain 'A' and resid 780 through 784 Processing helix chain 'A' and resid 785 through 801 Processing helix chain 'A' and resid 809 through 813 Processing helix chain 'A' and resid 946 through 962 removed outlier: 3.691A pdb=" N LEU A 950 " --> pdb=" O PRO A 946 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL A 957 " --> pdb=" O MET A 953 " (cutoff:3.500A) Processing helix chain 'A' and resid 1019 through 1024 Processing helix chain 'A' and resid 1025 through 1031 Processing helix chain 'A' and resid 1163 through 1169 Processing helix chain 'A' and resid 1179 through 1183 removed outlier: 3.704A pdb=" N ILE A1183 " --> pdb=" O TRP A1180 " (cutoff:3.500A) Processing helix chain 'A' and resid 1231 through 1247 Processing helix chain 'A' and resid 1254 through 1258 Processing helix chain 'A' and resid 1259 through 1264 Processing helix chain 'A' and resid 1300 through 1305 removed outlier: 3.737A pdb=" N MET A1305 " --> pdb=" O GLY A1302 " (cutoff:3.500A) Processing helix chain 'A' and resid 1322 through 1326 removed outlier: 3.610A pdb=" N LEU A1325 " --> pdb=" O LEU A1322 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASN A1326 " --> pdb=" O SER A1323 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1322 through 1326' Processing helix chain 'A' and resid 1331 through 1336 removed outlier: 3.800A pdb=" N ARG A1336 " --> pdb=" O LEU A1333 " (cutoff:3.500A) Processing helix chain 'A' and resid 1342 through 1348 Processing helix chain 'A' and resid 1395 through 1400 removed outlier: 4.030A pdb=" N SER A1399 " --> pdb=" O ARG A1395 " (cutoff:3.500A) Processing helix chain 'A' and resid 1420 through 1426 Processing helix chain 'A' and resid 1464 through 1477 Processing helix chain 'A' and resid 1488 through 1492 Processing helix chain 'A' and resid 1518 through 1534 Processing helix chain 'A' and resid 1538 through 1549 removed outlier: 4.170A pdb=" N GLU A1542 " --> pdb=" O LEU A1538 " (cutoff:3.500A) Processing helix chain 'A' and resid 1565 through 1569 Processing helix chain 'A' and resid 1575 through 1581 removed outlier: 3.866A pdb=" N ASP A1581 " --> pdb=" O GLU A1577 " (cutoff:3.500A) Processing helix chain 'A' and resid 1585 through 1587 No H-bonds generated for 'chain 'A' and resid 1585 through 1587' Processing helix chain 'A' and resid 1588 through 1594 removed outlier: 3.842A pdb=" N LYS A1592 " --> pdb=" O ASP A1588 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 14 removed outlier: 3.906A pdb=" N THR B 14 " --> pdb=" O ASP B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 39 removed outlier: 3.514A pdb=" N MET B 23 " --> pdb=" O ASN B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 46 Processing helix chain 'B' and resid 52 through 64 removed outlier: 3.593A pdb=" N SER B 58 " --> pdb=" O PRO B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 88 Processing helix chain 'B' and resid 92 through 109 removed outlier: 3.958A pdb=" N ASN B 109 " --> pdb=" O ARG B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 134 removed outlier: 3.575A pdb=" N LEU B 134 " --> pdb=" O HIS B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 164 removed outlier: 3.970A pdb=" N VAL B 147 " --> pdb=" O PRO B 143 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE B 160 " --> pdb=" O TYR B 156 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS B 163 " --> pdb=" O ILE B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 185 removed outlier: 3.590A pdb=" N ARG B 172 " --> pdb=" O SER B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 199 Processing helix chain 'B' and resid 200 through 202 No H-bonds generated for 'chain 'B' and resid 200 through 202' Processing helix chain 'B' and resid 207 through 222 removed outlier: 3.796A pdb=" N ILE B 211 " --> pdb=" O GLU B 207 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ARG B 212 " --> pdb=" O LEU B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 232 Processing helix chain 'B' and resid 239 through 254 Processing helix chain 'B' and resid 256 through 270 removed outlier: 3.725A pdb=" N VAL B 260 " --> pdb=" O GLN B 256 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ARG B 261 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ILE B 262 " --> pdb=" O ASN B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 293 removed outlier: 4.194A pdb=" N ASP B 281 " --> pdb=" O ASP B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 312 removed outlier: 3.742A pdb=" N ILE B 301 " --> pdb=" O LEU B 297 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ILE B 303 " --> pdb=" O LYS B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 340 Processing helix chain 'B' and resid 342 through 355 removed outlier: 3.866A pdb=" N ARG B 348 " --> pdb=" O GLU B 344 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU B 353 " --> pdb=" O ILE B 349 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS B 354 " --> pdb=" O ALA B 350 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N SER B 355 " --> pdb=" O ASP B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 437 removed outlier: 3.545A pdb=" N GLU B 437 " --> pdb=" O LEU B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 481 Processing helix chain 'B' and resid 485 through 500 removed outlier: 3.672A pdb=" N GLU B 497 " --> pdb=" O CYS B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 525 removed outlier: 3.510A pdb=" N HIS B 524 " --> pdb=" O GLY B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 546 Processing sheet with id=AA1, first strand: chain 'A' and resid 148 through 150 Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 17 removed outlier: 3.575A pdb=" N ASP A 185 " --> pdb=" O ARG A 175 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 41 through 42 Processing sheet with id=AA4, first strand: chain 'A' and resid 79 through 80 Processing sheet with id=AA5, first strand: chain 'A' and resid 106 through 107 removed outlier: 5.530A pdb=" N THR A 106 " --> pdb=" O VAL A 395 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 483 through 485 removed outlier: 4.777A pdb=" N GLU A 409 " --> pdb=" O ASN A 574 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N ASN A 574 " --> pdb=" O GLU A 409 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N VAL A 411 " --> pdb=" O MET A 572 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N MET A 572 " --> pdb=" O VAL A 411 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 483 through 485 removed outlier: 4.777A pdb=" N GLU A 409 " --> pdb=" O ASN A 574 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N ASN A 574 " --> pdb=" O GLU A 409 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N VAL A 411 " --> pdb=" O MET A 572 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N MET A 572 " --> pdb=" O VAL A 411 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 441 through 442 Processing sheet with id=AA9, first strand: chain 'A' and resid 497 through 504 removed outlier: 3.841A pdb=" N ARG A 503 " --> pdb=" O ALA A 515 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N ALA A 515 " --> pdb=" O ARG A 503 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 659 through 664 removed outlier: 7.373A pdb=" N CYS A 672 " --> pdb=" O PHE A 730 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N PHE A 730 " --> pdb=" O CYS A 672 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 659 through 664 removed outlier: 7.373A pdb=" N CYS A 672 " --> pdb=" O PHE A 730 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N PHE A 730 " --> pdb=" O CYS A 672 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 641 through 642 removed outlier: 3.915A pdb=" N VAL A 656 " --> pdb=" O ASP A 642 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N VAL A 655 " --> pdb=" O SER A 760 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N ALA A 743 " --> pdb=" O ALA A 752 " (cutoff:3.500A) removed outlier: 10.078A pdb=" N LYS A 754 " --> pdb=" O HIS A 741 " (cutoff:3.500A) removed outlier: 10.999A pdb=" N HIS A 741 " --> pdb=" O LYS A 754 " (cutoff:3.500A) removed outlier: 10.320A pdb=" N LYS A 756 " --> pdb=" O PHE A 739 " (cutoff:3.500A) removed outlier: 11.349A pdb=" N PHE A 739 " --> pdb=" O LYS A 756 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 692 through 693 Processing sheet with id=AB5, first strand: chain 'A' and resid 1558 through 1559 removed outlier: 6.691A pdb=" N VAL A 861 " --> pdb=" O TRP A1600 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 865 through 868 Processing sheet with id=AB7, first strand: chain 'A' and resid 944 through 945 removed outlier: 5.593A pdb=" N LEU A 891 " --> pdb=" O ASN A1462 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N THR A 892 " --> pdb=" O ARG A1506 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LYS A 898 " --> pdb=" O VAL A1500 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N VAL A1500 " --> pdb=" O LYS A 898 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ILE A 900 " --> pdb=" O ILE A1498 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N ILE A1498 " --> pdb=" O ILE A 900 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1357 through 1359 removed outlier: 5.593A pdb=" N LEU A 891 " --> pdb=" O ASN A1462 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N THR A 892 " --> pdb=" O ARG A1506 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LYS A 898 " --> pdb=" O VAL A1500 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N VAL A1500 " --> pdb=" O LYS A 898 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ILE A 900 " --> pdb=" O ILE A1498 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N ILE A1498 " --> pdb=" O ILE A 900 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 908 through 909 removed outlier: 4.427A pdb=" N ALA A 935 " --> pdb=" O ASP A 909 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 976 through 978 Processing sheet with id=AC2, first strand: chain 'A' and resid 1284 through 1288 removed outlier: 6.648A pdb=" N LYS A1278 " --> pdb=" O GLU A1285 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ILE A1287 " --> pdb=" O TYR A1276 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N TYR A1276 " --> pdb=" O ILE A1287 " (cutoff:3.500A) removed outlier: 9.059A pdb=" N HIS A1001 " --> pdb=" O GLU A1226 " (cutoff:3.500A) removed outlier: 10.265A pdb=" N GLU A1226 " --> pdb=" O HIS A1001 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N GLN A1003 " --> pdb=" O GLU A1224 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N GLU A1224 " --> pdb=" O GLN A1003 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N PHE A1005 " --> pdb=" O LEU A1222 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU A1222 " --> pdb=" O PHE A1005 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU A1007 " --> pdb=" O PHE A1220 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE A1220 " --> pdb=" O GLU A1007 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR A1217 " --> pdb=" O HIS A1149 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP A1221 " --> pdb=" O GLU A1145 " (cutoff:3.500A) removed outlier: 8.958A pdb=" N GLU A1145 " --> pdb=" O ASP A1221 " (cutoff:3.500A) removed outlier: 14.664A pdb=" N LYS A1223 " --> pdb=" O CYS A1143 " (cutoff:3.500A) removed outlier: 19.999A pdb=" N CYS A1143 " --> pdb=" O LYS A1223 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS A1128 " --> pdb=" O LYS A1040 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N ALA A1129 " --> pdb=" O THR A1008 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ARG A1010 " --> pdb=" O ALA A1129 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 1156 through 1159 removed outlier: 7.326A pdb=" N GLU A1196 " --> pdb=" O LYS A1189 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 457 through 462 removed outlier: 3.571A pdb=" N ALA B 425 " --> pdb=" O TYR B 447 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE B 428 " --> pdb=" O ILE B 518 " (cutoff:3.500A) 679 hydrogen bonds defined for protein. 1869 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 45 hydrogen bonds 90 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 23 stacking parallelities Total time for adding SS restraints: 8.57 Time building geometry restraints manager: 7.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 4876 1.33 - 1.45: 3168 1.45 - 1.57: 9172 1.57 - 1.69: 122 1.69 - 1.81: 108 Bond restraints: 17446 Sorted by residual: bond pdb=" C2' G R 19 " pdb=" C1' G R 19 " ideal model delta sigma weight residual 1.526 1.514 0.012 1.50e-02 4.44e+03 6.85e-01 bond pdb=" CB PRO A1138 " pdb=" CG PRO A1138 " ideal model delta sigma weight residual 1.492 1.529 -0.037 5.00e-02 4.00e+02 5.33e-01 bond pdb=" CA ALA A 420 " pdb=" C ALA A 420 " ideal model delta sigma weight residual 1.529 1.522 0.007 1.04e-02 9.25e+03 4.65e-01 bond pdb=" C VAL A 907 " pdb=" O VAL A 907 " ideal model delta sigma weight residual 1.240 1.231 0.008 1.26e-02 6.30e+03 4.46e-01 bond pdb=" CB PRO A 734 " pdb=" CG PRO A 734 " ideal model delta sigma weight residual 1.492 1.525 -0.033 5.00e-02 4.00e+02 4.41e-01 ... (remaining 17441 not shown) Histogram of bond angle deviations from ideal: 99.62 - 106.49: 847 106.49 - 113.36: 9223 113.36 - 120.23: 6232 120.23 - 127.10: 7154 127.10 - 133.97: 333 Bond angle restraints: 23789 Sorted by residual: angle pdb=" N ILE B 205 " pdb=" CA ILE B 205 " pdb=" C ILE B 205 " ideal model delta sigma weight residual 111.91 107.96 3.95 8.90e-01 1.26e+00 1.97e+01 angle pdb=" O4' G R 19 " pdb=" C1' G R 19 " pdb=" N9 G R 19 " ideal model delta sigma weight residual 108.20 114.01 -5.81 1.50e+00 4.44e-01 1.50e+01 angle pdb=" C SER A 81 " pdb=" CA SER A 81 " pdb=" CB SER A 81 " ideal model delta sigma weight residual 110.42 116.05 -5.63 1.99e+00 2.53e-01 8.00e+00 angle pdb=" C2' U R 1 " pdb=" C1' U R 1 " pdb=" N1 U R 1 " ideal model delta sigma weight residual 112.00 116.00 -4.00 1.50e+00 4.44e-01 7.13e+00 angle pdb=" C4' G R 19 " pdb=" O4' G R 19 " pdb=" C1' G R 19 " ideal model delta sigma weight residual 109.70 107.80 1.90 1.00e+00 1.00e+00 3.62e+00 ... (remaining 23784 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.93: 10033 18.93 - 37.85: 304 37.85 - 56.78: 61 56.78 - 75.70: 21 75.70 - 94.63: 9 Dihedral angle restraints: 10428 sinusoidal: 4879 harmonic: 5549 Sorted by residual: dihedral pdb=" O4' A R 12 " pdb=" C1' A R 12 " pdb=" N9 A R 12 " pdb=" C4 A R 12 " ideal model delta sinusoidal sigma weight residual -106.00 -159.14 53.14 1 1.70e+01 3.46e-03 1.33e+01 dihedral pdb=" CA ASP B 65 " pdb=" C ASP B 65 " pdb=" N SER B 66 " pdb=" CA SER B 66 " ideal model delta harmonic sigma weight residual -180.00 -161.93 -18.07 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" N GLN B 456 " pdb=" CA GLN B 456 " pdb=" CB GLN B 456 " pdb=" CG GLN B 456 " ideal model delta sinusoidal sigma weight residual -60.00 -119.67 59.67 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 10425 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 2254 0.057 - 0.114: 255 0.114 - 0.172: 22 0.172 - 0.229: 1 0.229 - 0.286: 1 Chirality restraints: 2533 Sorted by residual: chirality pdb=" C1' G R 19 " pdb=" O4' G R 19 " pdb=" C2' G R 19 " pdb=" N9 G R 19 " both_signs ideal model delta sigma weight residual False 2.44 2.15 0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" C1' U R 1 " pdb=" O4' U R 1 " pdb=" C2' U R 1 " pdb=" N1 U R 1 " both_signs ideal model delta sigma weight residual False 2.47 2.27 0.19 2.00e-01 2.50e+01 9.22e-01 chirality pdb=" CB ILE B 518 " pdb=" CA ILE B 518 " pdb=" CG1 ILE B 518 " pdb=" CG2 ILE B 518 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.15 2.00e-01 2.50e+01 5.39e-01 ... (remaining 2530 not shown) Planarity restraints: 2870 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G R 19 " -0.032 2.00e-02 2.50e+03 1.53e-02 7.05e+00 pdb=" N9 G R 19 " 0.041 2.00e-02 2.50e+03 pdb=" C8 G R 19 " -0.000 2.00e-02 2.50e+03 pdb=" N7 G R 19 " -0.003 2.00e-02 2.50e+03 pdb=" C5 G R 19 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G R 19 " -0.004 2.00e-02 2.50e+03 pdb=" O6 G R 19 " -0.006 2.00e-02 2.50e+03 pdb=" N1 G R 19 " -0.003 2.00e-02 2.50e+03 pdb=" C2 G R 19 " 0.002 2.00e-02 2.50e+03 pdb=" N2 G R 19 " 0.001 2.00e-02 2.50e+03 pdb=" N3 G R 19 " 0.002 2.00e-02 2.50e+03 pdb=" C4 G R 19 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U R 1 " 0.027 2.00e-02 2.50e+03 1.42e-02 4.57e+00 pdb=" N1 U R 1 " -0.032 2.00e-02 2.50e+03 pdb=" C2 U R 1 " -0.001 2.00e-02 2.50e+03 pdb=" O2 U R 1 " -0.003 2.00e-02 2.50e+03 pdb=" N3 U R 1 " 0.002 2.00e-02 2.50e+03 pdb=" C4 U R 1 " 0.003 2.00e-02 2.50e+03 pdb=" O4 U R 1 " 0.008 2.00e-02 2.50e+03 pdb=" C5 U R 1 " -0.002 2.00e-02 2.50e+03 pdb=" C6 U R 1 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U R 17 " -0.027 2.00e-02 2.50e+03 1.41e-02 4.45e+00 pdb=" N1 U R 17 " 0.031 2.00e-02 2.50e+03 pdb=" C2 U R 17 " 0.002 2.00e-02 2.50e+03 pdb=" O2 U R 17 " 0.002 2.00e-02 2.50e+03 pdb=" N3 U R 17 " -0.000 2.00e-02 2.50e+03 pdb=" C4 U R 17 " -0.004 2.00e-02 2.50e+03 pdb=" O4 U R 17 " -0.008 2.00e-02 2.50e+03 pdb=" C5 U R 17 " 0.000 2.00e-02 2.50e+03 pdb=" C6 U R 17 " 0.004 2.00e-02 2.50e+03 ... (remaining 2867 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.24: 4 2.24 - 2.91: 6376 2.91 - 3.57: 23120 3.57 - 4.24: 42263 4.24 - 4.90: 70837 Nonbonded interactions: 142600 Sorted by model distance: nonbonded pdb=" O3' G D 23 " pdb=" P C D 101 " model vdw 1.579 3.400 nonbonded pdb=" O3' C D 101 " pdb=" P A A1701 " model vdw 1.605 3.400 nonbonded pdb=" O3' A A1701 " pdb=" P A B 801 " model vdw 1.607 3.400 nonbonded pdb=" O CYS A 881 " pdb=" OH TYR A1353 " model vdw 2.201 2.440 nonbonded pdb=" OH TYR B 176 " pdb=" OD1 ASP B 210 " model vdw 2.247 2.440 ... (remaining 142595 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 Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 63 5.49 5 S 73 5.16 5 C 10487 2.51 5 N 2988 2.21 5 O 3320 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.530 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: 11.350 Check model and map are aligned: 0.260 Process input model: 56.720 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Set scattering table: 0.170 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8918 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 : 0.002 0.037 17446 Z= 0.134 Angle : 0.417 5.813 23789 Z= 0.229 Chirality : 0.037 0.286 2533 Planarity : 0.003 0.034 2870 Dihedral : 10.200 94.627 6844 Min Nonbonded Distance : 1.579 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer Outliers : 0.30 % 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: 1.18 (0.19), residues: 1892 helix: 1.51 (0.20), residues: 657 sheet: 0.98 (0.27), residues: 339 loop : 0.28 (0.21), residues: 896 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3784 Ramachandran restraints generated. 1892 Oldfield, 0 Emsley, 1892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3784 Ramachandran restraints generated. 1892 Oldfield, 0 Emsley, 1892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 345 time to evaluate : 2.058 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 350 average time/residue: 1.6813 time to fit residues: 641.3499 Evaluate side-chains 193 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 191 time to evaluate : 2.030 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 2.7621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 0.7980 chunk 148 optimal weight: 7.9990 chunk 82 optimal weight: 4.9990 chunk 50 optimal weight: 6.9990 chunk 100 optimal weight: 10.0000 chunk 79 optimal weight: 0.9990 chunk 153 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 114 optimal weight: 3.9990 chunk 177 optimal weight: 4.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN A 640 ASN A 871 HIS A1018 GLN ** A1127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1131 GLN A1167 ASN A1326 ASN A1419 HIS A1483 HIS B 36 GLN B 108 GLN B 224 ASN B 235 GLN B 477 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9012 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.046 17446 Z= 0.380 Angle : 0.580 6.942 23789 Z= 0.304 Chirality : 0.045 0.298 2533 Planarity : 0.005 0.046 2870 Dihedral : 9.365 95.882 2846 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer Outliers : 2.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.19), residues: 1892 helix: 1.57 (0.20), residues: 662 sheet: 0.71 (0.27), residues: 348 loop : 0.07 (0.21), residues: 882 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3784 Ramachandran restraints generated. 1892 Oldfield, 0 Emsley, 1892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3784 Ramachandran restraints generated. 1892 Oldfield, 0 Emsley, 1892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 197 time to evaluate : 2.009 Fit side-chains revert: symmetry clash outliers start: 46 outliers final: 17 residues processed: 230 average time/residue: 1.5783 time to fit residues: 399.8621 Evaluate side-chains 190 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 173 time to evaluate : 2.011 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 14 residues processed: 3 average time/residue: 1.3177 time to fit residues: 7.1480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 2.9990 chunk 55 optimal weight: 0.5980 chunk 148 optimal weight: 7.9990 chunk 121 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 178 optimal weight: 5.9990 chunk 192 optimal weight: 4.9990 chunk 158 optimal weight: 4.9990 chunk 176 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 143 optimal weight: 0.8980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1027 GLN B 108 GLN B 224 ASN B 256 GLN B 458 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9000 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 17446 Z= 0.263 Angle : 0.510 6.470 23789 Z= 0.269 Chirality : 0.041 0.289 2533 Planarity : 0.004 0.040 2870 Dihedral : 9.396 97.383 2846 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer Outliers : 3.17 % 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: 1.06 (0.19), residues: 1892 helix: 1.75 (0.20), residues: 654 sheet: 0.55 (0.27), residues: 348 loop : 0.06 (0.21), residues: 890 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3784 Ramachandran restraints generated. 1892 Oldfield, 0 Emsley, 1892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3784 Ramachandran restraints generated. 1892 Oldfield, 0 Emsley, 1892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 186 time to evaluate : 2.065 Fit side-chains revert: symmetry clash outliers start: 53 outliers final: 22 residues processed: 225 average time/residue: 1.5663 time to fit residues: 388.0315 Evaluate side-chains 192 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 170 time to evaluate : 2.045 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 21 residues processed: 1 average time/residue: 0.2052 time to fit residues: 3.0472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 176 optimal weight: 3.9990 chunk 134 optimal weight: 4.9990 chunk 92 optimal weight: 0.9980 chunk 19 optimal weight: 0.3980 chunk 85 optimal weight: 5.9990 chunk 119 optimal weight: 2.9990 chunk 178 optimal weight: 6.9990 chunk 189 optimal weight: 0.8980 chunk 93 optimal weight: 0.5980 chunk 169 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1186 ASN B 224 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8964 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.040 17446 Z= 0.157 Angle : 0.459 6.792 23789 Z= 0.244 Chirality : 0.039 0.264 2533 Planarity : 0.004 0.072 2870 Dihedral : 9.355 97.396 2846 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer Outliers : 2.46 % 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: 1.17 (0.19), residues: 1892 helix: 1.92 (0.20), residues: 660 sheet: 0.43 (0.27), residues: 345 loop : 0.14 (0.21), residues: 887 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3784 Ramachandran restraints generated. 1892 Oldfield, 0 Emsley, 1892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3784 Ramachandran restraints generated. 1892 Oldfield, 0 Emsley, 1892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 182 time to evaluate : 2.052 Fit side-chains revert: symmetry clash outliers start: 41 outliers final: 19 residues processed: 210 average time/residue: 1.4782 time to fit residues: 343.8622 Evaluate side-chains 185 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 166 time to evaluate : 1.857 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 18 residues processed: 1 average time/residue: 1.7150 time to fit residues: 4.3810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 157 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 141 optimal weight: 3.9990 chunk 78 optimal weight: 0.5980 chunk 161 optimal weight: 6.9990 chunk 130 optimal weight: 0.0020 chunk 0 optimal weight: 6.9990 chunk 96 optimal weight: 0.9980 chunk 170 optimal weight: 0.4980 chunk 47 optimal weight: 0.0970 overall best weight: 0.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8931 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 17446 Z= 0.122 Angle : 0.437 7.484 23789 Z= 0.230 Chirality : 0.038 0.247 2533 Planarity : 0.004 0.046 2870 Dihedral : 9.324 96.231 2846 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer Outliers : 2.22 % 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: 1.33 (0.19), residues: 1892 helix: 2.08 (0.20), residues: 660 sheet: 0.52 (0.27), residues: 330 loop : 0.21 (0.21), residues: 902 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3784 Ramachandran restraints generated. 1892 Oldfield, 0 Emsley, 1892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3784 Ramachandran restraints generated. 1892 Oldfield, 0 Emsley, 1892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 184 time to evaluate : 2.078 Fit side-chains revert: symmetry clash outliers start: 37 outliers final: 19 residues processed: 211 average time/residue: 1.5072 time to fit residues: 352.0774 Evaluate side-chains 183 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 164 time to evaluate : 1.990 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 18 residues processed: 1 average time/residue: 0.3019 time to fit residues: 3.1912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 63 optimal weight: 3.9990 chunk 170 optimal weight: 10.0000 chunk 37 optimal weight: 0.0170 chunk 111 optimal weight: 7.9990 chunk 46 optimal weight: 0.6980 chunk 189 optimal weight: 1.9990 chunk 157 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 99 optimal weight: 0.7980 overall best weight: 0.9022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 481 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8957 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 17446 Z= 0.166 Angle : 0.459 7.891 23789 Z= 0.240 Chirality : 0.039 0.265 2533 Planarity : 0.004 0.038 2870 Dihedral : 9.299 95.741 2846 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer Outliers : 2.40 % 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 (0.19), residues: 1892 helix: 2.03 (0.20), residues: 667 sheet: 0.54 (0.28), residues: 324 loop : 0.13 (0.21), residues: 901 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3784 Ramachandran restraints generated. 1892 Oldfield, 0 Emsley, 1892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3784 Ramachandran restraints generated. 1892 Oldfield, 0 Emsley, 1892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 174 time to evaluate : 1.943 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 20 residues processed: 204 average time/residue: 1.5008 time to fit residues: 339.3308 Evaluate side-chains 185 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 165 time to evaluate : 2.126 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 20 residues processed: 0 time to fit residues: 2.8954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 182 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 chunk 108 optimal weight: 6.9990 chunk 138 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 159 optimal weight: 7.9990 chunk 105 optimal weight: 5.9990 chunk 188 optimal weight: 5.9990 chunk 118 optimal weight: 0.9980 chunk 115 optimal weight: 3.9990 chunk 87 optimal weight: 0.0470 overall best weight: 1.3482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 640 ASN A1127 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8982 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 17446 Z= 0.218 Angle : 0.487 6.612 23789 Z= 0.255 Chirality : 0.040 0.284 2533 Planarity : 0.004 0.039 2870 Dihedral : 9.333 96.542 2846 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer Outliers : 2.51 % 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: 1.22 (0.19), residues: 1892 helix: 1.99 (0.20), residues: 667 sheet: 0.49 (0.28), residues: 324 loop : 0.11 (0.21), residues: 901 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3784 Ramachandran restraints generated. 1892 Oldfield, 0 Emsley, 1892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3784 Ramachandran restraints generated. 1892 Oldfield, 0 Emsley, 1892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 171 time to evaluate : 2.071 Fit side-chains revert: symmetry clash outliers start: 42 outliers final: 21 residues processed: 205 average time/residue: 1.5407 time to fit residues: 349.8092 Evaluate side-chains 186 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 165 time to evaluate : 2.111 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 19 residues processed: 2 average time/residue: 1.5505 time to fit residues: 6.2791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 116 optimal weight: 10.0000 chunk 75 optimal weight: 1.9990 chunk 112 optimal weight: 0.0970 chunk 56 optimal weight: 0.3980 chunk 37 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 120 optimal weight: 3.9990 chunk 128 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 148 optimal weight: 10.0000 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 640 ASN A1127 GLN B 232 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8972 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 17446 Z= 0.184 Angle : 0.476 8.718 23789 Z= 0.249 Chirality : 0.039 0.272 2533 Planarity : 0.004 0.038 2870 Dihedral : 9.339 96.848 2846 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer Outliers : 1.92 % 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: 1.23 (0.19), residues: 1892 helix: 2.01 (0.20), residues: 668 sheet: 0.51 (0.28), residues: 324 loop : 0.10 (0.21), residues: 900 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3784 Ramachandran restraints generated. 1892 Oldfield, 0 Emsley, 1892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3784 Ramachandran restraints generated. 1892 Oldfield, 0 Emsley, 1892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 165 time to evaluate : 2.068 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 20 residues processed: 190 average time/residue: 1.5157 time to fit residues: 319.8883 Evaluate side-chains 179 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 159 time to evaluate : 2.068 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 20 residues processed: 0 time to fit residues: 2.9320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 171 optimal weight: 6.9990 chunk 180 optimal weight: 1.9990 chunk 165 optimal weight: 0.7980 chunk 176 optimal weight: 7.9990 chunk 105 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 138 optimal weight: 0.5980 chunk 54 optimal weight: 6.9990 chunk 159 optimal weight: 6.9990 chunk 166 optimal weight: 0.0040 chunk 175 optimal weight: 5.9990 overall best weight: 1.2796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 640 ASN A1127 GLN B 232 GLN B 235 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8983 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 17446 Z= 0.212 Angle : 0.491 8.006 23789 Z= 0.257 Chirality : 0.040 0.280 2533 Planarity : 0.004 0.039 2870 Dihedral : 9.356 96.824 2846 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer Outliers : 1.62 % 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: 1.14 (0.19), residues: 1892 helix: 1.94 (0.20), residues: 668 sheet: 0.43 (0.28), residues: 329 loop : 0.05 (0.21), residues: 895 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3784 Ramachandran restraints generated. 1892 Oldfield, 0 Emsley, 1892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3784 Ramachandran restraints generated. 1892 Oldfield, 0 Emsley, 1892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 165 time to evaluate : 1.945 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 20 residues processed: 189 average time/residue: 1.5332 time to fit residues: 321.6337 Evaluate side-chains 181 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 161 time to evaluate : 1.947 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 20 residues processed: 0 time to fit residues: 2.8661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 115 optimal weight: 3.9990 chunk 186 optimal weight: 5.9990 chunk 113 optimal weight: 0.7980 chunk 88 optimal weight: 0.0020 chunk 129 optimal weight: 0.7980 chunk 195 optimal weight: 9.9990 chunk 179 optimal weight: 8.9990 chunk 155 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 chunk 120 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 640 ASN A1127 GLN B 232 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8944 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 17446 Z= 0.140 Angle : 0.453 7.491 23789 Z= 0.238 Chirality : 0.038 0.252 2533 Planarity : 0.003 0.038 2870 Dihedral : 9.341 96.461 2846 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer Outliers : 1.50 % 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: 1.31 (0.19), residues: 1892 helix: 2.07 (0.20), residues: 667 sheet: 0.58 (0.28), residues: 324 loop : 0.14 (0.21), residues: 901 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3784 Ramachandran restraints generated. 1892 Oldfield, 0 Emsley, 1892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3784 Ramachandran restraints generated. 1892 Oldfield, 0 Emsley, 1892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 169 time to evaluate : 1.948 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 20 residues processed: 191 average time/residue: 1.5693 time to fit residues: 331.3985 Evaluate side-chains 178 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 158 time to evaluate : 2.013 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 20 residues processed: 0 time to fit residues: 2.7628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 123 optimal weight: 2.9990 chunk 165 optimal weight: 6.9990 chunk 47 optimal weight: 0.0000 chunk 143 optimal weight: 0.0060 chunk 22 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 159 optimal weight: 7.9990 chunk 19 optimal weight: 0.5980 chunk 28 optimal weight: 0.5980 overall best weight: 0.3800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 640 ASN A1127 GLN B 232 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.146154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.110483 restraints weight = 19093.769| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 1.75 r_work: 0.2990 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8954 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 17446 Z= 0.119 Angle : 0.444 7.275 23789 Z= 0.232 Chirality : 0.037 0.234 2533 Planarity : 0.003 0.037 2870 Dihedral : 9.333 94.935 2846 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer Outliers : 1.56 % 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: 1892 helix: 2.15 (0.20), residues: 670 sheet: 0.59 (0.28), residues: 336 loop : 0.24 (0.21), residues: 886 =============================================================================== Job complete usr+sys time: 6302.96 seconds wall clock time: 112 minutes 17.29 seconds (6737.29 seconds total)