Starting phenix.real_space_refine on Sun Mar 17 06:35:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gs2_34218/03_2024/8gs2_34218.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gs2_34218/03_2024/8gs2_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_34218/03_2024/8gs2_34218.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gs2_34218/03_2024/8gs2_34218.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gs2_34218/03_2024/8gs2_34218.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gs2_34218/03_2024/8gs2_34218.pdb" } resolution = 2.84 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= 0.116 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 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. 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-5265/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: 27 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: 9.31, per 1000 atoms: 0.55 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: 6.80 Conformation dependent library (CDL) restraints added in 2.6 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: 6.06 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: 8.79 Time building geometry restraints manager: 7.35 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: 10101 18.93 - 37.85: 336 37.85 - 56.78: 103 56.78 - 75.70: 84 75.70 - 94.63: 10 Dihedral angle restraints: 10634 sinusoidal: 5085 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 10631 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 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: 3.100 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: 0.020 Extract box with map and model: 10.690 Check model and map are aligned: 0.260 Set scattering table: 0.190 Process input model: 56.250 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 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 : 12.543 94.627 7050 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 % Allowed : 2.46 % Favored : 97.25 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 544 HIS 0.003 0.001 HIS A 741 PHE 0.011 0.001 PHE A 416 TYR 0.009 0.001 TYR A 492 ARG 0.003 0.000 ARG A1356 *********************** 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 : 1.782 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 354 LYS cc_start: 0.8423 (mttt) cc_final: 0.8163 (mttm) REVERT: A 619 ASN cc_start: 0.7909 (m-40) cc_final: 0.7481 (t0) REVERT: A 669 LYS cc_start: 0.8291 (tttt) cc_final: 0.7343 (mmpt) REVERT: A 1028 GLU cc_start: 0.7526 (mt-10) cc_final: 0.7319 (mt-10) REVERT: A 1203 ASP cc_start: 0.7748 (t0) cc_final: 0.7482 (t0) REVERT: A 1214 TYR cc_start: 0.8182 (p90) cc_final: 0.7872 (p90) REVERT: A 1228 TYR cc_start: 0.7825 (m-10) cc_final: 0.7329 (m-10) REVERT: A 1254 GLU cc_start: 0.7541 (mm-30) cc_final: 0.6928 (mp0) REVERT: A 1511 GLN cc_start: 0.7744 (tt0) cc_final: 0.7544 (tm-30) REVERT: A 1580 LYS cc_start: 0.7530 (ttpt) cc_final: 0.6836 (mttp) REVERT: B 343 ILE cc_start: 0.8232 (mt) cc_final: 0.7951 (mm) REVERT: B 513 ARG cc_start: 0.6114 (mtp180) cc_final: 0.5114 (tpt170) outliers start: 5 outliers final: 2 residues processed: 350 average time/residue: 1.6050 time to fit residues: 611.7361 Evaluate side-chains 197 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 195 time to evaluate : 1.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1350 THR Chi-restraints excluded: chain B residue 201 ASN 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: 0.0770 chunk 82 optimal weight: 4.9990 chunk 50 optimal weight: 6.9990 chunk 100 optimal weight: 9.9990 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: 1.7744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN A 871 HIS A1018 GLN A1131 GLN A1186 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: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17446 Z= 0.278 Angle : 0.528 6.362 23789 Z= 0.278 Chirality : 0.042 0.289 2533 Planarity : 0.004 0.043 2870 Dihedral : 14.328 96.141 3055 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.57 % Allowed : 10.12 % Favored : 87.31 % 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: 1.18 (0.19), residues: 1892 helix: 1.70 (0.20), residues: 662 sheet: 0.74 (0.27), residues: 350 loop : 0.19 (0.21), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 517 HIS 0.009 0.001 HIS B 253 PHE 0.014 0.002 PHE A 517 TYR 0.010 0.001 TYR A 492 ARG 0.007 0.001 ARG B 288 *********************** 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 237 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 194 time to evaluate : 1.929 Fit side-chains revert: symmetry clash REVERT: A 28 LYS cc_start: 0.8816 (OUTLIER) cc_final: 0.8610 (pttt) REVERT: A 179 LYS cc_start: 0.8473 (mmpt) cc_final: 0.8236 (mmtt) REVERT: A 264 LYS cc_start: 0.7872 (OUTLIER) cc_final: 0.7504 (mttp) REVERT: A 305 ASP cc_start: 0.8295 (p0) cc_final: 0.8067 (p0) REVERT: A 354 LYS cc_start: 0.8473 (mttt) cc_final: 0.8188 (mttm) REVERT: A 451 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8681 (tt) REVERT: A 486 MET cc_start: 0.9003 (OUTLIER) cc_final: 0.8790 (ttm) REVERT: A 619 ASN cc_start: 0.7988 (m-40) cc_final: 0.7509 (t0) REVERT: A 669 LYS cc_start: 0.8377 (tttt) cc_final: 0.7390 (mmpt) REVERT: A 826 ASP cc_start: 0.7429 (t70) cc_final: 0.7169 (t0) REVERT: A 857 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7766 (mt-10) REVERT: A 859 GLU cc_start: 0.7801 (pm20) cc_final: 0.7382 (pm20) REVERT: A 942 GLN cc_start: 0.8052 (OUTLIER) cc_final: 0.6887 (tm-30) REVERT: A 1019 LYS cc_start: 0.8294 (mppt) cc_final: 0.7891 (mmtt) REVERT: A 1203 ASP cc_start: 0.7831 (t0) cc_final: 0.7572 (t0) REVERT: A 1214 TYR cc_start: 0.8231 (p90) cc_final: 0.7958 (p90) REVERT: A 1228 TYR cc_start: 0.7880 (m-10) cc_final: 0.7477 (m-10) REVERT: A 1239 LYS cc_start: 0.8893 (tttt) cc_final: 0.8209 (mptt) REVERT: A 1254 GLU cc_start: 0.7485 (mm-30) cc_final: 0.6814 (mp0) REVERT: B 24 MET cc_start: 0.8053 (OUTLIER) cc_final: 0.7426 (mtp) REVERT: B 83 GLU cc_start: 0.7484 (tm-30) cc_final: 0.7185 (tt0) REVERT: B 136 ARG cc_start: 0.7177 (OUTLIER) cc_final: 0.5115 (mtt90) REVERT: B 513 ARG cc_start: 0.6142 (mtp180) cc_final: 0.5065 (tpt170) outliers start: 43 outliers final: 13 residues processed: 225 average time/residue: 1.5344 time to fit residues: 379.4502 Evaluate side-chains 196 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 175 time to evaluate : 1.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 264 LYS Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 486 MET Chi-restraints excluded: chain A residue 631 SER Chi-restraints excluded: chain A residue 699 THR Chi-restraints excluded: chain A residue 707 GLU Chi-restraints excluded: chain A residue 830 SER Chi-restraints excluded: chain A residue 857 GLU Chi-restraints excluded: chain A residue 942 GLN Chi-restraints excluded: chain A residue 1003 GLN Chi-restraints excluded: chain A residue 1008 THR Chi-restraints excluded: chain A residue 1217 THR Chi-restraints excluded: chain A residue 1330 GLU Chi-restraints excluded: chain A residue 1350 THR Chi-restraints excluded: chain A residue 1502 SER Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 136 ARG Chi-restraints excluded: chain B residue 341 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 148 optimal weight: 5.9990 chunk 121 optimal weight: 0.0370 chunk 49 optimal weight: 3.9990 chunk 178 optimal weight: 7.9990 chunk 192 optimal weight: 2.9990 chunk 158 optimal weight: 10.0000 chunk 176 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 143 optimal weight: 0.9980 overall best weight: 1.6062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 108 GLN B 224 ASN B 256 GLN B 458 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17446 Z= 0.249 Angle : 0.500 6.275 23789 Z= 0.263 Chirality : 0.041 0.293 2533 Planarity : 0.004 0.040 2870 Dihedral : 14.267 97.322 3053 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 3.11 % Allowed : 10.84 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.19), residues: 1892 helix: 1.83 (0.20), residues: 654 sheet: 0.54 (0.27), residues: 350 loop : 0.14 (0.21), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 517 HIS 0.006 0.001 HIS B 253 PHE 0.014 0.001 PHE A 416 TYR 0.011 0.001 TYR A 492 ARG 0.009 0.000 ARG A 780 *********************** 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 241 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 189 time to evaluate : 1.987 Fit side-chains revert: symmetry clash REVERT: A 179 LYS cc_start: 0.8524 (mmpt) cc_final: 0.8267 (mmtt) REVERT: A 264 LYS cc_start: 0.7868 (OUTLIER) cc_final: 0.7510 (mttp) REVERT: A 354 LYS cc_start: 0.8482 (mttt) cc_final: 0.8203 (mttm) REVERT: A 451 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8669 (tt) REVERT: A 619 ASN cc_start: 0.8052 (m-40) cc_final: 0.7503 (t0) REVERT: A 669 LYS cc_start: 0.8329 (tttt) cc_final: 0.7372 (mmpt) REVERT: A 826 ASP cc_start: 0.7432 (t70) cc_final: 0.7078 (t0) REVERT: A 857 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7806 (mt-10) REVERT: A 942 GLN cc_start: 0.8016 (OUTLIER) cc_final: 0.6995 (tm-30) REVERT: A 1202 GLU cc_start: 0.8037 (tt0) cc_final: 0.7790 (mt-10) REVERT: A 1203 ASP cc_start: 0.7853 (t0) cc_final: 0.7502 (t0) REVERT: A 1214 TYR cc_start: 0.8249 (p90) cc_final: 0.7949 (p90) REVERT: A 1228 TYR cc_start: 0.7874 (m-10) cc_final: 0.7396 (m-10) REVERT: B 24 MET cc_start: 0.8060 (OUTLIER) cc_final: 0.7396 (mtp) REVERT: B 136 ARG cc_start: 0.7182 (OUTLIER) cc_final: 0.6442 (mtt90) REVERT: B 165 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7591 (mp0) REVERT: B 183 ARG cc_start: 0.8089 (ttm-80) cc_final: 0.7347 (ttm-80) REVERT: B 209 TYR cc_start: 0.7569 (OUTLIER) cc_final: 0.7160 (m-80) REVERT: B 212 ARG cc_start: 0.7963 (OUTLIER) cc_final: 0.6724 (ptm160) REVERT: B 328 ARG cc_start: 0.8152 (mmt90) cc_final: 0.7944 (mmt90) REVERT: B 513 ARG cc_start: 0.6134 (mtp180) cc_final: 0.5125 (tpt170) outliers start: 52 outliers final: 19 residues processed: 225 average time/residue: 1.5692 time to fit residues: 387.5549 Evaluate side-chains 201 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 173 time to evaluate : 1.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 264 LYS Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 599 ASP Chi-restraints excluded: chain A residue 631 SER Chi-restraints excluded: chain A residue 699 THR Chi-restraints excluded: chain A residue 707 GLU Chi-restraints excluded: chain A residue 830 SER Chi-restraints excluded: chain A residue 857 GLU Chi-restraints excluded: chain A residue 942 GLN Chi-restraints excluded: chain A residue 1008 THR Chi-restraints excluded: chain A residue 1185 THR Chi-restraints excluded: chain A residue 1217 THR Chi-restraints excluded: chain A residue 1330 GLU Chi-restraints excluded: chain A residue 1350 THR Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 136 ARG Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 209 TYR Chi-restraints excluded: chain B residue 212 ARG Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 341 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 176 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 85 optimal weight: 7.9990 chunk 119 optimal weight: 0.9980 chunk 178 optimal weight: 5.9990 chunk 189 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 169 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1027 GLN A1167 ASN B 224 ASN B 235 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.2151 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 : 0.481 6.628 23789 Z= 0.253 Chirality : 0.040 0.286 2533 Planarity : 0.004 0.040 2870 Dihedral : 14.236 97.544 3053 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.63 % Allowed : 11.98 % Favored : 85.39 % 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: 1.15 (0.19), residues: 1892 helix: 1.89 (0.20), residues: 660 sheet: 0.46 (0.27), residues: 341 loop : 0.11 (0.21), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 517 HIS 0.004 0.001 HIS A 741 PHE 0.013 0.001 PHE A 416 TYR 0.010 0.001 TYR A 492 ARG 0.006 0.000 ARG A1558 *********************** 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 224 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 180 time to evaluate : 1.877 Fit side-chains revert: symmetry clash REVERT: A 179 LYS cc_start: 0.8551 (mmpt) cc_final: 0.8274 (mmtt) REVERT: A 264 LYS cc_start: 0.7876 (OUTLIER) cc_final: 0.7504 (mttp) REVERT: A 354 LYS cc_start: 0.8473 (mttt) cc_final: 0.8203 (mttm) REVERT: A 451 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8688 (tt) REVERT: A 466 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7413 (mm-30) REVERT: A 619 ASN cc_start: 0.8132 (m-40) cc_final: 0.7521 (t0) REVERT: A 669 LYS cc_start: 0.8313 (tttt) cc_final: 0.7355 (mmpt) REVERT: A 826 ASP cc_start: 0.7528 (t70) cc_final: 0.7066 (t0) REVERT: A 857 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7728 (mt-10) REVERT: A 859 GLU cc_start: 0.7758 (pm20) cc_final: 0.7388 (pm20) REVERT: A 896 ARG cc_start: 0.8329 (OUTLIER) cc_final: 0.7708 (mmt180) REVERT: A 942 GLN cc_start: 0.8042 (OUTLIER) cc_final: 0.6995 (tm-30) REVERT: A 1038 TRP cc_start: 0.7742 (m100) cc_final: 0.7513 (m100) REVERT: A 1202 GLU cc_start: 0.8021 (tt0) cc_final: 0.7772 (mt-10) REVERT: A 1203 ASP cc_start: 0.7844 (t0) cc_final: 0.7509 (t0) REVERT: A 1214 TYR cc_start: 0.8286 (p90) cc_final: 0.8044 (p90) REVERT: A 1228 TYR cc_start: 0.7819 (m-10) cc_final: 0.7492 (m-10) REVERT: A 1229 GLU cc_start: 0.7335 (tp30) cc_final: 0.7099 (tp30) REVERT: A 1565 ARG cc_start: 0.7885 (OUTLIER) cc_final: 0.7062 (mtp85) REVERT: B 24 MET cc_start: 0.8052 (OUTLIER) cc_final: 0.7406 (mtp) REVERT: B 136 ARG cc_start: 0.7255 (OUTLIER) cc_final: 0.6442 (mtt90) REVERT: B 183 ARG cc_start: 0.8037 (ttm-80) cc_final: 0.7359 (ttm-80) REVERT: B 209 TYR cc_start: 0.7535 (OUTLIER) cc_final: 0.7084 (m-80) REVERT: B 212 ARG cc_start: 0.7948 (OUTLIER) cc_final: 0.6754 (ptm160) REVERT: B 513 ARG cc_start: 0.6129 (mtp180) cc_final: 0.5145 (tpt170) outliers start: 44 outliers final: 15 residues processed: 208 average time/residue: 1.4567 time to fit residues: 334.5502 Evaluate side-chains 193 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 167 time to evaluate : 1.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 264 LYS Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 599 ASP Chi-restraints excluded: chain A residue 631 SER Chi-restraints excluded: chain A residue 707 GLU Chi-restraints excluded: chain A residue 857 GLU Chi-restraints excluded: chain A residue 896 ARG Chi-restraints excluded: chain A residue 942 GLN Chi-restraints excluded: chain A residue 1008 THR Chi-restraints excluded: chain A residue 1185 THR Chi-restraints excluded: chain A residue 1323 SER Chi-restraints excluded: chain A residue 1330 GLU Chi-restraints excluded: chain A residue 1350 THR Chi-restraints excluded: chain A residue 1390 LEU Chi-restraints excluded: chain A residue 1502 SER Chi-restraints excluded: chain A residue 1565 ARG Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 136 ARG Chi-restraints excluded: chain B residue 201 ASN Chi-restraints excluded: chain B residue 209 TYR Chi-restraints excluded: chain B residue 212 ARG Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 341 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 157 optimal weight: 2.9990 chunk 107 optimal weight: 0.0170 chunk 2 optimal weight: 4.9990 chunk 141 optimal weight: 0.9990 chunk 78 optimal weight: 0.7980 chunk 161 optimal weight: 3.9990 chunk 130 optimal weight: 0.0000 chunk 0 optimal weight: 6.9990 chunk 96 optimal weight: 4.9990 chunk 170 optimal weight: 2.9990 chunk 47 optimal weight: 0.0370 overall best weight: 0.3702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1027 GLN B 235 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.2198 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= 0.116 Angle : 0.426 6.321 23789 Z= 0.225 Chirality : 0.038 0.249 2533 Planarity : 0.003 0.038 2870 Dihedral : 14.180 97.049 3053 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.92 % Allowed : 13.17 % Favored : 84.91 % 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: 1.36 (0.19), residues: 1892 helix: 2.10 (0.20), residues: 661 sheet: 0.59 (0.28), residues: 330 loop : 0.21 (0.21), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 517 HIS 0.003 0.001 HIS B 427 PHE 0.011 0.001 PHE A 776 TYR 0.009 0.001 TYR A 930 ARG 0.007 0.000 ARG B 328 *********************** 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 211 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 179 time to evaluate : 1.906 Fit side-chains revert: symmetry clash REVERT: A 354 LYS cc_start: 0.8459 (mttt) cc_final: 0.8200 (mttp) REVERT: A 466 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7383 (mm-30) REVERT: A 473 MET cc_start: 0.9162 (mmt) cc_final: 0.8746 (mmt) REVERT: A 619 ASN cc_start: 0.8125 (m-40) cc_final: 0.7550 (t0) REVERT: A 669 LYS cc_start: 0.8314 (tttt) cc_final: 0.7362 (mmpt) REVERT: A 826 ASP cc_start: 0.7520 (t70) cc_final: 0.7107 (t0) REVERT: A 857 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7685 (mt-10) REVERT: A 942 GLN cc_start: 0.7972 (OUTLIER) cc_final: 0.6964 (tm-30) REVERT: A 1202 GLU cc_start: 0.8002 (tt0) cc_final: 0.7728 (mt-10) REVERT: A 1203 ASP cc_start: 0.7785 (t0) cc_final: 0.7456 (t0) REVERT: A 1214 TYR cc_start: 0.8228 (p90) cc_final: 0.8004 (p90) REVERT: A 1387 MET cc_start: 0.9096 (ttm) cc_final: 0.8773 (ttm) REVERT: A 1565 ARG cc_start: 0.7849 (OUTLIER) cc_final: 0.7116 (mtp85) REVERT: A 1580 LYS cc_start: 0.7802 (ttpt) cc_final: 0.7377 (pttm) REVERT: B 24 MET cc_start: 0.8054 (OUTLIER) cc_final: 0.7353 (mtp) REVERT: B 101 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.8265 (mp0) REVERT: B 136 ARG cc_start: 0.7287 (OUTLIER) cc_final: 0.6331 (mtt90) REVERT: B 209 TYR cc_start: 0.7462 (OUTLIER) cc_final: 0.6945 (m-80) REVERT: B 513 ARG cc_start: 0.6097 (mtp180) cc_final: 0.5247 (mmt180) outliers start: 32 outliers final: 12 residues processed: 198 average time/residue: 1.6207 time to fit residues: 352.1425 Evaluate side-chains 187 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 167 time to evaluate : 1.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 699 THR Chi-restraints excluded: chain A residue 707 GLU Chi-restraints excluded: chain A residue 857 GLU Chi-restraints excluded: chain A residue 942 GLN Chi-restraints excluded: chain A residue 1008 THR Chi-restraints excluded: chain A residue 1217 THR Chi-restraints excluded: chain A residue 1350 THR Chi-restraints excluded: chain A residue 1390 LEU Chi-restraints excluded: chain A residue 1565 ARG Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 136 ARG Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 209 TYR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 341 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 63 optimal weight: 2.9990 chunk 170 optimal weight: 10.0000 chunk 37 optimal weight: 0.6980 chunk 111 optimal weight: 6.9990 chunk 46 optimal weight: 0.9990 chunk 189 optimal weight: 0.8980 chunk 157 optimal weight: 1.9990 chunk 87 optimal weight: 0.0070 chunk 15 optimal weight: 0.6980 chunk 62 optimal weight: 10.0000 chunk 99 optimal weight: 0.9990 overall best weight: 0.6600 ------------------------------------------------------------------------------- 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: 0.8690 moved from start: 0.2239 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= 0.139 Angle : 0.439 6.898 23789 Z= 0.229 Chirality : 0.038 0.260 2533 Planarity : 0.004 0.057 2870 Dihedral : 14.163 96.181 3053 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.28 % Allowed : 13.59 % Favored : 84.13 % 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: 1.41 (0.19), residues: 1892 helix: 2.15 (0.20), residues: 662 sheet: 0.59 (0.28), residues: 330 loop : 0.23 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1038 HIS 0.003 0.001 HIS B 427 PHE 0.010 0.001 PHE A 776 TYR 0.009 0.001 TYR A 492 ARG 0.006 0.000 ARG B 328 *********************** 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 215 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 177 time to evaluate : 1.930 Fit side-chains revert: symmetry clash REVERT: A 354 LYS cc_start: 0.8464 (mttt) cc_final: 0.8203 (mttp) REVERT: A 451 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8674 (tt) REVERT: A 466 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7387 (mm-30) REVERT: A 619 ASN cc_start: 0.8121 (m-40) cc_final: 0.7542 (t0) REVERT: A 669 LYS cc_start: 0.8319 (tttt) cc_final: 0.7361 (mmpt) REVERT: A 826 ASP cc_start: 0.7552 (t70) cc_final: 0.7146 (t0) REVERT: A 857 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7647 (mt-10) REVERT: A 859 GLU cc_start: 0.7720 (pm20) cc_final: 0.7373 (pm20) REVERT: A 942 GLN cc_start: 0.7990 (OUTLIER) cc_final: 0.6985 (tm-30) REVERT: A 1202 GLU cc_start: 0.8004 (tt0) cc_final: 0.7723 (mt-10) REVERT: A 1203 ASP cc_start: 0.7787 (t0) cc_final: 0.7449 (t0) REVERT: A 1214 TYR cc_start: 0.8208 (p90) cc_final: 0.7974 (p90) REVERT: A 1387 MET cc_start: 0.9099 (ttm) cc_final: 0.8759 (ttm) REVERT: A 1565 ARG cc_start: 0.7841 (OUTLIER) cc_final: 0.7108 (mtp85) REVERT: A 1580 LYS cc_start: 0.7814 (ttpt) cc_final: 0.7381 (pttm) REVERT: A 1591 LYS cc_start: 0.8435 (OUTLIER) cc_final: 0.8233 (tmtp) REVERT: B 24 MET cc_start: 0.8057 (OUTLIER) cc_final: 0.7355 (mtp) REVERT: B 101 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.8250 (mp0) REVERT: B 136 ARG cc_start: 0.7284 (OUTLIER) cc_final: 0.6193 (mtt90) REVERT: B 209 TYR cc_start: 0.7524 (OUTLIER) cc_final: 0.7034 (m-80) REVERT: B 513 ARG cc_start: 0.6156 (mtp180) cc_final: 0.5254 (mmt180) outliers start: 38 outliers final: 17 residues processed: 206 average time/residue: 1.5553 time to fit residues: 352.0209 Evaluate side-chains 193 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 166 time to evaluate : 1.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 631 SER Chi-restraints excluded: chain A residue 699 THR Chi-restraints excluded: chain A residue 707 GLU Chi-restraints excluded: chain A residue 857 GLU Chi-restraints excluded: chain A residue 898 LYS Chi-restraints excluded: chain A residue 942 GLN Chi-restraints excluded: chain A residue 1008 THR Chi-restraints excluded: chain A residue 1217 THR Chi-restraints excluded: chain A residue 1323 SER Chi-restraints excluded: chain A residue 1350 THR Chi-restraints excluded: chain A residue 1390 LEU Chi-restraints excluded: chain A residue 1565 ARG Chi-restraints excluded: chain A residue 1591 LYS Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 136 ARG Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 209 TYR Chi-restraints excluded: chain B residue 341 ASP Chi-restraints excluded: chain B residue 542 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 182 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 108 optimal weight: 9.9990 chunk 138 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 159 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 188 optimal weight: 5.9990 chunk 118 optimal weight: 0.9980 chunk 115 optimal weight: 1.9990 chunk 87 optimal weight: 0.0050 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1127 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 17446 Z= 0.145 Angle : 0.444 8.205 23789 Z= 0.231 Chirality : 0.038 0.263 2533 Planarity : 0.004 0.051 2870 Dihedral : 14.153 96.038 3053 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.69 % Allowed : 13.35 % Favored : 83.95 % 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: 1.41 (0.19), residues: 1892 helix: 2.15 (0.20), residues: 663 sheet: 0.61 (0.27), residues: 338 loop : 0.22 (0.21), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1038 HIS 0.003 0.001 HIS A 741 PHE 0.010 0.001 PHE A 776 TYR 0.009 0.001 TYR A 492 ARG 0.007 0.000 ARG A1558 *********************** 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 217 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 172 time to evaluate : 1.836 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 354 LYS cc_start: 0.8463 (mttt) cc_final: 0.8201 (mttm) REVERT: A 451 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8677 (tt) REVERT: A 466 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7407 (mm-30) REVERT: A 619 ASN cc_start: 0.8112 (m-40) cc_final: 0.7536 (t0) REVERT: A 669 LYS cc_start: 0.8324 (tttt) cc_final: 0.7360 (mmpt) REVERT: A 826 ASP cc_start: 0.7562 (t70) cc_final: 0.7174 (t0) REVERT: A 857 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7638 (mt-10) REVERT: A 859 GLU cc_start: 0.7711 (pm20) cc_final: 0.7343 (pm20) REVERT: A 888 GLU cc_start: 0.7349 (mt-10) cc_final: 0.7100 (mp0) REVERT: A 942 GLN cc_start: 0.7982 (OUTLIER) cc_final: 0.6987 (tm-30) REVERT: A 1202 GLU cc_start: 0.7994 (tt0) cc_final: 0.7713 (mt-10) REVERT: A 1203 ASP cc_start: 0.7766 (t0) cc_final: 0.7457 (t0) REVERT: A 1214 TYR cc_start: 0.8189 (p90) cc_final: 0.7965 (p90) REVERT: A 1387 MET cc_start: 0.9102 (ttm) cc_final: 0.8769 (ttm) REVERT: A 1565 ARG cc_start: 0.7834 (OUTLIER) cc_final: 0.7117 (mtp85) REVERT: A 1580 LYS cc_start: 0.7830 (ttpt) cc_final: 0.7404 (pttm) REVERT: A 1591 LYS cc_start: 0.8444 (OUTLIER) cc_final: 0.8239 (tmtp) REVERT: B 24 MET cc_start: 0.8071 (OUTLIER) cc_final: 0.7362 (mtp) REVERT: B 136 ARG cc_start: 0.7260 (OUTLIER) cc_final: 0.6131 (mtt90) REVERT: B 183 ARG cc_start: 0.8089 (ttm-80) cc_final: 0.7883 (ttm110) REVERT: B 209 TYR cc_start: 0.7514 (OUTLIER) cc_final: 0.6963 (m-80) REVERT: B 448 ASP cc_start: 0.7333 (t0) cc_final: 0.6465 (t70) REVERT: B 513 ARG cc_start: 0.6007 (mtp180) cc_final: 0.5225 (mmt180) outliers start: 45 outliers final: 17 residues processed: 204 average time/residue: 1.5157 time to fit residues: 340.7168 Evaluate side-chains 191 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 165 time to evaluate : 1.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 699 THR Chi-restraints excluded: chain A residue 707 GLU Chi-restraints excluded: chain A residue 857 GLU Chi-restraints excluded: chain A residue 898 LYS Chi-restraints excluded: chain A residue 942 GLN Chi-restraints excluded: chain A residue 1008 THR Chi-restraints excluded: chain A residue 1185 THR Chi-restraints excluded: chain A residue 1350 THR Chi-restraints excluded: chain A residue 1390 LEU Chi-restraints excluded: chain A residue 1502 SER Chi-restraints excluded: chain A residue 1565 ARG Chi-restraints excluded: chain A residue 1591 LYS Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 136 ARG Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 209 TYR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 341 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 116 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 112 optimal weight: 0.0370 chunk 56 optimal weight: 0.2980 chunk 37 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 120 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 148 optimal weight: 0.5980 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1127 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.2365 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= 0.123 Angle : 0.436 7.121 23789 Z= 0.227 Chirality : 0.038 0.250 2533 Planarity : 0.003 0.041 2870 Dihedral : 14.138 95.478 3053 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.10 % Allowed : 13.89 % Favored : 84.01 % 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: 1.48 (0.20), residues: 1892 helix: 2.23 (0.20), residues: 662 sheet: 0.65 (0.27), residues: 338 loop : 0.25 (0.21), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A1038 HIS 0.003 0.001 HIS B 427 PHE 0.010 0.001 PHE A 776 TYR 0.009 0.001 TYR A 930 ARG 0.008 0.000 ARG A 199 *********************** 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 215 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 180 time to evaluate : 1.780 Fit side-chains revert: symmetry clash REVERT: A 354 LYS cc_start: 0.8435 (mttt) cc_final: 0.8176 (mttm) REVERT: A 391 LYS cc_start: 0.7471 (mtmm) cc_final: 0.7258 (mppt) REVERT: A 451 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8682 (tt) REVERT: A 466 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7372 (mm-30) REVERT: A 473 MET cc_start: 0.9170 (mmt) cc_final: 0.8717 (mmt) REVERT: A 619 ASN cc_start: 0.8109 (m-40) cc_final: 0.7553 (t0) REVERT: A 669 LYS cc_start: 0.8305 (tttt) cc_final: 0.7352 (mmpt) REVERT: A 784 GLU cc_start: 0.8326 (mm-30) cc_final: 0.7301 (mm-30) REVERT: A 826 ASP cc_start: 0.7587 (t70) cc_final: 0.7206 (t0) REVERT: A 857 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7628 (mt-10) REVERT: A 888 GLU cc_start: 0.7345 (mt-10) cc_final: 0.7088 (mp0) REVERT: A 942 GLN cc_start: 0.7955 (OUTLIER) cc_final: 0.7000 (tm-30) REVERT: A 1202 GLU cc_start: 0.7990 (tt0) cc_final: 0.7715 (mt-10) REVERT: A 1203 ASP cc_start: 0.7760 (t0) cc_final: 0.7444 (t0) REVERT: A 1387 MET cc_start: 0.9096 (ttm) cc_final: 0.8754 (ttm) REVERT: A 1565 ARG cc_start: 0.7819 (OUTLIER) cc_final: 0.7129 (mtp85) REVERT: A 1580 LYS cc_start: 0.7811 (ttpt) cc_final: 0.7404 (pttm) REVERT: A 1591 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.8229 (tmtp) REVERT: B 24 MET cc_start: 0.8070 (ttm) cc_final: 0.7372 (mtp) REVERT: B 136 ARG cc_start: 0.7257 (OUTLIER) cc_final: 0.6029 (mtt90) REVERT: B 209 TYR cc_start: 0.7464 (OUTLIER) cc_final: 0.6884 (m-80) REVERT: B 448 ASP cc_start: 0.7304 (t0) cc_final: 0.6430 (t70) REVERT: B 513 ARG cc_start: 0.5929 (mtp180) cc_final: 0.5198 (mmt180) outliers start: 35 outliers final: 16 residues processed: 204 average time/residue: 1.5345 time to fit residues: 344.3748 Evaluate side-chains 196 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 172 time to evaluate : 1.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 631 SER Chi-restraints excluded: chain A residue 699 THR Chi-restraints excluded: chain A residue 707 GLU Chi-restraints excluded: chain A residue 857 GLU Chi-restraints excluded: chain A residue 898 LYS Chi-restraints excluded: chain A residue 942 GLN Chi-restraints excluded: chain A residue 1008 THR Chi-restraints excluded: chain A residue 1185 THR Chi-restraints excluded: chain A residue 1350 THR Chi-restraints excluded: chain A residue 1390 LEU Chi-restraints excluded: chain A residue 1502 SER Chi-restraints excluded: chain A residue 1565 ARG Chi-restraints excluded: chain A residue 1591 LYS Chi-restraints excluded: chain B residue 136 ARG Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 209 TYR Chi-restraints excluded: chain B residue 341 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 171 optimal weight: 0.9990 chunk 180 optimal weight: 3.9990 chunk 165 optimal weight: 3.9990 chunk 176 optimal weight: 7.9990 chunk 105 optimal weight: 0.8980 chunk 76 optimal weight: 0.7980 chunk 138 optimal weight: 0.5980 chunk 54 optimal weight: 5.9990 chunk 159 optimal weight: 0.6980 chunk 166 optimal weight: 0.1980 chunk 175 optimal weight: 5.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1127 GLN B 235 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.2385 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= 0.137 Angle : 0.450 9.237 23789 Z= 0.233 Chirality : 0.038 0.255 2533 Planarity : 0.004 0.073 2870 Dihedral : 14.133 95.166 3053 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.92 % Allowed : 14.49 % Favored : 83.59 % 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: 1.50 (0.20), residues: 1892 helix: 2.25 (0.20), residues: 661 sheet: 0.69 (0.28), residues: 338 loop : 0.25 (0.21), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A1038 HIS 0.003 0.001 HIS B 427 PHE 0.010 0.001 PHE A 776 TYR 0.021 0.001 TYR A1214 ARG 0.008 0.000 ARG B 183 *********************** 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 201 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 169 time to evaluate : 1.818 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 354 LYS cc_start: 0.8444 (mttt) cc_final: 0.8188 (mttm) REVERT: A 391 LYS cc_start: 0.7476 (mtmm) cc_final: 0.7247 (mppt) REVERT: A 451 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8684 (tt) REVERT: A 466 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7402 (mm-30) REVERT: A 473 MET cc_start: 0.9181 (mmt) cc_final: 0.8710 (mmt) REVERT: A 619 ASN cc_start: 0.8071 (m-40) cc_final: 0.7534 (t0) REVERT: A 669 LYS cc_start: 0.8311 (tttt) cc_final: 0.7356 (mmpt) REVERT: A 784 GLU cc_start: 0.8319 (mm-30) cc_final: 0.7292 (mm-30) REVERT: A 826 ASP cc_start: 0.7597 (t70) cc_final: 0.7207 (t0) REVERT: A 857 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7641 (mt-10) REVERT: A 888 GLU cc_start: 0.7351 (mt-10) cc_final: 0.7096 (mp0) REVERT: A 942 GLN cc_start: 0.7970 (OUTLIER) cc_final: 0.7015 (tm-30) REVERT: A 1190 ASN cc_start: 0.7919 (t0) cc_final: 0.7555 (t0) REVERT: A 1202 GLU cc_start: 0.7994 (tt0) cc_final: 0.7717 (mt-10) REVERT: A 1203 ASP cc_start: 0.7764 (t0) cc_final: 0.7445 (t0) REVERT: A 1387 MET cc_start: 0.9097 (ttm) cc_final: 0.8762 (ttm) REVERT: A 1565 ARG cc_start: 0.7838 (OUTLIER) cc_final: 0.7133 (mtp85) REVERT: A 1580 LYS cc_start: 0.7833 (ttpt) cc_final: 0.7415 (pttm) REVERT: A 1591 LYS cc_start: 0.8442 (OUTLIER) cc_final: 0.8239 (tmtp) REVERT: B 24 MET cc_start: 0.8084 (ttm) cc_final: 0.7379 (mtp) REVERT: B 136 ARG cc_start: 0.7253 (OUTLIER) cc_final: 0.6025 (mtt90) REVERT: B 209 TYR cc_start: 0.7468 (OUTLIER) cc_final: 0.6893 (m-80) REVERT: B 448 ASP cc_start: 0.7296 (t0) cc_final: 0.6436 (t70) REVERT: B 513 ARG cc_start: 0.5890 (mtp180) cc_final: 0.5175 (mmt180) outliers start: 32 outliers final: 17 residues processed: 193 average time/residue: 1.4901 time to fit residues: 317.1235 Evaluate side-chains 194 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 169 time to evaluate : 1.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 631 SER Chi-restraints excluded: chain A residue 699 THR Chi-restraints excluded: chain A residue 707 GLU Chi-restraints excluded: chain A residue 857 GLU Chi-restraints excluded: chain A residue 898 LYS Chi-restraints excluded: chain A residue 942 GLN Chi-restraints excluded: chain A residue 1008 THR Chi-restraints excluded: chain A residue 1185 THR Chi-restraints excluded: chain A residue 1350 THR Chi-restraints excluded: chain A residue 1390 LEU Chi-restraints excluded: chain A residue 1502 SER Chi-restraints excluded: chain A residue 1565 ARG Chi-restraints excluded: chain A residue 1591 LYS Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 136 ARG Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 209 TYR Chi-restraints excluded: chain B residue 341 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 115 optimal weight: 4.9990 chunk 186 optimal weight: 2.9990 chunk 113 optimal weight: 0.5980 chunk 88 optimal weight: 0.0770 chunk 129 optimal weight: 1.9990 chunk 195 optimal weight: 9.9990 chunk 179 optimal weight: 9.9990 chunk 155 optimal weight: 0.6980 chunk 16 optimal weight: 0.0060 chunk 120 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 overall best weight: 0.4754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 232 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 17446 Z= 0.122 Angle : 0.439 8.581 23789 Z= 0.228 Chirality : 0.037 0.243 2533 Planarity : 0.003 0.054 2870 Dihedral : 14.117 94.816 3053 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 1.68 % Allowed : 15.03 % Favored : 83.29 % 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: 1.54 (0.20), residues: 1892 helix: 2.24 (0.20), residues: 665 sheet: 0.74 (0.28), residues: 338 loop : 0.27 (0.21), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A1038 HIS 0.003 0.001 HIS B 427 PHE 0.010 0.001 PHE A 776 TYR 0.013 0.001 TYR A1214 ARG 0.007 0.000 ARG B 183 ********************** 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 202 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 174 time to evaluate : 1.967 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 354 LYS cc_start: 0.8436 (mttt) cc_final: 0.8181 (mttm) REVERT: A 391 LYS cc_start: 0.7443 (mtmm) cc_final: 0.7224 (mppt) REVERT: A 451 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8684 (tt) REVERT: A 466 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7369 (mm-30) REVERT: A 473 MET cc_start: 0.9170 (mmt) cc_final: 0.8743 (mmt) REVERT: A 619 ASN cc_start: 0.8119 (m-40) cc_final: 0.7571 (t0) REVERT: A 669 LYS cc_start: 0.8297 (tttt) cc_final: 0.7348 (mmpt) REVERT: A 784 GLU cc_start: 0.8297 (mm-30) cc_final: 0.7266 (mm-30) REVERT: A 826 ASP cc_start: 0.7615 (t70) cc_final: 0.7224 (t0) REVERT: A 859 GLU cc_start: 0.7695 (pm20) cc_final: 0.7366 (pm20) REVERT: A 888 GLU cc_start: 0.7331 (mt-10) cc_final: 0.7097 (mp0) REVERT: A 942 GLN cc_start: 0.7955 (OUTLIER) cc_final: 0.7005 (tm-30) REVERT: A 1019 LYS cc_start: 0.8248 (mppt) cc_final: 0.7852 (mmtm) REVERT: A 1190 ASN cc_start: 0.7906 (t0) cc_final: 0.7523 (t0) REVERT: A 1202 GLU cc_start: 0.7996 (tt0) cc_final: 0.7719 (mt-10) REVERT: A 1203 ASP cc_start: 0.7755 (t0) cc_final: 0.7436 (t0) REVERT: A 1387 MET cc_start: 0.9062 (ttm) cc_final: 0.8714 (ttm) REVERT: A 1565 ARG cc_start: 0.7833 (OUTLIER) cc_final: 0.7159 (mtp85) REVERT: A 1580 LYS cc_start: 0.7807 (ttpt) cc_final: 0.7410 (pttm) REVERT: A 1591 LYS cc_start: 0.8434 (OUTLIER) cc_final: 0.8230 (tmtp) REVERT: B 24 MET cc_start: 0.8081 (ttm) cc_final: 0.7372 (mtp) REVERT: B 101 GLU cc_start: 0.8496 (mt-10) cc_final: 0.8158 (mp0) REVERT: B 136 ARG cc_start: 0.7216 (OUTLIER) cc_final: 0.5964 (mtt90) REVERT: B 209 TYR cc_start: 0.7515 (OUTLIER) cc_final: 0.6927 (m-80) REVERT: B 448 ASP cc_start: 0.7234 (t0) cc_final: 0.6391 (t70) REVERT: B 513 ARG cc_start: 0.5927 (mtp180) cc_final: 0.5206 (mmt180) outliers start: 28 outliers final: 14 residues processed: 196 average time/residue: 1.5594 time to fit residues: 336.7908 Evaluate side-chains 186 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 165 time to evaluate : 1.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 699 THR Chi-restraints excluded: chain A residue 707 GLU Chi-restraints excluded: chain A residue 898 LYS Chi-restraints excluded: chain A residue 942 GLN Chi-restraints excluded: chain A residue 1008 THR Chi-restraints excluded: chain A residue 1185 THR Chi-restraints excluded: chain A residue 1350 THR Chi-restraints excluded: chain A residue 1390 LEU Chi-restraints excluded: chain A residue 1502 SER Chi-restraints excluded: chain A residue 1565 ARG Chi-restraints excluded: chain A residue 1591 LYS Chi-restraints excluded: chain B residue 136 ARG Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 209 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 123 optimal weight: 0.9980 chunk 165 optimal weight: 6.9990 chunk 47 optimal weight: 0.0970 chunk 143 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 chunk 43 optimal weight: 0.9980 chunk 155 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 chunk 159 optimal weight: 0.6980 chunk 19 optimal weight: 0.0770 chunk 28 optimal weight: 0.5980 overall best weight: 0.4136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 232 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.146722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.109937 restraints weight = 19026.635| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 1.67 r_work: 0.2937 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 17446 Z= 0.117 Angle : 0.439 8.418 23789 Z= 0.227 Chirality : 0.037 0.239 2533 Planarity : 0.004 0.078 2870 Dihedral : 14.112 94.328 3053 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.74 % Allowed : 15.21 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.20), residues: 1892 helix: 2.26 (0.20), residues: 665 sheet: 0.76 (0.28), residues: 338 loop : 0.31 (0.21), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A1038 HIS 0.003 0.001 HIS B 427 PHE 0.011 0.001 PHE B 286 TYR 0.012 0.001 TYR A1214 ARG 0.009 0.000 ARG B 183 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6476.95 seconds wall clock time: 115 minutes 10.55 seconds (6910.55 seconds total)