Starting phenix.real_space_refine on Sun Aug 24 05:26:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gs2_34218/08_2025/8gs2_34218.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gs2_34218/08_2025/8gs2_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/cci-nas-00/data/ceres_data/8gs2_34218/08_2025/8gs2_34218.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gs2_34218/08_2025/8gs2_34218.map" model { file = "/net/cci-nas-00/data/ceres_data/8gs2_34218/08_2025/8gs2_34218.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gs2_34218/08_2025/8gs2_34218.cif" } resolution = 2.84 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16935 Number of models: 1 Model: "" Number of chains: 8 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: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNA': 1} Modifications used: {'rna3p_pur': 1} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} 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: 2.90, per 1000 atoms: 0.17 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 - 3.00 Amino acid : True - 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: 1.10 Conformation dependent library (CDL) restraints added in 560.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 2.28 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: 3.32 Time building geometry restraints manager: 1.38 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: 0.00 - 1.16: 23300 1.16 - 2.33: 367 2.33 - 3.49: 110 3.49 - 4.65: 9 4.65 - 5.81: 3 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 3.040 nonbonded pdb=" OH TYR B 176 " pdb=" OD1 ASP B 210 " model vdw 2.247 3.040 ... (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 Time spend for trying shortcut: 0.00 ========== 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: 3.030 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: 0.000 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 17.540 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.840 ------------------------------------------------------------------------------- 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 17461 Z= 0.096 Angle : 0.421 5.813 23804 Z= 0.230 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.003 0.000 ARG A1356 TYR 0.009 0.001 TYR A 492 PHE 0.011 0.001 PHE A 416 TRP 0.010 0.001 TRP B 544 HIS 0.003 0.001 HIS A 741 Details of bonding type rmsd covalent geometry : bond 0.00210 (17446) covalent geometry : angle 0.41685 (23789) hydrogen bonds : bond 0.19637 ( 682) hydrogen bonds : angle 6.11785 ( 1959) metal coordination : bond 0.00391 ( 15) metal coordination : angle 2.25955 ( 15) *********************** 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 to be fit. rotamer outliers: 5 poor density : 345 time to evaluate : 0.646 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: 0.7188 time to fit residues: 273.6559 Evaluate side-chains 197 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 195 time to evaluate : 0.669 ------------------------------------------------------------------------------- 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 98 optimal weight: 5.9990 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 0.2980 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.0270 chunk 91 optimal weight: 6.9990 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN A 531 GLN A 871 HIS A1018 GLN A1131 GLN A1186 ASN A1326 ASN A1419 HIS A1483 HIS B 108 GLN B 224 ASN B 235 GLN B 477 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.146563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.110765 restraints weight = 19034.994| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 1.80 r_work: 0.3021 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 17461 Z= 0.112 Angle : 0.490 6.571 23804 Z= 0.260 Chirality : 0.039 0.321 2533 Planarity : 0.004 0.043 2870 Dihedral : 14.147 96.461 3055 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 1.86 % Allowed : 10.18 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.40 (0.20), residues: 1892 helix: 1.84 (0.20), residues: 669 sheet: 0.88 (0.27), residues: 344 loop : 0.33 (0.22), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 780 TYR 0.010 0.001 TYR B 246 PHE 0.013 0.001 PHE B 252 TRP 0.028 0.001 TRP B 517 HIS 0.005 0.001 HIS B 427 Details of bonding type rmsd covalent geometry : bond 0.00242 (17446) covalent geometry : angle 0.48856 (23789) hydrogen bonds : bond 0.04218 ( 682) hydrogen bonds : angle 4.48739 ( 1959) metal coordination : bond 0.00439 ( 15) metal coordination : angle 1.62220 ( 15) *********************** 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 234 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 203 time to evaluate : 0.548 Fit side-chains revert: symmetry clash REVERT: A 28 LYS cc_start: 0.8783 (OUTLIER) cc_final: 0.8530 (pttt) REVERT: A 354 LYS cc_start: 0.8597 (mttt) cc_final: 0.8331 (mttm) REVERT: A 451 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8567 (tt) REVERT: A 619 ASN cc_start: 0.8137 (m-40) cc_final: 0.7507 (t0) REVERT: A 669 LYS cc_start: 0.8387 (tttt) cc_final: 0.7301 (mmpt) REVERT: A 857 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7738 (mt-10) REVERT: A 859 GLU cc_start: 0.7908 (pm20) cc_final: 0.7558 (pm20) REVERT: A 930 TYR cc_start: 0.7683 (p90) cc_final: 0.7348 (p90) REVERT: A 942 GLN cc_start: 0.7995 (OUTLIER) cc_final: 0.6795 (tm-30) REVERT: A 1019 LYS cc_start: 0.8201 (mppt) cc_final: 0.7785 (mmtm) REVERT: A 1028 GLU cc_start: 0.7769 (mt-10) cc_final: 0.7497 (mt-10) REVERT: A 1203 ASP cc_start: 0.7982 (t0) cc_final: 0.7712 (t0) REVERT: A 1228 TYR cc_start: 0.7869 (m-10) cc_final: 0.7341 (m-10) REVERT: A 1239 LYS cc_start: 0.9129 (tttt) cc_final: 0.8316 (mmtt) REVERT: A 1254 GLU cc_start: 0.7841 (mm-30) cc_final: 0.7323 (mm-30) REVERT: A 1580 LYS cc_start: 0.7579 (ttpt) cc_final: 0.6828 (mttp) REVERT: B 11 ARG cc_start: 0.7796 (mmt180) cc_final: 0.7587 (mmt-90) REVERT: B 24 MET cc_start: 0.8005 (OUTLIER) cc_final: 0.7264 (mtp) REVERT: B 83 GLU cc_start: 0.7819 (tm-30) cc_final: 0.7412 (tt0) REVERT: B 101 GLU cc_start: 0.8255 (mt-10) cc_final: 0.7955 (mp0) REVERT: B 117 ASP cc_start: 0.7652 (t70) cc_final: 0.6632 (p0) REVERT: B 136 ARG cc_start: 0.6911 (OUTLIER) cc_final: 0.6344 (mtt90) REVERT: B 165 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7604 (mp0) REVERT: B 513 ARG cc_start: 0.6025 (mtp180) cc_final: 0.4981 (tpt170) outliers start: 31 outliers final: 7 residues processed: 225 average time/residue: 0.7009 time to fit residues: 172.9667 Evaluate side-chains 194 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 180 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 631 SER 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 1217 THR 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 136 ARG Chi-restraints excluded: chain B residue 165 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 173 optimal weight: 8.9990 chunk 57 optimal weight: 5.9990 chunk 10 optimal weight: 0.5980 chunk 187 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 167 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 93 optimal weight: 0.6980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 GLN B 224 ASN B 256 GLN B 458 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.143476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.107072 restraints weight = 19248.822| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 1.80 r_work: 0.2972 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17461 Z= 0.144 Angle : 0.497 6.141 23804 Z= 0.260 Chirality : 0.040 0.302 2533 Planarity : 0.004 0.038 2870 Dihedral : 14.093 97.233 3053 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.34 % Allowed : 10.72 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.33 (0.19), residues: 1892 helix: 1.91 (0.20), residues: 661 sheet: 0.69 (0.27), residues: 341 loop : 0.27 (0.21), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 780 TYR 0.010 0.001 TYR A 492 PHE 0.012 0.001 PHE A 416 TRP 0.015 0.001 TRP B 517 HIS 0.006 0.001 HIS B 253 Details of bonding type rmsd covalent geometry : bond 0.00337 (17446) covalent geometry : angle 0.49459 (23789) hydrogen bonds : bond 0.03896 ( 682) hydrogen bonds : angle 4.21158 ( 1959) metal coordination : bond 0.00564 ( 15) metal coordination : angle 1.84567 ( 15) *********************** 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 235 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 196 time to evaluate : 0.596 Fit side-chains revert: symmetry clash REVERT: A 28 LYS cc_start: 0.8800 (OUTLIER) cc_final: 0.8588 (pttt) REVERT: A 354 LYS cc_start: 0.8634 (mttt) cc_final: 0.8370 (mttm) REVERT: A 451 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8558 (tt) REVERT: A 466 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7396 (mm-30) REVERT: A 559 MET cc_start: 0.9016 (OUTLIER) cc_final: 0.8769 (mtm) REVERT: A 619 ASN cc_start: 0.8192 (m-40) cc_final: 0.7549 (t0) REVERT: A 669 LYS cc_start: 0.8437 (tttt) cc_final: 0.7314 (mmpt) REVERT: A 826 ASP cc_start: 0.7801 (t70) cc_final: 0.7422 (t0) REVERT: A 930 TYR cc_start: 0.7704 (p90) cc_final: 0.7406 (p90) REVERT: A 942 GLN cc_start: 0.8070 (OUTLIER) cc_final: 0.6999 (tm-30) REVERT: A 1038 TRP cc_start: 0.7823 (m100) cc_final: 0.7614 (m100) REVERT: A 1202 GLU cc_start: 0.8228 (tt0) cc_final: 0.7991 (mt-10) REVERT: A 1203 ASP cc_start: 0.8034 (t0) cc_final: 0.7803 (t0) REVERT: A 1228 TYR cc_start: 0.7883 (m-10) cc_final: 0.7539 (m-10) REVERT: A 1229 GLU cc_start: 0.7235 (tp30) cc_final: 0.6937 (tp30) REVERT: A 1239 LYS cc_start: 0.9143 (tttt) cc_final: 0.8342 (mptt) REVERT: A 1254 GLU cc_start: 0.7860 (mm-30) cc_final: 0.7048 (mp0) REVERT: A 1457 GLU cc_start: 0.8622 (mt-10) cc_final: 0.8356 (mt-10) REVERT: B 11 ARG cc_start: 0.7830 (mmt180) cc_final: 0.7589 (mmt-90) REVERT: B 24 MET cc_start: 0.7977 (OUTLIER) cc_final: 0.7288 (mtp) REVERT: B 83 GLU cc_start: 0.7730 (tm-30) cc_final: 0.7379 (tt0) REVERT: B 101 GLU cc_start: 0.8282 (mt-10) cc_final: 0.7981 (mp0) REVERT: B 136 ARG cc_start: 0.6968 (OUTLIER) cc_final: 0.6252 (mtt90) REVERT: B 183 ARG cc_start: 0.8229 (ttm-80) cc_final: 0.7398 (ttm-80) REVERT: B 202 ASP cc_start: 0.6883 (OUTLIER) cc_final: 0.6659 (m-30) REVERT: B 209 TYR cc_start: 0.7373 (OUTLIER) cc_final: 0.6833 (m-80) REVERT: B 212 ARG cc_start: 0.7847 (OUTLIER) cc_final: 0.6584 (ptm160) REVERT: B 513 ARG cc_start: 0.5759 (mtp180) cc_final: 0.5118 (tpt170) outliers start: 39 outliers final: 9 residues processed: 222 average time/residue: 0.6688 time to fit residues: 162.7455 Evaluate side-chains 193 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 174 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 559 MET Chi-restraints excluded: chain A residue 830 SER 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 1330 GLU Chi-restraints excluded: chain A residue 1350 THR Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 136 ARG Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 202 ASP 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 243 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 60 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 189 optimal weight: 4.9990 chunk 110 optimal weight: 7.9990 chunk 12 optimal weight: 4.9990 chunk 21 optimal weight: 0.3980 chunk 53 optimal weight: 4.9990 chunk 152 optimal weight: 6.9990 chunk 50 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 132 optimal weight: 0.2980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 531 GLN A1167 ASN A1573 ASN B 224 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.143323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.106712 restraints weight = 19153.330| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 1.73 r_work: 0.2965 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17461 Z= 0.131 Angle : 0.482 6.551 23804 Z= 0.253 Chirality : 0.040 0.306 2533 Planarity : 0.004 0.037 2870 Dihedral : 14.049 98.640 3053 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.63 % Allowed : 11.56 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.30 (0.19), residues: 1892 helix: 1.97 (0.20), residues: 660 sheet: 0.59 (0.28), residues: 333 loop : 0.24 (0.21), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1558 TYR 0.011 0.001 TYR A1214 PHE 0.012 0.001 PHE A 416 TRP 0.017 0.001 TRP B 517 HIS 0.006 0.001 HIS B 253 Details of bonding type rmsd covalent geometry : bond 0.00307 (17446) covalent geometry : angle 0.47993 (23789) hydrogen bonds : bond 0.03487 ( 682) hydrogen bonds : angle 4.08130 ( 1959) metal coordination : bond 0.00467 ( 15) metal coordination : angle 1.73332 ( 15) *********************** 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 227 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 183 time to evaluate : 0.584 Fit side-chains revert: symmetry clash REVERT: A 28 LYS cc_start: 0.8790 (OUTLIER) cc_final: 0.8588 (pttt) REVERT: A 264 LYS cc_start: 0.7977 (OUTLIER) cc_final: 0.7604 (mttp) REVERT: A 354 LYS cc_start: 0.8586 (mttt) cc_final: 0.8324 (mttp) REVERT: A 402 LYS cc_start: 0.9027 (OUTLIER) cc_final: 0.8807 (mttp) REVERT: A 451 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8579 (tt) REVERT: A 466 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7348 (mm-30) REVERT: A 619 ASN cc_start: 0.8171 (m-40) cc_final: 0.7523 (t0) REVERT: A 669 LYS cc_start: 0.8396 (tttt) cc_final: 0.7272 (mmpt) REVERT: A 826 ASP cc_start: 0.7860 (t70) cc_final: 0.7416 (t0) REVERT: A 857 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7775 (mt-10) REVERT: A 859 GLU cc_start: 0.7920 (pm20) cc_final: 0.7648 (pm20) REVERT: A 896 ARG cc_start: 0.8522 (OUTLIER) cc_final: 0.7874 (mmt180) REVERT: A 930 TYR cc_start: 0.7641 (p90) cc_final: 0.7419 (p90) REVERT: A 942 GLN cc_start: 0.8004 (OUTLIER) cc_final: 0.6918 (tm-30) REVERT: A 1202 GLU cc_start: 0.8213 (tt0) cc_final: 0.7956 (mt-10) REVERT: A 1203 ASP cc_start: 0.8011 (t0) cc_final: 0.7649 (t0) REVERT: A 1228 TYR cc_start: 0.7824 (m-10) cc_final: 0.7491 (m-10) REVERT: A 1229 GLU cc_start: 0.7205 (tp30) cc_final: 0.6811 (tp30) REVERT: A 1239 LYS cc_start: 0.9107 (tttt) cc_final: 0.8279 (mptt) REVERT: A 1457 GLU cc_start: 0.8570 (mt-10) cc_final: 0.8153 (mt-10) REVERT: B 11 ARG cc_start: 0.7797 (mmt180) cc_final: 0.7545 (mmt-90) REVERT: B 24 MET cc_start: 0.7906 (OUTLIER) cc_final: 0.7187 (mtp) REVERT: B 83 GLU cc_start: 0.7610 (tm-30) cc_final: 0.7400 (tt0) REVERT: B 101 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7928 (mp0) REVERT: B 136 ARG cc_start: 0.6976 (OUTLIER) cc_final: 0.6157 (mtt90) REVERT: B 202 ASP cc_start: 0.6879 (OUTLIER) cc_final: 0.6658 (m-30) REVERT: B 209 TYR cc_start: 0.7280 (OUTLIER) cc_final: 0.6674 (m-80) REVERT: B 513 ARG cc_start: 0.5998 (mtp180) cc_final: 0.5018 (tpt170) outliers start: 44 outliers final: 13 residues processed: 213 average time/residue: 0.6345 time to fit residues: 148.5025 Evaluate side-chains 200 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 175 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 264 LYS Chi-restraints excluded: chain A residue 402 LYS 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 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 1217 THR 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 1591 LYS Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 136 ARG Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 209 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 191 optimal weight: 8.9990 chunk 54 optimal weight: 6.9990 chunk 63 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 172 optimal weight: 6.9990 chunk 28 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 119 optimal weight: 0.9990 chunk 74 optimal weight: 4.9990 chunk 39 optimal weight: 0.0270 chunk 47 optimal weight: 0.7980 overall best weight: 0.9242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 235 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.143743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.107014 restraints weight = 19120.221| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 1.76 r_work: 0.2875 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2766 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 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 : 0.003 0.031 17461 Z= 0.117 Angle : 0.467 6.382 23804 Z= 0.244 Chirality : 0.039 0.302 2533 Planarity : 0.004 0.057 2870 Dihedral : 14.028 98.351 3053 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.57 % Allowed : 11.98 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.33 (0.19), residues: 1892 helix: 2.03 (0.20), residues: 661 sheet: 0.53 (0.28), residues: 322 loop : 0.24 (0.21), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 328 TYR 0.010 0.001 TYR A1214 PHE 0.011 0.001 PHE A 416 TRP 0.014 0.001 TRP B 517 HIS 0.005 0.001 HIS B 253 Details of bonding type rmsd covalent geometry : bond 0.00271 (17446) covalent geometry : angle 0.46523 (23789) hydrogen bonds : bond 0.03279 ( 682) hydrogen bonds : angle 3.98595 ( 1959) metal coordination : bond 0.00433 ( 15) metal coordination : angle 1.68281 ( 15) *********************** 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 227 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 184 time to evaluate : 0.396 Fit side-chains revert: symmetry clash REVERT: A 264 LYS cc_start: 0.7890 (OUTLIER) cc_final: 0.7523 (mttp) REVERT: A 354 LYS cc_start: 0.8486 (mttt) cc_final: 0.8200 (mttp) REVERT: A 451 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8595 (tt) REVERT: A 466 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7395 (mm-30) REVERT: A 619 ASN cc_start: 0.8207 (m-40) cc_final: 0.7456 (t0) REVERT: A 669 LYS cc_start: 0.8326 (tttt) cc_final: 0.7148 (mmpt) REVERT: A 826 ASP cc_start: 0.7810 (t70) cc_final: 0.7329 (t0) REVERT: A 857 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7797 (mt-10) REVERT: A 896 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.7765 (mmt180) REVERT: A 930 TYR cc_start: 0.7542 (p90) cc_final: 0.7322 (p90) REVERT: A 942 GLN cc_start: 0.7987 (OUTLIER) cc_final: 0.6818 (tm-30) REVERT: A 1202 GLU cc_start: 0.8220 (tt0) cc_final: 0.7912 (mt-10) REVERT: A 1203 ASP cc_start: 0.7930 (t0) cc_final: 0.7552 (t0) REVERT: A 1229 GLU cc_start: 0.7159 (tp30) cc_final: 0.6720 (tp30) REVERT: A 1239 LYS cc_start: 0.9049 (tttt) cc_final: 0.8139 (mptt) REVERT: A 1457 GLU cc_start: 0.8617 (mt-10) cc_final: 0.8161 (mt-10) REVERT: A 1580 LYS cc_start: 0.7779 (ttpp) cc_final: 0.6582 (mttp) REVERT: B 11 ARG cc_start: 0.7722 (mmt180) cc_final: 0.7417 (mmt-90) REVERT: B 19 ASN cc_start: 0.6981 (t0) cc_final: 0.6687 (t0) REVERT: B 24 MET cc_start: 0.7833 (OUTLIER) cc_final: 0.7083 (mtp) REVERT: B 83 GLU cc_start: 0.7585 (tm-30) cc_final: 0.7376 (tt0) REVERT: B 101 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7847 (mp0) REVERT: B 136 ARG cc_start: 0.7039 (OUTLIER) cc_final: 0.6124 (mtt90) REVERT: B 202 ASP cc_start: 0.6821 (OUTLIER) cc_final: 0.6600 (m-30) REVERT: B 209 TYR cc_start: 0.7153 (OUTLIER) cc_final: 0.6769 (m-80) REVERT: B 294 LYS cc_start: 0.7881 (OUTLIER) cc_final: 0.7335 (mtmm) REVERT: B 513 ARG cc_start: 0.5777 (mtp180) cc_final: 0.4917 (tpt170) outliers start: 43 outliers final: 13 residues processed: 212 average time/residue: 0.6340 time to fit residues: 147.6205 Evaluate side-chains 195 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 171 time to evaluate : 0.542 ------------------------------------------------------------------------------- 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 264 LYS 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 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 1217 THR 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 1591 LYS Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 136 ARG Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 209 TYR Chi-restraints excluded: chain B residue 294 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 60 optimal weight: 0.0980 chunk 20 optimal weight: 1.9990 chunk 126 optimal weight: 3.9990 chunk 144 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 182 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 chunk 174 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 104 optimal weight: 8.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 640 ASN A1027 GLN B 235 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.141459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.105385 restraints weight = 19012.208| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 1.78 r_work: 0.2907 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 17461 Z= 0.167 Angle : 0.514 7.436 23804 Z= 0.266 Chirality : 0.041 0.324 2533 Planarity : 0.004 0.044 2870 Dihedral : 14.053 98.962 3053 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.75 % Allowed : 12.22 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.17 (0.19), residues: 1892 helix: 1.91 (0.20), residues: 661 sheet: 0.44 (0.28), residues: 321 loop : 0.15 (0.21), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1558 TYR 0.013 0.001 TYR A1214 PHE 0.013 0.001 PHE A 517 TRP 0.013 0.001 TRP A1038 HIS 0.005 0.001 HIS B 253 Details of bonding type rmsd covalent geometry : bond 0.00398 (17446) covalent geometry : angle 0.51111 (23789) hydrogen bonds : bond 0.03601 ( 682) hydrogen bonds : angle 4.08921 ( 1959) metal coordination : bond 0.00586 ( 15) metal coordination : angle 2.04591 ( 15) *********************** 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 225 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 179 time to evaluate : 0.467 Fit side-chains revert: symmetry clash REVERT: A 264 LYS cc_start: 0.7969 (OUTLIER) cc_final: 0.7625 (mttp) REVERT: A 354 LYS cc_start: 0.8592 (mttt) cc_final: 0.8323 (mttm) REVERT: A 451 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8593 (tt) REVERT: A 466 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7459 (mm-30) REVERT: A 559 MET cc_start: 0.9087 (OUTLIER) cc_final: 0.8847 (mtm) REVERT: A 619 ASN cc_start: 0.8170 (m-40) cc_final: 0.7489 (t0) REVERT: A 669 LYS cc_start: 0.8365 (tttt) cc_final: 0.7252 (mmpt) REVERT: A 826 ASP cc_start: 0.8021 (t70) cc_final: 0.7536 (t0) REVERT: A 857 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7803 (mt-10) REVERT: A 859 GLU cc_start: 0.7974 (pm20) cc_final: 0.7676 (pm20) REVERT: A 896 ARG cc_start: 0.8480 (OUTLIER) cc_final: 0.7887 (mmt180) REVERT: A 930 TYR cc_start: 0.7627 (p90) cc_final: 0.7403 (p90) REVERT: A 942 GLN cc_start: 0.8089 (OUTLIER) cc_final: 0.6997 (tm-30) REVERT: A 1202 GLU cc_start: 0.8210 (tt0) cc_final: 0.7694 (tp30) REVERT: A 1203 ASP cc_start: 0.8091 (t0) cc_final: 0.7722 (t0) REVERT: A 1229 GLU cc_start: 0.7266 (tp30) cc_final: 0.6866 (tp30) REVERT: A 1239 LYS cc_start: 0.9094 (tttt) cc_final: 0.8274 (mptt) REVERT: A 1457 GLU cc_start: 0.8611 (mt-10) cc_final: 0.8294 (mt-10) REVERT: B 11 ARG cc_start: 0.7828 (mmt180) cc_final: 0.7566 (mmt-90) REVERT: B 24 MET cc_start: 0.7957 (OUTLIER) cc_final: 0.7227 (mtp) REVERT: B 83 GLU cc_start: 0.7632 (tm-30) cc_final: 0.7398 (tt0) REVERT: B 101 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7910 (mp0) REVERT: B 136 ARG cc_start: 0.7030 (OUTLIER) cc_final: 0.5987 (mtt90) REVERT: B 209 TYR cc_start: 0.7278 (OUTLIER) cc_final: 0.6751 (m-80) REVERT: B 513 ARG cc_start: 0.5733 (mtp180) cc_final: 0.5030 (mmt180) outliers start: 46 outliers final: 15 residues processed: 211 average time/residue: 0.6371 time to fit residues: 148.3406 Evaluate side-chains 195 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 170 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 MET Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 264 LYS 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 559 MET 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 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 1330 GLU Chi-restraints excluded: chain A residue 1350 THR Chi-restraints excluded: chain A residue 1502 SER Chi-restraints excluded: chain A residue 1508 ASP 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 209 TYR Chi-restraints excluded: chain B residue 262 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 15 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 chunk 186 optimal weight: 7.9990 chunk 44 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 90 optimal weight: 0.7980 chunk 111 optimal weight: 4.9990 chunk 174 optimal weight: 0.7980 chunk 106 optimal weight: 3.9990 chunk 5 optimal weight: 8.9990 chunk 180 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.143904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.107374 restraints weight = 19050.940| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 1.67 r_work: 0.2894 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 17461 Z= 0.106 Angle : 0.468 7.672 23804 Z= 0.244 Chirality : 0.039 0.300 2533 Planarity : 0.004 0.062 2870 Dihedral : 14.020 99.049 3053 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.74 % Allowed : 13.83 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.30 (0.19), residues: 1892 helix: 2.03 (0.20), residues: 662 sheet: 0.50 (0.28), residues: 316 loop : 0.22 (0.21), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 183 TYR 0.013 0.001 TYR A1214 PHE 0.011 0.001 PHE A 416 TRP 0.018 0.001 TRP A1038 HIS 0.004 0.001 HIS B 253 Details of bonding type rmsd covalent geometry : bond 0.00244 (17446) covalent geometry : angle 0.46599 (23789) hydrogen bonds : bond 0.03099 ( 682) hydrogen bonds : angle 3.93676 ( 1959) metal coordination : bond 0.00401 ( 15) metal coordination : angle 1.61079 ( 15) *********************** 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 211 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 182 time to evaluate : 2.093 Fit side-chains revert: symmetry clash REVERT: A 354 LYS cc_start: 0.8494 (mttt) cc_final: 0.8206 (mttm) REVERT: A 451 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8560 (tt) REVERT: A 466 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7398 (mm-30) REVERT: A 559 MET cc_start: 0.9014 (OUTLIER) cc_final: 0.8751 (mtm) REVERT: A 619 ASN cc_start: 0.8178 (m-40) cc_final: 0.7473 (t0) REVERT: A 669 LYS cc_start: 0.8297 (tttt) cc_final: 0.7157 (mmpt) REVERT: A 826 ASP cc_start: 0.7956 (t70) cc_final: 0.7451 (t0) REVERT: A 857 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7772 (mt-10) REVERT: A 859 GLU cc_start: 0.7947 (pm20) cc_final: 0.7702 (pm20) REVERT: A 896 ARG cc_start: 0.8424 (OUTLIER) cc_final: 0.7786 (mmt180) REVERT: A 930 TYR cc_start: 0.7574 (p90) cc_final: 0.7371 (p90) REVERT: A 942 GLN cc_start: 0.7969 (OUTLIER) cc_final: 0.6794 (tm-30) REVERT: A 1202 GLU cc_start: 0.8210 (tt0) cc_final: 0.7876 (mt-10) REVERT: A 1203 ASP cc_start: 0.7975 (t0) cc_final: 0.7622 (t0) REVERT: A 1229 GLU cc_start: 0.7193 (tp30) cc_final: 0.6763 (tp30) REVERT: A 1239 LYS cc_start: 0.9025 (tttt) cc_final: 0.8133 (mptt) REVERT: A 1387 MET cc_start: 0.9110 (ttm) cc_final: 0.8817 (ttm) REVERT: A 1457 GLU cc_start: 0.8585 (mt-10) cc_final: 0.8203 (mt-10) REVERT: A 1580 LYS cc_start: 0.7775 (ttpp) cc_final: 0.6641 (mttp) REVERT: B 11 ARG cc_start: 0.7746 (mmt180) cc_final: 0.7457 (mmt-90) REVERT: B 24 MET cc_start: 0.7854 (OUTLIER) cc_final: 0.7106 (mtp) REVERT: B 101 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7835 (mp0) REVERT: B 136 ARG cc_start: 0.7026 (OUTLIER) cc_final: 0.5799 (mtt90) REVERT: B 209 TYR cc_start: 0.7191 (OUTLIER) cc_final: 0.6689 (m-80) REVERT: B 513 ARG cc_start: 0.5550 (mtp180) cc_final: 0.5005 (mmt180) outliers start: 29 outliers final: 11 residues processed: 199 average time/residue: 0.6596 time to fit residues: 143.9050 Evaluate side-chains 190 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 170 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 559 MET 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 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 1350 THR Chi-restraints excluded: chain A residue 1390 LEU Chi-restraints excluded: chain A residue 1502 SER 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 209 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 106 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 126 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 114 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.142937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.108881 restraints weight = 19226.543| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 1.79 r_work: 0.2939 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17461 Z= 0.132 Angle : 0.493 9.133 23804 Z= 0.255 Chirality : 0.040 0.312 2533 Planarity : 0.004 0.053 2870 Dihedral : 14.018 98.641 3053 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.86 % Allowed : 14.25 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.23 (0.19), residues: 1892 helix: 2.01 (0.20), residues: 663 sheet: 0.41 (0.28), residues: 321 loop : 0.16 (0.21), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 199 TYR 0.011 0.001 TYR A1214 PHE 0.012 0.001 PHE A 416 TRP 0.020 0.001 TRP A1038 HIS 0.004 0.001 HIS B 253 Details of bonding type rmsd covalent geometry : bond 0.00311 (17446) covalent geometry : angle 0.49136 (23789) hydrogen bonds : bond 0.03274 ( 682) hydrogen bonds : angle 3.98506 ( 1959) metal coordination : bond 0.00450 ( 15) metal coordination : angle 1.80529 ( 15) *********************** 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 208 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 177 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 354 LYS cc_start: 0.8620 (mttt) cc_final: 0.8359 (mttm) REVERT: A 451 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8564 (tt) REVERT: A 466 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7532 (mm-30) REVERT: A 559 MET cc_start: 0.9048 (OUTLIER) cc_final: 0.8782 (mtm) REVERT: A 619 ASN cc_start: 0.8265 (m-40) cc_final: 0.7545 (t0) REVERT: A 669 LYS cc_start: 0.8378 (tttt) cc_final: 0.7288 (mmpt) REVERT: A 826 ASP cc_start: 0.8103 (t70) cc_final: 0.7648 (t0) REVERT: A 857 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7797 (mt-10) REVERT: A 859 GLU cc_start: 0.8028 (pm20) cc_final: 0.7789 (pm20) REVERT: A 896 ARG cc_start: 0.8462 (OUTLIER) cc_final: 0.7869 (mmt180) REVERT: A 930 TYR cc_start: 0.7666 (p90) cc_final: 0.7433 (p90) REVERT: A 942 GLN cc_start: 0.8148 (OUTLIER) cc_final: 0.7059 (tm-30) REVERT: A 1202 GLU cc_start: 0.8219 (tt0) cc_final: 0.7968 (mt-10) REVERT: A 1203 ASP cc_start: 0.8074 (t0) cc_final: 0.7731 (t0) REVERT: A 1229 GLU cc_start: 0.7264 (tp30) cc_final: 0.6874 (tp30) REVERT: A 1239 LYS cc_start: 0.9151 (tttt) cc_final: 0.8374 (mptt) REVERT: A 1387 MET cc_start: 0.9141 (ttm) cc_final: 0.8836 (ttm) REVERT: A 1457 GLU cc_start: 0.8599 (mt-10) cc_final: 0.8241 (mt-10) REVERT: A 1580 LYS cc_start: 0.7951 (ttpp) cc_final: 0.6869 (mttp) REVERT: B 11 ARG cc_start: 0.7844 (mmt180) cc_final: 0.7615 (mmt-90) REVERT: B 24 MET cc_start: 0.7987 (OUTLIER) cc_final: 0.7291 (mtp) REVERT: B 101 GLU cc_start: 0.8252 (mt-10) cc_final: 0.7998 (mp0) REVERT: B 136 ARG cc_start: 0.7131 (OUTLIER) cc_final: 0.5965 (mtt90) REVERT: B 209 TYR cc_start: 0.7280 (OUTLIER) cc_final: 0.6733 (m-80) REVERT: B 448 ASP cc_start: 0.7074 (t0) cc_final: 0.6318 (t70) REVERT: B 513 ARG cc_start: 0.5620 (mtp180) cc_final: 0.5017 (mmt180) outliers start: 31 outliers final: 16 residues processed: 200 average time/residue: 0.6918 time to fit residues: 151.2403 Evaluate side-chains 191 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 166 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 205 THR 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 559 MET 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 896 ARG 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 1591 LYS Chi-restraints excluded: chain B residue 24 MET 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 49 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 139 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 112 optimal weight: 7.9990 chunk 74 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 99 optimal weight: 0.0980 chunk 179 optimal weight: 7.9990 chunk 158 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 ASN B 235 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.142645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.106361 restraints weight = 19021.915| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 1.81 r_work: 0.2864 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17461 Z= 0.132 Angle : 0.494 7.947 23804 Z= 0.256 Chirality : 0.040 0.312 2533 Planarity : 0.004 0.067 2870 Dihedral : 14.019 98.921 3053 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.80 % Allowed : 14.55 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.23 (0.19), residues: 1892 helix: 2.00 (0.20), residues: 663 sheet: 0.41 (0.28), residues: 321 loop : 0.16 (0.21), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 199 TYR 0.012 0.001 TYR A1214 PHE 0.012 0.001 PHE A 416 TRP 0.022 0.001 TRP A1038 HIS 0.003 0.001 HIS A 741 Details of bonding type rmsd covalent geometry : bond 0.00312 (17446) covalent geometry : angle 0.49188 (23789) hydrogen bonds : bond 0.03267 ( 682) hydrogen bonds : angle 4.01297 ( 1959) metal coordination : bond 0.00452 ( 15) metal coordination : angle 1.83589 ( 15) *********************** 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 202 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 172 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 354 LYS cc_start: 0.8478 (mttt) cc_final: 0.8180 (mttm) REVERT: A 451 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8599 (tt) REVERT: A 466 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7436 (mm-30) REVERT: A 559 MET cc_start: 0.9081 (OUTLIER) cc_final: 0.8820 (mtm) REVERT: A 619 ASN cc_start: 0.8252 (m-40) cc_final: 0.7474 (t0) REVERT: A 669 LYS cc_start: 0.8314 (tttt) cc_final: 0.7161 (mmpt) REVERT: A 826 ASP cc_start: 0.8026 (t70) cc_final: 0.7577 (t0) REVERT: A 857 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7824 (mt-10) REVERT: A 859 GLU cc_start: 0.7987 (pm20) cc_final: 0.7737 (pm20) REVERT: A 896 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.7779 (mmt180) REVERT: A 930 TYR cc_start: 0.7573 (p90) cc_final: 0.7361 (p90) REVERT: A 942 GLN cc_start: 0.8053 (OUTLIER) cc_final: 0.6889 (tm-30) REVERT: A 1202 GLU cc_start: 0.8225 (tt0) cc_final: 0.7889 (mt-10) REVERT: A 1203 ASP cc_start: 0.7998 (t0) cc_final: 0.7635 (t0) REVERT: A 1229 GLU cc_start: 0.7275 (tp30) cc_final: 0.6861 (tp30) REVERT: A 1239 LYS cc_start: 0.9069 (tttt) cc_final: 0.8165 (mptt) REVERT: A 1387 MET cc_start: 0.9135 (ttm) cc_final: 0.8851 (ttm) REVERT: A 1457 GLU cc_start: 0.8655 (mt-10) cc_final: 0.8270 (mt-10) REVERT: A 1580 LYS cc_start: 0.7790 (ttpp) cc_final: 0.6652 (mttp) REVERT: B 11 ARG cc_start: 0.7757 (mmt180) cc_final: 0.7475 (mmt-90) REVERT: B 24 MET cc_start: 0.7876 (OUTLIER) cc_final: 0.7122 (mtp) REVERT: B 101 GLU cc_start: 0.8199 (mt-10) cc_final: 0.7872 (mp0) REVERT: B 136 ARG cc_start: 0.7020 (OUTLIER) cc_final: 0.5907 (mtt90) REVERT: B 209 TYR cc_start: 0.7206 (OUTLIER) cc_final: 0.6683 (m-80) REVERT: B 448 ASP cc_start: 0.6997 (t0) cc_final: 0.6207 (t70) REVERT: B 513 ARG cc_start: 0.5710 (mtp180) cc_final: 0.5039 (mmt180) outliers start: 30 outliers final: 17 residues processed: 194 average time/residue: 0.6833 time to fit residues: 146.0800 Evaluate side-chains 194 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 168 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 205 THR 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 559 MET 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 896 ARG 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 1508 ASP Chi-restraints excluded: chain A residue 1591 LYS Chi-restraints excluded: chain B residue 24 MET 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 78 optimal weight: 0.7980 chunk 160 optimal weight: 0.5980 chunk 173 optimal weight: 6.9990 chunk 128 optimal weight: 7.9990 chunk 167 optimal weight: 3.9990 chunk 166 optimal weight: 0.0070 chunk 92 optimal weight: 4.9990 chunk 175 optimal weight: 0.4980 chunk 27 optimal weight: 8.9990 chunk 115 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 overall best weight: 0.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.144216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.107732 restraints weight = 19044.414| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 1.83 r_work: 0.2871 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17461 Z= 0.109 Angle : 0.475 7.440 23804 Z= 0.248 Chirality : 0.039 0.300 2533 Planarity : 0.004 0.062 2870 Dihedral : 14.003 98.551 3053 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.68 % Allowed : 14.49 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.33 (0.19), residues: 1892 helix: 2.07 (0.20), residues: 663 sheet: 0.47 (0.28), residues: 331 loop : 0.23 (0.21), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 199 TYR 0.012 0.001 TYR A1214 PHE 0.011 0.001 PHE A 416 TRP 0.023 0.001 TRP A1038 HIS 0.003 0.001 HIS B 253 Details of bonding type rmsd covalent geometry : bond 0.00252 (17446) covalent geometry : angle 0.47358 (23789) hydrogen bonds : bond 0.03052 ( 682) hydrogen bonds : angle 3.91792 ( 1959) metal coordination : bond 0.00399 ( 15) metal coordination : angle 1.71582 ( 15) ********************** 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 206 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 178 time to evaluate : 0.668 Fit side-chains revert: symmetry clash REVERT: A 354 LYS cc_start: 0.8416 (mttt) cc_final: 0.8111 (mttm) REVERT: A 451 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8587 (tt) REVERT: A 466 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7447 (mm-30) REVERT: A 559 MET cc_start: 0.9095 (OUTLIER) cc_final: 0.8821 (mtm) REVERT: A 619 ASN cc_start: 0.8330 (m-40) cc_final: 0.7509 (t0) REVERT: A 669 LYS cc_start: 0.8258 (tttt) cc_final: 0.7091 (mmpt) REVERT: A 826 ASP cc_start: 0.8046 (t70) cc_final: 0.7594 (t0) REVERT: A 857 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7792 (mt-10) REVERT: A 859 GLU cc_start: 0.8018 (pm20) cc_final: 0.7744 (pm20) REVERT: A 896 ARG cc_start: 0.8424 (OUTLIER) cc_final: 0.7726 (mmt180) REVERT: A 942 GLN cc_start: 0.8008 (OUTLIER) cc_final: 0.6805 (tm-30) REVERT: A 1202 GLU cc_start: 0.8211 (tt0) cc_final: 0.7854 (mt-10) REVERT: A 1203 ASP cc_start: 0.7928 (t0) cc_final: 0.7582 (t0) REVERT: A 1229 GLU cc_start: 0.7083 (tp30) cc_final: 0.6752 (tp30) REVERT: A 1239 LYS cc_start: 0.9045 (tttt) cc_final: 0.8134 (mptt) REVERT: A 1387 MET cc_start: 0.9111 (ttm) cc_final: 0.8810 (ttm) REVERT: A 1457 GLU cc_start: 0.8641 (mt-10) cc_final: 0.8026 (mt-10) REVERT: A 1580 LYS cc_start: 0.7706 (ttpp) cc_final: 0.6591 (mttp) REVERT: B 11 ARG cc_start: 0.7676 (mmt180) cc_final: 0.7362 (mmt-90) REVERT: B 19 ASN cc_start: 0.7074 (t0) cc_final: 0.6697 (t0) REVERT: B 24 MET cc_start: 0.7837 (OUTLIER) cc_final: 0.7076 (mtp) REVERT: B 101 GLU cc_start: 0.8135 (mt-10) cc_final: 0.7801 (mp0) REVERT: B 136 ARG cc_start: 0.6958 (OUTLIER) cc_final: 0.5552 (mtt90) REVERT: B 209 TYR cc_start: 0.7115 (OUTLIER) cc_final: 0.6753 (m-80) REVERT: B 329 GLN cc_start: 0.8013 (tt0) cc_final: 0.7744 (tt0) REVERT: B 448 ASP cc_start: 0.6957 (t0) cc_final: 0.6228 (t70) REVERT: B 511 GLU cc_start: 0.7472 (pm20) cc_final: 0.7203 (pm20) REVERT: B 513 ARG cc_start: 0.5531 (mtp180) cc_final: 0.4916 (mmt180) outliers start: 28 outliers final: 16 residues processed: 197 average time/residue: 0.6867 time to fit residues: 148.3406 Evaluate side-chains 194 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 169 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 205 THR 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 559 MET 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 896 ARG 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 1591 LYS Chi-restraints excluded: chain B residue 24 MET 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 15 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 58 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 128 optimal weight: 0.0970 chunk 138 optimal weight: 0.9990 chunk 191 optimal weight: 8.9990 chunk 132 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1003 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1127 GLN B 224 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.144049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.107822 restraints weight = 18994.690| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 1.79 r_work: 0.2885 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17461 Z= 0.110 Angle : 0.483 11.051 23804 Z= 0.250 Chirality : 0.039 0.299 2533 Planarity : 0.004 0.070 2870 Dihedral : 14.001 98.181 3053 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.68 % Allowed : 14.61 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.36 (0.20), residues: 1892 helix: 2.07 (0.20), residues: 664 sheet: 0.53 (0.27), residues: 347 loop : 0.23 (0.21), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 199 TYR 0.011 0.001 TYR A1214 PHE 0.011 0.001 PHE A 776 TRP 0.028 0.001 TRP A1038 HIS 0.003 0.001 HIS B 253 Details of bonding type rmsd covalent geometry : bond 0.00255 (17446) covalent geometry : angle 0.48172 (23789) hydrogen bonds : bond 0.03046 ( 682) hydrogen bonds : angle 3.91114 ( 1959) metal coordination : bond 0.00395 ( 15) metal coordination : angle 1.71664 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5340.01 seconds wall clock time: 91 minutes 34.39 seconds (5494.39 seconds total)