Starting phenix.real_space_refine on Sun Aug 24 00:04:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gu6_34270/08_2025/8gu6_34270.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gu6_34270/08_2025/8gu6_34270.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8gu6_34270/08_2025/8gu6_34270.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gu6_34270/08_2025/8gu6_34270.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8gu6_34270/08_2025/8gu6_34270.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gu6_34270/08_2025/8gu6_34270.map" } resolution = 3.1 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= 0.036 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 50 5.49 5 S 51 5.16 5 C 9590 2.51 5 N 2670 2.21 5 O 2896 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 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: 15261 Number of models: 1 Model: "" Number of chains: 5 Chain: "D" Number of atoms: 4880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 659, 4880 Classifications: {'peptide': 659} Incomplete info: {'truncation_to_alanine': 125} Link IDs: {'PTRANS': 19, 'TRANS': 639} Chain breaks: 4 Unresolved non-hydrogen bonds: 479 Unresolved non-hydrogen angles: 598 Unresolved non-hydrogen dihedrals: 391 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'ARG:plan': 8, 'GLU:plan': 19, 'ASP:plan': 22, 'ASN:plan1': 15, 'PHE:plan': 5, 'GLN:plan1': 4, 'TYR:plan': 2, 'HIS:plan': 4, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 316 Chain: "A" Number of atoms: 9314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1211, 9314 Classifications: {'peptide': 1211} Incomplete info: {'truncation_to_alanine': 133} Link IDs: {'PTRANS': 59, 'TRANS': 1151} Chain breaks: 13 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 485 Unresolved non-hydrogen angles: 598 Unresolved non-hydrogen dihedrals: 385 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLU:plan': 34, 'ASP:plan': 26, 'GLN:plan1': 5, 'ASN:plan1': 14, 'ARG:plan': 6, 'HIS:plan': 1, 'PHE:plan': 2, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 337 Chain: "C" Number of atoms: 689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 689 Classifications: {'RNA': 33} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 9, 'rna3p_pur': 2, 'rna3p_pyr': 12} Link IDs: {'rna2p': 18, 'rna3p': 14} Chain: "J" Number of atoms: 374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 374 Classifications: {'RNA': 17} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 12, 'rna3p_pyr': 3} Link IDs: {'rna2p': 1, 'rna3p': 15} 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 8188 SG CYS A 491 42.410 50.382 109.592 1.00 56.88 S ATOM 8256 SG CYS A 501 42.340 50.002 113.239 1.00 43.26 S ATOM 8270 SG CYS A 503 39.054 50.135 111.347 1.00 51.40 S ATOM 8292 SG CYS A 506 41.174 47.041 110.957 1.00 42.41 S ATOM 5526 SG CYS A 88 41.869 29.986 135.607 1.00 52.94 S ATOM 5769 SG CYS A 121 42.592 27.562 138.440 1.00 80.14 S ATOM 5800 SG CYS A 127 41.344 26.344 135.032 1.00 50.36 S ATOM 5824 SG CYS A 130 44.895 27.615 135.412 1.00 49.35 S ATOM 10157 SG CYS A 750 48.196 66.675 85.818 1.00 94.35 S ATOM 10170 SG CYS A 752 45.399 65.843 83.413 1.00 72.34 S ATOM 10192 SG CYS A 755 47.298 62.993 84.983 1.00 66.08 S ATOM 12065 SG CYS A1018 57.375 61.363 49.287 1.00 82.93 S ATOM 12218 SG CYS A1406 57.984 62.296 52.978 1.00 87.64 S ATOM 12269 SG CYS A1414 57.266 64.947 50.377 1.00 79.23 S ATOM 12286 SG CYS A1417 54.544 62.425 51.493 1.00 64.66 S Time building chain proxies: 3.01, per 1000 atoms: 0.20 Number of scatterers: 15261 At special positions: 0 Unit cell: (101.65, 95, 158.65, 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 51 16.00 P 50 15.00 O 2896 8.00 N 2670 7.00 C 9590 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: 1.34 Conformation dependent library (CDL) restraints added in 709.6 milliseconds Enol-peptide restraints added in 953.7 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1801 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 491 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 503 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 501 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 506 " pdb=" ZN A1802 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 127 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 88 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 121 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 130 " pdb=" ZN A1803 " pdb="ZN ZN A1803 " - pdb=" ND1 HIS A 747 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 752 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 755 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 750 " pdb=" ZN A1804 " pdb="ZN ZN A1804 " - pdb=" SG CYS A1018 " pdb="ZN ZN A1804 " - pdb=" SG CYS A1417 " pdb="ZN ZN A1804 " - pdb=" SG CYS A1406 " pdb="ZN ZN A1804 " - pdb=" SG CYS A1414 " Number of angles added : 21 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3464 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 22 sheets defined 41.7% alpha, 11.9% beta 11 base pairs and 14 stacking pairs defined. Time for finding SS restraints: 1.75 Creating SS restraints... Processing helix chain 'D' and resid 15 through 33 Processing helix chain 'D' and resid 37 through 59 removed outlier: 3.938A pdb=" N LYS D 43 " --> pdb=" O VAL D 39 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLU D 58 " --> pdb=" O GLY D 54 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS D 59 " --> pdb=" O LEU D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 82 removed outlier: 3.643A pdb=" N ILE D 82 " --> pdb=" O VAL D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 110 removed outlier: 3.550A pdb=" N LYS D 94 " --> pdb=" O PRO D 90 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ARG D 106 " --> pdb=" O GLU D 102 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ALA D 107 " --> pdb=" O PHE D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 136 Processing helix chain 'D' and resid 141 through 156 Processing helix chain 'D' and resid 163 through 176 removed outlier: 3.611A pdb=" N ILE D 167 " --> pdb=" O TYR D 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 182 No H-bonds generated for 'chain 'D' and resid 180 through 182' Processing helix chain 'D' and resid 183 through 190 removed outlier: 3.942A pdb=" N LYS D 189 " --> pdb=" O ASP D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 205 Processing helix chain 'D' and resid 208 through 224 removed outlier: 3.703A pdb=" N LYS D 218 " --> pdb=" O GLU D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 246 removed outlier: 4.095A pdb=" N ASP D 234 " --> pdb=" O HIS D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 269 removed outlier: 3.602A pdb=" N PHE D 254 " --> pdb=" O LEU D 250 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N GLU D 268 " --> pdb=" O VAL D 264 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N THR D 269 " --> pdb=" O GLN D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 297 Processing helix chain 'D' and resid 302 through 322 removed outlier: 3.559A pdb=" N LYS D 306 " --> pdb=" O ASP D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 332 Processing helix chain 'D' and resid 339 through 359 removed outlier: 3.601A pdb=" N GLU D 344 " --> pdb=" O GLU D 340 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLN D 357 " --> pdb=" O VAL D 353 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLY D 359 " --> pdb=" O ALA D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 433 through 448 Processing helix chain 'D' and resid 451 through 453 No H-bonds generated for 'chain 'D' and resid 451 through 453' Processing helix chain 'D' and resid 454 through 469 Processing helix chain 'D' and resid 470 through 473 removed outlier: 3.501A pdb=" N PHE D 473 " --> pdb=" O PRO D 470 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 470 through 473' Processing helix chain 'D' and resid 496 through 500 Processing helix chain 'D' and resid 509 through 514 removed outlier: 4.261A pdb=" N ASN D 513 " --> pdb=" O LEU D 509 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N HIS D 514 " --> pdb=" O PHE D 510 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 509 through 514' Processing helix chain 'D' and resid 521 through 525 Processing helix chain 'D' and resid 566 through 572 Processing helix chain 'D' and resid 592 through 595 Processing helix chain 'D' and resid 607 through 613 Processing helix chain 'D' and resid 628 through 632 removed outlier: 3.550A pdb=" N VAL D 632 " --> pdb=" O THR D 629 " (cutoff:3.500A) Processing helix chain 'D' and resid 644 through 653 removed outlier: 3.684A pdb=" N ALA D 648 " --> pdb=" O SER D 644 " (cutoff:3.500A) Processing helix chain 'D' and resid 665 through 675 removed outlier: 3.851A pdb=" N THR D 669 " --> pdb=" O ARG D 665 " (cutoff:3.500A) Processing helix chain 'D' and resid 685 through 691 removed outlier: 4.165A pdb=" N LYS D 689 " --> pdb=" O ASN D 685 " (cutoff:3.500A) Processing helix chain 'D' and resid 699 through 708 removed outlier: 3.999A pdb=" N ALA D 708 " --> pdb=" O TYR D 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 30 removed outlier: 4.404A pdb=" N LYS A 30 " --> pdb=" O TRP A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 38 Processing helix chain 'A' and resid 59 through 78 Processing helix chain 'A' and resid 127 through 134 Processing helix chain 'A' and resid 168 through 173 removed outlier: 3.563A pdb=" N ILE A 172 " --> pdb=" O ARG A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 215 No H-bonds generated for 'chain 'A' and resid 213 through 215' Processing helix chain 'A' and resid 216 through 227 removed outlier: 3.548A pdb=" N LEU A 220 " --> pdb=" O ALA A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 287 Processing helix chain 'A' and resid 292 through 303 Processing helix chain 'A' and resid 308 through 313 Processing helix chain 'A' and resid 338 through 350 Processing helix chain 'A' and resid 354 through 375 Processing helix chain 'A' and resid 471 through 488 Processing helix chain 'A' and resid 503 through 510 removed outlier: 3.582A pdb=" N GLU A 508 " --> pdb=" O LYS A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 580 Processing helix chain 'A' and resid 594 through 598 Processing helix chain 'A' and resid 617 through 624 removed outlier: 3.631A pdb=" N TYR A 621 " --> pdb=" O LYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 628 Processing helix chain 'A' and resid 630 through 637 removed outlier: 3.579A pdb=" N LEU A 634 " --> pdb=" O LYS A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 657 Processing helix chain 'A' and resid 658 through 665 Processing helix chain 'A' and resid 687 through 693 removed outlier: 3.546A pdb=" N LEU A 691 " --> pdb=" O THR A 687 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N THR A 692 " --> pdb=" O ILE A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 740 Processing helix chain 'A' and resid 752 through 759 Processing helix chain 'A' and resid 831 through 848 Processing helix chain 'A' and resid 873 through 881 removed outlier: 3.670A pdb=" N MET A 879 " --> pdb=" O ASP A 875 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE A 880 " --> pdb=" O PHE A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 914 removed outlier: 3.889A pdb=" N ASP A 914 " --> pdb=" O SER A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 999 through 1015 removed outlier: 3.745A pdb=" N LEU A1003 " --> pdb=" O PRO A 999 " (cutoff:3.500A) Processing helix chain 'A' and resid 1395 through 1399 removed outlier: 3.574A pdb=" N LYS A1398 " --> pdb=" O LEU A1395 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU A1399 " --> pdb=" O GLY A1396 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1395 through 1399' Processing helix chain 'A' and resid 1408 through 1412 removed outlier: 3.625A pdb=" N ASP A1411 " --> pdb=" O GLY A1408 " (cutoff:3.500A) Processing helix chain 'A' and resid 1414 through 1421 Processing helix chain 'A' and resid 1463 through 1468 removed outlier: 4.064A pdb=" N SER A1467 " --> pdb=" O ARG A1463 " (cutoff:3.500A) Processing helix chain 'A' and resid 1486 through 1493 removed outlier: 3.791A pdb=" N ILE A1490 " --> pdb=" O GLY A1486 " (cutoff:3.500A) Processing helix chain 'A' and resid 1493 through 1499 Processing helix chain 'A' and resid 1528 through 1540 removed outlier: 3.779A pdb=" N GLY A1533 " --> pdb=" O GLU A1529 " (cutoff:3.500A) Processing helix chain 'A' and resid 1552 through 1556 Processing helix chain 'A' and resid 1583 through 1588 Processing helix chain 'A' and resid 1590 through 1601 removed outlier: 3.541A pdb=" N GLU A1600 " --> pdb=" O GLN A1596 " (cutoff:3.500A) Processing helix chain 'A' and resid 1615 through 1618 Processing helix chain 'A' and resid 1619 through 1629 Processing helix chain 'A' and resid 1675 through 1681 Processing sheet with id=AA1, first strand: chain 'D' and resid 425 through 431 removed outlier: 3.765A pdb=" N ASP D 420 " --> pdb=" O SER D 425 " (cutoff:3.500A) removed outlier: 8.609A pdb=" N CYS D 516 " --> pdb=" O PHE D 709 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N SER D 711 " --> pdb=" O CYS D 516 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 562 through 563 removed outlier: 6.583A pdb=" N VAL D 537 " --> pdb=" O THR D 581 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N LEU D 583 " --> pdb=" O VAL D 537 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LEU D 539 " --> pdb=" O LEU D 583 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 597 through 598 Processing sheet with id=AA4, first strand: chain 'A' and resid 20 through 22 removed outlier: 6.507A pdb=" N VAL A 21 " --> pdb=" O TRP A 44 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N SER A 56 " --> pdb=" O LEU A 158 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 20 through 22 removed outlier: 6.507A pdb=" N VAL A 21 " --> pdb=" O TRP A 44 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N SER A 56 " --> pdb=" O LEU A 158 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 81 through 82 Processing sheet with id=AA7, first strand: chain 'A' and resid 110 through 111 removed outlier: 6.008A pdb=" N THR A 110 " --> pdb=" O VAL A 405 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 176 through 181 removed outlier: 3.701A pdb=" N PHE A 192 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ASP A 190 " --> pdb=" O ARG A 180 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 229 through 230 Processing sheet with id=AB1, first strand: chain 'A' and resid 512 through 514 removed outlier: 3.515A pdb=" N PHE A 557 " --> pdb=" O LEU A 422 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ILE A 417 " --> pdb=" O ILE A 609 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ILE A 609 " --> pdb=" O ILE A 417 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL A 419 " --> pdb=" O ILE A 607 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ILE A 607 " --> pdb=" O VAL A 419 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 431 through 432 removed outlier: 4.258A pdb=" N ASN A 459 " --> pdb=" O VAL A 432 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 469 through 470 removed outlier: 3.587A pdb=" N SER A 517 " --> pdb=" O ILE A 470 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 526 through 530 Processing sheet with id=AB5, first strand: chain 'A' and resid 721 through 722 removed outlier: 3.872A pdb=" N GLU A 773 " --> pdb=" O LYS A 821 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 721 through 722 removed outlier: 3.872A pdb=" N GLU A 773 " --> pdb=" O LYS A 821 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N GLN A 673 " --> pdb=" O ILE A 868 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N ILE A 868 " --> pdb=" O GLN A 673 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N THR A 675 " --> pdb=" O ILE A 866 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ILE A 866 " --> pdb=" O THR A 675 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N GLU A 677 " --> pdb=" O ALA A 864 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 699 through 700 removed outlier: 7.161A pdb=" N ALA A 699 " --> pdb=" O TYR A 808 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 920 through 921 removed outlier: 3.672A pdb=" N TYR A 921 " --> pdb=" O ASP A1642 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 924 through 927 Processing sheet with id=AC1, first strand: chain 'A' and resid 1519 through 1522 removed outlier: 6.819A pdb=" N ASN A 955 " --> pdb=" O ASP A1565 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 985 through 987 removed outlier: 3.917A pdb=" N GLU A1510 " --> pdb=" O TYR A 987 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N THR A1509 " --> pdb=" O LEU A1454 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 991 through 992 Processing sheet with id=AC4, first strand: chain 'A' and resid 1647 through 1648 removed outlier: 6.753A pdb=" N VAL A1647 " --> pdb=" O TYR A1663 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 589 hydrogen bonds defined for protein. 1647 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 29 hydrogen bonds 58 hydrogen bond angles 0 basepair planarities 11 basepair parallelities 14 stacking parallelities Total time for adding SS restraints: 3.13 Time building geometry restraints manager: 1.79 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: 4328 1.33 - 1.45: 2854 1.45 - 1.57: 8353 1.57 - 1.69: 98 1.69 - 1.81: 69 Bond restraints: 15702 Sorted by residual: bond pdb=" C SER A 910 " pdb=" N PRO A 911 " ideal model delta sigma weight residual 1.336 1.350 -0.014 9.80e-03 1.04e+04 1.96e+00 bond pdb=" CB GLU D 398 " pdb=" CG GLU D 398 " ideal model delta sigma weight residual 1.520 1.545 -0.025 3.00e-02 1.11e+03 7.16e-01 bond pdb=" C PRO D 700 " pdb=" N PRO D 701 " ideal model delta sigma weight residual 1.336 1.345 -0.010 1.23e-02 6.61e+03 6.44e-01 bond pdb=" CG1 ILE D 45 " pdb=" CD1 ILE D 45 " ideal model delta sigma weight residual 1.513 1.483 0.030 3.90e-02 6.57e+02 5.92e-01 bond pdb=" CB GLU D 23 " pdb=" CG GLU D 23 " ideal model delta sigma weight residual 1.520 1.543 -0.023 3.00e-02 1.11e+03 5.85e-01 ... (remaining 15697 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.02: 21432 3.02 - 6.04: 69 6.04 - 9.06: 4 9.06 - 12.08: 0 12.08 - 15.10: 1 Bond angle restraints: 21506 Sorted by residual: angle pdb=" O4' G C 11 " pdb=" C1' G C 11 " pdb=" N9 G C 11 " ideal model delta sigma weight residual 108.20 115.61 -7.41 1.50e+00 4.44e-01 2.44e+01 angle pdb=" CA LEU A 366 " pdb=" CB LEU A 366 " pdb=" CG LEU A 366 " ideal model delta sigma weight residual 116.30 131.40 -15.10 3.50e+00 8.16e-02 1.86e+01 angle pdb=" O4' A C -2 " pdb=" C1' A C -2 " pdb=" N9 A C -2 " ideal model delta sigma weight residual 108.20 112.52 -4.32 1.50e+00 4.44e-01 8.29e+00 angle pdb=" N GLU A1441 " pdb=" CA GLU A1441 " pdb=" C GLU A1441 " ideal model delta sigma weight residual 110.97 114.10 -3.13 1.09e+00 8.42e-01 8.23e+00 angle pdb=" N LEU A 366 " pdb=" CA LEU A 366 " pdb=" CB LEU A 366 " ideal model delta sigma weight residual 110.28 114.68 -4.40 1.55e+00 4.16e-01 8.07e+00 ... (remaining 21501 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.68: 8925 35.68 - 71.36: 417 71.36 - 107.04: 21 107.04 - 142.72: 2 142.72 - 178.40: 2 Dihedral angle restraints: 9367 sinusoidal: 3991 harmonic: 5376 Sorted by residual: dihedral pdb=" O4' U C -9 " pdb=" C1' U C -9 " pdb=" N1 U C -9 " pdb=" C2 U C -9 " ideal model delta sinusoidal sigma weight residual 232.00 53.60 178.40 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U C 10 " pdb=" C1' U C 10 " pdb=" N1 U C 10 " pdb=" C2 U C 10 " ideal model delta sinusoidal sigma weight residual -128.00 44.11 -172.11 1 1.70e+01 3.46e-03 6.61e+01 dihedral pdb=" O4' U C -15 " pdb=" C1' U C -15 " pdb=" N1 U C -15 " pdb=" C2 U C -15 " ideal model delta sinusoidal sigma weight residual -160.00 -91.17 -68.83 1 1.50e+01 4.44e-03 2.73e+01 ... (remaining 9364 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 2239 0.073 - 0.146: 186 0.146 - 0.218: 6 0.218 - 0.291: 0 0.291 - 0.364: 1 Chirality restraints: 2432 Sorted by residual: chirality pdb=" C1' G C 11 " pdb=" O4' G C 11 " pdb=" C2' G C 11 " pdb=" N9 G C 11 " both_signs ideal model delta sigma weight residual False 2.44 2.07 0.36 2.00e-01 2.50e+01 3.31e+00 chirality pdb=" C1' A C -2 " pdb=" O4' A C -2 " pdb=" C2' A C -2 " pdb=" N9 A C -2 " both_signs ideal model delta sigma weight residual False 2.44 2.25 0.18 2.00e-01 2.50e+01 8.42e-01 chirality pdb=" CB ILE D 80 " pdb=" CA ILE D 80 " pdb=" CG1 ILE D 80 " pdb=" CG2 ILE D 80 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.88e-01 ... (remaining 2429 not shown) Planarity restraints: 2558 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G C 11 " -0.047 2.00e-02 2.50e+03 2.16e-02 1.40e+01 pdb=" N9 G C 11 " 0.056 2.00e-02 2.50e+03 pdb=" C8 G C 11 " 0.004 2.00e-02 2.50e+03 pdb=" N7 G C 11 " -0.001 2.00e-02 2.50e+03 pdb=" C5 G C 11 " -0.002 2.00e-02 2.50e+03 pdb=" C6 G C 11 " -0.005 2.00e-02 2.50e+03 pdb=" O6 G C 11 " -0.010 2.00e-02 2.50e+03 pdb=" N1 G C 11 " -0.005 2.00e-02 2.50e+03 pdb=" C2 G C 11 " -0.003 2.00e-02 2.50e+03 pdb=" N2 G C 11 " 0.008 2.00e-02 2.50e+03 pdb=" N3 G C 11 " 0.003 2.00e-02 2.50e+03 pdb=" C4 G C 11 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A1475 " -0.051 5.00e-02 4.00e+02 7.76e-02 9.63e+00 pdb=" N PRO A1476 " 0.134 5.00e-02 4.00e+02 pdb=" CA PRO A1476 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO A1476 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' A C 3 " -0.031 2.00e-02 2.50e+03 1.45e-02 5.78e+00 pdb=" N9 A C 3 " 0.036 2.00e-02 2.50e+03 pdb=" C8 A C 3 " 0.000 2.00e-02 2.50e+03 pdb=" N7 A C 3 " -0.002 2.00e-02 2.50e+03 pdb=" C5 A C 3 " -0.001 2.00e-02 2.50e+03 pdb=" C6 A C 3 " -0.004 2.00e-02 2.50e+03 pdb=" N6 A C 3 " -0.006 2.00e-02 2.50e+03 pdb=" N1 A C 3 " -0.003 2.00e-02 2.50e+03 pdb=" C2 A C 3 " 0.003 2.00e-02 2.50e+03 pdb=" N3 A C 3 " 0.002 2.00e-02 2.50e+03 pdb=" C4 A C 3 " 0.006 2.00e-02 2.50e+03 ... (remaining 2555 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 295 2.65 - 3.21: 14000 3.21 - 3.78: 25283 3.78 - 4.34: 34607 4.34 - 4.90: 56189 Nonbonded interactions: 130374 Sorted by model distance: nonbonded pdb=" O GLY A 186 " pdb=" O2' C C -1 " model vdw 2.091 3.040 nonbonded pdb=" O LYS D 321 " pdb=" OH TYR D 643 " model vdw 2.136 3.040 nonbonded pdb=" O ALA A 685 " pdb=" O2' U C 5 " model vdw 2.163 3.040 nonbonded pdb=" O ASN A 179 " pdb=" O2' G C -4 " model vdw 2.189 3.040 nonbonded pdb=" N THR D 629 " pdb=" O THR D 660 " model vdw 2.194 3.120 ... (remaining 130369 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: 2.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 16.460 Find NCS groups from input model: 0.060 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: 0.010 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 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 0.036 15718 Z= 0.110 Angle : 0.539 15.101 21527 Z= 0.283 Chirality : 0.040 0.364 2432 Planarity : 0.004 0.078 2558 Dihedral : 18.657 178.395 5903 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 0.14 % Allowed : 28.99 % Favored : 70.86 % 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: -0.34 (0.19), residues: 1832 helix: 1.28 (0.21), residues: 647 sheet: -0.79 (0.35), residues: 221 loop : -1.15 (0.19), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1581 TYR 0.022 0.001 TYR D 259 PHE 0.019 0.001 PHE A1011 TRP 0.022 0.001 TRP D 165 HIS 0.012 0.001 HIS A1621 Details of bonding type rmsd covalent geometry : bond 0.00235 (15702) covalent geometry : angle 0.53426 (21506) hydrogen bonds : bond 0.18317 ( 606) hydrogen bonds : angle 6.53707 ( 1705) metal coordination : bond 0.01080 ( 16) metal coordination : angle 2.43043 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 167 time to evaluate : 0.403 Fit side-chains REVERT: D 420 ASP cc_start: 0.7551 (p0) cc_final: 0.7033 (p0) REVERT: D 630 ASP cc_start: 0.7911 (p0) cc_final: 0.7527 (p0) REVERT: D 666 SER cc_start: 0.7254 (m) cc_final: 0.6776 (p) REVERT: A 308 GLU cc_start: 0.6421 (pm20) cc_final: 0.5741 (pt0) REVERT: A 762 HIS cc_start: 0.7015 (m170) cc_final: 0.6804 (m-70) REVERT: A 771 ASP cc_start: 0.8249 (m-30) cc_final: 0.7603 (m-30) REVERT: A 995 GLU cc_start: 0.7704 (pt0) cc_final: 0.7268 (pt0) outliers start: 2 outliers final: 2 residues processed: 169 average time/residue: 0.1402 time to fit residues: 34.3072 Evaluate side-chains 155 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 153 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 195 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 0.0870 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 overall best weight: 0.9962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 448 ASN A 306 HIS ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 786 HIS A1494 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.174770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.134519 restraints weight = 17101.370| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 2.00 r_work: 0.3364 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.0954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15718 Z= 0.152 Angle : 0.556 8.340 21527 Z= 0.289 Chirality : 0.042 0.417 2432 Planarity : 0.004 0.060 2558 Dihedral : 15.044 175.307 2777 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 3.83 % Allowed : 26.25 % Favored : 69.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.34 (0.19), residues: 1832 helix: 1.26 (0.20), residues: 662 sheet: -0.91 (0.35), residues: 215 loop : -1.15 (0.19), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1581 TYR 0.016 0.001 TYR D 607 PHE 0.014 0.001 PHE D 547 TRP 0.027 0.001 TRP A 330 HIS 0.010 0.001 HIS A1621 Details of bonding type rmsd covalent geometry : bond 0.00344 (15702) covalent geometry : angle 0.54869 (21506) hydrogen bonds : bond 0.03867 ( 606) hydrogen bonds : angle 4.91064 ( 1705) metal coordination : bond 0.00972 ( 16) metal coordination : angle 2.90131 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 163 time to evaluate : 0.477 Fit side-chains REVERT: D 231 ARG cc_start: 0.7484 (ttm-80) cc_final: 0.6639 (ttp-110) REVERT: D 280 ARG cc_start: 0.7713 (OUTLIER) cc_final: 0.7337 (tpp-160) REVERT: D 542 PHE cc_start: 0.7320 (OUTLIER) cc_final: 0.6319 (m-80) REVERT: A 107 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.8028 (pttt) REVERT: A 308 GLU cc_start: 0.6709 (pm20) cc_final: 0.5859 (pt0) REVERT: A 389 TYR cc_start: 0.8275 (t80) cc_final: 0.7984 (t80) REVERT: A 877 LYS cc_start: 0.7019 (tptm) cc_final: 0.6617 (mtpp) REVERT: A 927 LEU cc_start: 0.7370 (OUTLIER) cc_final: 0.7099 (tt) outliers start: 53 outliers final: 23 residues processed: 203 average time/residue: 0.1400 time to fit residues: 40.9732 Evaluate side-chains 173 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 146 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 246 ASP Chi-restraints excluded: chain D residue 280 ARG Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain D residue 468 THR Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 491 PHE Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain A residue 867 SER Chi-restraints excluded: chain A residue 927 LEU Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 970 SER Chi-restraints excluded: chain A residue 997 MET Chi-restraints excluded: chain A residue 1006 MET Chi-restraints excluded: chain A residue 1441 GLU Chi-restraints excluded: chain A residue 1456 LEU Chi-restraints excluded: chain A residue 1468 ILE Chi-restraints excluded: chain A residue 1507 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 130 optimal weight: 0.9980 chunk 131 optimal weight: 0.5980 chunk 142 optimal weight: 0.9980 chunk 174 optimal weight: 0.7980 chunk 182 optimal weight: 0.0870 chunk 45 optimal weight: 0.9980 chunk 133 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 44 optimal weight: 0.4980 chunk 154 optimal weight: 6.9990 chunk 112 optimal weight: 0.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 133 ASN ** D 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 685 ASN ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1494 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.177166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.137086 restraints weight = 17162.744| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 1.96 r_work: 0.3397 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.1168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15718 Z= 0.117 Angle : 0.518 9.695 21527 Z= 0.269 Chirality : 0.041 0.427 2432 Planarity : 0.004 0.051 2558 Dihedral : 14.933 177.467 2772 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 4.41 % Allowed : 25.16 % Favored : 70.43 % 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: -0.27 (0.19), residues: 1832 helix: 1.35 (0.20), residues: 666 sheet: -0.92 (0.35), residues: 215 loop : -1.13 (0.19), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1581 TYR 0.014 0.001 TYR D 607 PHE 0.014 0.001 PHE D 289 TRP 0.030 0.001 TRP A 330 HIS 0.007 0.001 HIS A1621 Details of bonding type rmsd covalent geometry : bond 0.00263 (15702) covalent geometry : angle 0.51084 (21506) hydrogen bonds : bond 0.03337 ( 606) hydrogen bonds : angle 4.52162 ( 1705) metal coordination : bond 0.01090 ( 16) metal coordination : angle 2.79246 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 162 time to evaluate : 0.431 Fit side-chains revert: symmetry clash REVERT: D 260 ARG cc_start: 0.6977 (mtt90) cc_final: 0.6755 (mtt90) REVERT: D 280 ARG cc_start: 0.7627 (OUTLIER) cc_final: 0.7395 (tpp-160) REVERT: D 542 PHE cc_start: 0.7395 (OUTLIER) cc_final: 0.6313 (m-80) REVERT: D 585 HIS cc_start: 0.6150 (OUTLIER) cc_final: 0.5845 (p-80) REVERT: A 308 GLU cc_start: 0.6493 (pm20) cc_final: 0.5685 (pt0) REVERT: A 389 TYR cc_start: 0.8249 (t80) cc_final: 0.7956 (t80) REVERT: A 605 LYS cc_start: 0.8571 (OUTLIER) cc_final: 0.7910 (ptpt) REVERT: A 877 LYS cc_start: 0.7064 (tptm) cc_final: 0.6616 (mtpp) REVERT: A 927 LEU cc_start: 0.7411 (OUTLIER) cc_final: 0.7141 (tt) REVERT: A 1487 TRP cc_start: 0.8060 (p-90) cc_final: 0.7488 (p-90) outliers start: 61 outliers final: 29 residues processed: 207 average time/residue: 0.1418 time to fit residues: 42.9408 Evaluate side-chains 188 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 154 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 190 SER Chi-restraints excluded: chain D residue 246 ASP Chi-restraints excluded: chain D residue 280 ARG Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 491 PHE Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 585 HIS Chi-restraints excluded: chain D residue 594 PHE Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 542 ASP Chi-restraints excluded: chain A residue 605 LYS Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 867 SER Chi-restraints excluded: chain A residue 927 LEU Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 995 GLU Chi-restraints excluded: chain A residue 997 MET Chi-restraints excluded: chain A residue 1006 MET Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1456 LEU Chi-restraints excluded: chain A residue 1468 ILE Chi-restraints excluded: chain A residue 1507 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 176 optimal weight: 0.0770 chunk 188 optimal weight: 4.9990 chunk 124 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 162 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 158 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 overall best weight: 1.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1494 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.173604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.133176 restraints weight = 17215.545| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 2.02 r_work: 0.3343 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.1313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15718 Z= 0.165 Angle : 0.554 10.080 21527 Z= 0.284 Chirality : 0.042 0.426 2432 Planarity : 0.004 0.045 2558 Dihedral : 14.917 174.476 2772 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 4.99 % Allowed : 24.44 % Favored : 70.57 % 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: -0.35 (0.19), residues: 1832 helix: 1.28 (0.20), residues: 668 sheet: -1.08 (0.34), residues: 215 loop : -1.15 (0.19), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1581 TYR 0.015 0.001 TYR D 607 PHE 0.013 0.001 PHE D 289 TRP 0.028 0.002 TRP A 330 HIS 0.006 0.001 HIS A1621 Details of bonding type rmsd covalent geometry : bond 0.00385 (15702) covalent geometry : angle 0.54421 (21506) hydrogen bonds : bond 0.03403 ( 606) hydrogen bonds : angle 4.50977 ( 1705) metal coordination : bond 0.00888 ( 16) metal coordination : angle 3.27942 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 158 time to evaluate : 0.583 Fit side-chains REVERT: D 260 ARG cc_start: 0.6914 (mtt90) cc_final: 0.6689 (mtt90) REVERT: D 542 PHE cc_start: 0.7605 (OUTLIER) cc_final: 0.6355 (m-80) REVERT: D 585 HIS cc_start: 0.6268 (OUTLIER) cc_final: 0.5875 (p-80) REVERT: A 107 LYS cc_start: 0.8456 (OUTLIER) cc_final: 0.8071 (pttt) REVERT: A 308 GLU cc_start: 0.6574 (pm20) cc_final: 0.5789 (pt0) REVERT: A 389 TYR cc_start: 0.8296 (t80) cc_final: 0.7977 (t80) REVERT: A 605 LYS cc_start: 0.8611 (OUTLIER) cc_final: 0.7925 (ptpt) REVERT: A 765 SER cc_start: 0.8507 (t) cc_final: 0.7947 (p) REVERT: A 877 LYS cc_start: 0.7105 (tptm) cc_final: 0.6607 (mtpp) REVERT: A 927 LEU cc_start: 0.7462 (OUTLIER) cc_final: 0.7207 (tt) REVERT: A 972 GLU cc_start: 0.6907 (mm-30) cc_final: 0.6548 (mm-30) REVERT: A 984 HIS cc_start: 0.7527 (t70) cc_final: 0.7230 (t-170) REVERT: A 1487 TRP cc_start: 0.8078 (p-90) cc_final: 0.7698 (p-90) outliers start: 69 outliers final: 39 residues processed: 210 average time/residue: 0.1468 time to fit residues: 44.9285 Evaluate side-chains 198 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 154 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 190 SER Chi-restraints excluded: chain D residue 246 ASP Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 329 SER Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 491 PHE Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 585 HIS Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 605 LYS Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 867 SER Chi-restraints excluded: chain A residue 927 LEU Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 970 SER Chi-restraints excluded: chain A residue 995 GLU Chi-restraints excluded: chain A residue 997 MET Chi-restraints excluded: chain A residue 1006 MET Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1456 LEU Chi-restraints excluded: chain A residue 1468 ILE Chi-restraints excluded: chain A residue 1507 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 159 optimal weight: 0.7980 chunk 146 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 chunk 85 optimal weight: 0.8980 chunk 118 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 177 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 125 optimal weight: 0.6980 chunk 80 optimal weight: 5.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1494 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.175516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.133691 restraints weight = 17200.808| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 2.10 r_work: 0.3365 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15718 Z= 0.134 Angle : 0.535 10.848 21527 Z= 0.274 Chirality : 0.041 0.423 2432 Planarity : 0.004 0.046 2558 Dihedral : 14.889 176.207 2772 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 5.13 % Allowed : 25.16 % Favored : 69.70 % 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: -0.29 (0.19), residues: 1832 helix: 1.38 (0.20), residues: 667 sheet: -1.02 (0.35), residues: 209 loop : -1.16 (0.19), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1581 TYR 0.014 0.001 TYR D 607 PHE 0.013 0.001 PHE D 289 TRP 0.036 0.001 TRP A 330 HIS 0.006 0.001 HIS A1621 Details of bonding type rmsd covalent geometry : bond 0.00310 (15702) covalent geometry : angle 0.52744 (21506) hydrogen bonds : bond 0.03177 ( 606) hydrogen bonds : angle 4.37297 ( 1705) metal coordination : bond 0.00957 ( 16) metal coordination : angle 3.00362 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 158 time to evaluate : 0.571 Fit side-chains REVERT: D 260 ARG cc_start: 0.6924 (mtt90) cc_final: 0.6693 (mtt90) REVERT: D 542 PHE cc_start: 0.7640 (OUTLIER) cc_final: 0.6399 (m-80) REVERT: D 585 HIS cc_start: 0.6219 (OUTLIER) cc_final: 0.5893 (p-80) REVERT: A 107 LYS cc_start: 0.8311 (OUTLIER) cc_final: 0.7973 (pttt) REVERT: A 389 TYR cc_start: 0.8275 (t80) cc_final: 0.7967 (t80) REVERT: A 719 ARG cc_start: 0.8427 (mmt-90) cc_final: 0.8224 (mmt-90) REVERT: A 765 SER cc_start: 0.8473 (t) cc_final: 0.7919 (p) REVERT: A 877 LYS cc_start: 0.7092 (tptm) cc_final: 0.6579 (mtpp) REVERT: A 899 ILE cc_start: 0.6809 (tt) cc_final: 0.6592 (tt) REVERT: A 927 LEU cc_start: 0.7557 (OUTLIER) cc_final: 0.7305 (tt) REVERT: A 972 GLU cc_start: 0.6857 (mm-30) cc_final: 0.6577 (mm-30) REVERT: A 984 HIS cc_start: 0.7612 (t70) cc_final: 0.7289 (t-170) REVERT: A 1487 TRP cc_start: 0.8158 (p-90) cc_final: 0.7886 (p-90) outliers start: 71 outliers final: 43 residues processed: 211 average time/residue: 0.1384 time to fit residues: 43.3439 Evaluate side-chains 199 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 152 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 190 SER Chi-restraints excluded: chain D residue 246 ASP Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 329 SER Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 491 PHE Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 585 HIS Chi-restraints excluded: chain D residue 594 PHE Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 750 CYS Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 867 SER Chi-restraints excluded: chain A residue 927 LEU Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 970 SER Chi-restraints excluded: chain A residue 995 GLU Chi-restraints excluded: chain A residue 997 MET Chi-restraints excluded: chain A residue 1006 MET Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1456 LEU Chi-restraints excluded: chain A residue 1468 ILE Chi-restraints excluded: chain A residue 1497 ILE Chi-restraints excluded: chain A residue 1507 VAL Chi-restraints excluded: chain A residue 1601 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 90 optimal weight: 0.6980 chunk 50 optimal weight: 8.9990 chunk 15 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 101 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 147 optimal weight: 9.9990 chunk 127 optimal weight: 0.1980 chunk 82 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1494 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.176859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.131439 restraints weight = 16766.210| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 1.89 r_work: 0.3391 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3250 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15718 Z= 0.123 Angle : 0.529 11.998 21527 Z= 0.270 Chirality : 0.041 0.422 2432 Planarity : 0.004 0.044 2558 Dihedral : 14.795 176.381 2772 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 5.35 % Allowed : 24.22 % Favored : 70.43 % 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: -0.25 (0.19), residues: 1832 helix: 1.40 (0.20), residues: 673 sheet: -1.02 (0.35), residues: 209 loop : -1.13 (0.19), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1581 TYR 0.014 0.001 TYR D 607 PHE 0.013 0.001 PHE D 289 TRP 0.045 0.001 TRP A 330 HIS 0.005 0.001 HIS A1621 Details of bonding type rmsd covalent geometry : bond 0.00282 (15702) covalent geometry : angle 0.52125 (21506) hydrogen bonds : bond 0.03047 ( 606) hydrogen bonds : angle 4.26250 ( 1705) metal coordination : bond 0.00936 ( 16) metal coordination : angle 2.89666 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 161 time to evaluate : 0.631 Fit side-chains REVERT: D 260 ARG cc_start: 0.6898 (mtt90) cc_final: 0.6652 (mtt90) REVERT: D 398 GLU cc_start: 0.8670 (tp30) cc_final: 0.8085 (tt0) REVERT: D 542 PHE cc_start: 0.7650 (OUTLIER) cc_final: 0.6274 (m-80) REVERT: D 585 HIS cc_start: 0.6170 (OUTLIER) cc_final: 0.5782 (p-80) REVERT: A 107 LYS cc_start: 0.8234 (OUTLIER) cc_final: 0.7924 (pttt) REVERT: A 141 LYS cc_start: 0.8275 (OUTLIER) cc_final: 0.7794 (mttp) REVERT: A 214 GLU cc_start: 0.7532 (pm20) cc_final: 0.7121 (mm-30) REVERT: A 389 TYR cc_start: 0.8297 (t80) cc_final: 0.7983 (t80) REVERT: A 605 LYS cc_start: 0.8693 (OUTLIER) cc_final: 0.8099 (ptpt) REVERT: A 765 SER cc_start: 0.8445 (t) cc_final: 0.7928 (p) REVERT: A 877 LYS cc_start: 0.7086 (tptm) cc_final: 0.6549 (mtpp) REVERT: A 899 ILE cc_start: 0.6499 (tt) cc_final: 0.6260 (tt) REVERT: A 927 LEU cc_start: 0.7502 (OUTLIER) cc_final: 0.7261 (tt) REVERT: A 972 GLU cc_start: 0.6911 (mm-30) cc_final: 0.6642 (mm-30) REVERT: A 1487 TRP cc_start: 0.8156 (p-90) cc_final: 0.7915 (p-90) outliers start: 74 outliers final: 52 residues processed: 219 average time/residue: 0.1361 time to fit residues: 44.2478 Evaluate side-chains 209 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 151 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 190 SER Chi-restraints excluded: chain D residue 246 ASP Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 329 SER Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 491 PHE Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 585 HIS Chi-restraints excluded: chain D residue 594 PHE Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 141 LYS Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 542 ASP Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 605 LYS Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 750 CYS Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 867 SER Chi-restraints excluded: chain A residue 927 LEU Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 970 SER Chi-restraints excluded: chain A residue 995 GLU Chi-restraints excluded: chain A residue 997 MET Chi-restraints excluded: chain A residue 1006 MET Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1441 GLU Chi-restraints excluded: chain A residue 1456 LEU Chi-restraints excluded: chain A residue 1468 ILE Chi-restraints excluded: chain A residue 1497 ILE Chi-restraints excluded: chain A residue 1507 VAL Chi-restraints excluded: chain A residue 1517 VAL Chi-restraints excluded: chain A residue 1582 VAL Chi-restraints excluded: chain A residue 1601 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 107 optimal weight: 0.0770 chunk 148 optimal weight: 9.9990 chunk 79 optimal weight: 0.8980 chunk 0 optimal weight: 40.0000 chunk 83 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 120 optimal weight: 0.9980 chunk 161 optimal weight: 1.9990 chunk 60 optimal weight: 8.9990 chunk 64 optimal weight: 0.8980 overall best weight: 0.7738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1494 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.176817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.134716 restraints weight = 16876.216| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 2.02 r_work: 0.3382 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15718 Z= 0.127 Angle : 0.534 11.883 21527 Z= 0.272 Chirality : 0.041 0.415 2432 Planarity : 0.004 0.042 2558 Dihedral : 14.748 176.095 2772 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 5.06 % Allowed : 24.87 % Favored : 70.07 % 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: -0.24 (0.19), residues: 1832 helix: 1.45 (0.20), residues: 669 sheet: -1.13 (0.34), residues: 217 loop : -1.12 (0.19), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1581 TYR 0.014 0.001 TYR D 607 PHE 0.014 0.001 PHE A1011 TRP 0.036 0.001 TRP A 330 HIS 0.005 0.001 HIS A1621 Details of bonding type rmsd covalent geometry : bond 0.00294 (15702) covalent geometry : angle 0.52598 (21506) hydrogen bonds : bond 0.03031 ( 606) hydrogen bonds : angle 4.23080 ( 1705) metal coordination : bond 0.00916 ( 16) metal coordination : angle 2.92013 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 157 time to evaluate : 0.577 Fit side-chains REVERT: D 260 ARG cc_start: 0.6903 (mtt90) cc_final: 0.6658 (mtt90) REVERT: D 398 GLU cc_start: 0.8734 (tp30) cc_final: 0.8143 (tt0) REVERT: D 542 PHE cc_start: 0.7631 (OUTLIER) cc_final: 0.6349 (m-80) REVERT: D 585 HIS cc_start: 0.6171 (OUTLIER) cc_final: 0.5780 (p-80) REVERT: A 107 LYS cc_start: 0.8218 (OUTLIER) cc_final: 0.7902 (pttt) REVERT: A 141 LYS cc_start: 0.8295 (OUTLIER) cc_final: 0.7804 (mttp) REVERT: A 214 GLU cc_start: 0.7561 (pm20) cc_final: 0.7064 (mm-30) REVERT: A 389 TYR cc_start: 0.8308 (t80) cc_final: 0.7996 (t80) REVERT: A 605 LYS cc_start: 0.8698 (OUTLIER) cc_final: 0.8155 (ptpt) REVERT: A 765 SER cc_start: 0.8472 (t) cc_final: 0.7971 (p) REVERT: A 877 LYS cc_start: 0.7048 (tptm) cc_final: 0.6549 (mtpp) REVERT: A 899 ILE cc_start: 0.6402 (tt) cc_final: 0.6155 (tt) REVERT: A 927 LEU cc_start: 0.7526 (OUTLIER) cc_final: 0.7307 (tt) REVERT: A 972 GLU cc_start: 0.6897 (mm-30) cc_final: 0.6625 (mm-30) REVERT: A 1487 TRP cc_start: 0.8137 (p-90) cc_final: 0.7885 (p-90) outliers start: 70 outliers final: 54 residues processed: 213 average time/residue: 0.1398 time to fit residues: 43.8596 Evaluate side-chains 208 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 148 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 190 SER Chi-restraints excluded: chain D residue 246 ASP Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 329 SER Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 491 PHE Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 585 HIS Chi-restraints excluded: chain D residue 671 SER Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 141 LYS Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 542 ASP Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 605 LYS Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 750 CYS Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 867 SER Chi-restraints excluded: chain A residue 927 LEU Chi-restraints excluded: chain A residue 936 GLU Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 970 SER Chi-restraints excluded: chain A residue 995 GLU Chi-restraints excluded: chain A residue 997 MET Chi-restraints excluded: chain A residue 1006 MET Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1441 GLU Chi-restraints excluded: chain A residue 1456 LEU Chi-restraints excluded: chain A residue 1468 ILE Chi-restraints excluded: chain A residue 1497 ILE Chi-restraints excluded: chain A residue 1507 VAL Chi-restraints excluded: chain A residue 1582 VAL Chi-restraints excluded: chain A residue 1601 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 153 optimal weight: 9.9990 chunk 1 optimal weight: 0.9980 chunk 144 optimal weight: 0.0970 chunk 188 optimal weight: 4.9990 chunk 115 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 25 optimal weight: 8.9990 chunk 103 optimal weight: 6.9990 chunk 94 optimal weight: 4.9990 chunk 154 optimal weight: 3.9990 chunk 32 optimal weight: 7.9990 overall best weight: 1.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1494 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.172960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.132381 restraints weight = 17216.358| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 1.83 r_work: 0.3343 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15718 Z= 0.182 Angle : 0.584 11.847 21527 Z= 0.295 Chirality : 0.043 0.415 2432 Planarity : 0.004 0.043 2558 Dihedral : 14.798 174.223 2772 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 5.35 % Allowed : 25.16 % Favored : 69.49 % 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: -0.41 (0.19), residues: 1832 helix: 1.28 (0.20), residues: 673 sheet: -1.26 (0.33), residues: 225 loop : -1.19 (0.19), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1581 TYR 0.015 0.001 TYR D 607 PHE 0.015 0.002 PHE D 324 TRP 0.038 0.002 TRP A 330 HIS 0.006 0.001 HIS A1484 Details of bonding type rmsd covalent geometry : bond 0.00428 (15702) covalent geometry : angle 0.57321 (21506) hydrogen bonds : bond 0.03281 ( 606) hydrogen bonds : angle 4.40642 ( 1705) metal coordination : bond 0.01001 ( 16) metal coordination : angle 3.60537 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 155 time to evaluate : 0.580 Fit side-chains REVERT: D 260 ARG cc_start: 0.6878 (mtt90) cc_final: 0.6629 (mtt90) REVERT: D 278 TRP cc_start: 0.8337 (OUTLIER) cc_final: 0.8125 (p-90) REVERT: D 542 PHE cc_start: 0.7706 (OUTLIER) cc_final: 0.6396 (m-80) REVERT: D 585 HIS cc_start: 0.6318 (OUTLIER) cc_final: 0.5860 (p-80) REVERT: A 107 LYS cc_start: 0.8507 (OUTLIER) cc_final: 0.8110 (pttt) REVERT: A 141 LYS cc_start: 0.8342 (OUTLIER) cc_final: 0.7857 (mttp) REVERT: A 389 TYR cc_start: 0.8302 (t80) cc_final: 0.7981 (t80) REVERT: A 605 LYS cc_start: 0.8693 (OUTLIER) cc_final: 0.8139 (ptpt) REVERT: A 719 ARG cc_start: 0.8417 (mmt-90) cc_final: 0.8195 (mmt-90) REVERT: A 765 SER cc_start: 0.8534 (t) cc_final: 0.7971 (p) REVERT: A 877 LYS cc_start: 0.6997 (tptm) cc_final: 0.6399 (mtpp) REVERT: A 899 ILE cc_start: 0.6331 (tt) cc_final: 0.6093 (tt) REVERT: A 927 LEU cc_start: 0.7578 (OUTLIER) cc_final: 0.7358 (tt) REVERT: A 972 GLU cc_start: 0.6877 (mm-30) cc_final: 0.6595 (mm-30) outliers start: 74 outliers final: 54 residues processed: 215 average time/residue: 0.1375 time to fit residues: 43.9510 Evaluate side-chains 211 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 150 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 190 SER Chi-restraints excluded: chain D residue 246 ASP Chi-restraints excluded: chain D residue 278 TRP Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 329 SER Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 491 PHE Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 585 HIS Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 671 SER Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 141 LYS Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 605 LYS Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 750 CYS Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 867 SER Chi-restraints excluded: chain A residue 927 LEU Chi-restraints excluded: chain A residue 936 GLU Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 970 SER Chi-restraints excluded: chain A residue 995 GLU Chi-restraints excluded: chain A residue 997 MET Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1441 GLU Chi-restraints excluded: chain A residue 1456 LEU Chi-restraints excluded: chain A residue 1468 ILE Chi-restraints excluded: chain A residue 1507 VAL Chi-restraints excluded: chain A residue 1582 VAL Chi-restraints excluded: chain A residue 1601 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 97 optimal weight: 4.9990 chunk 171 optimal weight: 0.9990 chunk 154 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 5 optimal weight: 6.9990 chunk 114 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 132 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 chunk 160 optimal weight: 0.9980 chunk 162 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1494 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.175584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.129829 restraints weight = 16753.083| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 1.91 r_work: 0.3371 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15718 Z= 0.142 Angle : 0.555 12.291 21527 Z= 0.281 Chirality : 0.042 0.413 2432 Planarity : 0.004 0.042 2558 Dihedral : 14.771 175.814 2772 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 4.99 % Allowed : 25.74 % Favored : 69.27 % 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: -0.35 (0.19), residues: 1832 helix: 1.34 (0.20), residues: 673 sheet: -1.22 (0.34), residues: 217 loop : -1.17 (0.19), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1581 TYR 0.014 0.001 TYR D 607 PHE 0.015 0.001 PHE A1011 TRP 0.019 0.001 TRP A1487 HIS 0.005 0.001 HIS A1484 Details of bonding type rmsd covalent geometry : bond 0.00330 (15702) covalent geometry : angle 0.54653 (21506) hydrogen bonds : bond 0.03085 ( 606) hydrogen bonds : angle 4.31121 ( 1705) metal coordination : bond 0.00942 ( 16) metal coordination : angle 3.16619 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 147 time to evaluate : 0.606 Fit side-chains REVERT: D 260 ARG cc_start: 0.6850 (mtt90) cc_final: 0.6595 (mtt90) REVERT: D 278 TRP cc_start: 0.8301 (OUTLIER) cc_final: 0.8083 (p-90) REVERT: D 398 GLU cc_start: 0.8729 (tp30) cc_final: 0.8184 (tt0) REVERT: D 542 PHE cc_start: 0.7729 (OUTLIER) cc_final: 0.6354 (m-80) REVERT: D 585 HIS cc_start: 0.6182 (OUTLIER) cc_final: 0.5776 (p-80) REVERT: A 107 LYS cc_start: 0.8325 (OUTLIER) cc_final: 0.7995 (pttt) REVERT: A 141 LYS cc_start: 0.8285 (OUTLIER) cc_final: 0.7803 (mttp) REVERT: A 361 MET cc_start: 0.6705 (tpp) cc_final: 0.6369 (mmp) REVERT: A 765 SER cc_start: 0.8471 (t) cc_final: 0.7947 (p) REVERT: A 877 LYS cc_start: 0.7107 (tptm) cc_final: 0.6552 (mtpp) REVERT: A 927 LEU cc_start: 0.7529 (OUTLIER) cc_final: 0.7304 (tt) REVERT: A 972 GLU cc_start: 0.6817 (mm-30) cc_final: 0.6554 (mm-30) REVERT: A 1487 TRP cc_start: 0.8072 (p-90) cc_final: 0.7837 (p-90) outliers start: 69 outliers final: 55 residues processed: 201 average time/residue: 0.1298 time to fit residues: 39.2369 Evaluate side-chains 202 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 141 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 190 SER Chi-restraints excluded: chain D residue 246 ASP Chi-restraints excluded: chain D residue 278 TRP Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 329 SER Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 491 PHE Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 585 HIS Chi-restraints excluded: chain D residue 671 SER Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 141 LYS Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 750 CYS Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 867 SER Chi-restraints excluded: chain A residue 927 LEU Chi-restraints excluded: chain A residue 936 GLU Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 970 SER Chi-restraints excluded: chain A residue 995 GLU Chi-restraints excluded: chain A residue 997 MET Chi-restraints excluded: chain A residue 1006 MET Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1463 ARG Chi-restraints excluded: chain A residue 1468 ILE Chi-restraints excluded: chain A residue 1507 VAL Chi-restraints excluded: chain A residue 1534 LEU Chi-restraints excluded: chain A residue 1582 VAL Chi-restraints excluded: chain A residue 1601 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 79 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 106 optimal weight: 0.6980 chunk 4 optimal weight: 7.9990 chunk 176 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 181 optimal weight: 0.0270 chunk 93 optimal weight: 0.6980 chunk 110 optimal weight: 0.3980 chunk 0 optimal weight: 40.0000 chunk 44 optimal weight: 0.7980 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 905 HIS A1494 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.178690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.133406 restraints weight = 16840.009| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 1.91 r_work: 0.3413 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 15718 Z= 0.108 Angle : 0.530 13.665 21527 Z= 0.269 Chirality : 0.041 0.406 2432 Planarity : 0.004 0.042 2558 Dihedral : 14.659 177.794 2772 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 4.27 % Allowed : 26.39 % Favored : 69.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.21 (0.19), residues: 1832 helix: 1.51 (0.20), residues: 669 sheet: -1.04 (0.34), residues: 219 loop : -1.15 (0.19), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1581 TYR 0.015 0.001 TYR A 702 PHE 0.017 0.001 PHE A1011 TRP 0.031 0.001 TRP A1530 HIS 0.006 0.001 HIS A 905 Details of bonding type rmsd covalent geometry : bond 0.00246 (15702) covalent geometry : angle 0.52224 (21506) hydrogen bonds : bond 0.02871 ( 606) hydrogen bonds : angle 4.23349 ( 1705) metal coordination : bond 0.01004 ( 16) metal coordination : angle 2.86606 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 150 time to evaluate : 0.613 Fit side-chains REVERT: D 190 SER cc_start: 0.7166 (OUTLIER) cc_final: 0.6811 (m) REVERT: D 260 ARG cc_start: 0.6887 (mtt90) cc_final: 0.6636 (mtt90) REVERT: D 278 TRP cc_start: 0.8078 (OUTLIER) cc_final: 0.7849 (p-90) REVERT: D 398 GLU cc_start: 0.8630 (tp30) cc_final: 0.8097 (tt0) REVERT: D 542 PHE cc_start: 0.7665 (OUTLIER) cc_final: 0.6315 (m-80) REVERT: D 585 HIS cc_start: 0.6085 (OUTLIER) cc_final: 0.5678 (p-80) REVERT: A 141 LYS cc_start: 0.8254 (OUTLIER) cc_final: 0.7754 (mttp) REVERT: A 389 TYR cc_start: 0.8234 (t80) cc_final: 0.7907 (t80) REVERT: A 529 TYR cc_start: 0.8665 (m-80) cc_final: 0.8371 (m-80) REVERT: A 765 SER cc_start: 0.8428 (t) cc_final: 0.7955 (p) REVERT: A 877 LYS cc_start: 0.7021 (tptm) cc_final: 0.6378 (mtpp) REVERT: A 927 LEU cc_start: 0.7555 (OUTLIER) cc_final: 0.7329 (tt) REVERT: A 972 GLU cc_start: 0.6811 (mm-30) cc_final: 0.6586 (mm-30) REVERT: A 1487 TRP cc_start: 0.7920 (p-90) cc_final: 0.7451 (p-90) outliers start: 59 outliers final: 49 residues processed: 196 average time/residue: 0.1256 time to fit residues: 36.1183 Evaluate side-chains 197 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 142 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 190 SER Chi-restraints excluded: chain D residue 246 ASP Chi-restraints excluded: chain D residue 278 TRP Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 329 SER Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 491 PHE Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 585 HIS Chi-restraints excluded: chain D residue 671 SER Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 141 LYS Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 750 CYS Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 867 SER Chi-restraints excluded: chain A residue 927 LEU Chi-restraints excluded: chain A residue 936 GLU Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 970 SER Chi-restraints excluded: chain A residue 995 GLU Chi-restraints excluded: chain A residue 997 MET Chi-restraints excluded: chain A residue 1006 MET Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1463 ARG Chi-restraints excluded: chain A residue 1468 ILE Chi-restraints excluded: chain A residue 1507 VAL Chi-restraints excluded: chain A residue 1582 VAL Chi-restraints excluded: chain A residue 1601 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 8 optimal weight: 10.0000 chunk 137 optimal weight: 6.9990 chunk 146 optimal weight: 0.9990 chunk 9 optimal weight: 9.9990 chunk 79 optimal weight: 0.5980 chunk 127 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 64 optimal weight: 0.5980 chunk 165 optimal weight: 2.9990 chunk 110 optimal weight: 0.0030 chunk 69 optimal weight: 0.2980 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1494 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.179470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.134163 restraints weight = 16756.034| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 1.90 r_work: 0.3424 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 15718 Z= 0.108 Angle : 0.528 13.647 21527 Z= 0.268 Chirality : 0.041 0.399 2432 Planarity : 0.004 0.042 2558 Dihedral : 14.580 177.257 2772 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 4.34 % Allowed : 26.25 % Favored : 69.41 % 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: -0.19 (0.20), residues: 1832 helix: 1.55 (0.20), residues: 669 sheet: -1.10 (0.35), residues: 213 loop : -1.13 (0.19), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1581 TYR 0.013 0.001 TYR D 607 PHE 0.016 0.001 PHE A1011 TRP 0.032 0.001 TRP A1530 HIS 0.005 0.001 HIS A1621 Details of bonding type rmsd covalent geometry : bond 0.00247 (15702) covalent geometry : angle 0.52156 (21506) hydrogen bonds : bond 0.02830 ( 606) hydrogen bonds : angle 4.18757 ( 1705) metal coordination : bond 0.00983 ( 16) metal coordination : angle 2.78168 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4395.64 seconds wall clock time: 76 minutes 2.94 seconds (4562.94 seconds total)