Starting phenix.real_space_refine on Sun Jun 15 12:42:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y8y_33686/06_2025/7y8y_33686.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y8y_33686/06_2025/7y8y_33686.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7y8y_33686/06_2025/7y8y_33686.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y8y_33686/06_2025/7y8y_33686.map" model { file = "/net/cci-nas-00/data/ceres_data/7y8y_33686/06_2025/7y8y_33686.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y8y_33686/06_2025/7y8y_33686.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.085 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 55 5.49 5 S 59 5.16 5 C 10611 2.51 5 N 2951 2.21 5 O 3343 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 17023 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 5468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 680, 5468 Classifications: {'peptide': 680} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 20, 'TRANS': 659} Chain breaks: 1 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "A" Number of atoms: 10378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1291, 10378 Classifications: {'peptide': 1291} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'CIS': 1, 'PTRANS': 62, 'TRANS': 1227} Chain breaks: 4 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "D" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 780 Classifications: {'RNA': 37} Modifications used: {'rna2p_pur': 12, 'rna2p_pyr': 10, 'rna3p_pur': 4, 'rna3p_pyr': 11} Link IDs: {'rna2p': 21, 'rna3p': 15} Chain: "E" Number of atoms: 393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 393 Classifications: {'RNA': 18} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 13, 'rna3p_pyr': 4} Link IDs: {'rna3p': 17} 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 9104 SG CYS A 491 47.965 49.179 114.332 1.00 41.16 S ATOM 9172 SG CYS A 501 47.679 48.247 117.979 1.00 36.50 S ATOM 9186 SG CYS A 503 44.704 47.764 115.662 1.00 32.57 S ATOM 9208 SG CYS A 506 47.602 45.453 115.318 1.00 33.14 S ATOM 13309 SG CYS A1018 59.236 69.245 52.513 1.00 67.92 S ATOM 13536 SG CYS A1406 60.052 70.341 56.116 1.00 58.40 S ATOM 13587 SG CYS A1414 57.111 71.800 54.150 1.00 55.83 S ATOM 13604 SG CYS A1417 56.898 68.283 55.418 1.00 43.89 S ATOM 6144 SG CYS A 88 52.917 25.609 139.837 1.00 40.36 S ATOM 6415 SG CYS A 121 54.618 22.965 142.014 1.00 68.04 S ATOM 6461 SG CYS A 127 53.378 22.155 138.467 1.00 36.89 S ATOM 6485 SG CYS A 130 56.407 24.331 138.934 1.00 43.43 S ATOM 11179 SG CYS A 750 51.016 68.821 89.708 1.00 67.10 S ATOM 11192 SG CYS A 752 47.968 67.670 87.742 1.00 50.21 S ATOM 11214 SG CYS A 755 50.020 65.099 89.750 1.00 50.68 S Time building chain proxies: 11.08, per 1000 atoms: 0.65 Number of scatterers: 17023 At special positions: 0 Unit cell: (107.8, 106.7, 167.2, 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 59 16.00 P 55 15.00 O 3343 8.00 N 2951 7.00 C 10611 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: 4.27 Conformation dependent library (CDL) restraints added in 2.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1801 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 503 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 491 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 506 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 501 " pdb=" ZN A1802 " pdb="ZN ZN A1802 " - pdb=" SG CYS A1414 " pdb="ZN ZN A1802 " - pdb=" SG CYS A1417 " pdb="ZN ZN A1802 " - pdb=" SG CYS A1018 " pdb="ZN ZN A1802 " - pdb=" SG CYS A1406 " pdb=" ZN A1803 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 88 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 127 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 130 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 121 " pdb=" ZN A1804 " pdb="ZN ZN A1804 " - pdb=" ND1 HIS A 747 " pdb="ZN ZN A1804 " - pdb=" SG CYS A 750 " pdb="ZN ZN A1804 " - pdb=" SG CYS A 752 " pdb="ZN ZN A1804 " - pdb=" SG CYS A 755 " Number of angles added : 21 3914 Ramachandran restraints generated. 1957 Oldfield, 0 Emsley, 1957 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3654 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 20 sheets defined 37.6% alpha, 16.7% beta 4 base pairs and 15 stacking pairs defined. Time for finding SS restraints: 5.50 Creating SS restraints... Processing helix chain 'B' and resid 14 through 30 removed outlier: 3.747A pdb=" N ILE B 19 " --> pdb=" O THR B 15 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG B 26 " --> pdb=" O LYS B 22 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LEU B 27 " --> pdb=" O GLU B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 33 No H-bonds generated for 'chain 'B' and resid 31 through 33' Processing helix chain 'B' and resid 37 through 59 removed outlier: 4.160A pdb=" N LYS B 43 " --> pdb=" O VAL B 39 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU B 52 " --> pdb=" O ALA B 48 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY B 54 " --> pdb=" O LYS B 50 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N LEU B 55 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR B 56 " --> pdb=" O LEU B 52 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS B 57 " --> pdb=" O ILE B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 79 removed outlier: 3.566A pdb=" N ILE B 71 " --> pdb=" O SER B 67 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA B 72 " --> pdb=" O PHE B 68 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER B 79 " --> pdb=" O TYR B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 109 removed outlier: 3.945A pdb=" N LYS B 94 " --> pdb=" O PRO B 90 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU B 95 " --> pdb=" O GLU B 91 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU B 97 " --> pdb=" O LYS B 93 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU B 102 " --> pdb=" O ARG B 98 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG B 106 " --> pdb=" O GLU B 102 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ALA B 107 " --> pdb=" O PHE B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 136 Processing helix chain 'B' and resid 141 through 155 Processing helix chain 'B' and resid 163 through 177 removed outlier: 4.085A pdb=" N ILE B 167 " --> pdb=" O TYR B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 182 No H-bonds generated for 'chain 'B' and resid 180 through 182' Processing helix chain 'B' and resid 183 through 190 Processing helix chain 'B' and resid 194 through 207 removed outlier: 3.535A pdb=" N LYS B 206 " --> pdb=" O TYR B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 223 Processing helix chain 'B' and resid 224 through 226 No H-bonds generated for 'chain 'B' and resid 224 through 226' Processing helix chain 'B' and resid 231 through 246 Processing helix chain 'B' and resid 250 through 267 removed outlier: 3.698A pdb=" N ILE B 256 " --> pdb=" O ARG B 252 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LYS B 267 " --> pdb=" O ARG B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 297 Processing helix chain 'B' and resid 303 through 322 Processing helix chain 'B' and resid 327 through 333 removed outlier: 3.501A pdb=" N LYS B 333 " --> pdb=" O SER B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 357 Processing helix chain 'B' and resid 435 through 448 Processing helix chain 'B' and resid 454 through 469 removed outlier: 3.918A pdb=" N LEU B 458 " --> pdb=" O ALA B 454 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL B 459 " --> pdb=" O ALA B 455 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR B 460 " --> pdb=" O GLU B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 474 Processing helix chain 'B' and resid 489 through 495 removed outlier: 3.743A pdb=" N HIS B 493 " --> pdb=" O ASP B 490 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG B 494 " --> pdb=" O PHE B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 500 removed outlier: 3.845A pdb=" N SER B 500 " --> pdb=" O LEU B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 525 Processing helix chain 'B' and resid 569 through 573 removed outlier: 3.693A pdb=" N ILE B 573 " --> pdb=" O LEU B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 595 Processing helix chain 'B' and resid 607 through 614 removed outlier: 3.738A pdb=" N VAL B 614 " --> pdb=" O ILE B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 644 through 653 removed outlier: 4.053A pdb=" N ALA B 648 " --> pdb=" O SER B 644 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY B 653 " --> pdb=" O LEU B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 679 removed outlier: 3.879A pdb=" N THR B 669 " --> pdb=" O ARG B 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 691 removed outlier: 3.850A pdb=" N TRP B 687 " --> pdb=" O LYS B 683 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 707 Processing helix chain 'A' and resid 27 through 31 removed outlier: 4.068A pdb=" N LYS A 30 " --> pdb=" O ASP A 27 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS A 31 " --> pdb=" O ALA A 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 27 through 31' Processing helix chain 'A' and resid 32 through 38 Processing helix chain 'A' and resid 59 through 78 removed outlier: 3.748A pdb=" N VAL A 63 " --> pdb=" O THR A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 133 Processing helix chain 'A' and resid 216 through 227 Processing helix chain 'A' and resid 267 through 287 Processing helix chain 'A' and resid 292 through 297 Processing helix chain 'A' and resid 299 through 306 removed outlier: 3.806A pdb=" N THR A 302 " --> pdb=" O ALA A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 314 Processing helix chain 'A' and resid 342 through 345 Processing helix chain 'A' and resid 346 through 351 Processing helix chain 'A' and resid 354 through 375 Processing helix chain 'A' and resid 434 through 438 Processing helix chain 'A' and resid 471 through 488 removed outlier: 3.538A pdb=" N LEU A 475 " --> pdb=" O PRO A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 510 removed outlier: 3.588A pdb=" N ILE A 507 " --> pdb=" O CYS A 503 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLU A 508 " --> pdb=" O LYS A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 580 removed outlier: 3.748A pdb=" N SER A 573 " --> pdb=" O PRO A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 625 Processing helix chain 'A' and resid 626 through 628 No H-bonds generated for 'chain 'A' and resid 626 through 628' Processing helix chain 'A' and resid 630 through 636 removed outlier: 3.771A pdb=" N LEU A 634 " --> pdb=" O LYS A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 667 No H-bonds generated for 'chain 'A' and resid 665 through 667' Processing helix chain 'A' and resid 686 through 693 removed outlier: 3.617A pdb=" N ALA A 690 " --> pdb=" O ASP A 686 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 712 Processing helix chain 'A' and resid 723 through 740 removed outlier: 3.536A pdb=" N PHE A 731 " --> pdb=" O HIS A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 758 Processing helix chain 'A' and resid 776 through 780 removed outlier: 3.576A pdb=" N GLU A 779 " --> pdb=" O ASN A 776 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N PHE A 780 " --> pdb=" O GLY A 777 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 776 through 780' Processing helix chain 'A' and resid 831 through 848 removed outlier: 3.518A pdb=" N GLY A 848 " --> pdb=" O ASP A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 859 removed outlier: 3.523A pdb=" N VAL A 858 " --> pdb=" O LYS A 855 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLY A 859 " --> pdb=" O GLY A 856 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 855 through 859' Processing helix chain 'A' and resid 873 through 884 Processing helix chain 'A' and resid 999 through 1016 removed outlier: 3.984A pdb=" N LEU A1003 " --> pdb=" O PRO A 999 " (cutoff:3.500A) Processing helix chain 'A' and resid 1414 through 1421 Processing helix chain 'A' and resid 1486 through 1494 removed outlier: 4.257A pdb=" N ILE A1490 " --> pdb=" O GLY A1486 " (cutoff:3.500A) Processing helix chain 'A' and resid 1528 through 1540 removed outlier: 3.721A pdb=" N LEU A1532 " --> pdb=" O ARG A1528 " (cutoff:3.500A) Processing helix chain 'A' and resid 1552 through 1556 Processing helix chain 'A' and resid 1583 through 1603 removed outlier: 3.783A pdb=" N ILE A1587 " --> pdb=" O PRO A1583 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY A1603 " --> pdb=" O ILE A1599 " (cutoff:3.500A) Processing helix chain 'A' and resid 1619 through 1628 removed outlier: 3.655A pdb=" N LEU A1628 " --> pdb=" O LYS A1624 " (cutoff:3.500A) Processing helix chain 'A' and resid 1664 through 1668 removed outlier: 3.650A pdb=" N GLY A1667 " --> pdb=" O LYS A1664 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ASP A1668 " --> pdb=" O LYS A1665 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1664 through 1668' Processing helix chain 'A' and resid 1673 through 1682 Processing sheet with id=AA1, first strand: chain 'B' and resid 425 through 431 removed outlier: 3.586A pdb=" N SER B 425 " --> pdb=" O ASP B 420 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA B 416 " --> pdb=" O LYS B 429 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE B 431 " --> pdb=" O GLY B 414 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TYR B 406 " --> pdb=" O ASN B 415 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL B 402 " --> pdb=" O PHE B 419 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 536 through 540 removed outlier: 7.105A pdb=" N VAL B 537 " --> pdb=" O THR B 581 " (cutoff:3.500A) removed outlier: 8.552A pdb=" N LEU B 583 " --> pdb=" O VAL B 537 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N LEU B 539 " --> pdb=" O LEU B 583 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N LEU B 580 " --> pdb=" O ILE B 623 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N THR B 660 " --> pdb=" O LEU B 624 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY B 659 " --> pdb=" O ARG B 710 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 585 through 587 removed outlier: 3.842A pdb=" N HIS B 585 " --> pdb=" O LYS B 599 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N MET B 597 " --> pdb=" O GLU B 587 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE B 605 " --> pdb=" O LEU B 598 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 20 through 22 removed outlier: 7.326A pdb=" N SER A 56 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU A 158 " --> pdb=" O SER A 56 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 151 through 153 removed outlier: 3.783A pdb=" N LEU A 158 " --> pdb=" O SER A 56 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N SER A 56 " --> pdb=" O LEU A 158 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 53 through 58 current: chain 'A' and resid 233 through 239 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: 6.214A 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 173 through 181 removed outlier: 4.621A pdb=" N ARG A 180 " --> pdb=" O ASP A 190 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N ASP A 190 " --> pdb=" O ARG A 180 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 512 through 513 removed outlier: 3.701A pdb=" N GLY A 565 " --> pdb=" O LYS A 414 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU A 415 " --> pdb=" O TRP A 612 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N ARG A 421 " --> pdb=" O ASP A 606 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N ASP A 606 " --> pdb=" O ARG A 421 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N LYS A 423 " --> pdb=" O LEU A 604 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N LEU A 604 " --> pdb=" O LYS A 423 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA A 589 " --> pdb=" O PHE A 602 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 512 through 513 removed outlier: 3.701A pdb=" N GLY A 565 " --> pdb=" O LYS A 414 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU A 415 " --> pdb=" O TRP A 612 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N ARG A 421 " --> pdb=" O ASP A 606 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N ASP A 606 " --> pdb=" O ARG A 421 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N LYS A 423 " --> pdb=" O LEU A 604 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N LEU A 604 " --> pdb=" O LYS A 423 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE A 647 " --> pdb=" O GLU A 611 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 469 through 470 removed outlier: 3.528A pdb=" N SER A 517 " --> pdb=" O ILE A 470 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 526 through 533 removed outlier: 3.691A pdb=" N ALA A 532 " --> pdb=" O SER A 544 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N SER A 544 " --> pdb=" O ALA A 532 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 703 through 704 removed outlier: 3.513A pdb=" N ARG A 719 " --> pdb=" O LYS A 704 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N PHE A 720 " --> pdb=" O LEU A 774 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 703 through 704 removed outlier: 3.513A pdb=" N ARG A 719 " --> pdb=" O LYS A 704 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N PHE A 720 " --> pdb=" O LEU A 774 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR A 674 " --> pdb=" O GLY A 822 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N GLN A 673 " --> pdb=" O ILE A 868 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N ILE A 868 " --> pdb=" O GLN A 673 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N THR A 675 " --> pdb=" O ILE A 866 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ILE A 866 " --> pdb=" O THR A 675 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N GLU A 677 " --> pdb=" O ALA A 864 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 707 through 708 removed outlier: 3.620A pdb=" N ALA A 713 " --> pdb=" O ASN A 708 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 789 Processing sheet with id=AB8, first strand: chain 'A' and resid 925 through 927 Processing sheet with id=AB9, first strand: chain 'A' and resid 997 through 998 removed outlier: 7.198A pdb=" N VAL A1517 " --> pdb=" O GLU A1437 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE A1524 " --> pdb=" O GLY A 952 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLY A 952 " --> pdb=" O PHE A1524 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N LEU A 950 " --> pdb=" O ASN A1526 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N SER A 951 " --> pdb=" O THR A1569 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N THR A1569 " --> pdb=" O SER A 951 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N LYS A 953 " --> pdb=" O LEU A1567 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N LEU A1567 " --> pdb=" O LYS A 953 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ASN A 955 " --> pdb=" O ASP A1565 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1429 through 1431 removed outlier: 3.608A pdb=" N PHE A1524 " --> pdb=" O GLY A 952 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLY A 952 " --> pdb=" O PHE A1524 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N LEU A 950 " --> pdb=" O ASN A1526 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N SER A 951 " --> pdb=" O THR A1569 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N THR A1569 " --> pdb=" O SER A 951 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N LYS A 953 " --> pdb=" O LEU A1567 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N LEU A1567 " --> pdb=" O LYS A 953 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ASN A 955 " --> pdb=" O ASP A1565 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1453 through 1455 591 hydrogen bonds defined for protein. 1662 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 11 hydrogen bonds 22 hydrogen bond angles 0 basepair planarities 4 basepair parallelities 15 stacking parallelities Total time for adding SS restraints: 6.71 Time building geometry restraints manager: 5.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4410 1.33 - 1.45: 3495 1.45 - 1.57: 9422 1.57 - 1.69: 108 1.69 - 1.81: 83 Bond restraints: 17518 Sorted by residual: bond pdb=" C LYS A1553 " pdb=" N PRO A1554 " ideal model delta sigma weight residual 1.337 1.351 -0.014 9.80e-03 1.04e+04 2.06e+00 bond pdb=" CB GLU B 23 " pdb=" CG GLU B 23 " ideal model delta sigma weight residual 1.520 1.562 -0.042 3.00e-02 1.11e+03 2.00e+00 bond pdb=" C ASN A1449 " pdb=" N PRO A1450 " ideal model delta sigma weight residual 1.332 1.349 -0.018 1.30e-02 5.92e+03 1.89e+00 bond pdb=" CB GLU A 639 " pdb=" CG GLU A 639 " ideal model delta sigma weight residual 1.520 1.561 -0.041 3.00e-02 1.11e+03 1.89e+00 bond pdb=" CB ARG B 16 " pdb=" CG ARG B 16 " ideal model delta sigma weight residual 1.520 1.561 -0.041 3.00e-02 1.11e+03 1.86e+00 ... (remaining 17513 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 23591 2.29 - 4.58: 268 4.58 - 6.87: 30 6.87 - 9.16: 11 9.16 - 11.45: 2 Bond angle restraints: 23902 Sorted by residual: angle pdb=" C ASP B 62 " pdb=" N LEU B 63 " pdb=" CA LEU B 63 " ideal model delta sigma weight residual 121.54 130.09 -8.55 1.91e+00 2.74e-01 2.00e+01 angle pdb=" CA LYS A 147 " pdb=" CB LYS A 147 " pdb=" CG LYS A 147 " ideal model delta sigma weight residual 114.10 122.28 -8.18 2.00e+00 2.50e-01 1.67e+01 angle pdb=" C LEU A1495 " pdb=" N GLU A1496 " pdb=" CA GLU A1496 " ideal model delta sigma weight residual 121.54 129.20 -7.66 1.91e+00 2.74e-01 1.61e+01 angle pdb=" CB LYS B 389 " pdb=" CG LYS B 389 " pdb=" CD LYS B 389 " ideal model delta sigma weight residual 111.30 120.08 -8.78 2.30e+00 1.89e-01 1.46e+01 angle pdb=" N LYS B 85 " pdb=" CA LYS B 85 " pdb=" C LYS B 85 " ideal model delta sigma weight residual 112.58 108.25 4.33 1.22e+00 6.72e-01 1.26e+01 ... (remaining 23897 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.34: 10117 35.34 - 70.68: 435 70.68 - 106.01: 35 106.01 - 141.35: 2 141.35 - 176.69: 9 Dihedral angle restraints: 10598 sinusoidal: 4914 harmonic: 5684 Sorted by residual: dihedral pdb=" O4' U E -4 " pdb=" C1' U E -4 " pdb=" N1 U E -4 " pdb=" C2 U E -4 " ideal model delta sinusoidal sigma weight residual 200.00 33.31 166.69 1 1.50e+01 4.44e-03 8.42e+01 dihedral pdb=" O4' U D 7 " pdb=" C1' U D 7 " pdb=" N1 U D 7 " pdb=" C2 U D 7 " ideal model delta sinusoidal sigma weight residual 200.00 33.47 166.53 1 1.50e+01 4.44e-03 8.42e+01 dihedral pdb=" O4' C D 1 " pdb=" C1' C D 1 " pdb=" N1 C D 1 " pdb=" C2 C D 1 " ideal model delta sinusoidal sigma weight residual -160.00 5.18 -165.18 1 1.50e+01 4.44e-03 8.39e+01 ... (remaining 10595 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1924 0.040 - 0.079: 496 0.079 - 0.119: 153 0.119 - 0.159: 25 0.159 - 0.198: 5 Chirality restraints: 2603 Sorted by residual: chirality pdb=" C1' U D 7 " pdb=" O4' U D 7 " pdb=" C2' U D 7 " pdb=" N1 U D 7 " both_signs ideal model delta sigma weight residual False 2.47 2.27 0.20 2.00e-01 2.50e+01 9.82e-01 chirality pdb=" CG LEU A 691 " pdb=" CB LEU A 691 " pdb=" CD1 LEU A 691 " pdb=" CD2 LEU A 691 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.84e-01 chirality pdb=" CA ASP A 190 " pdb=" N ASP A 190 " pdb=" C ASP A 190 " pdb=" CB ASP A 190 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.60e-01 ... (remaining 2600 not shown) Planarity restraints: 2878 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A1463 " -0.042 5.00e-02 4.00e+02 6.46e-02 6.68e+00 pdb=" N PRO A1464 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO A1464 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A1464 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' C D 9 " -0.028 2.00e-02 2.50e+03 1.48e-02 4.93e+00 pdb=" N1 C D 9 " 0.032 2.00e-02 2.50e+03 pdb=" C2 C D 9 " -0.002 2.00e-02 2.50e+03 pdb=" O2 C D 9 " 0.006 2.00e-02 2.50e+03 pdb=" N3 C D 9 " -0.002 2.00e-02 2.50e+03 pdb=" C4 C D 9 " -0.003 2.00e-02 2.50e+03 pdb=" N4 C D 9 " -0.008 2.00e-02 2.50e+03 pdb=" C5 C D 9 " 0.001 2.00e-02 2.50e+03 pdb=" C6 C D 9 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 146 " 0.010 2.00e-02 2.50e+03 2.08e-02 4.32e+00 pdb=" C ASN A 146 " -0.036 2.00e-02 2.50e+03 pdb=" O ASN A 146 " 0.013 2.00e-02 2.50e+03 pdb=" N LYS A 147 " 0.012 2.00e-02 2.50e+03 ... (remaining 2875 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1421 2.74 - 3.28: 15445 3.28 - 3.82: 26245 3.82 - 4.36: 31196 4.36 - 4.90: 54802 Nonbonded interactions: 129109 Sorted by model distance: nonbonded pdb=" O THR A 456 " pdb=" OG1 THR A 456 " model vdw 2.201 3.040 nonbonded pdb=" OG1 THR A 739 " pdb=" OD1 ASP A 741 " model vdw 2.215 3.040 nonbonded pdb=" N GLU B 181 " pdb=" OE1 GLU B 181 " model vdw 2.226 3.120 nonbonded pdb=" O LEU A 961 " pdb=" NZ LYS A1514 " model vdw 2.262 3.120 nonbonded pdb=" OG SER A 680 " pdb=" O GLY A 859 " model vdw 2.272 3.040 ... (remaining 129104 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: 4.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.700 Check model and map are aligned: 0.140 Set scattering table: 0.140 Process input model: 48.070 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 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 : 0.003 0.042 17534 Z= 0.124 Angle : 0.609 11.452 23923 Z= 0.327 Chirality : 0.040 0.198 2603 Planarity : 0.004 0.065 2878 Dihedral : 18.861 176.689 6944 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.72 % Favored : 94.12 % Rotamer: Outliers : 2.51 % Allowed : 24.13 % Favored : 73.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.19), residues: 1957 helix: 1.67 (0.22), residues: 626 sheet: -0.07 (0.32), residues: 268 loop : -1.83 (0.18), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 26 HIS 0.003 0.001 HIS A1617 PHE 0.029 0.001 PHE A 795 TYR 0.020 0.001 TYR B 76 ARG 0.008 0.000 ARG A 719 Details of bonding type rmsd hydrogen bonds : bond 0.19146 ( 564) hydrogen bonds : angle 6.26117 ( 1684) metal coordination : bond 0.00285 ( 16) metal coordination : angle 1.87675 ( 21) covalent geometry : bond 0.00254 (17518) covalent geometry : angle 0.60680 (23902) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3914 Ramachandran restraints generated. 1957 Oldfield, 0 Emsley, 1957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3914 Ramachandran restraints generated. 1957 Oldfield, 0 Emsley, 1957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 125 time to evaluate : 1.824 Fit side-chains REVERT: A 880 ILE cc_start: 0.6215 (OUTLIER) cc_final: 0.5829 (mp) outliers start: 43 outliers final: 38 residues processed: 166 average time/residue: 1.1831 time to fit residues: 224.7492 Evaluate side-chains 160 residues out of total 1733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 121 time to evaluate : 2.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 523 SER Chi-restraints excluded: chain B residue 555 ILE Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 328 HIS Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 489 SER Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 542 ASP Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 751 THR Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 880 ILE Chi-restraints excluded: chain A residue 956 CYS Chi-restraints excluded: chain A residue 1001 SER Chi-restraints excluded: chain A residue 1009 THR Chi-restraints excluded: chain A residue 1454 LEU Chi-restraints excluded: chain A residue 1467 SER Chi-restraints excluded: chain A residue 1586 ASP Chi-restraints excluded: chain A residue 1652 SER Chi-restraints excluded: chain A residue 1671 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 169 optimal weight: 5.9990 chunk 152 optimal weight: 0.4980 chunk 84 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 157 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 95 optimal weight: 0.6980 chunk 117 optimal weight: 0.9990 chunk 182 optimal weight: 4.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN A 286 GLN A 394 HIS A1544 ASN ** A1617 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.173622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.137297 restraints weight = 22474.986| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 2.65 r_work: 0.3457 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.0672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17534 Z= 0.131 Angle : 0.580 10.158 23923 Z= 0.299 Chirality : 0.041 0.206 2603 Planarity : 0.004 0.052 2878 Dihedral : 17.489 178.642 3038 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.39 % Favored : 93.51 % Rotamer: Outliers : 4.49 % Allowed : 20.75 % Favored : 74.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.19), residues: 1957 helix: 1.52 (0.21), residues: 638 sheet: -0.20 (0.32), residues: 273 loop : -1.79 (0.18), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 26 HIS 0.004 0.001 HIS B 585 PHE 0.015 0.001 PHE B 491 TYR 0.018 0.001 TYR B 704 ARG 0.007 0.000 ARG A 719 Details of bonding type rmsd hydrogen bonds : bond 0.04561 ( 564) hydrogen bonds : angle 4.65239 ( 1684) metal coordination : bond 0.00504 ( 16) metal coordination : angle 1.83323 ( 21) covalent geometry : bond 0.00291 (17518) covalent geometry : angle 0.57754 (23902) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3914 Ramachandran restraints generated. 1957 Oldfield, 0 Emsley, 1957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3914 Ramachandran restraints generated. 1957 Oldfield, 0 Emsley, 1957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 131 time to evaluate : 2.828 Fit side-chains revert: symmetry clash REVERT: B 348 PHE cc_start: 0.6279 (OUTLIER) cc_final: 0.5631 (t80) REVERT: B 395 GLN cc_start: 0.8131 (OUTLIER) cc_final: 0.7893 (tt0) REVERT: B 559 GLN cc_start: 0.5471 (OUTLIER) cc_final: 0.5174 (mp10) REVERT: A 415 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7294 (tp30) REVERT: A 639 GLU cc_start: 0.7450 (tm-30) cc_final: 0.7225 (tm-30) REVERT: A 1588 ARG cc_start: 0.7381 (OUTLIER) cc_final: 0.6661 (mmt180) outliers start: 77 outliers final: 27 residues processed: 192 average time/residue: 1.3408 time to fit residues: 291.8689 Evaluate side-chains 154 residues out of total 1733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 122 time to evaluate : 1.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 235 GLU Chi-restraints excluded: chain B residue 348 PHE Chi-restraints excluded: chain B residue 395 GLN Chi-restraints excluded: chain B residue 551 GLN Chi-restraints excluded: chain B residue 559 GLN Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 627 CYS Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 1454 LEU Chi-restraints excluded: chain A residue 1475 ILE Chi-restraints excluded: chain A residue 1529 GLU Chi-restraints excluded: chain A residue 1586 ASP Chi-restraints excluded: chain A residue 1588 ARG Chi-restraints excluded: chain A residue 1643 VAL Chi-restraints excluded: chain A residue 1652 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 83 optimal weight: 4.9990 chunk 26 optimal weight: 0.4980 chunk 64 optimal weight: 0.5980 chunk 44 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 20 optimal weight: 7.9990 chunk 120 optimal weight: 0.8980 chunk 67 optimal weight: 0.1980 chunk 102 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 432 GLN A 116 ASN A 668 GLN ** A1615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1617 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.171822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.135649 restraints weight = 22390.068| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 2.59 r_work: 0.3432 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.0965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17534 Z= 0.144 Angle : 0.595 10.358 23923 Z= 0.305 Chirality : 0.042 0.214 2603 Planarity : 0.004 0.048 2878 Dihedral : 17.296 178.499 3003 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.69 % Favored : 93.15 % Rotamer: Outliers : 4.55 % Allowed : 20.80 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.19), residues: 1957 helix: 1.43 (0.21), residues: 636 sheet: -0.23 (0.32), residues: 272 loop : -1.87 (0.18), residues: 1049 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 278 HIS 0.007 0.001 HIS B 699 PHE 0.016 0.001 PHE B 491 TYR 0.020 0.001 TYR B 704 ARG 0.008 0.000 ARG A 719 Details of bonding type rmsd hydrogen bonds : bond 0.04650 ( 564) hydrogen bonds : angle 4.43912 ( 1684) metal coordination : bond 0.00587 ( 16) metal coordination : angle 1.92006 ( 21) covalent geometry : bond 0.00331 (17518) covalent geometry : angle 0.59221 (23902) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3914 Ramachandran restraints generated. 1957 Oldfield, 0 Emsley, 1957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3914 Ramachandran restraints generated. 1957 Oldfield, 0 Emsley, 1957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 128 time to evaluate : 2.234 Fit side-chains REVERT: B 348 PHE cc_start: 0.6336 (OUTLIER) cc_final: 0.5649 (t80) REVERT: B 395 GLN cc_start: 0.8164 (OUTLIER) cc_final: 0.7938 (tt0) REVERT: B 559 GLN cc_start: 0.5463 (OUTLIER) cc_final: 0.5233 (mp10) REVERT: B 631 LEU cc_start: 0.6111 (OUTLIER) cc_final: 0.5640 (mt) REVERT: B 663 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.8135 (tttm) REVERT: A 293 ILE cc_start: 0.4658 (OUTLIER) cc_final: 0.4252 (tp) REVERT: A 415 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7031 (tp30) REVERT: A 639 GLU cc_start: 0.7497 (tm-30) cc_final: 0.7289 (tm-30) REVERT: A 697 ARG cc_start: 0.7324 (OUTLIER) cc_final: 0.6829 (mmt90) REVERT: A 880 ILE cc_start: 0.6035 (OUTLIER) cc_final: 0.5678 (mp) REVERT: A 996 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8565 (mt) REVERT: A 1588 ARG cc_start: 0.7439 (OUTLIER) cc_final: 0.6748 (mmt180) outliers start: 78 outliers final: 39 residues processed: 188 average time/residue: 1.2364 time to fit residues: 262.3700 Evaluate side-chains 170 residues out of total 1733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 120 time to evaluate : 1.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 216 MET Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 318 ASP Chi-restraints excluded: chain B residue 348 PHE Chi-restraints excluded: chain B residue 395 GLN Chi-restraints excluded: chain B residue 413 MET Chi-restraints excluded: chain B residue 516 CYS Chi-restraints excluded: chain B residue 551 GLN Chi-restraints excluded: chain B residue 559 GLN Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 627 CYS Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 638 VAL Chi-restraints excluded: chain B residue 663 LYS Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 567 LYS Chi-restraints excluded: chain A residue 697 ARG Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 880 ILE Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1454 LEU Chi-restraints excluded: chain A residue 1468 ILE Chi-restraints excluded: chain A residue 1475 ILE Chi-restraints excluded: chain A residue 1529 GLU Chi-restraints excluded: chain A residue 1586 ASP Chi-restraints excluded: chain A residue 1588 ARG Chi-restraints excluded: chain A residue 1643 VAL Chi-restraints excluded: chain A residue 1652 SER Chi-restraints excluded: chain A residue 1671 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 63 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 12 optimal weight: 7.9990 chunk 13 optimal weight: 4.9990 chunk 194 optimal weight: 9.9990 chunk 177 optimal weight: 0.8980 chunk 32 optimal weight: 0.0980 chunk 70 optimal weight: 0.9990 chunk 55 optimal weight: 0.3980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN ** A1617 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.173164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.136977 restraints weight = 22293.120| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 2.80 r_work: 0.3456 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.1052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17534 Z= 0.115 Angle : 0.555 9.403 23923 Z= 0.285 Chirality : 0.041 0.216 2603 Planarity : 0.004 0.049 2878 Dihedral : 17.204 178.331 3003 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.03 % Favored : 93.82 % Rotamer: Outliers : 4.49 % Allowed : 21.79 % Favored : 73.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.19), residues: 1957 helix: 1.59 (0.21), residues: 636 sheet: -0.21 (0.32), residues: 272 loop : -1.84 (0.18), residues: 1049 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 278 HIS 0.003 0.001 HIS B 699 PHE 0.012 0.001 PHE B 491 TYR 0.016 0.001 TYR B 704 ARG 0.009 0.000 ARG A 719 Details of bonding type rmsd hydrogen bonds : bond 0.03861 ( 564) hydrogen bonds : angle 4.28576 ( 1684) metal coordination : bond 0.00367 ( 16) metal coordination : angle 1.86985 ( 21) covalent geometry : bond 0.00257 (17518) covalent geometry : angle 0.55234 (23902) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3914 Ramachandran restraints generated. 1957 Oldfield, 0 Emsley, 1957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3914 Ramachandran restraints generated. 1957 Oldfield, 0 Emsley, 1957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 123 time to evaluate : 1.643 Fit side-chains REVERT: B 59 LYS cc_start: 0.6445 (OUTLIER) cc_final: 0.6243 (tppp) REVERT: B 210 HIS cc_start: 0.6812 (m90) cc_final: 0.6583 (m90) REVERT: B 348 PHE cc_start: 0.6300 (OUTLIER) cc_final: 0.5664 (t80) REVERT: B 395 GLN cc_start: 0.8125 (OUTLIER) cc_final: 0.7896 (tt0) REVERT: B 631 LEU cc_start: 0.6111 (OUTLIER) cc_final: 0.5627 (mt) REVERT: B 663 LYS cc_start: 0.8359 (OUTLIER) cc_final: 0.8127 (tttm) REVERT: A 293 ILE cc_start: 0.4515 (OUTLIER) cc_final: 0.4143 (tp) REVERT: A 415 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.6983 (tp30) REVERT: A 639 GLU cc_start: 0.7447 (tm-30) cc_final: 0.7246 (tm-30) REVERT: A 697 ARG cc_start: 0.7217 (OUTLIER) cc_final: 0.6760 (mmt90) REVERT: A 1588 ARG cc_start: 0.7435 (OUTLIER) cc_final: 0.6902 (mmm-85) outliers start: 77 outliers final: 41 residues processed: 184 average time/residue: 1.3113 time to fit residues: 274.1305 Evaluate side-chains 169 residues out of total 1733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 119 time to evaluate : 1.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 318 ASP Chi-restraints excluded: chain B residue 348 PHE Chi-restraints excluded: chain B residue 395 GLN Chi-restraints excluded: chain B residue 491 PHE Chi-restraints excluded: chain B residue 516 CYS Chi-restraints excluded: chain B residue 551 GLN Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 627 CYS Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 638 VAL Chi-restraints excluded: chain B residue 663 LYS Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 229 LYS Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 542 ASP Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 567 LYS Chi-restraints excluded: chain A residue 697 ARG Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 1454 LEU Chi-restraints excluded: chain A residue 1468 ILE Chi-restraints excluded: chain A residue 1475 ILE Chi-restraints excluded: chain A residue 1529 GLU Chi-restraints excluded: chain A residue 1549 LEU Chi-restraints excluded: chain A residue 1586 ASP Chi-restraints excluded: chain A residue 1588 ARG Chi-restraints excluded: chain A residue 1631 VAL Chi-restraints excluded: chain A residue 1643 VAL Chi-restraints excluded: chain A residue 1652 SER Chi-restraints excluded: chain A residue 1671 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 123 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 72 optimal weight: 0.0980 chunk 49 optimal weight: 8.9990 chunk 184 optimal weight: 1.9990 chunk 173 optimal weight: 9.9990 chunk 149 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 178 optimal weight: 9.9990 overall best weight: 1.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN A 146 ASN ** A1617 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.168978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.132872 restraints weight = 22588.884| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 2.95 r_work: 0.3395 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 17534 Z= 0.215 Angle : 0.672 10.556 23923 Z= 0.346 Chirality : 0.045 0.240 2603 Planarity : 0.005 0.053 2878 Dihedral : 17.399 178.012 3003 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.31 % Favored : 92.49 % Rotamer: Outliers : 5.07 % Allowed : 21.15 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.19), residues: 1957 helix: 1.19 (0.21), residues: 636 sheet: -0.31 (0.32), residues: 266 loop : -1.96 (0.18), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 612 HIS 0.006 0.001 HIS B 493 PHE 0.023 0.002 PHE A 795 TYR 0.023 0.002 TYR B 277 ARG 0.010 0.001 ARG A 719 Details of bonding type rmsd hydrogen bonds : bond 0.05635 ( 564) hydrogen bonds : angle 4.51938 ( 1684) metal coordination : bond 0.00773 ( 16) metal coordination : angle 1.91967 ( 21) covalent geometry : bond 0.00512 (17518) covalent geometry : angle 0.67027 (23902) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3914 Ramachandran restraints generated. 1957 Oldfield, 0 Emsley, 1957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3914 Ramachandran restraints generated. 1957 Oldfield, 0 Emsley, 1957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 123 time to evaluate : 2.051 Fit side-chains revert: symmetry clash REVERT: B 22 LYS cc_start: 0.7609 (OUTLIER) cc_final: 0.7207 (tptp) REVERT: B 41 ARG cc_start: 0.5201 (OUTLIER) cc_final: 0.4839 (ttt-90) REVERT: B 395 GLN cc_start: 0.8231 (OUTLIER) cc_final: 0.7983 (tt0) REVERT: B 631 LEU cc_start: 0.6109 (OUTLIER) cc_final: 0.5678 (mt) REVERT: B 663 LYS cc_start: 0.8386 (OUTLIER) cc_final: 0.8135 (tttm) REVERT: A 293 ILE cc_start: 0.4778 (OUTLIER) cc_final: 0.4387 (tp) REVERT: A 415 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.7130 (tp30) REVERT: A 582 ASN cc_start: 0.7322 (p0) cc_final: 0.7115 (p0) REVERT: A 639 GLU cc_start: 0.7642 (tm-30) cc_final: 0.7401 (tm-30) REVERT: A 697 ARG cc_start: 0.7225 (OUTLIER) cc_final: 0.6743 (mmt90) REVERT: A 880 ILE cc_start: 0.6128 (OUTLIER) cc_final: 0.5744 (mp) REVERT: A 1588 ARG cc_start: 0.7587 (OUTLIER) cc_final: 0.6859 (mmt180) outliers start: 87 outliers final: 52 residues processed: 189 average time/residue: 1.3365 time to fit residues: 285.2461 Evaluate side-chains 182 residues out of total 1733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 120 time to evaluate : 1.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 LYS Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 41 ARG Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 216 MET Chi-restraints excluded: chain B residue 219 CYS Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 235 GLU Chi-restraints excluded: chain B residue 318 ASP Chi-restraints excluded: chain B residue 395 GLN Chi-restraints excluded: chain B residue 413 MET Chi-restraints excluded: chain B residue 491 PHE Chi-restraints excluded: chain B residue 516 CYS Chi-restraints excluded: chain B residue 523 SER Chi-restraints excluded: chain B residue 551 GLN Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 627 CYS Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 638 VAL Chi-restraints excluded: chain B residue 663 LYS Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 229 LYS Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 542 ASP Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 567 LYS Chi-restraints excluded: chain A residue 697 ARG Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 839 THR Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 880 ILE Chi-restraints excluded: chain A residue 1001 SER Chi-restraints excluded: chain A residue 1454 LEU Chi-restraints excluded: chain A residue 1468 ILE Chi-restraints excluded: chain A residue 1475 ILE Chi-restraints excluded: chain A residue 1529 GLU Chi-restraints excluded: chain A residue 1549 LEU Chi-restraints excluded: chain A residue 1586 ASP Chi-restraints excluded: chain A residue 1588 ARG Chi-restraints excluded: chain A residue 1643 VAL Chi-restraints excluded: chain A residue 1652 SER Chi-restraints excluded: chain A residue 1671 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 90 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 135 optimal weight: 1.9990 chunk 185 optimal weight: 5.9990 chunk 146 optimal weight: 1.9990 chunk 119 optimal weight: 0.5980 chunk 181 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 165 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN A 146 ASN A1617 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.171504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.135483 restraints weight = 22572.445| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 2.84 r_work: 0.3426 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17534 Z= 0.128 Angle : 0.592 10.611 23923 Z= 0.302 Chirality : 0.042 0.226 2603 Planarity : 0.004 0.053 2878 Dihedral : 17.255 177.719 3002 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.34 % Favored : 93.51 % Rotamer: Outliers : 4.43 % Allowed : 22.61 % Favored : 72.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.19), residues: 1957 helix: 1.41 (0.21), residues: 637 sheet: -0.34 (0.31), residues: 277 loop : -1.89 (0.18), residues: 1043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 612 HIS 0.004 0.001 HIS A 789 PHE 0.023 0.001 PHE A 795 TYR 0.018 0.001 TYR B 704 ARG 0.007 0.000 ARG A 719 Details of bonding type rmsd hydrogen bonds : bond 0.04198 ( 564) hydrogen bonds : angle 4.32819 ( 1684) metal coordination : bond 0.00407 ( 16) metal coordination : angle 1.98741 ( 21) covalent geometry : bond 0.00289 (17518) covalent geometry : angle 0.58921 (23902) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3914 Ramachandran restraints generated. 1957 Oldfield, 0 Emsley, 1957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3914 Ramachandran restraints generated. 1957 Oldfield, 0 Emsley, 1957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 118 time to evaluate : 1.813 Fit side-chains revert: symmetry clash REVERT: B 22 LYS cc_start: 0.7628 (OUTLIER) cc_final: 0.7246 (tptp) REVERT: B 348 PHE cc_start: 0.6439 (OUTLIER) cc_final: 0.5754 (t80) REVERT: B 395 GLN cc_start: 0.8148 (OUTLIER) cc_final: 0.7906 (tt0) REVERT: B 631 LEU cc_start: 0.6090 (OUTLIER) cc_final: 0.5635 (mt) REVERT: B 663 LYS cc_start: 0.8388 (OUTLIER) cc_final: 0.8156 (tttm) REVERT: A 293 ILE cc_start: 0.4687 (OUTLIER) cc_final: 0.4313 (tp) REVERT: A 415 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.6846 (tp30) REVERT: A 639 GLU cc_start: 0.7557 (tm-30) cc_final: 0.7338 (tm-30) REVERT: A 697 ARG cc_start: 0.7129 (OUTLIER) cc_final: 0.6685 (mmt90) REVERT: A 870 ASP cc_start: 0.7297 (m-30) cc_final: 0.7073 (m-30) REVERT: A 1493 LYS cc_start: 0.5496 (mppt) cc_final: 0.5292 (mppt) REVERT: A 1588 ARG cc_start: 0.7436 (OUTLIER) cc_final: 0.6722 (mmt180) REVERT: A 1677 ARG cc_start: 0.7556 (ttp-170) cc_final: 0.7320 (ttp-170) outliers start: 76 outliers final: 51 residues processed: 177 average time/residue: 1.1923 time to fit residues: 237.7328 Evaluate side-chains 176 residues out of total 1733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 116 time to evaluate : 1.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 LYS Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 85 LYS Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 216 MET Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 235 GLU Chi-restraints excluded: chain B residue 318 ASP Chi-restraints excluded: chain B residue 348 PHE Chi-restraints excluded: chain B residue 395 GLN Chi-restraints excluded: chain B residue 413 MET Chi-restraints excluded: chain B residue 491 PHE Chi-restraints excluded: chain B residue 516 CYS Chi-restraints excluded: chain B residue 523 SER Chi-restraints excluded: chain B residue 551 GLN Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 627 CYS Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 638 VAL Chi-restraints excluded: chain B residue 641 GLU Chi-restraints excluded: chain B residue 663 LYS Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 229 LYS Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 542 ASP Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 567 LYS Chi-restraints excluded: chain A residue 697 ARG Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 1454 LEU Chi-restraints excluded: chain A residue 1468 ILE Chi-restraints excluded: chain A residue 1475 ILE Chi-restraints excluded: chain A residue 1529 GLU Chi-restraints excluded: chain A residue 1549 LEU Chi-restraints excluded: chain A residue 1586 ASP Chi-restraints excluded: chain A residue 1588 ARG Chi-restraints excluded: chain A residue 1643 VAL Chi-restraints excluded: chain A residue 1652 SER Chi-restraints excluded: chain A residue 1671 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 26 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 7 optimal weight: 0.0970 chunk 80 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 117 optimal weight: 0.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN A 146 ASN A1617 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.171798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.136158 restraints weight = 22355.634| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 2.54 r_work: 0.3437 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17534 Z= 0.125 Angle : 0.591 14.034 23923 Z= 0.301 Chirality : 0.042 0.223 2603 Planarity : 0.004 0.054 2878 Dihedral : 17.191 177.842 3001 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.64 % Favored : 93.20 % Rotamer: Outliers : 4.25 % Allowed : 23.08 % Favored : 72.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.19), residues: 1957 helix: 1.51 (0.21), residues: 637 sheet: -0.26 (0.32), residues: 267 loop : -1.86 (0.18), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 612 HIS 0.004 0.001 HIS B 699 PHE 0.024 0.001 PHE A 795 TYR 0.017 0.001 TYR B 704 ARG 0.009 0.000 ARG A 719 Details of bonding type rmsd hydrogen bonds : bond 0.04050 ( 564) hydrogen bonds : angle 4.26432 ( 1684) metal coordination : bond 0.00361 ( 16) metal coordination : angle 1.88200 ( 21) covalent geometry : bond 0.00281 (17518) covalent geometry : angle 0.58816 (23902) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3914 Ramachandran restraints generated. 1957 Oldfield, 0 Emsley, 1957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3914 Ramachandran restraints generated. 1957 Oldfield, 0 Emsley, 1957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 119 time to evaluate : 2.343 Fit side-chains revert: symmetry clash REVERT: B 22 LYS cc_start: 0.7684 (OUTLIER) cc_final: 0.7268 (tptp) REVERT: B 181 GLU cc_start: 0.8009 (pm20) cc_final: 0.7798 (pm20) REVERT: B 348 PHE cc_start: 0.6452 (OUTLIER) cc_final: 0.5726 (t80) REVERT: B 395 GLN cc_start: 0.8135 (OUTLIER) cc_final: 0.7889 (tt0) REVERT: B 631 LEU cc_start: 0.6277 (OUTLIER) cc_final: 0.5806 (mt) REVERT: B 663 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.8162 (tttm) REVERT: A 293 ILE cc_start: 0.4531 (OUTLIER) cc_final: 0.4100 (tp) REVERT: A 415 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7001 (tp30) REVERT: A 639 GLU cc_start: 0.7568 (tm-30) cc_final: 0.7358 (tm-30) REVERT: A 697 ARG cc_start: 0.7174 (OUTLIER) cc_final: 0.6719 (mmt90) REVERT: A 830 PHE cc_start: 0.8560 (OUTLIER) cc_final: 0.8201 (m-80) REVERT: A 870 ASP cc_start: 0.7261 (m-30) cc_final: 0.7045 (m-30) REVERT: A 880 ILE cc_start: 0.6157 (OUTLIER) cc_final: 0.5782 (mp) REVERT: A 1586 ASP cc_start: 0.7294 (OUTLIER) cc_final: 0.7044 (OUTLIER) REVERT: A 1588 ARG cc_start: 0.7396 (OUTLIER) cc_final: 0.6681 (mmt180) REVERT: A 1677 ARG cc_start: 0.7638 (ttp-170) cc_final: 0.7385 (ttp-170) outliers start: 73 outliers final: 49 residues processed: 175 average time/residue: 1.2366 time to fit residues: 244.6797 Evaluate side-chains 176 residues out of total 1733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 116 time to evaluate : 1.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 LYS Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 216 MET Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 235 GLU Chi-restraints excluded: chain B residue 318 ASP Chi-restraints excluded: chain B residue 348 PHE Chi-restraints excluded: chain B residue 395 GLN Chi-restraints excluded: chain B residue 413 MET Chi-restraints excluded: chain B residue 491 PHE Chi-restraints excluded: chain B residue 516 CYS Chi-restraints excluded: chain B residue 523 SER Chi-restraints excluded: chain B residue 551 GLN Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 627 CYS Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 638 VAL Chi-restraints excluded: chain B residue 641 GLU Chi-restraints excluded: chain B residue 663 LYS Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 229 LYS Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 542 ASP Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 567 LYS Chi-restraints excluded: chain A residue 697 ARG Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 830 PHE Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 880 ILE Chi-restraints excluded: chain A residue 1001 SER Chi-restraints excluded: chain A residue 1454 LEU Chi-restraints excluded: chain A residue 1468 ILE Chi-restraints excluded: chain A residue 1475 ILE Chi-restraints excluded: chain A residue 1529 GLU Chi-restraints excluded: chain A residue 1549 LEU Chi-restraints excluded: chain A residue 1586 ASP Chi-restraints excluded: chain A residue 1588 ARG Chi-restraints excluded: chain A residue 1643 VAL Chi-restraints excluded: chain A residue 1652 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 87 optimal weight: 5.9990 chunk 183 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 105 optimal weight: 0.3980 chunk 26 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 9 optimal weight: 0.4980 chunk 139 optimal weight: 0.6980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN A1617 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.171452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.135701 restraints weight = 22353.816| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 2.84 r_work: 0.3436 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.1382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17534 Z= 0.136 Angle : 0.598 13.414 23923 Z= 0.306 Chirality : 0.042 0.224 2603 Planarity : 0.004 0.055 2878 Dihedral : 17.183 177.801 3001 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.59 % Favored : 93.25 % Rotamer: Outliers : 4.14 % Allowed : 23.43 % Favored : 72.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.19), residues: 1957 helix: 1.50 (0.21), residues: 637 sheet: -0.25 (0.32), residues: 267 loop : -1.89 (0.18), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 278 HIS 0.004 0.001 HIS B 699 PHE 0.025 0.001 PHE A 795 TYR 0.019 0.001 TYR B 704 ARG 0.015 0.000 ARG A 145 Details of bonding type rmsd hydrogen bonds : bond 0.04202 ( 564) hydrogen bonds : angle 4.27540 ( 1684) metal coordination : bond 0.00443 ( 16) metal coordination : angle 1.88948 ( 21) covalent geometry : bond 0.00311 (17518) covalent geometry : angle 0.59588 (23902) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3914 Ramachandran restraints generated. 1957 Oldfield, 0 Emsley, 1957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3914 Ramachandran restraints generated. 1957 Oldfield, 0 Emsley, 1957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 120 time to evaluate : 1.749 Fit side-chains revert: symmetry clash REVERT: B 22 LYS cc_start: 0.7660 (OUTLIER) cc_final: 0.7274 (tptp) REVERT: B 348 PHE cc_start: 0.6374 (OUTLIER) cc_final: 0.5655 (t80) REVERT: B 395 GLN cc_start: 0.8161 (OUTLIER) cc_final: 0.7910 (tt0) REVERT: B 631 LEU cc_start: 0.6254 (OUTLIER) cc_final: 0.5780 (mt) REVERT: B 663 LYS cc_start: 0.8395 (OUTLIER) cc_final: 0.8162 (tttm) REVERT: A 293 ILE cc_start: 0.4727 (OUTLIER) cc_final: 0.4263 (tp) REVERT: A 296 LEU cc_start: 0.6403 (OUTLIER) cc_final: 0.5825 (tp) REVERT: A 415 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7008 (tp30) REVERT: A 582 ASN cc_start: 0.7278 (p0) cc_final: 0.7066 (p0) REVERT: A 639 GLU cc_start: 0.7540 (tm-30) cc_final: 0.7318 (tm-30) REVERT: A 697 ARG cc_start: 0.7031 (OUTLIER) cc_final: 0.6637 (mmt90) REVERT: A 870 ASP cc_start: 0.7288 (m-30) cc_final: 0.7086 (m-30) REVERT: A 880 ILE cc_start: 0.6116 (OUTLIER) cc_final: 0.5748 (mp) REVERT: A 1586 ASP cc_start: 0.7262 (OUTLIER) cc_final: 0.7012 (OUTLIER) REVERT: A 1588 ARG cc_start: 0.7429 (OUTLIER) cc_final: 0.6700 (mmt180) REVERT: A 1677 ARG cc_start: 0.7558 (ttp-170) cc_final: 0.7304 (ttp-170) outliers start: 71 outliers final: 48 residues processed: 176 average time/residue: 1.2667 time to fit residues: 252.4861 Evaluate side-chains 174 residues out of total 1733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 115 time to evaluate : 1.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 LYS Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 85 LYS Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 216 MET Chi-restraints excluded: chain B residue 219 CYS Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 235 GLU Chi-restraints excluded: chain B residue 318 ASP Chi-restraints excluded: chain B residue 348 PHE Chi-restraints excluded: chain B residue 395 GLN Chi-restraints excluded: chain B residue 413 MET Chi-restraints excluded: chain B residue 491 PHE Chi-restraints excluded: chain B residue 516 CYS Chi-restraints excluded: chain B residue 523 SER Chi-restraints excluded: chain B residue 551 GLN Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 627 CYS Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 638 VAL Chi-restraints excluded: chain B residue 641 GLU Chi-restraints excluded: chain B residue 663 LYS Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 229 LYS Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 542 ASP Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 697 ARG Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 880 ILE Chi-restraints excluded: chain A residue 1001 SER Chi-restraints excluded: chain A residue 1468 ILE Chi-restraints excluded: chain A residue 1475 ILE Chi-restraints excluded: chain A residue 1529 GLU Chi-restraints excluded: chain A residue 1549 LEU Chi-restraints excluded: chain A residue 1586 ASP Chi-restraints excluded: chain A residue 1588 ARG Chi-restraints excluded: chain A residue 1643 VAL Chi-restraints excluded: chain A residue 1652 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 37 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 199 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 77 optimal weight: 0.0070 chunk 159 optimal weight: 0.1980 chunk 64 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 190 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 120 optimal weight: 1.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN A1617 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.172963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.136900 restraints weight = 22531.400| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 2.82 r_work: 0.3464 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 17534 Z= 0.113 Angle : 0.577 13.595 23923 Z= 0.293 Chirality : 0.041 0.219 2603 Planarity : 0.004 0.053 2878 Dihedral : 17.086 177.656 2995 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.13 % Favored : 93.77 % Rotamer: Outliers : 3.38 % Allowed : 24.24 % Favored : 72.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.19), residues: 1957 helix: 1.64 (0.21), residues: 637 sheet: -0.14 (0.32), residues: 260 loop : -1.82 (0.18), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 612 HIS 0.004 0.001 HIS B 699 PHE 0.026 0.001 PHE A 795 TYR 0.014 0.001 TYR B 704 ARG 0.010 0.000 ARG A 145 Details of bonding type rmsd hydrogen bonds : bond 0.03652 ( 564) hydrogen bonds : angle 4.18429 ( 1684) metal coordination : bond 0.00304 ( 16) metal coordination : angle 1.90839 ( 21) covalent geometry : bond 0.00249 (17518) covalent geometry : angle 0.57425 (23902) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3914 Ramachandran restraints generated. 1957 Oldfield, 0 Emsley, 1957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3914 Ramachandran restraints generated. 1957 Oldfield, 0 Emsley, 1957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 120 time to evaluate : 2.093 Fit side-chains REVERT: B 22 LYS cc_start: 0.7623 (OUTLIER) cc_final: 0.7231 (tptp) REVERT: B 348 PHE cc_start: 0.6366 (OUTLIER) cc_final: 0.5687 (t80) REVERT: B 395 GLN cc_start: 0.8115 (OUTLIER) cc_final: 0.7873 (tt0) REVERT: B 663 LYS cc_start: 0.8396 (OUTLIER) cc_final: 0.8168 (tttm) REVERT: A 212 ARG cc_start: 0.8107 (OUTLIER) cc_final: 0.7039 (ttm110) REVERT: A 293 ILE cc_start: 0.4801 (OUTLIER) cc_final: 0.4324 (tp) REVERT: A 296 LEU cc_start: 0.6279 (OUTLIER) cc_final: 0.5746 (tp) REVERT: A 415 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.6941 (tp30) REVERT: A 582 ASN cc_start: 0.7248 (p0) cc_final: 0.7037 (p0) REVERT: A 639 GLU cc_start: 0.7506 (tm-30) cc_final: 0.7306 (tm-30) REVERT: A 697 ARG cc_start: 0.7012 (OUTLIER) cc_final: 0.6642 (mmt90) REVERT: A 830 PHE cc_start: 0.8553 (OUTLIER) cc_final: 0.8185 (m-80) REVERT: A 870 ASP cc_start: 0.7156 (m-30) cc_final: 0.6946 (m-30) REVERT: A 880 ILE cc_start: 0.6140 (OUTLIER) cc_final: 0.5766 (mp) REVERT: A 1586 ASP cc_start: 0.7247 (OUTLIER) cc_final: 0.7003 (OUTLIER) REVERT: A 1588 ARG cc_start: 0.7441 (OUTLIER) cc_final: 0.6899 (mmm-85) REVERT: A 1677 ARG cc_start: 0.7531 (ttp-170) cc_final: 0.7268 (ttp-170) outliers start: 58 outliers final: 39 residues processed: 166 average time/residue: 1.5975 time to fit residues: 301.8266 Evaluate side-chains 165 residues out of total 1733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 114 time to evaluate : 3.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 LYS Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 85 LYS Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 216 MET Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 318 ASP Chi-restraints excluded: chain B residue 348 PHE Chi-restraints excluded: chain B residue 395 GLN Chi-restraints excluded: chain B residue 413 MET Chi-restraints excluded: chain B residue 491 PHE Chi-restraints excluded: chain B residue 516 CYS Chi-restraints excluded: chain B residue 551 GLN Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 627 CYS Chi-restraints excluded: chain B residue 638 VAL Chi-restraints excluded: chain B residue 641 GLU Chi-restraints excluded: chain B residue 663 LYS Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 212 ARG Chi-restraints excluded: chain A residue 229 LYS Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 542 ASP Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 697 ARG Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 830 PHE Chi-restraints excluded: chain A residue 880 ILE Chi-restraints excluded: chain A residue 1468 ILE Chi-restraints excluded: chain A residue 1475 ILE Chi-restraints excluded: chain A residue 1529 GLU Chi-restraints excluded: chain A residue 1549 LEU Chi-restraints excluded: chain A residue 1586 ASP Chi-restraints excluded: chain A residue 1588 ARG Chi-restraints excluded: chain A residue 1643 VAL Chi-restraints excluded: chain A residue 1652 SER Chi-restraints excluded: chain A residue 1671 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 163 optimal weight: 0.8980 chunk 192 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 chunk 168 optimal weight: 7.9990 chunk 8 optimal weight: 0.6980 chunk 153 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 74 optimal weight: 0.5980 chunk 63 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN A1617 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.172143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.135970 restraints weight = 22312.629| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 2.89 r_work: 0.3451 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17534 Z= 0.128 Angle : 0.598 15.375 23923 Z= 0.305 Chirality : 0.042 0.231 2603 Planarity : 0.004 0.055 2878 Dihedral : 17.080 177.728 2992 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.59 % Favored : 93.25 % Rotamer: Outliers : 3.21 % Allowed : 24.53 % Favored : 72.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.19), residues: 1957 helix: 1.62 (0.21), residues: 636 sheet: -0.13 (0.32), residues: 262 loop : -1.86 (0.18), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 330 HIS 0.004 0.001 HIS B 699 PHE 0.026 0.001 PHE A 795 TYR 0.019 0.001 TYR B 704 ARG 0.009 0.000 ARG A 719 Details of bonding type rmsd hydrogen bonds : bond 0.03998 ( 564) hydrogen bonds : angle 4.19805 ( 1684) metal coordination : bond 0.00407 ( 16) metal coordination : angle 1.86692 ( 21) covalent geometry : bond 0.00291 (17518) covalent geometry : angle 0.59523 (23902) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3914 Ramachandran restraints generated. 1957 Oldfield, 0 Emsley, 1957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3914 Ramachandran restraints generated. 1957 Oldfield, 0 Emsley, 1957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 117 time to evaluate : 1.849 Fit side-chains REVERT: B 22 LYS cc_start: 0.7631 (OUTLIER) cc_final: 0.7261 (tptp) REVERT: B 348 PHE cc_start: 0.6389 (OUTLIER) cc_final: 0.5669 (t80) REVERT: B 395 GLN cc_start: 0.8146 (OUTLIER) cc_final: 0.7900 (tt0) REVERT: B 631 LEU cc_start: 0.6141 (OUTLIER) cc_final: 0.5661 (mt) REVERT: B 663 LYS cc_start: 0.8400 (OUTLIER) cc_final: 0.8169 (tttm) REVERT: A 212 ARG cc_start: 0.8047 (OUTLIER) cc_final: 0.7124 (ttm110) REVERT: A 293 ILE cc_start: 0.5003 (OUTLIER) cc_final: 0.4543 (tp) REVERT: A 296 LEU cc_start: 0.6391 (OUTLIER) cc_final: 0.5857 (tp) REVERT: A 415 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.6972 (tp30) REVERT: A 582 ASN cc_start: 0.7256 (p0) cc_final: 0.7041 (p0) REVERT: A 639 GLU cc_start: 0.7530 (tm-30) cc_final: 0.7323 (tm-30) REVERT: A 697 ARG cc_start: 0.7018 (OUTLIER) cc_final: 0.6627 (mmt90) REVERT: A 830 PHE cc_start: 0.8553 (OUTLIER) cc_final: 0.8176 (m-80) REVERT: A 880 ILE cc_start: 0.6046 (OUTLIER) cc_final: 0.5698 (mp) REVERT: A 1586 ASP cc_start: 0.7269 (OUTLIER) cc_final: 0.7014 (OUTLIER) REVERT: A 1588 ARG cc_start: 0.7486 (OUTLIER) cc_final: 0.6928 (mmm-85) REVERT: A 1677 ARG cc_start: 0.7543 (ttp-170) cc_final: 0.7267 (ttp-170) outliers start: 55 outliers final: 40 residues processed: 160 average time/residue: 1.2161 time to fit residues: 220.2899 Evaluate side-chains 167 residues out of total 1733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 114 time to evaluate : 1.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 LYS Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 85 LYS Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 216 MET Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 318 ASP Chi-restraints excluded: chain B residue 348 PHE Chi-restraints excluded: chain B residue 395 GLN Chi-restraints excluded: chain B residue 413 MET Chi-restraints excluded: chain B residue 491 PHE Chi-restraints excluded: chain B residue 516 CYS Chi-restraints excluded: chain B residue 551 GLN Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 627 CYS Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 638 VAL Chi-restraints excluded: chain B residue 641 GLU Chi-restraints excluded: chain B residue 663 LYS Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 212 ARG Chi-restraints excluded: chain A residue 229 LYS Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 542 ASP Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 697 ARG Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 830 PHE Chi-restraints excluded: chain A residue 880 ILE Chi-restraints excluded: chain A residue 1468 ILE Chi-restraints excluded: chain A residue 1475 ILE Chi-restraints excluded: chain A residue 1529 GLU Chi-restraints excluded: chain A residue 1549 LEU Chi-restraints excluded: chain A residue 1586 ASP Chi-restraints excluded: chain A residue 1588 ARG Chi-restraints excluded: chain A residue 1643 VAL Chi-restraints excluded: chain A residue 1652 SER Chi-restraints excluded: chain A residue 1671 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 24 optimal weight: 0.8980 chunk 165 optimal weight: 2.9990 chunk 127 optimal weight: 0.9980 chunk 88 optimal weight: 0.3980 chunk 129 optimal weight: 1.9990 chunk 114 optimal weight: 0.0870 chunk 92 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 75 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN A1617 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.173495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.137638 restraints weight = 22407.234| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 2.79 r_work: 0.3467 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 17534 Z= 0.111 Angle : 0.578 15.252 23923 Z= 0.294 Chirality : 0.041 0.232 2603 Planarity : 0.004 0.054 2878 Dihedral : 17.034 177.512 2992 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.93 % Favored : 93.97 % Rotamer: Outliers : 3.44 % Allowed : 24.24 % Favored : 72.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.19), residues: 1957 helix: 1.72 (0.21), residues: 636 sheet: -0.08 (0.32), residues: 260 loop : -1.81 (0.18), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 330 HIS 0.005 0.001 HIS B 699 PHE 0.026 0.001 PHE A 795 TYR 0.016 0.001 TYR B 163 ARG 0.009 0.000 ARG A 719 Details of bonding type rmsd hydrogen bonds : bond 0.03535 ( 564) hydrogen bonds : angle 4.13656 ( 1684) metal coordination : bond 0.00320 ( 16) metal coordination : angle 1.92391 ( 21) covalent geometry : bond 0.00247 (17518) covalent geometry : angle 0.57509 (23902) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10705.33 seconds wall clock time: 186 minutes 57.06 seconds (11217.06 seconds total)