Starting phenix.real_space_refine on Fri Mar 6 03:06:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6mzb_9297/03_2026/6mzb_9297_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/6mzb_9297/03_2026/6mzb_9297.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6mzb_9297/03_2026/6mzb_9297.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6mzb_9297/03_2026/6mzb_9297.map" model { file = "/net/cci-nas-00/data/ceres_data/6mzb_9297/03_2026/6mzb_9297_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6mzb_9297/03_2026/6mzb_9297_trim.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.157 sd= 1.341 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: 8 Type Number sf(0) Gaussians Zn 2 6.06 5 P 2 5.49 5 Mg 2 5.21 5 S 97 5.16 5 C 8991 2.51 5 N 2367 2.21 5 O 2605 1.98 5 H 13839 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27905 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 12982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 807, 12982 Classifications: {'peptide': 807} Link IDs: {'PTRANS': 31, 'TRANS': 775} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "A" Number of atoms: 13314 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 820, 13306 Classifications: {'peptide': 820} Link IDs: {'PTRANS': 31, 'TRANS': 788} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Conformer: "B" Number of residues, atoms: 820, 13306 Classifications: {'peptide': 820} Link IDs: {'PTRANS': 31, 'TRANS': 788} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 bond proxies already assigned to first conformer: 13450 Chain: "C" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 796 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 4, 'TRANS': 43} Chain breaks: 1 Chain: "D" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 763 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 4, 'TRANS': 41} Chain breaks: 1 Chain: "B" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 25 Unusual residues: {' MG': 1, ' ZN': 1, '35G%rna3p': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 2} Modifications used: {'rna3p': 1} Link IDs: {None: 2} Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 25 Unusual residues: {' MG': 1, ' ZN': 1, '35G%rna3p': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 2} Modifications used: {'rna3p': 1} Link IDs: {None: 2} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AGLY A 345 " occ=0.50 ... (12 atoms not shown) pdb=" HA3BGLY A 345 " occ=0.50 Time building chain proxies: 6.17, per 1000 atoms: 0.22 Number of scatterers: 27905 At special positions: 0 Unit cell: (165.048, 122.728, 119.554, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 2 29.99 S 97 16.00 P 2 15.00 Mg 2 11.99 O 2605 8.00 N 2367 7.00 C 8991 6.00 H 13839 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 84 " - pdb=" SG CYS B 92 " distance=2.03 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: 2.52 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 901 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 563 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 599 " pdb=" ZN B 901 " pdb="ZN ZN B 901 " - pdb=" NE2 HIS B 561 " pdb="ZN ZN B 901 " - pdb=" NE2 HIS B 597 " 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3288 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 5 sheets defined 56.3% alpha, 7.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'B' and resid 47 through 66 removed outlier: 3.713A pdb=" N GLN B 52 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N VAL B 53 " --> pdb=" O GLU B 49 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU B 54 " --> pdb=" O LEU B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 88 removed outlier: 3.593A pdb=" N LYS B 78 " --> pdb=" O ARG B 74 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG B 82 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N SER B 85 " --> pdb=" O ARG B 81 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE B 86 " --> pdb=" O ARG B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 123 removed outlier: 3.807A pdb=" N CYS B 122 " --> pdb=" O VAL B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 129 removed outlier: 4.022A pdb=" N GLU B 129 " --> pdb=" O PRO B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 146 removed outlier: 3.679A pdb=" N ALA B 143 " --> pdb=" O VAL B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 167 removed outlier: 4.219A pdb=" N LEU B 167 " --> pdb=" O PHE B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 213 removed outlier: 3.955A pdb=" N GLU B 206 " --> pdb=" O THR B 202 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL B 208 " --> pdb=" O GLU B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 247 removed outlier: 3.842A pdb=" N LEU B 220 " --> pdb=" O GLY B 216 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N PHE B 247 " --> pdb=" O ALA B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 264 removed outlier: 3.955A pdb=" N VAL B 264 " --> pdb=" O ALA B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 294 Processing helix chain 'B' and resid 344 through 351 removed outlier: 3.562A pdb=" N ALA B 349 " --> pdb=" O PRO B 345 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU B 350 " --> pdb=" O THR B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 428 Processing helix chain 'B' and resid 429 through 457 Processing helix chain 'B' and resid 459 through 466 removed outlier: 4.537A pdb=" N GLN B 464 " --> pdb=" O GLU B 461 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU B 465 " --> pdb=" O GLU B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 473 removed outlier: 3.864A pdb=" N ARG B 472 " --> pdb=" O PRO B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 493 removed outlier: 3.758A pdb=" N LYS B 487 " --> pdb=" O ASP B 483 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ILE B 488 " --> pdb=" O GLU B 484 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU B 489 " --> pdb=" O LEU B 485 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU B 491 " --> pdb=" O LYS B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 527 removed outlier: 3.892A pdb=" N VAL B 517 " --> pdb=" O GLU B 513 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LYS B 518 " --> pdb=" O LEU B 514 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU B 527 " --> pdb=" O MET B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 551 removed outlier: 3.691A pdb=" N TYR B 551 " --> pdb=" O VAL B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 576 Processing helix chain 'B' and resid 583 through 596 removed outlier: 3.871A pdb=" N MET B 590 " --> pdb=" O GLU B 586 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR B 592 " --> pdb=" O PHE B 588 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA B 593 " --> pdb=" O ALA B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 613 removed outlier: 3.784A pdb=" N GLN B 609 " --> pdb=" O ASN B 605 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N MET B 610 " --> pdb=" O ASN B 606 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS B 611 " --> pdb=" O LEU B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 620 removed outlier: 3.564A pdb=" N LYS B 618 " --> pdb=" O ASN B 614 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 637 removed outlier: 3.773A pdb=" N LEU B 630 " --> pdb=" O GLU B 626 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLU B 631 " --> pdb=" O ARG B 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 667 removed outlier: 4.147A pdb=" N ILE B 665 " --> pdb=" O ASP B 661 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA B 666 " --> pdb=" O ILE B 662 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR B 667 " --> pdb=" O ALA B 663 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 675 removed outlier: 3.627A pdb=" N LYS B 674 " --> pdb=" O ALA B 670 " (cutoff:3.500A) Processing helix chain 'B' and resid 676 through 686 Processing helix chain 'B' and resid 691 through 700 removed outlier: 3.586A pdb=" N VAL B 696 " --> pdb=" O ARG B 692 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLU B 697 " --> pdb=" O LYS B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 702 through 719 removed outlier: 3.868A pdb=" N LYS B 706 " --> pdb=" O GLU B 702 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR B 715 " --> pdb=" O ALA B 711 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N CYS B 717 " --> pdb=" O MET B 713 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASP B 718 " --> pdb=" O MET B 714 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU B 719 " --> pdb=" O THR B 715 " (cutoff:3.500A) Processing helix chain 'B' and resid 725 through 751 removed outlier: 3.782A pdb=" N LYS B 731 " --> pdb=" O GLU B 727 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N THR B 749 " --> pdb=" O ASP B 745 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL B 750 " --> pdb=" O LEU B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 756 through 764 removed outlier: 5.985A pdb=" N ARG B 761 " --> pdb=" O MET B 758 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ASN B 762 " --> pdb=" O MET B 759 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA B 764 " --> pdb=" O ARG B 761 " (cutoff:3.500A) Processing helix chain 'B' and resid 766 through 778 removed outlier: 3.953A pdb=" N LEU B 770 " --> pdb=" O GLU B 766 " (cutoff:3.500A) Processing helix chain 'B' and resid 781 through 790 removed outlier: 3.901A pdb=" N SER B 787 " --> pdb=" O TYR B 783 " (cutoff:3.500A) Processing helix chain 'B' and resid 793 through 823 removed outlier: 4.235A pdb=" N PHE B 797 " --> pdb=" O ILE B 793 " (cutoff:3.500A) Processing helix chain 'A' and resid 11 through 16 Processing helix chain 'A' and resid 20 through 35 removed outlier: 3.909A pdb=" N LEU A 26 " --> pdb=" O GLN A 22 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ALA A 30 " --> pdb=" O LEU A 26 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N LYS A 31 " --> pdb=" O ARG A 27 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP A 35 " --> pdb=" O LYS A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 66 removed outlier: 3.904A pdb=" N GLU A 59 " --> pdb=" O VAL A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 89 removed outlier: 3.602A pdb=" N PHE A 87 " --> pdb=" O LYS A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 124 Processing helix chain 'A' and resid 138 through 148 removed outlier: 3.857A pdb=" N GLY A 142 " --> pdb=" O MET A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 159 Processing helix chain 'A' and resid 164 through 170 removed outlier: 3.828A pdb=" N THR A 168 " --> pdb=" O ASP A 164 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU A 169 " --> pdb=" O PHE A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 215 removed outlier: 3.786A pdb=" N GLU A 208 " --> pdb=" O THR A 204 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU A 209 " --> pdb=" O GLU A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 220 removed outlier: 3.502A pdb=" N LEU A 220 " --> pdb=" O ASN A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 250 removed outlier: 3.744A pdb=" N PHE A 225 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLY A 245 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N SER A 246 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS A 247 " --> pdb=" O TRP A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 266 removed outlier: 3.800A pdb=" N VAL A 266 " --> pdb=" O ALA A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 290 Processing helix chain 'A' and resid 291 through 297 Processing helix chain 'A' and resid 345 through 354 Processing helix chain 'A' and resid 413 through 430 removed outlier: 3.788A pdb=" N LEU A 419 " --> pdb=" O MET A 415 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N MET A 420 " --> pdb=" O ASP A 416 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER A 422 " --> pdb=" O THR A 418 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU A 423 " --> pdb=" O LEU A 419 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN A 425 " --> pdb=" O GLU A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 458 removed outlier: 3.614A pdb=" N GLU A 438 " --> pdb=" O PRO A 434 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASN A 441 " --> pdb=" O TYR A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 466 removed outlier: 4.146A pdb=" N GLN A 466 " --> pdb=" O ASN A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 482 Processing helix chain 'A' and resid 483 through 493 removed outlier: 4.492A pdb=" N GLU A 489 " --> pdb=" O GLU A 485 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N ILE A 490 " --> pdb=" O GLU A 486 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LEU A 491 " --> pdb=" O LEU A 487 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLN A 492 " --> pdb=" O ALA A 488 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLY A 493 " --> pdb=" O GLU A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 502 Processing helix chain 'A' and resid 514 through 529 removed outlier: 3.622A pdb=" N LEU A 518 " --> pdb=" O THR A 514 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N VAL A 519 " --> pdb=" O GLU A 515 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR A 526 " --> pdb=" O GLY A 522 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N TYR A 527 " --> pdb=" O ILE A 523 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU A 529 " --> pdb=" O MET A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 536 Processing helix chain 'A' and resid 538 through 553 removed outlier: 3.606A pdb=" N SER A 550 " --> pdb=" O MET A 546 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS A 551 " --> pdb=" O TYR A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 577 removed outlier: 3.503A pdb=" N GLY A 564 " --> pdb=" O ASN A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 598 removed outlier: 3.644A pdb=" N THR A 594 " --> pdb=" O LEU A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 615 Processing helix chain 'A' and resid 616 through 622 removed outlier: 3.525A pdb=" N LEU A 621 " --> pdb=" O PRO A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 640 removed outlier: 3.559A pdb=" N LYS A 636 " --> pdb=" O LEU A 632 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N THR A 637 " --> pdb=" O GLU A 633 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU A 638 " --> pdb=" O PHE A 634 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU A 639 " --> pdb=" O GLY A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 669 removed outlier: 3.602A pdb=" N HIS A 660 " --> pdb=" O GLU A 656 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASP A 663 " --> pdb=" O ILE A 659 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE A 664 " --> pdb=" O HIS A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 677 removed outlier: 3.743A pdb=" N LYS A 677 " --> pdb=" O LEU A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 689 removed outlier: 3.982A pdb=" N LYS A 683 " --> pdb=" O THR A 679 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ILE A 684 " --> pdb=" O MET A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 705 removed outlier: 4.420A pdb=" N TYR A 700 " --> pdb=" O GLU A 696 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU A 703 " --> pdb=" O GLN A 699 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN A 705 " --> pdb=" O MET A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 721 removed outlier: 3.911A pdb=" N THR A 717 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU A 721 " --> pdb=" O THR A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 722 through 726 removed outlier: 3.540A pdb=" N LYS A 726 " --> pdb=" O ALA A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 754 removed outlier: 4.653A pdb=" N LYS A 733 " --> pdb=" O GLU A 729 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR A 751 " --> pdb=" O ASP A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 767 removed outlier: 5.461A pdb=" N ARG A 763 " --> pdb=" O MET A 760 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ASN A 764 " --> pdb=" O MET A 761 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N ASP A 767 " --> pdb=" O ASN A 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 780 removed outlier: 3.552A pdb=" N GLY A 775 " --> pdb=" O LYS A 771 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE A 776 " --> pdb=" O LEU A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 792 removed outlier: 3.607A pdb=" N SER A 789 " --> pdb=" O TYR A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 796 through 827 removed outlier: 3.697A pdb=" N ASP A 800 " --> pdb=" O THR A 796 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN A 805 " --> pdb=" O GLY A 801 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA A 811 " --> pdb=" O LYS A 807 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LEU A 812 " --> pdb=" O GLU A 808 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 84 removed outlier: 3.776A pdb=" N ALA C 82 " --> pdb=" O LEU C 78 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N TYR C 84 " --> pdb=" O GLU C 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 81 removed outlier: 4.029A pdb=" N LEU D 81 " --> pdb=" O LEU D 78 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 110 through 113 removed outlier: 4.996A pdb=" N PHE B 111 " --> pdb=" O LEU B 94 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N LEU B 94 " --> pdb=" O PHE B 111 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER B 93 " --> pdb=" O MET B 191 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ILE B 180 " --> pdb=" O VAL B 187 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N VAL B 189 " --> pdb=" O THR B 178 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N THR B 178 " --> pdb=" O VAL B 189 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N MET B 191 " --> pdb=" O LEU B 176 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N LEU B 176 " --> pdb=" O MET B 191 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE B 175 " --> pdb=" O VAL B 151 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL B 151 " --> pdb=" O ILE B 175 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 98 through 100 Processing sheet with id=AA3, first strand: chain 'B' and resid 328 through 330 removed outlier: 3.695A pdb=" N LYS B 328 " --> pdb=" O ASP B 318 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N LYS B 315 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N VAL B 396 " --> pdb=" O LEU B 278 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ILE B 388 " --> pdb=" O VAL B 396 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N VAL B 398 " --> pdb=" O MET B 386 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N MET B 386 " --> pdb=" O VAL B 398 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N THR B 400 " --> pdb=" O LEU B 384 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N LEU B 384 " --> pdb=" O THR B 400 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 133 through 134 removed outlier: 6.542A pdb=" N LEU A 96 " --> pdb=" O ARG A 111 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N PHE A 113 " --> pdb=" O MET A 94 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N MET A 94 " --> pdb=" O PHE A 113 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N VAL A 115 " --> pdb=" O ASP A 92 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ASP A 92 " --> pdb=" O VAL A 115 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N ARG A 93 " --> pdb=" O VAL A 195 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL A 195 " --> pdb=" O ARG A 93 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N VAL A 189 " --> pdb=" O TYR A 99 " (cutoff:3.500A) removed outlier: 11.631A pdb=" N ALA A 101 " --> pdb=" O ASP A 187 " (cutoff:3.500A) removed outlier: 14.548A pdb=" N ASP A 187 " --> pdb=" O ALA A 101 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N ILE A 182 " --> pdb=" O VAL A 189 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N ILE A 191 " --> pdb=" O SER A 180 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N SER A 180 " --> pdb=" O ILE A 191 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N MET A 193 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N LEU A 178 " --> pdb=" O MET A 193 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 328 through 333 removed outlier: 3.641A pdb=" N VAL A 318 " --> pdb=" O ILE A 332 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LYS A 317 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N VAL A 398 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ILE A 390 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N VAL A 400 " --> pdb=" O MET A 388 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N MET A 388 " --> pdb=" O VAL A 400 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N THR A 402 " --> pdb=" O LEU A 386 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N LEU A 386 " --> pdb=" O THR A 402 " (cutoff:3.500A) 621 hydrogen bonds defined for protein. 1761 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.15 Time building geometry restraints manager: 3.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 13809 1.02 - 1.22: 31 1.22 - 1.42: 6045 1.42 - 1.62: 8176 1.62 - 1.82: 162 Bond restraints: 28223 Sorted by residual: bond pdb=" O2P 35G A 903 " pdb=" P 35G A 903 " ideal model delta sigma weight residual 1.587 1.469 0.118 2.00e-02 2.50e+03 3.46e+01 bond pdb=" O1P 35G A 903 " pdb=" P 35G A 903 " ideal model delta sigma weight residual 1.462 1.562 -0.100 2.00e-02 2.50e+03 2.48e+01 bond pdb=" N MET A 798 " pdb=" CA MET A 798 " ideal model delta sigma weight residual 1.459 1.413 0.046 1.28e-02 6.10e+03 1.30e+01 bond pdb=" C MET A 798 " pdb=" O MET A 798 " ideal model delta sigma weight residual 1.236 1.196 0.040 1.26e-02 6.30e+03 1.01e+01 bond pdb=" CA MET A 798 " pdb=" CB MET A 798 " ideal model delta sigma weight residual 1.528 1.481 0.047 1.66e-02 3.63e+03 8.03e+00 ... (remaining 28218 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.81: 51023 8.81 - 17.63: 0 17.63 - 26.44: 1 26.44 - 35.25: 2 35.25 - 44.06: 3 Bond angle restraints: 51029 Sorted by residual: angle pdb=" O1P 35G B 903 " pdb=" P 35G B 903 " pdb=" O5' 35G B 903 " ideal model delta sigma weight residual 113.89 69.83 44.06 3.00e+00 1.11e-01 2.16e+02 angle pdb=" O1P 35G A 903 " pdb=" P 35G A 903 " pdb=" O2P 35G A 903 " ideal model delta sigma weight residual 116.51 80.79 35.72 3.00e+00 1.11e-01 1.42e+02 angle pdb=" O1P 35G B 903 " pdb=" P 35G B 903 " pdb=" O2P 35G B 903 " ideal model delta sigma weight residual 116.51 80.85 35.66 3.00e+00 1.11e-01 1.41e+02 angle pdb=" O2P 35G B 903 " pdb=" P 35G B 903 " pdb=" O5' 35G B 903 " ideal model delta sigma weight residual 101.38 134.85 -33.47 3.00e+00 1.11e-01 1.24e+02 angle pdb=" O2P 35G A 903 " pdb=" P 35G A 903 " pdb=" O5' 35G A 903 " ideal model delta sigma weight residual 101.38 68.89 32.49 3.00e+00 1.11e-01 1.17e+02 ... (remaining 51024 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.56: 12574 26.56 - 53.12: 640 53.12 - 79.68: 68 79.68 - 106.24: 11 106.24 - 132.80: 2 Dihedral angle restraints: 13295 sinusoidal: 7217 harmonic: 6078 Sorted by residual: dihedral pdb=" CB CYS B 84 " pdb=" SG CYS B 84 " pdb=" SG CYS B 92 " pdb=" CB CYS B 92 " ideal model delta sinusoidal sigma weight residual -86.00 -175.31 89.31 1 1.00e+01 1.00e-02 9.49e+01 dihedral pdb=" CA HIS C 75 " pdb=" C HIS C 75 " pdb=" N LEU C 76 " pdb=" CA LEU C 76 " ideal model delta harmonic sigma weight residual 180.00 157.00 23.00 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" C5' 35G B 903 " pdb=" O5' 35G B 903 " pdb=" P 35G B 903 " pdb=" O2P 35G B 903 " ideal model delta sinusoidal sigma weight residual 68.89 -158.31 -132.80 1 3.00e+01 1.11e-03 1.79e+01 ... (remaining 13292 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.466: 2120 0.466 - 0.932: 0 0.932 - 1.398: 0 1.398 - 1.864: 0 1.864 - 2.330: 1 Chirality restraints: 2121 Sorted by residual: chirality pdb=" P 35G B 903 " pdb=" O2P 35G B 903 " pdb=" O3' 35G B 903 " pdb=" O5' 35G B 903 " both_signs ideal model delta sigma weight residual True 3.54 1.21 2.33 2.00e-01 2.50e+01 1.36e+02 chirality pdb=" CA THR A 796 " pdb=" N THR A 796 " pdb=" C THR A 796 " pdb=" CB THR A 796 " both_signs ideal model delta sigma weight residual False 2.53 2.21 0.31 2.00e-01 2.50e+01 2.45e+00 chirality pdb=" P 35G A 903 " pdb=" O2P 35G A 903 " pdb=" O3' 35G A 903 " pdb=" O5' 35G A 903 " both_signs ideal model delta sigma weight residual True 3.54 3.23 0.31 2.00e-01 2.50e+01 2.34e+00 ... (remaining 2118 not shown) Planarity restraints: 4151 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' 35G A 903 " 0.062 2.00e-02 2.50e+03 2.56e-02 1.97e+01 pdb=" C2 35G A 903 " -0.003 2.00e-02 2.50e+03 pdb=" C4 35G A 903 " -0.010 2.00e-02 2.50e+03 pdb=" C5 35G A 903 " -0.009 2.00e-02 2.50e+03 pdb=" C6 35G A 903 " 0.011 2.00e-02 2.50e+03 pdb=" C8 35G A 903 " -0.030 2.00e-02 2.50e+03 pdb=" N1 35G A 903 " 0.012 2.00e-02 2.50e+03 pdb=" N2 35G A 903 " -0.023 2.00e-02 2.50e+03 pdb=" N3 35G A 903 " -0.010 2.00e-02 2.50e+03 pdb=" N7 35G A 903 " -0.025 2.00e-02 2.50e+03 pdb=" N9 35G A 903 " -0.013 2.00e-02 2.50e+03 pdb=" O6 35G A 903 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET A 798 " -0.019 2.00e-02 2.50e+03 3.53e-02 1.25e+01 pdb=" N LEU A 799 " 0.061 2.00e-02 2.50e+03 pdb=" CA LEU A 799 " -0.015 2.00e-02 2.50e+03 pdb=" H LEU A 799 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO C 27 " -0.056 5.00e-02 4.00e+02 8.36e-02 1.12e+01 pdb=" N PRO C 28 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO C 28 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO C 28 " -0.046 5.00e-02 4.00e+02 ... (remaining 4148 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.15: 878 2.15 - 2.76: 52078 2.76 - 3.37: 77531 3.37 - 3.99: 97482 3.99 - 4.60: 156089 Nonbonded interactions: 384058 Sorted by model distance: nonbonded pdb=" HG1 THR A 693 " pdb=" OE1 GLN A 694 " model vdw 1.533 2.450 nonbonded pdb=" HE1 TRP B 290 " pdb=" OE2 GLU A 709 " model vdw 1.567 2.450 nonbonded pdb=" O VAL A 685 " pdb=" HG SER A 688 " model vdw 1.576 2.450 nonbonded pdb=" O GLY A 801 " pdb="HD22 ASN A 805 " model vdw 1.583 2.450 nonbonded pdb=" OD1 ASN A 645 " pdb=" H PHE A 647 " model vdw 1.595 2.450 ... (remaining 384053 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 Found NCS groups: ncs_group { reference = (chain 'C' and (resid 10 through 39 or resid 72 through 87)) selection = chain 'D' } 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=0.50 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: 0.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.150 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 35.610 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 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 0.118 14389 Z= 0.146 Angle : 0.812 44.065 19450 Z= 0.351 Chirality : 0.064 2.330 2121 Planarity : 0.004 0.084 2504 Dihedral : 14.944 132.796 5447 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 0.13 % Allowed : 0.33 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.21), residues: 1712 helix: 0.66 (0.20), residues: 821 sheet: -0.86 (0.48), residues: 129 loop : -1.35 (0.22), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 15 TYR 0.009 0.001 TYR B 454 PHE 0.014 0.001 PHE A 788 TRP 0.028 0.001 TRP A 697 HIS 0.004 0.001 HIS A 792 Details of bonding type rmsd covalent geometry : bond 0.00298 (14384) covalent geometry : angle 0.81148 (19448) SS BOND : bond 0.00011 ( 1) SS BOND : angle 3.43633 ( 2) hydrogen bonds : bond 0.20003 ( 621) hydrogen bonds : angle 6.89772 ( 1761) metal coordination : bond 0.00082 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 9 is missing expected H atoms. Skipping. Residue LYS 11 is missing expected H atoms. Skipping. Evaluate side-chains 546 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 544 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 273 TYR cc_start: 0.8617 (p90) cc_final: 0.8295 (p90) REVERT: A 86 CYS cc_start: 0.5899 (m) cc_final: 0.5588 (m) REVERT: A 180 SER cc_start: 0.8096 (t) cc_final: 0.7735 (p) REVERT: A 550 SER cc_start: 0.8364 (t) cc_final: 0.8116 (p) REVERT: A 798 MET cc_start: 0.6570 (OUTLIER) cc_final: 0.6288 (ttp) outliers start: 2 outliers final: 0 residues processed: 544 average time/residue: 0.2957 time to fit residues: 224.5106 Evaluate side-chains 365 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 364 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 798 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.0270 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.1644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 522 GLN B 597 HIS A 361 ASN A 608 ASN A 804 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.084372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.075363 restraints weight = 93679.359| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 2.69 r_work: 0.3049 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2915 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2915 r_free = 0.2915 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2915 r_free = 0.2915 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2915 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.599 14389 Z= 0.221 Angle : 0.749 33.294 19450 Z= 0.353 Chirality : 0.059 2.000 2121 Planarity : 0.005 0.057 2504 Dihedral : 7.060 109.046 1928 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.73 % Favored : 94.15 % Rotamer: Outliers : 1.17 % Allowed : 12.23 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.21), residues: 1712 helix: 0.80 (0.19), residues: 827 sheet: -0.72 (0.46), residues: 141 loop : -1.48 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 48 TYR 0.011 0.001 TYR A 404 PHE 0.016 0.001 PHE B 215 TRP 0.009 0.001 TRP A 480 HIS 0.007 0.001 HIS A 507 Details of bonding type rmsd covalent geometry : bond 0.00320 (14384) covalent geometry : angle 0.74939 (19448) SS BOND : bond 0.00248 ( 1) SS BOND : angle 1.22334 ( 2) hydrogen bonds : bond 0.05506 ( 621) hydrogen bonds : angle 5.40798 ( 1761) metal coordination : bond 0.29958 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 9 is missing expected H atoms. Skipping. Residue LYS 11 is missing expected H atoms. Skipping. Evaluate side-chains 388 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 370 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 273 TYR cc_start: 0.9209 (p90) cc_final: 0.8578 (p90) REVERT: B 442 GLU cc_start: 0.7636 (tm-30) cc_final: 0.7366 (tm-30) REVERT: B 487 LYS cc_start: 0.8943 (mttp) cc_final: 0.8662 (tptp) REVERT: B 515 GLU cc_start: 0.8685 (mp0) cc_final: 0.8288 (mp0) REVERT: B 636 LEU cc_start: 0.8992 (tp) cc_final: 0.8639 (tp) REVERT: B 815 GLU cc_start: 0.8352 (tt0) cc_final: 0.8116 (tt0) REVERT: A 108 LEU cc_start: 0.8778 (mt) cc_final: 0.8509 (mp) REVERT: A 180 SER cc_start: 0.9283 (t) cc_final: 0.8882 (p) REVERT: A 550 SER cc_start: 0.9354 (t) cc_final: 0.9115 (p) REVERT: D 32 GLN cc_start: 0.7466 (pp30) cc_final: 0.7177 (pp30) outliers start: 18 outliers final: 15 residues processed: 376 average time/residue: 0.2718 time to fit residues: 145.0107 Evaluate side-chains 368 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 353 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 207 ASP Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 350 GLU Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 511 CYS Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain A residue 175 LYS Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 361 ASN Chi-restraints excluded: chain A residue 448 ASP Chi-restraints excluded: chain A residue 804 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 126 optimal weight: 5.9990 chunk 47 optimal weight: 0.0770 chunk 14 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 108 optimal weight: 0.4980 chunk 57 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 chunk 151 optimal weight: 5.9990 chunk 98 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 78 optimal weight: 4.9990 overall best weight: 1.0340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.084055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.074968 restraints weight = 93793.932| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 2.69 r_work: 0.3046 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2902 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2902 r_free = 0.2902 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2902 r_free = 0.2902 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2902 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14389 Z= 0.130 Angle : 0.725 33.469 19450 Z= 0.336 Chirality : 0.058 1.982 2121 Planarity : 0.004 0.064 2504 Dihedral : 6.862 114.301 1925 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.44 % Favored : 94.44 % Rotamer: Outliers : 1.37 % Allowed : 13.60 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.21), residues: 1712 helix: 0.77 (0.19), residues: 848 sheet: -0.63 (0.47), residues: 141 loop : -1.56 (0.22), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 48 TYR 0.010 0.001 TYR A 583 PHE 0.010 0.001 PHE B 215 TRP 0.013 0.001 TRP A 697 HIS 0.009 0.001 HIS A 599 Details of bonding type rmsd covalent geometry : bond 0.00287 (14384) covalent geometry : angle 0.72482 (19448) SS BOND : bond 0.00140 ( 1) SS BOND : angle 1.12980 ( 2) hydrogen bonds : bond 0.04657 ( 621) hydrogen bonds : angle 5.11354 ( 1761) metal coordination : bond 0.00835 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 9 is missing expected H atoms. Skipping. Residue LYS 11 is missing expected H atoms. Skipping. Evaluate side-chains 384 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 363 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 105 GLU cc_start: 0.7171 (mp0) cc_final: 0.6961 (mp0) REVERT: B 462 GLU cc_start: 0.8355 (pt0) cc_final: 0.8119 (pm20) REVERT: B 481 GLU cc_start: 0.7440 (tp30) cc_final: 0.7183 (tp30) REVERT: B 487 LYS cc_start: 0.8970 (mttp) cc_final: 0.8749 (tptp) REVERT: B 515 GLU cc_start: 0.8720 (mp0) cc_final: 0.8395 (mp0) REVERT: B 584 ASP cc_start: 0.8312 (t0) cc_final: 0.8034 (t0) REVERT: A 180 SER cc_start: 0.9275 (t) cc_final: 0.8874 (p) REVERT: A 464 GLU cc_start: 0.8731 (pt0) cc_final: 0.8497 (pm20) REVERT: A 550 SER cc_start: 0.9346 (t) cc_final: 0.9119 (p) REVERT: A 814 ASP cc_start: 0.8461 (m-30) cc_final: 0.7897 (p0) REVERT: D 32 GLN cc_start: 0.7585 (pp30) cc_final: 0.7378 (pp30) outliers start: 21 outliers final: 15 residues processed: 369 average time/residue: 0.2757 time to fit residues: 144.4995 Evaluate side-chains 368 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 353 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 350 GLU Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 511 CYS Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 622 SER Chi-restraints excluded: chain A residue 175 LYS Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 448 ASP Chi-restraints excluded: chain A residue 804 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 124 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 106 optimal weight: 5.9990 chunk 158 optimal weight: 5.9990 chunk 131 optimal weight: 4.9990 chunk 86 optimal weight: 5.9990 chunk 134 optimal weight: 4.9990 chunk 1 optimal weight: 0.2980 chunk 73 optimal weight: 0.1980 chunk 0 optimal weight: 5.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 ASN B 67 GLN ** B 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 646 GLN A 361 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.080262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.071399 restraints weight = 94704.961| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 2.60 r_work: 0.2971 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2831 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2831 r_free = 0.2831 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2831 r_free = 0.2831 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2831 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 14389 Z= 0.215 Angle : 0.753 34.737 19450 Z= 0.356 Chirality : 0.058 1.928 2121 Planarity : 0.005 0.057 2504 Dihedral : 7.003 131.331 1925 Min Nonbonded Distance : 1.763 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.79 % Favored : 93.10 % Rotamer: Outliers : 1.69 % Allowed : 14.44 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.21), residues: 1712 helix: 0.68 (0.18), residues: 859 sheet: -0.71 (0.46), residues: 143 loop : -1.72 (0.22), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 707 TYR 0.013 0.001 TYR A 583 PHE 0.014 0.002 PHE B 632 TRP 0.014 0.001 TRP A 697 HIS 0.006 0.001 HIS A 507 Details of bonding type rmsd covalent geometry : bond 0.00491 (14384) covalent geometry : angle 0.75253 (19448) SS BOND : bond 0.00196 ( 1) SS BOND : angle 1.13389 ( 2) hydrogen bonds : bond 0.04502 ( 621) hydrogen bonds : angle 5.05664 ( 1761) metal coordination : bond 0.00815 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 9 is missing expected H atoms. Skipping. Residue LYS 11 is missing expected H atoms. Skipping. Evaluate side-chains 380 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 354 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 121 ASP cc_start: 0.8754 (m-30) cc_final: 0.8543 (m-30) REVERT: B 215 PHE cc_start: 0.8212 (p90) cc_final: 0.7759 (p90) REVERT: B 481 GLU cc_start: 0.7808 (tp30) cc_final: 0.7605 (tp30) REVERT: B 487 LYS cc_start: 0.9078 (mttp) cc_final: 0.8858 (tptp) REVERT: B 584 ASP cc_start: 0.8348 (t0) cc_final: 0.8073 (t0) REVERT: B 815 GLU cc_start: 0.8224 (tm-30) cc_final: 0.7953 (tm-30) REVERT: A 155 ASN cc_start: 0.7804 (t0) cc_final: 0.7527 (m110) REVERT: A 180 SER cc_start: 0.9284 (t) cc_final: 0.8889 (p) REVERT: A 242 LEU cc_start: 0.9258 (tp) cc_final: 0.9010 (tp) REVERT: A 478 GLU cc_start: 0.8220 (pm20) cc_final: 0.8013 (pm20) REVERT: A 550 SER cc_start: 0.9342 (t) cc_final: 0.9135 (p) REVERT: D 32 GLN cc_start: 0.7520 (pp30) cc_final: 0.7237 (pp30) outliers start: 26 outliers final: 19 residues processed: 364 average time/residue: 0.2705 time to fit residues: 140.2010 Evaluate side-chains 363 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 344 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 66 MET Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain B residue 479 ASP Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 511 CYS Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 622 SER Chi-restraints excluded: chain B residue 639 GLU Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain A residue 175 LYS Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 361 ASN Chi-restraints excluded: chain A residue 448 ASP Chi-restraints excluded: chain A residue 758 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 137 optimal weight: 1.9990 chunk 125 optimal weight: 3.9990 chunk 146 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 126 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 chunk 60 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 ASN A 384 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.081383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.072434 restraints weight = 94530.126| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 2.62 r_work: 0.2998 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2873 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2873 r_free = 0.2873 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2873 r_free = 0.2873 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2873 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.3467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14389 Z= 0.137 Angle : 0.726 34.202 19450 Z= 0.336 Chirality : 0.058 1.940 2121 Planarity : 0.004 0.075 2504 Dihedral : 6.907 126.732 1925 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.62 % Favored : 94.27 % Rotamer: Outliers : 1.56 % Allowed : 15.81 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.21), residues: 1712 helix: 0.80 (0.19), residues: 859 sheet: -0.62 (0.46), residues: 139 loop : -1.67 (0.22), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 48 TYR 0.012 0.001 TYR B 273 PHE 0.012 0.001 PHE A 565 TRP 0.014 0.001 TRP A 697 HIS 0.004 0.001 HIS A 599 Details of bonding type rmsd covalent geometry : bond 0.00315 (14384) covalent geometry : angle 0.72615 (19448) SS BOND : bond 0.00198 ( 1) SS BOND : angle 0.91020 ( 2) hydrogen bonds : bond 0.04130 ( 621) hydrogen bonds : angle 4.86263 ( 1761) metal coordination : bond 0.00173 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 9 is missing expected H atoms. Skipping. Residue LYS 11 is missing expected H atoms. Skipping. Evaluate side-chains 373 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 349 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 462 GLU cc_start: 0.8463 (pt0) cc_final: 0.8168 (pm20) REVERT: B 510 GLU cc_start: 0.8256 (mt-10) cc_final: 0.8041 (mt-10) REVERT: B 584 ASP cc_start: 0.8320 (t0) cc_final: 0.8096 (t0) REVERT: A 180 SER cc_start: 0.9255 (t) cc_final: 0.8849 (p) REVERT: A 420 MET cc_start: 0.8525 (pmm) cc_final: 0.8315 (pmm) REVERT: A 486 GLU cc_start: 0.7784 (tt0) cc_final: 0.7558 (tt0) REVERT: A 550 SER cc_start: 0.9290 (t) cc_final: 0.9073 (p) REVERT: A 697 TRP cc_start: 0.8656 (t-100) cc_final: 0.8441 (t-100) REVERT: D 32 GLN cc_start: 0.7489 (pp30) cc_final: 0.7232 (pp30) outliers start: 24 outliers final: 20 residues processed: 359 average time/residue: 0.2873 time to fit residues: 146.1355 Evaluate side-chains 362 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 342 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 66 MET Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 479 ASP Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 523 MET Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 598 ASP Chi-restraints excluded: chain B residue 766 GLU Chi-restraints excluded: chain A residue 94 MET Chi-restraints excluded: chain A residue 175 LYS Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 448 ASP Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain D residue 22 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 78 optimal weight: 5.9990 chunk 124 optimal weight: 4.9990 chunk 123 optimal weight: 2.9990 chunk 133 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 105 optimal weight: 0.9980 chunk 83 optimal weight: 0.7980 chunk 57 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 129 optimal weight: 2.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 69 ASN ** B 219 ASN ** 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 = 0.3221 r_free = 0.3221 target = 0.080234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.071374 restraints weight = 95138.186| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 2.60 r_work: 0.2974 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2848 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2848 r_free = 0.2848 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2848 r_free = 0.2848 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2848 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.3684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14389 Z= 0.171 Angle : 0.734 34.547 19450 Z= 0.343 Chirality : 0.058 1.924 2121 Planarity : 0.004 0.062 2504 Dihedral : 6.937 131.002 1925 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.85 % Favored : 93.04 % Rotamer: Outliers : 1.76 % Allowed : 16.20 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.21), residues: 1712 helix: 0.86 (0.19), residues: 860 sheet: -0.74 (0.46), residues: 143 loop : -1.66 (0.22), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 707 TYR 0.012 0.001 TYR B 273 PHE 0.014 0.001 PHE B 287 TRP 0.013 0.001 TRP A 697 HIS 0.005 0.001 HIS D 75 Details of bonding type rmsd covalent geometry : bond 0.00396 (14384) covalent geometry : angle 0.73402 (19448) SS BOND : bond 0.00211 ( 1) SS BOND : angle 0.86813 ( 2) hydrogen bonds : bond 0.04060 ( 621) hydrogen bonds : angle 4.82549 ( 1761) metal coordination : bond 0.00311 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 9 is missing expected H atoms. Skipping. Residue LYS 11 is missing expected H atoms. Skipping. Evaluate side-chains 367 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 340 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 417 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8241 (tp) REVERT: B 462 GLU cc_start: 0.8509 (pt0) cc_final: 0.8153 (pm20) REVERT: B 502 TYR cc_start: 0.8103 (m-80) cc_final: 0.7071 (m-10) REVERT: B 584 ASP cc_start: 0.8327 (t0) cc_final: 0.8104 (t0) REVERT: B 812 ASP cc_start: 0.8767 (t0) cc_final: 0.8365 (t0) REVERT: A 70 ASP cc_start: 0.7961 (t0) cc_final: 0.7750 (t70) REVERT: A 180 SER cc_start: 0.9260 (t) cc_final: 0.8867 (p) REVERT: A 420 MET cc_start: 0.8550 (pmm) cc_final: 0.8325 (pmm) REVERT: A 550 SER cc_start: 0.9264 (t) cc_final: 0.9046 (p) REVERT: D 32 GLN cc_start: 0.7506 (pp30) cc_final: 0.7263 (pp30) outliers start: 27 outliers final: 25 residues processed: 353 average time/residue: 0.2793 time to fit residues: 139.9148 Evaluate side-chains 363 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 337 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 66 MET Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 479 ASP Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 523 MET Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 571 THR Chi-restraints excluded: chain B residue 598 ASP Chi-restraints excluded: chain B residue 622 SER Chi-restraints excluded: chain B residue 639 GLU Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain A residue 94 MET Chi-restraints excluded: chain A residue 157 GLU Chi-restraints excluded: chain A residue 175 LYS Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 448 ASP Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain D residue 22 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 93 optimal weight: 1.9990 chunk 102 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 154 optimal weight: 0.0970 chunk 146 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 162 optimal weight: 6.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 384 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.086015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.076179 restraints weight = 97354.653| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 2.75 r_work: 0.3038 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2903 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2903 r_free = 0.2903 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2903 r_free = 0.2903 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2903 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.3822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14389 Z= 0.169 Angle : 0.734 34.604 19450 Z= 0.343 Chirality : 0.058 1.924 2121 Planarity : 0.004 0.063 2504 Dihedral : 6.951 130.635 1925 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.44 % Favored : 93.45 % Rotamer: Outliers : 1.76 % Allowed : 16.27 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.21), residues: 1712 helix: 0.92 (0.19), residues: 859 sheet: -0.76 (0.46), residues: 143 loop : -1.68 (0.22), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 48 TYR 0.013 0.001 TYR B 273 PHE 0.013 0.001 PHE B 632 TRP 0.015 0.001 TRP A 697 HIS 0.005 0.001 HIS D 75 Details of bonding type rmsd covalent geometry : bond 0.00393 (14384) covalent geometry : angle 0.73432 (19448) SS BOND : bond 0.00216 ( 1) SS BOND : angle 0.81589 ( 2) hydrogen bonds : bond 0.04010 ( 621) hydrogen bonds : angle 4.76214 ( 1761) metal coordination : bond 0.00280 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 9 is missing expected H atoms. Skipping. Residue LYS 11 is missing expected H atoms. Skipping. Evaluate side-chains 367 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 340 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 417 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8409 (tp) REVERT: B 462 GLU cc_start: 0.8466 (pt0) cc_final: 0.8227 (pm20) REVERT: B 502 TYR cc_start: 0.7868 (m-80) cc_final: 0.7624 (m-10) REVERT: A 70 ASP cc_start: 0.8016 (t0) cc_final: 0.7753 (t70) REVERT: A 180 SER cc_start: 0.9240 (t) cc_final: 0.8856 (p) REVERT: A 550 SER cc_start: 0.9291 (t) cc_final: 0.9066 (p) REVERT: D 32 GLN cc_start: 0.7540 (pp30) cc_final: 0.7335 (pp30) outliers start: 27 outliers final: 25 residues processed: 356 average time/residue: 0.2830 time to fit residues: 143.0087 Evaluate side-chains 357 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 331 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 66 MET Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 479 ASP Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 523 MET Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 571 THR Chi-restraints excluded: chain B residue 598 ASP Chi-restraints excluded: chain B residue 622 SER Chi-restraints excluded: chain B residue 766 GLU Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 94 MET Chi-restraints excluded: chain A residue 175 LYS Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 448 ASP Chi-restraints excluded: chain A residue 661 MET Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain D residue 22 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 166 optimal weight: 7.9990 chunk 146 optimal weight: 4.9990 chunk 111 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 131 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 114 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 2 optimal weight: 9.9990 chunk 102 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.084392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.074677 restraints weight = 98629.129| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 2.72 r_work: 0.3001 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2871 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2871 r_free = 0.2871 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2871 r_free = 0.2871 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2871 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.4016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 14389 Z= 0.242 Angle : 0.768 35.126 19450 Z= 0.366 Chirality : 0.059 1.904 2121 Planarity : 0.005 0.093 2504 Dihedral : 7.098 133.125 1925 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.43 % Favored : 92.45 % Rotamer: Outliers : 2.02 % Allowed : 16.85 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.21), residues: 1712 helix: 0.84 (0.19), residues: 858 sheet: -0.87 (0.45), residues: 145 loop : -1.78 (0.22), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 48 TYR 0.015 0.002 TYR B 273 PHE 0.017 0.002 PHE B 632 TRP 0.015 0.001 TRP A 697 HIS 0.007 0.001 HIS D 75 Details of bonding type rmsd covalent geometry : bond 0.00559 (14384) covalent geometry : angle 0.76831 (19448) SS BOND : bond 0.00245 ( 1) SS BOND : angle 0.86146 ( 2) hydrogen bonds : bond 0.04294 ( 621) hydrogen bonds : angle 4.87954 ( 1761) metal coordination : bond 0.00467 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 9 is missing expected H atoms. Skipping. Residue LYS 11 is missing expected H atoms. Skipping. Evaluate side-chains 364 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 333 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 417 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8443 (tp) REVERT: B 510 GLU cc_start: 0.8164 (mt-10) cc_final: 0.7937 (mt-10) REVERT: B 523 MET cc_start: 0.9072 (OUTLIER) cc_final: 0.8820 (ptm) REVERT: A 124 CYS cc_start: 0.8648 (m) cc_final: 0.8404 (m) REVERT: A 180 SER cc_start: 0.9282 (t) cc_final: 0.8875 (p) REVERT: A 550 SER cc_start: 0.9294 (t) cc_final: 0.9083 (p) outliers start: 31 outliers final: 26 residues processed: 349 average time/residue: 0.2792 time to fit residues: 138.5658 Evaluate side-chains 360 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 332 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 66 MET Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 479 ASP Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 523 MET Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 571 THR Chi-restraints excluded: chain B residue 598 ASP Chi-restraints excluded: chain B residue 622 SER Chi-restraints excluded: chain B residue 639 GLU Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 94 MET Chi-restraints excluded: chain A residue 175 LYS Chi-restraints excluded: chain A residue 186 LYS Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 448 ASP Chi-restraints excluded: chain A residue 661 MET Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain D residue 22 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 164 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 87 optimal weight: 0.0980 chunk 151 optimal weight: 4.9990 chunk 97 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 120 optimal weight: 0.8980 chunk 111 optimal weight: 4.9990 chunk 119 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 628 HIS A 804 ASN C 32 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.086957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.077190 restraints weight = 97537.664| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 2.74 r_work: 0.3055 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2921 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2921 r_free = 0.2921 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2921 r_free = 0.2921 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2921 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.4057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14389 Z= 0.116 Angle : 0.730 33.895 19450 Z= 0.337 Chirality : 0.057 1.942 2121 Planarity : 0.004 0.093 2504 Dihedral : 6.895 127.352 1925 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.79 % Favored : 94.09 % Rotamer: Outliers : 1.43 % Allowed : 17.70 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.21), residues: 1712 helix: 1.06 (0.19), residues: 855 sheet: -0.77 (0.45), residues: 143 loop : -1.67 (0.23), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 48 TYR 0.012 0.001 TYR B 273 PHE 0.012 0.001 PHE B 287 TRP 0.012 0.001 TRP A 697 HIS 0.007 0.001 HIS D 75 Details of bonding type rmsd covalent geometry : bond 0.00272 (14384) covalent geometry : angle 0.72996 (19448) SS BOND : bond 0.00225 ( 1) SS BOND : angle 0.62522 ( 2) hydrogen bonds : bond 0.03777 ( 621) hydrogen bonds : angle 4.60676 ( 1761) metal coordination : bond 0.00121 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 9 is missing expected H atoms. Skipping. Residue LYS 11 is missing expected H atoms. Skipping. Evaluate side-chains 368 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 346 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 358 MET cc_start: 0.8604 (mmm) cc_final: 0.8217 (tpt) REVERT: B 417 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8393 (tp) REVERT: B 462 GLU cc_start: 0.8460 (pt0) cc_final: 0.8237 (pm20) REVERT: B 812 ASP cc_start: 0.8701 (t0) cc_final: 0.8290 (t0) REVERT: A 180 SER cc_start: 0.9234 (t) cc_final: 0.8853 (p) REVERT: A 550 SER cc_start: 0.9295 (t) cc_final: 0.9071 (p) REVERT: A 682 GLN cc_start: 0.8286 (mt0) cc_final: 0.8067 (mt0) outliers start: 22 outliers final: 21 residues processed: 356 average time/residue: 0.2763 time to fit residues: 140.4546 Evaluate side-chains 357 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 335 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 479 ASP Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 523 MET Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 598 ASP Chi-restraints excluded: chain B residue 622 SER Chi-restraints excluded: chain B residue 639 GLU Chi-restraints excluded: chain A residue 94 MET Chi-restraints excluded: chain A residue 175 LYS Chi-restraints excluded: chain A residue 186 LYS Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 448 ASP Chi-restraints excluded: chain A residue 661 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 147 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 47 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 61 optimal weight: 5.9990 chunk 82 optimal weight: 4.9990 chunk 159 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.085924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.076238 restraints weight = 97389.314| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 2.71 r_work: 0.3035 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2903 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2903 r_free = 0.2903 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2903 r_free = 0.2903 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2903 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.4112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 14389 Z= 0.161 Angle : 0.740 34.446 19450 Z= 0.345 Chirality : 0.058 1.923 2121 Planarity : 0.004 0.085 2504 Dihedral : 6.920 132.330 1925 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.37 % Favored : 92.51 % Rotamer: Outliers : 1.63 % Allowed : 18.09 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.21), residues: 1712 helix: 1.06 (0.19), residues: 855 sheet: -0.80 (0.45), residues: 143 loop : -1.70 (0.23), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 48 TYR 0.012 0.001 TYR A 404 PHE 0.012 0.001 PHE B 632 TRP 0.012 0.001 TRP A 697 HIS 0.008 0.001 HIS D 75 Details of bonding type rmsd covalent geometry : bond 0.00375 (14384) covalent geometry : angle 0.74042 (19448) SS BOND : bond 0.00224 ( 1) SS BOND : angle 0.72947 ( 2) hydrogen bonds : bond 0.03831 ( 621) hydrogen bonds : angle 4.64321 ( 1761) metal coordination : bond 0.00279 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 9 is missing expected H atoms. Skipping. Residue LYS 11 is missing expected H atoms. Skipping. Evaluate side-chains 360 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 335 time to evaluate : 0.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 358 MET cc_start: 0.8642 (mmm) cc_final: 0.8238 (tpt) REVERT: B 417 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8404 (tp) REVERT: A 180 SER cc_start: 0.9265 (t) cc_final: 0.8852 (p) REVERT: A 550 SER cc_start: 0.9281 (t) cc_final: 0.9065 (p) REVERT: A 682 GLN cc_start: 0.8408 (mt0) cc_final: 0.8200 (mt0) outliers start: 25 outliers final: 24 residues processed: 348 average time/residue: 0.2766 time to fit residues: 137.1221 Evaluate side-chains 360 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 335 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 66 MET Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 479 ASP Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 523 MET Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 571 THR Chi-restraints excluded: chain B residue 598 ASP Chi-restraints excluded: chain B residue 622 SER Chi-restraints excluded: chain B residue 639 GLU Chi-restraints excluded: chain B residue 766 GLU Chi-restraints excluded: chain A residue 94 MET Chi-restraints excluded: chain A residue 175 LYS Chi-restraints excluded: chain A residue 186 LYS Chi-restraints excluded: chain A residue 448 ASP Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 661 MET Chi-restraints excluded: chain D residue 22 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 12 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 chunk 151 optimal weight: 4.9990 chunk 128 optimal weight: 0.0570 chunk 121 optimal weight: 0.1980 chunk 11 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 112 optimal weight: 0.2980 chunk 80 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 overall best weight: 0.5102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.088008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.078207 restraints weight = 96596.370| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 2.75 r_work: 0.3076 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2943 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2943 r_free = 0.2943 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2943 r_free = 0.2943 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2943 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.4141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14389 Z= 0.110 Angle : 0.730 33.767 19450 Z= 0.334 Chirality : 0.057 1.944 2121 Planarity : 0.004 0.089 2504 Dihedral : 6.763 128.634 1925 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.38 % Favored : 94.50 % Rotamer: Outliers : 1.11 % Allowed : 18.41 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.21), residues: 1712 helix: 1.24 (0.19), residues: 848 sheet: -0.67 (0.45), residues: 143 loop : -1.58 (0.23), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 48 TYR 0.010 0.001 TYR B 273 PHE 0.010 0.001 PHE B 287 TRP 0.010 0.001 TRP A 697 HIS 0.007 0.001 HIS D 75 Details of bonding type rmsd covalent geometry : bond 0.00258 (14384) covalent geometry : angle 0.72998 (19448) SS BOND : bond 0.00204 ( 1) SS BOND : angle 0.61631 ( 2) hydrogen bonds : bond 0.03470 ( 621) hydrogen bonds : angle 4.45280 ( 1761) metal coordination : bond 0.00081 ( 4) =============================================================================== Job complete usr+sys time: 7227.50 seconds wall clock time: 122 minutes 53.03 seconds (7373.03 seconds total)