Starting phenix.real_space_refine on Fri Jul 3 16:11:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7epb_31236/07_2026/7epb_31236.cif Found real_map, /net/cci-nas-00/data/ceres_data/7epb_31236/07_2026/7epb_31236.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7epb_31236/07_2026/7epb_31236.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7epb_31236/07_2026/7epb_31236.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7epb_31236/07_2026/7epb_31236.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7epb_31236/07_2026/7epb_31236.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7epb_31236/07_2026/7epb_31236.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7epb_31236/07_2026/7epb_31236.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.198 sd= 0.783 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2352 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 84 5.16 5 C 8214 2.51 5 N 2344 2.21 5 O 2462 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 89 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13104 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 779, 5632 Classifications: {'peptide': 779} Incomplete info: {'truncation_to_alanine': 107} Link IDs: {'PTRANS': 37, 'TRANS': 741} Chain breaks: 1 Unresolved non-hydrogen bonds: 444 Unresolved non-hydrogen angles: 577 Unresolved non-hydrogen dihedrals: 382 Unresolved non-hydrogen chiralities: 46 Planarities with less than four sites: {'ARG:plan': 9, 'HIS:plan': 3, 'GLU:plan': 4, 'ASP:plan': 3, 'PHE:plan': 13, 'GLN:plan1': 3, 'TYR:plan': 6, 'TRP:plan': 3, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 253 Chain: "B" Number of atoms: 5638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 779, 5638 Classifications: {'peptide': 779} Incomplete info: {'truncation_to_alanine': 106} Link IDs: {'PTRANS': 37, 'TRANS': 741} Chain breaks: 1 Unresolved non-hydrogen bonds: 436 Unresolved non-hydrogen angles: 566 Unresolved non-hydrogen dihedrals: 374 Unresolved non-hydrogen chiralities: 45 Planarities with less than four sites: {'ARG:plan': 9, 'HIS:plan': 3, 'GLU:plan': 5, 'ASP:plan': 3, 'PHE:plan': 10, 'GLN:plan1': 3, 'TYR:plan': 7, 'TRP:plan': 3, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 246 Chain: "C" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 902 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 115} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 906 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 2, 'TRANS': 115} Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'40F': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'40F': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.25, per 1000 atoms: 0.25 Number of scatterers: 13104 At special positions: 0 Unit cell: (105.04, 91.52, 189.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 84 16.00 O 2462 8.00 N 2344 7.00 C 8214 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 92 " distance=2.03 Simple disulfide: pdb=" SG CYS A 121 " - pdb=" SG CYS B 121 " distance=2.03 Simple disulfide: pdb=" SG CYS A 234 " - pdb=" SG CYS A 518 " distance=2.03 Simple disulfide: pdb=" SG CYS A 355 " - pdb=" SG CYS A 362 " distance=2.03 Simple disulfide: pdb=" SG CYS A 400 " - pdb=" SG CYS A 407 " distance=2.03 Simple disulfide: pdb=" SG CYS A 500 " - pdb=" SG CYS A 519 " distance=2.03 Simple disulfide: pdb=" SG CYS A 504 " - pdb=" SG CYS A 522 " distance=2.03 Simple disulfide: pdb=" SG CYS A 525 " - pdb=" SG CYS A 537 " distance=2.03 Simple disulfide: pdb=" SG CYS A 540 " - pdb=" SG CYS A 553 " distance=2.04 Simple disulfide: pdb=" SG CYS A 632 " - pdb=" SG CYS A 721 " distance=2.03 Simple disulfide: pdb=" SG CYS B 50 " - pdb=" SG CYS B 92 " distance=2.03 Simple disulfide: pdb=" SG CYS B 234 " - pdb=" SG CYS B 518 " distance=2.03 Simple disulfide: pdb=" SG CYS B 355 " - pdb=" SG CYS B 362 " distance=2.03 Simple disulfide: pdb=" SG CYS B 400 " - pdb=" SG CYS B 407 " distance=2.03 Simple disulfide: pdb=" SG CYS B 500 " - pdb=" SG CYS B 519 " distance=2.03 Simple disulfide: pdb=" SG CYS B 504 " - pdb=" SG CYS B 522 " distance=2.03 Simple disulfide: pdb=" SG CYS B 525 " - pdb=" SG CYS B 537 " distance=2.03 Simple disulfide: pdb=" SG CYS B 540 " - pdb=" SG CYS B 553 " distance=2.03 Simple disulfide: pdb=" SG CYS B 632 " - pdb=" SG CYS B 721 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 95 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 95 " 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: 1.07 Conformation dependent library (CDL) restraints added in 559.2 milliseconds 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3320 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 13 sheets defined 41.8% alpha, 11.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 58 through 74 Processing helix chain 'A' and resid 94 through 115 removed outlier: 3.577A pdb=" N ALA A 98 " --> pdb=" O LYS A 94 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N ASP A 104 " --> pdb=" O GLU A 100 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N PHE A 105 " --> pdb=" O GLN A 101 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL A 106 " --> pdb=" O ALA A 102 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N SER A 109 " --> pdb=" O PHE A 105 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG A 112 " --> pdb=" O ALA A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 157 removed outlier: 3.919A pdb=" N ASN A 153 " --> pdb=" O ILE A 149 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N LEU A 154 " --> pdb=" O GLN A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 173 removed outlier: 3.540A pdb=" N LEU A 172 " --> pdb=" O SER A 169 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER A 173 " --> pdb=" O ALA A 170 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 169 through 173' Processing helix chain 'A' and resid 187 through 202 removed outlier: 3.979A pdb=" N GLN A 191 " --> pdb=" O PRO A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 231 Processing helix chain 'A' and resid 246 through 258 Processing helix chain 'A' and resid 271 through 285 Processing helix chain 'A' and resid 324 through 333 Processing helix chain 'A' and resid 344 through 354 Processing helix chain 'A' and resid 377 through 400 Processing helix chain 'A' and resid 407 through 411 Processing helix chain 'A' and resid 414 through 422 Processing helix chain 'A' and resid 489 through 493 Processing helix chain 'A' and resid 556 through 560 removed outlier: 4.313A pdb=" N GLU A 559 " --> pdb=" O LEU A 556 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TYR A 560 " --> pdb=" O PRO A 557 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 556 through 560' Processing helix chain 'A' and resid 568 through 592 Processing helix chain 'A' and resid 597 through 601 Processing helix chain 'A' and resid 602 through 625 removed outlier: 4.513A pdb=" N CYS A 606 " --> pdb=" O GLY A 602 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N TYR A 607 " --> pdb=" O ARG A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 659 removed outlier: 3.818A pdb=" N CYS A 646 " --> pdb=" O ALA A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 701 removed outlier: 3.622A pdb=" N GLU A 701 " --> pdb=" O TRP A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 747 removed outlier: 4.157A pdb=" N MET A 728 " --> pdb=" O ARG A 724 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 783 removed outlier: 3.741A pdb=" N PHE A 761 " --> pdb=" O ASN A 757 " (cutoff:3.500A) Proline residue: A 778 - end of helix removed outlier: 3.651A pdb=" N THR A 783 " --> pdb=" O ILE A 779 " (cutoff:3.500A) Processing helix chain 'A' and resid 786 through 816 removed outlier: 3.768A pdb=" N THR A 791 " --> pdb=" O TYR A 787 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N THR A 792 " --> pdb=" O ARG A 788 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR A 793 " --> pdb=" O VAL A 789 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N MET A 794 " --> pdb=" O GLN A 790 " (cutoff:3.500A) Proline residue: A 812 - end of helix Processing helix chain 'B' and resid 58 through 74 Processing helix chain 'B' and resid 94 through 115 removed outlier: 4.977A pdb=" N ASP B 104 " --> pdb=" O GLU B 100 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N PHE B 105 " --> pdb=" O GLN B 101 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL B 106 " --> pdb=" O ALA B 102 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N SER B 109 " --> pdb=" O PHE B 105 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ARG B 112 " --> pdb=" O ALA B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 157 removed outlier: 3.843A pdb=" N ASN B 153 " --> pdb=" O ILE B 149 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LEU B 154 " --> pdb=" O GLN B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 173 removed outlier: 3.535A pdb=" N LEU B 172 " --> pdb=" O SER B 169 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER B 173 " --> pdb=" O ALA B 170 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 169 through 173' Processing helix chain 'B' and resid 187 through 202 removed outlier: 3.919A pdb=" N GLN B 191 " --> pdb=" O PRO B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 230 Processing helix chain 'B' and resid 246 through 258 Processing helix chain 'B' and resid 271 through 285 Processing helix chain 'B' and resid 324 through 333 Processing helix chain 'B' and resid 344 through 354 Processing helix chain 'B' and resid 377 through 397 Processing helix chain 'B' and resid 407 through 411 Processing helix chain 'B' and resid 414 through 422 removed outlier: 3.630A pdb=" N LEU B 418 " --> pdb=" O ASN B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 493 Processing helix chain 'B' and resid 568 through 592 removed outlier: 3.533A pdb=" N VAL B 572 " --> pdb=" O ALA B 568 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 600 removed outlier: 3.614A pdb=" N ALA B 600 " --> pdb=" O PRO B 596 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 626 removed outlier: 4.432A pdb=" N CYS B 606 " --> pdb=" O GLY B 602 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ILE B 624 " --> pdb=" O THR B 620 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ALA B 625 " --> pdb=" O PHE B 621 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 657 removed outlier: 3.878A pdb=" N CYS B 646 " --> pdb=" O ALA B 642 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 701 removed outlier: 3.578A pdb=" N GLU B 701 " --> pdb=" O TRP B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 725 through 747 Processing helix chain 'B' and resid 748 through 750 No H-bonds generated for 'chain 'B' and resid 748 through 750' Processing helix chain 'B' and resid 757 through 783 removed outlier: 3.554A pdb=" N PHE B 761 " --> pdb=" O ASN B 757 " (cutoff:3.500A) Proline residue: B 778 - end of helix Processing helix chain 'B' and resid 784 through 786 No H-bonds generated for 'chain 'B' and resid 784 through 786' Processing helix chain 'B' and resid 787 through 816 removed outlier: 3.913A pdb=" N THR B 791 " --> pdb=" O TYR B 787 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N THR B 792 " --> pdb=" O ARG B 788 " (cutoff:3.500A) Proline residue: B 812 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 28 removed outlier: 4.622A pdb=" N GLY A 138 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N VAL A 139 " --> pdb=" O ILE A 163 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 234 through 239 removed outlier: 7.510A pdb=" N VAL A 207 " --> pdb=" O THR A 237 " (cutoff:3.500A) removed outlier: 8.596A pdb=" N GLU A 239 " --> pdb=" O VAL A 207 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N THR A 209 " --> pdb=" O GLU A 239 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N TYR A 206 " --> pdb=" O VAL A 265 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N VAL A 267 " --> pdb=" O TYR A 206 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N SER A 208 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N TRP A 291 " --> pdb=" O ILE A 315 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N ILE A 317 " --> pdb=" O TRP A 291 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ALA A 293 " --> pdb=" O ILE A 317 " (cutoff:3.500A) removed outlier: 9.072A pdb=" N LEU A 319 " --> pdb=" O ALA A 293 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLY A 472 " --> pdb=" O ILE A 455 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N THR A 457 " --> pdb=" O LYS A 470 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LYS A 470 " --> pdb=" O THR A 457 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N LEU A 459 " --> pdb=" O TYR A 468 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N TYR A 468 " --> pdb=" O LEU A 459 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 427 through 429 Processing sheet with id=AA4, first strand: chain 'A' and resid 510 through 511 Processing sheet with id=AA5, first strand: chain 'B' and resid 26 through 28 removed outlier: 4.761A pdb=" N GLY B 138 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL B 139 " --> pdb=" O ILE B 163 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 234 through 239 removed outlier: 7.577A pdb=" N VAL B 207 " --> pdb=" O THR B 237 " (cutoff:3.500A) removed outlier: 8.613A pdb=" N GLU B 239 " --> pdb=" O VAL B 207 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N THR B 209 " --> pdb=" O GLU B 239 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N TYR B 206 " --> pdb=" O VAL B 265 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N VAL B 267 " --> pdb=" O TYR B 206 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N SER B 208 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N ALA B 266 " --> pdb=" O VAL B 292 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N TRP B 291 " --> pdb=" O ILE B 315 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N ILE B 317 " --> pdb=" O TRP B 291 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ALA B 293 " --> pdb=" O ILE B 317 " (cutoff:3.500A) removed outlier: 9.168A pdb=" N LEU B 319 " --> pdb=" O ALA B 293 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLY B 472 " --> pdb=" O ILE B 455 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N THR B 457 " --> pdb=" O LYS B 470 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LYS B 470 " --> pdb=" O THR B 457 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N LEU B 459 " --> pdb=" O TYR B 468 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N TYR B 468 " --> pdb=" O LEU B 459 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 427 through 429 Processing sheet with id=AA8, first strand: chain 'B' and resid 509 through 511 Processing sheet with id=AA9, first strand: chain 'C' and resid 4 through 7 Processing sheet with id=AB1, first strand: chain 'C' and resid 46 through 51 removed outlier: 6.402A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ASP C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N MET C 34 " --> pdb=" O ASP C 50 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ASP C 98 " --> pdb=" O ASN C 32 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N MET C 34 " --> pdb=" O HIS C 96 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N HIS C 96 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N TRP C 36 " --> pdb=" O TYR C 94 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N TYR C 94 " --> pdb=" O TRP C 36 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ARG C 38 " --> pdb=" O VAL C 92 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL C 92 " --> pdb=" O ARG C 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AB3, first strand: chain 'D' and resid 10 through 12 Processing sheet with id=AB4, first strand: chain 'D' and resid 57 through 59 removed outlier: 5.381A pdb=" N LEU D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N ARG D 38 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR D 33 " --> pdb=" O ASP D 98 " (cutoff:3.500A) 623 hydrogen bonds defined for protein. 1803 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: 1.97 Time building geometry restraints manager: 1.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 4456 1.35 - 1.46: 3173 1.46 - 1.58: 5641 1.58 - 1.70: 4 1.70 - 1.82: 108 Bond restraints: 13382 Sorted by residual: bond pdb=" C6 40F A 901 " pdb=" C7 40F A 901 " ideal model delta sigma weight residual 1.534 1.393 0.141 2.00e-02 2.50e+03 4.95e+01 bond pdb=" C6 40F B 901 " pdb=" C7 40F B 901 " ideal model delta sigma weight residual 1.534 1.394 0.140 2.00e-02 2.50e+03 4.92e+01 bond pdb=" C 40F B 901 " pdb=" C1 40F B 901 " ideal model delta sigma weight residual 1.554 1.415 0.139 2.00e-02 2.50e+03 4.86e+01 bond pdb=" C 40F A 901 " pdb=" C1 40F A 901 " ideal model delta sigma weight residual 1.554 1.415 0.139 2.00e-02 2.50e+03 4.81e+01 bond pdb=" C5 40F A 901 " pdb=" C6 40F A 901 " ideal model delta sigma weight residual 1.522 1.653 -0.131 2.00e-02 2.50e+03 4.32e+01 ... (remaining 13377 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.90: 18236 6.90 - 13.79: 2 13.79 - 20.69: 0 20.69 - 27.59: 0 27.59 - 34.48: 2 Bond angle restraints: 18240 Sorted by residual: angle pdb=" C3 40F A 901 " pdb=" C5 40F A 901 " pdb=" C6 40F A 901 " ideal model delta sigma weight residual 116.92 151.40 -34.48 3.00e+00 1.11e-01 1.32e+02 angle pdb=" C3 40F B 901 " pdb=" C5 40F B 901 " pdb=" C6 40F B 901 " ideal model delta sigma weight residual 116.92 151.33 -34.41 3.00e+00 1.11e-01 1.32e+02 angle pdb=" C1 40F B 901 " pdb=" C2 40F B 901 " pdb=" C3 40F B 901 " ideal model delta sigma weight residual 118.97 130.97 -12.00 3.00e+00 1.11e-01 1.60e+01 angle pdb=" C1 40F A 901 " pdb=" C2 40F A 901 " pdb=" C3 40F A 901 " ideal model delta sigma weight residual 118.97 130.90 -11.93 3.00e+00 1.11e-01 1.58e+01 angle pdb=" N VAL D 48 " pdb=" CA VAL D 48 " pdb=" C VAL D 48 " ideal model delta sigma weight residual 113.53 109.76 3.77 9.80e-01 1.04e+00 1.48e+01 ... (remaining 18235 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 7270 17.89 - 35.78: 555 35.78 - 53.67: 126 53.67 - 71.55: 14 71.55 - 89.44: 21 Dihedral angle restraints: 7986 sinusoidal: 2821 harmonic: 5165 Sorted by residual: dihedral pdb=" CB CYS A 50 " pdb=" SG CYS A 50 " pdb=" SG CYS A 92 " pdb=" CB CYS A 92 " ideal model delta sinusoidal sigma weight residual -86.00 -2.71 -83.29 1 1.00e+01 1.00e-02 8.48e+01 dihedral pdb=" CB CYS B 50 " pdb=" SG CYS B 50 " pdb=" SG CYS B 92 " pdb=" CB CYS B 92 " ideal model delta sinusoidal sigma weight residual -86.00 -3.94 -82.06 1 1.00e+01 1.00e-02 8.27e+01 dihedral pdb=" CB CYS A 504 " pdb=" SG CYS A 504 " pdb=" SG CYS A 522 " pdb=" CB CYS A 522 " ideal model delta sinusoidal sigma weight residual -86.00 -166.26 80.26 1 1.00e+01 1.00e-02 7.98e+01 ... (remaining 7983 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.259: 2061 0.259 - 0.518: 2 0.518 - 0.777: 0 0.777 - 1.035: 0 1.035 - 1.294: 2 Chirality restraints: 2065 Sorted by residual: chirality pdb=" C5 40F A 901 " pdb=" C2 40F A 901 " pdb=" C3 40F A 901 " pdb=" C6 40F A 901 " both_signs ideal model delta sigma weight residual True 2.64 1.34 1.29 2.00e-01 2.50e+01 4.19e+01 chirality pdb=" C5 40F B 901 " pdb=" C2 40F B 901 " pdb=" C3 40F B 901 " pdb=" C6 40F B 901 " both_signs ideal model delta sigma weight residual True 2.64 1.35 1.29 2.00e-01 2.50e+01 4.16e+01 chirality pdb=" C2 40F B 901 " pdb=" C1 40F B 901 " pdb=" C3 40F B 901 " pdb=" C5 40F B 901 " both_signs ideal model delta sigma weight residual True 2.60 2.13 0.46 2.00e-01 2.50e+01 5.37e+00 ... (remaining 2062 not shown) Planarity restraints: 2402 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C 40 " 0.027 5.00e-02 4.00e+02 4.10e-02 2.69e+00 pdb=" N PRO C 41 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO C 41 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 41 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN B 526 " -0.024 5.00e-02 4.00e+02 3.72e-02 2.21e+00 pdb=" N PRO B 527 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO B 527 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 527 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D 40 " -0.022 5.00e-02 4.00e+02 3.36e-02 1.81e+00 pdb=" N PRO D 41 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO D 41 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO D 41 " -0.019 5.00e-02 4.00e+02 ... (remaining 2399 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 3910 2.81 - 3.33: 12469 3.33 - 3.86: 21950 3.86 - 4.38: 24167 4.38 - 4.90: 41194 Nonbonded interactions: 103690 Sorted by model distance: nonbonded pdb=" O TYR A 206 " pdb=" OG SER A 498 " model vdw 2.292 3.040 nonbonded pdb=" OD1 ASP C 98 " pdb=" OG1 THR C 106 " model vdw 2.297 3.040 nonbonded pdb=" OG SER A 321 " pdb=" O SER A 376 " model vdw 2.301 3.040 nonbonded pdb=" O SER A 628 " pdb=" OG SER A 628 " model vdw 2.306 3.040 nonbonded pdb=" O SER B 628 " pdb=" OG SER B 628 " model vdw 2.313 3.040 ... (remaining 103685 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 'A' and (resid 22 through 558 or (resid 559 through 562 and (name N or na \ me CA or name C or name O or name CB )) or resid 563 through 716 or (resid 717 a \ nd (name N or name CA or name C or name O or name CB )) or resid 718 or (resid 7 \ 19 and (name N or name CA or name C or name O or name CB )) or resid 720 through \ 747 or (resid 748 and (name N or name CA or name C or name O or name CB )) or r \ esid 749 through 754 or (resid 755 and (name N or name CA or name C or name O or \ name CB )) or resid 756 through 780 or (resid 781 and (name N or name CA or nam \ e C or name O or name CB )) or resid 782 through 901)) selection = (chain 'B' and (resid 22 through 571 or (resid 572 through 575 and (name N or na \ me CA or name C or name O or name CB )) or resid 576 through 623 or (resid 624 t \ hrough 626 and (name N or name CA or name C or name O or name CB )) or resid 627 \ through 642 or (resid 643 through 644 and (name N or name CA or name C or name \ O or name CB )) or resid 645 through 756 or (resid 757 through 759 and (name N o \ r name CA or name C or name O or name CB )) or resid 760 through 770 or (resid 7 \ 71 and (name N or name CA or name C or name O or name CB )) or resid 772 through \ 775 or (resid 776 and (name N or name CA or name C or name O or name CB )) or r \ esid 777 through 779 or (resid 780 through 781 and (name N or name CA or name C \ or name O or name CB )) or resid 782 through 901)) } ncs_group { reference = chain 'C' selection = (chain 'D' and (resid 1 through 5 or (resid 6 and (name N or name CA or name C o \ r name O or name CB )) or resid 7 through 118)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.230 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 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 : 0.004 0.141 13403 Z= 0.192 Angle : 0.619 34.483 18282 Z= 0.297 Chirality : 0.058 1.294 2065 Planarity : 0.003 0.041 2402 Dihedral : 13.654 89.443 4603 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 0.08 % Allowed : 6.94 % Favored : 92.98 % 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: -1.65 (0.18), residues: 1782 helix: 0.17 (0.18), residues: 722 sheet: -1.23 (0.32), residues: 242 loop : -2.25 (0.18), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 229 TYR 0.011 0.001 TYR A 787 PHE 0.018 0.001 PHE A 456 TRP 0.005 0.000 TRP B 297 HIS 0.002 0.000 HIS D 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.19 (13382) covalent geometry : angle 0.61862 / 0.30 (18240) SS BOND : bond 0.00163 / 0.11 ( 21) SS BOND : angle 0.65148 / 0.42 ( 42) hydrogen bonds : bond 0.13524 / 9.00 ( 623) hydrogen bonds : angle 5.46082 / 3.97 ( 1803) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 269 time to evaluate : 0.438 Fit side-chains REVERT: A 149 ILE cc_start: 0.8899 (pt) cc_final: 0.8664 (pt) REVERT: A 150 GLN cc_start: 0.8443 (mm-40) cc_final: 0.8165 (mm110) REVERT: A 251 GLU cc_start: 0.7655 (mt-10) cc_final: 0.7412 (mt-10) REVERT: A 414 ASN cc_start: 0.7330 (p0) cc_final: 0.7073 (p0) REVERT: A 725 ASP cc_start: 0.4939 (m-30) cc_final: 0.4425 (m-30) REVERT: B 149 ILE cc_start: 0.8956 (pt) cc_final: 0.8672 (pt) REVERT: B 189 PHE cc_start: 0.7856 (m-80) cc_final: 0.7638 (m-80) REVERT: B 229 ARG cc_start: 0.7729 (mtm-85) cc_final: 0.7452 (mtt180) REVERT: B 251 GLU cc_start: 0.7916 (mt-10) cc_final: 0.7685 (mt-10) REVERT: C 45 ARG cc_start: 0.7546 (ptp90) cc_final: 0.7103 (ptt180) REVERT: C 46 GLU cc_start: 0.7513 (mp0) cc_final: 0.7058 (mp0) outliers start: 1 outliers final: 0 residues processed: 270 average time/residue: 0.0906 time to fit residues: 37.2572 Evaluate side-chains 233 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 233 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.1980 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 10.0000 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 87 HIS B 101 GLN B 790 GLN D 1 GLN ** D 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 GLN ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 76 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.144977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.124963 restraints weight = 28831.925| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 3.08 r_work: 0.3754 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13403 Z= 0.156 Angle : 0.566 13.797 18282 Z= 0.286 Chirality : 0.042 0.182 2065 Planarity : 0.004 0.041 2402 Dihedral : 3.462 15.616 1959 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 1.67 % Allowed : 14.27 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.82 (0.20), residues: 1782 helix: 1.06 (0.20), residues: 728 sheet: -1.16 (0.32), residues: 260 loop : -1.88 (0.20), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 243 TYR 0.011 0.001 TYR D 99 PHE 0.045 0.002 PHE A 456 TRP 0.012 0.001 TRP B 297 HIS 0.004 0.001 HIS D 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.16 (13382) covalent geometry : angle 0.56556 / 0.29 (18240) SS BOND : bond 0.00233 / 0.15 ( 21) SS BOND : angle 0.80096 / 0.51 ( 42) hydrogen bonds : bond 0.03216 / 2.19 ( 623) hydrogen bonds : angle 4.15990 / 2.94 ( 1803) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 248 time to evaluate : 0.417 Fit side-chains revert: symmetry clash REVERT: A 149 ILE cc_start: 0.9096 (pt) cc_final: 0.8631 (pt) REVERT: A 150 GLN cc_start: 0.8935 (mm-40) cc_final: 0.8553 (mm-40) REVERT: A 350 GLU cc_start: 0.8301 (mt-10) cc_final: 0.7961 (mt-10) REVERT: A 396 HIS cc_start: 0.7126 (t70) cc_final: 0.6893 (t-90) REVERT: A 414 ASN cc_start: 0.7960 (p0) cc_final: 0.7673 (p0) REVERT: B 25 VAL cc_start: 0.8650 (t) cc_final: 0.8249 (p) REVERT: B 146 ASP cc_start: 0.8211 (p0) cc_final: 0.7744 (p0) REVERT: B 342 ASN cc_start: 0.8379 (t0) cc_final: 0.8164 (t0) REVERT: B 718 THR cc_start: 0.5410 (p) cc_final: 0.4043 (m) REVERT: C 38 ARG cc_start: 0.8253 (ptm160) cc_final: 0.7646 (ptm160) REVERT: C 46 GLU cc_start: 0.8059 (mp0) cc_final: 0.7552 (mp0) REVERT: C 100 LYS cc_start: 0.9085 (tmtt) cc_final: 0.8847 (tptt) REVERT: D 76 ASN cc_start: 0.7781 (OUTLIER) cc_final: 0.7562 (p0) REVERT: D 79 TYR cc_start: 0.7484 (m-80) cc_final: 0.7135 (m-80) REVERT: D 110 GLN cc_start: 0.8167 (mp10) cc_final: 0.7922 (mp10) outliers start: 21 outliers final: 14 residues processed: 257 average time/residue: 0.0979 time to fit residues: 37.6254 Evaluate side-chains 246 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 231 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 749 THR Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 396 HIS Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 76 ASN Chi-restraints excluded: chain D residue 115 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 44 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 12 optimal weight: 4.9990 chunk 63 optimal weight: 10.0000 chunk 105 optimal weight: 3.9990 chunk 9 optimal weight: 9.9990 chunk 50 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 19 optimal weight: 0.0870 chunk 128 optimal weight: 30.0000 chunk 54 optimal weight: 20.0000 overall best weight: 3.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 101 GLN A 338 ASN B 506 GLN D 1 GLN D 6 GLN ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 76 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.128027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.107303 restraints weight = 28118.254| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 2.98 r_work: 0.3479 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3357 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.4209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.067 13403 Z= 0.373 Angle : 0.736 6.848 18282 Z= 0.396 Chirality : 0.048 0.192 2065 Planarity : 0.005 0.055 2402 Dihedral : 4.774 19.435 1959 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 3.75 % Allowed : 17.15 % Favored : 79.11 % 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: -1.03 (0.20), residues: 1782 helix: 0.96 (0.20), residues: 722 sheet: -1.37 (0.32), residues: 252 loop : -2.02 (0.20), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 411 TYR 0.017 0.002 TYR D 99 PHE 0.048 0.003 PHE A 456 TRP 0.025 0.002 TRP C 108 HIS 0.008 0.002 HIS B 396 Details of bonding type rmsd/Z covalent geometry : bond 0.00783 / 0.37 (13382) covalent geometry : angle 0.73171 / 0.39 (18240) SS BOND : bond 0.00689 / 0.39 ( 21) SS BOND : angle 1.86835 / 1.21 ( 42) hydrogen bonds : bond 0.04624 / 3.17 ( 623) hydrogen bonds : angle 4.74255 / 3.34 ( 1803) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 269 time to evaluate : 0.383 Fit side-chains REVERT: A 43 LYS cc_start: 0.8920 (tppp) cc_final: 0.8696 (tppp) REVERT: A 93 SER cc_start: 0.9453 (m) cc_final: 0.9160 (p) REVERT: A 95 ASP cc_start: 0.8189 (m-30) cc_final: 0.7984 (m-30) REVERT: A 112 ARG cc_start: 0.6515 (tpm170) cc_final: 0.6297 (tpp-160) REVERT: A 149 ILE cc_start: 0.9143 (pt) cc_final: 0.8789 (pt) REVERT: A 193 LYS cc_start: 0.8689 (mtmt) cc_final: 0.8356 (mtmm) REVERT: A 197 GLU cc_start: 0.8433 (mt-10) cc_final: 0.8158 (mt-10) REVERT: A 218 GLU cc_start: 0.8003 (mp0) cc_final: 0.7797 (mp0) REVERT: A 274 ASP cc_start: 0.8423 (t0) cc_final: 0.8124 (t0) REVERT: A 350 GLU cc_start: 0.8554 (mt-10) cc_final: 0.8250 (mt-10) REVERT: A 388 MET cc_start: 0.9001 (tpp) cc_final: 0.8604 (tpp) REVERT: A 399 LEU cc_start: 0.9141 (mt) cc_final: 0.8889 (mp) REVERT: A 414 ASN cc_start: 0.8454 (p0) cc_final: 0.8201 (p0) REVERT: A 417 ARG cc_start: 0.8418 (ttt90) cc_final: 0.8175 (ttt-90) REVERT: A 728 MET cc_start: 0.8566 (tpp) cc_final: 0.8338 (tmm) REVERT: A 735 ASN cc_start: 0.8134 (m110) cc_final: 0.7896 (m110) REVERT: A 772 ILE cc_start: 0.7688 (tp) cc_final: 0.7440 (pt) REVERT: B 49 ASP cc_start: 0.8684 (OUTLIER) cc_final: 0.8439 (t0) REVERT: B 146 ASP cc_start: 0.8508 (OUTLIER) cc_final: 0.8237 (p0) REVERT: B 149 ILE cc_start: 0.8942 (pt) cc_final: 0.8729 (mt) REVERT: B 227 GLU cc_start: 0.8672 (mm-30) cc_final: 0.8450 (mm-30) REVERT: B 277 GLU cc_start: 0.8475 (mm-30) cc_final: 0.8136 (mm-30) REVERT: B 350 GLU cc_start: 0.8734 (mt-10) cc_final: 0.8394 (mt-10) REVERT: B 392 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8905 (mt) REVERT: B 396 HIS cc_start: 0.8348 (OUTLIER) cc_final: 0.7888 (t-90) REVERT: B 619 MET cc_start: 0.5774 (tpt) cc_final: 0.4936 (mmt) REVERT: B 756 PHE cc_start: 0.8092 (p90) cc_final: 0.7509 (p90) REVERT: C 27 ARG cc_start: 0.7516 (tpp80) cc_final: 0.7311 (mmp80) REVERT: C 100 LYS cc_start: 0.9326 (tmtt) cc_final: 0.9092 (tptt) REVERT: D 110 GLN cc_start: 0.8483 (mp10) cc_final: 0.8175 (mp10) outliers start: 47 outliers final: 27 residues processed: 293 average time/residue: 0.1016 time to fit residues: 43.5134 Evaluate side-chains 275 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 244 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 400 CYS Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 749 THR Chi-restraints excluded: chain A residue 781 TYR Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 396 HIS Chi-restraints excluded: chain B residue 400 CYS Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 83 ASN Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 83 ASN Chi-restraints excluded: chain D residue 115 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 2 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 125 optimal weight: 0.7980 chunk 94 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 143 optimal weight: 0.0000 chunk 123 optimal weight: 3.9990 chunk 110 optimal weight: 0.8980 chunk 66 optimal weight: 4.9990 chunk 47 optimal weight: 9.9990 chunk 12 optimal weight: 0.7980 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 191 GLN C 39 GLN D 76 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.134119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.113352 restraints weight = 28251.562| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 3.00 r_work: 0.3565 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.3952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13403 Z= 0.130 Angle : 0.574 10.720 18282 Z= 0.292 Chirality : 0.042 0.170 2065 Planarity : 0.004 0.041 2402 Dihedral : 4.068 16.875 1959 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 3.27 % Allowed : 19.86 % Favored : 76.87 % 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: -0.72 (0.20), residues: 1782 helix: 1.32 (0.20), residues: 724 sheet: -1.46 (0.32), residues: 248 loop : -1.87 (0.20), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 243 TYR 0.011 0.001 TYR D 99 PHE 0.026 0.002 PHE A 456 TRP 0.012 0.001 TRP A 291 HIS 0.004 0.001 HIS B 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (13382) covalent geometry : angle 0.57342 / 0.29 (18240) SS BOND : bond 0.00286 / 0.18 ( 21) SS BOND : angle 0.93141 / 0.63 ( 42) hydrogen bonds : bond 0.03404 / 2.33 ( 623) hydrogen bonds : angle 4.24248 / 2.98 ( 1803) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 273 time to evaluate : 0.472 Fit side-chains REVERT: A 95 ASP cc_start: 0.7773 (m-30) cc_final: 0.6919 (m-30) REVERT: A 146 ASP cc_start: 0.8160 (p0) cc_final: 0.7942 (p0) REVERT: A 149 ILE cc_start: 0.8944 (pt) cc_final: 0.8542 (pt) REVERT: A 180 TYR cc_start: 0.8365 (m-10) cc_final: 0.7859 (m-10) REVERT: A 193 LYS cc_start: 0.8553 (mtmt) cc_final: 0.8191 (mtmm) REVERT: A 197 GLU cc_start: 0.8170 (mt-10) cc_final: 0.7849 (mt-10) REVERT: A 245 MET cc_start: 0.8020 (tpp) cc_final: 0.7162 (tpt) REVERT: A 274 ASP cc_start: 0.8066 (t0) cc_final: 0.7790 (t0) REVERT: A 277 GLU cc_start: 0.8421 (mm-30) cc_final: 0.8023 (mm-30) REVERT: A 350 GLU cc_start: 0.8344 (mt-10) cc_final: 0.8037 (mt-10) REVERT: A 388 MET cc_start: 0.8699 (tpp) cc_final: 0.8375 (tpp) REVERT: A 399 LEU cc_start: 0.8897 (mt) cc_final: 0.8657 (mp) REVERT: A 414 ASN cc_start: 0.8186 (p0) cc_final: 0.7906 (p0) REVERT: A 772 ILE cc_start: 0.7663 (tp) cc_final: 0.7444 (pt) REVERT: B 146 ASP cc_start: 0.8268 (OUTLIER) cc_final: 0.7945 (p0) REVERT: B 273 GLU cc_start: 0.7901 (pm20) cc_final: 0.7618 (pm20) REVERT: B 277 GLU cc_start: 0.8422 (mm-30) cc_final: 0.8081 (mm-30) REVERT: B 342 ASN cc_start: 0.8649 (t0) cc_final: 0.8389 (t0) REVERT: B 350 GLU cc_start: 0.8434 (mt-10) cc_final: 0.8123 (mt-10) REVERT: B 392 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8804 (mt) REVERT: B 396 HIS cc_start: 0.7970 (OUTLIER) cc_final: 0.7705 (t-90) REVERT: B 619 MET cc_start: 0.5574 (tpt) cc_final: 0.5159 (mmp) REVERT: B 756 PHE cc_start: 0.8083 (p90) cc_final: 0.7464 (p90) REVERT: C 34 MET cc_start: 0.8348 (mtp) cc_final: 0.8135 (mtp) REVERT: C 76 ASN cc_start: 0.7791 (p0) cc_final: 0.7578 (p0) REVERT: C 100 LYS cc_start: 0.9188 (tmtt) cc_final: 0.8954 (tptt) REVERT: D 3 GLN cc_start: 0.8176 (pm20) cc_final: 0.7878 (pm20) REVERT: D 110 GLN cc_start: 0.8308 (mp10) cc_final: 0.8015 (mp10) outliers start: 41 outliers final: 31 residues processed: 295 average time/residue: 0.1074 time to fit residues: 45.7512 Evaluate side-chains 282 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 248 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 519 CYS Chi-restraints excluded: chain A residue 632 CYS Chi-restraints excluded: chain A residue 749 THR Chi-restraints excluded: chain A residue 781 TYR Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 396 HIS Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 117 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 145 optimal weight: 0.0470 chunk 135 optimal weight: 0.9990 chunk 108 optimal weight: 3.9990 chunk 9 optimal weight: 10.0000 chunk 87 optimal weight: 3.9990 chunk 131 optimal weight: 3.9990 chunk 133 optimal weight: 0.9990 chunk 121 optimal weight: 5.9990 chunk 79 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 94 optimal weight: 0.7980 overall best weight: 0.7082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 191 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.134588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.113914 restraints weight = 28568.761| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 3.04 r_work: 0.3577 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.3990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 13403 Z= 0.124 Angle : 0.558 10.337 18282 Z= 0.282 Chirality : 0.041 0.165 2065 Planarity : 0.004 0.044 2402 Dihedral : 3.901 16.422 1959 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 3.35 % Allowed : 20.81 % Favored : 75.84 % 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: -0.59 (0.20), residues: 1782 helix: 1.44 (0.20), residues: 732 sheet: -1.52 (0.32), residues: 248 loop : -1.80 (0.21), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 276 TYR 0.012 0.001 TYR D 59 PHE 0.016 0.001 PHE A 456 TRP 0.009 0.001 TRP A 291 HIS 0.004 0.001 HIS B 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (13382) covalent geometry : angle 0.55757 / 0.28 (18240) SS BOND : bond 0.00182 / 0.11 ( 21) SS BOND : angle 0.85727 / 0.56 ( 42) hydrogen bonds : bond 0.03258 / 2.23 ( 623) hydrogen bonds : angle 4.13557 / 2.90 ( 1803) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 267 time to evaluate : 0.496 Fit side-chains REVERT: A 146 ASP cc_start: 0.8201 (p0) cc_final: 0.7954 (p0) REVERT: A 149 ILE cc_start: 0.8912 (pt) cc_final: 0.8517 (pt) REVERT: A 193 LYS cc_start: 0.8559 (mtmt) cc_final: 0.8124 (mtmm) REVERT: A 197 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7811 (mt-10) REVERT: A 243 ARG cc_start: 0.8061 (mmm160) cc_final: 0.7651 (mmm160) REVERT: A 245 MET cc_start: 0.7887 (tpp) cc_final: 0.7163 (tpt) REVERT: A 274 ASP cc_start: 0.8176 (t0) cc_final: 0.7884 (t0) REVERT: A 277 GLU cc_start: 0.8448 (mm-30) cc_final: 0.8016 (mm-30) REVERT: A 350 GLU cc_start: 0.8329 (mt-10) cc_final: 0.8016 (mt-10) REVERT: A 388 MET cc_start: 0.8604 (tpp) cc_final: 0.8259 (tpp) REVERT: A 414 ASN cc_start: 0.8178 (p0) cc_final: 0.7919 (p0) REVERT: A 631 VAL cc_start: 0.1983 (OUTLIER) cc_final: 0.1687 (t) REVERT: A 639 LEU cc_start: 0.8419 (mt) cc_final: 0.8165 (pt) REVERT: A 772 ILE cc_start: 0.7728 (tp) cc_final: 0.7511 (pt) REVERT: B 146 ASP cc_start: 0.8227 (OUTLIER) cc_final: 0.7940 (p0) REVERT: B 273 GLU cc_start: 0.7918 (pm20) cc_final: 0.7529 (pm20) REVERT: B 277 GLU cc_start: 0.8468 (mm-30) cc_final: 0.7923 (mm-30) REVERT: B 342 ASN cc_start: 0.8574 (t0) cc_final: 0.8354 (t0) REVERT: B 350 GLU cc_start: 0.8393 (mt-10) cc_final: 0.8081 (mt-10) REVERT: B 392 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8810 (mt) REVERT: B 619 MET cc_start: 0.5503 (tpt) cc_final: 0.4950 (mtp) REVERT: B 756 PHE cc_start: 0.8089 (p90) cc_final: 0.7444 (p90) REVERT: C 34 MET cc_start: 0.8348 (mtp) cc_final: 0.8121 (mtp) REVERT: C 38 ARG cc_start: 0.8270 (ptm160) cc_final: 0.8046 (ptm160) REVERT: C 76 ASN cc_start: 0.7810 (p0) cc_final: 0.7533 (p0) REVERT: C 100 LYS cc_start: 0.9171 (tmtt) cc_final: 0.8922 (tptt) REVERT: C 108 TRP cc_start: 0.8945 (m100) cc_final: 0.8724 (m100) REVERT: D 3 GLN cc_start: 0.8241 (pm20) cc_final: 0.7957 (pm20) REVERT: D 110 GLN cc_start: 0.8275 (mp10) cc_final: 0.7989 (mp10) outliers start: 42 outliers final: 28 residues processed: 294 average time/residue: 0.1121 time to fit residues: 48.0323 Evaluate side-chains 279 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 248 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 400 CYS Chi-restraints excluded: chain A residue 519 CYS Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 632 CYS Chi-restraints excluded: chain A residue 749 THR Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 115 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 127 optimal weight: 4.9990 chunk 57 optimal weight: 9.9990 chunk 145 optimal weight: 10.0000 chunk 11 optimal weight: 4.9990 chunk 56 optimal weight: 0.6980 chunk 105 optimal weight: 3.9990 chunk 47 optimal weight: 8.9990 chunk 92 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 123 optimal weight: 0.0770 overall best weight: 2.1544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 76 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.128732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.108022 restraints weight = 28034.622| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 2.91 r_work: 0.3485 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3365 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.4725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 13403 Z= 0.254 Angle : 0.646 9.385 18282 Z= 0.336 Chirality : 0.044 0.257 2065 Planarity : 0.005 0.042 2402 Dihedral : 4.418 17.321 1959 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 4.07 % Allowed : 20.81 % Favored : 75.12 % 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: -0.74 (0.20), residues: 1782 helix: 1.31 (0.20), residues: 728 sheet: -1.56 (0.32), residues: 248 loop : -1.88 (0.21), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 352 TYR 0.012 0.002 TYR A 781 PHE 0.029 0.002 PHE A 456 TRP 0.017 0.002 TRP B 297 HIS 0.004 0.001 HIS A 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00544 / 0.25 (13382) covalent geometry : angle 0.64273 / 0.33 (18240) SS BOND : bond 0.00376 / 0.26 ( 21) SS BOND : angle 1.55031 / 0.99 ( 42) hydrogen bonds : bond 0.04033 / 2.77 ( 623) hydrogen bonds : angle 4.39233 / 3.09 ( 1803) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 257 time to evaluate : 0.394 Fit side-chains REVERT: A 95 ASP cc_start: 0.8182 (OUTLIER) cc_final: 0.7292 (m-30) REVERT: A 140 ILE cc_start: 0.9166 (OUTLIER) cc_final: 0.8889 (pt) REVERT: A 149 ILE cc_start: 0.9102 (pt) cc_final: 0.8737 (pt) REVERT: A 193 LYS cc_start: 0.8729 (mtmt) cc_final: 0.8325 (mtmm) REVERT: A 197 GLU cc_start: 0.8456 (mt-10) cc_final: 0.8202 (mt-10) REVERT: A 273 GLU cc_start: 0.8413 (pm20) cc_final: 0.8144 (pm20) REVERT: A 277 GLU cc_start: 0.8707 (mm-30) cc_final: 0.8442 (mm-30) REVERT: A 350 GLU cc_start: 0.8499 (mt-10) cc_final: 0.8183 (mt-10) REVERT: A 388 MET cc_start: 0.8980 (tpp) cc_final: 0.8623 (tpp) REVERT: A 619 MET cc_start: 0.7129 (mmm) cc_final: 0.6870 (mmp) REVERT: A 631 VAL cc_start: 0.1742 (OUTLIER) cc_final: 0.1378 (t) REVERT: A 772 ILE cc_start: 0.7916 (tp) cc_final: 0.7659 (pt) REVERT: B 146 ASP cc_start: 0.8533 (OUTLIER) cc_final: 0.8229 (p0) REVERT: B 197 GLU cc_start: 0.8954 (mm-30) cc_final: 0.8752 (mm-30) REVERT: B 227 GLU cc_start: 0.8603 (mm-30) cc_final: 0.8214 (mp0) REVERT: B 273 GLU cc_start: 0.8337 (pm20) cc_final: 0.7979 (pm20) REVERT: B 277 GLU cc_start: 0.8691 (mm-30) cc_final: 0.8232 (mm-30) REVERT: B 350 GLU cc_start: 0.8711 (mt-10) cc_final: 0.8426 (mt-10) REVERT: B 392 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.8963 (mt) REVERT: B 410 MET cc_start: 0.8290 (mmp) cc_final: 0.7609 (mmt) REVERT: B 619 MET cc_start: 0.5900 (tpt) cc_final: 0.5268 (mmp) REVERT: B 756 PHE cc_start: 0.8218 (p90) cc_final: 0.7601 (p90) REVERT: C 34 MET cc_start: 0.8760 (mtp) cc_final: 0.8549 (mtp) REVERT: C 46 GLU cc_start: 0.8129 (mp0) cc_final: 0.7558 (mp0) REVERT: C 100 LYS cc_start: 0.9332 (tmtt) cc_final: 0.9106 (tptt) REVERT: D 3 GLN cc_start: 0.8562 (pm20) cc_final: 0.7966 (pm20) REVERT: D 110 GLN cc_start: 0.8570 (mp10) cc_final: 0.8327 (mp10) outliers start: 51 outliers final: 39 residues processed: 290 average time/residue: 0.1028 time to fit residues: 44.0700 Evaluate side-chains 286 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 242 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 400 CYS Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 519 CYS Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 749 THR Chi-restraints excluded: chain A residue 781 TYR Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 400 CYS Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 105 ASN Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 83 ASN Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 117 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 7 optimal weight: 0.9980 chunk 101 optimal weight: 0.5980 chunk 51 optimal weight: 7.9990 chunk 134 optimal weight: 9.9990 chunk 175 optimal weight: 5.9990 chunk 162 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 117 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 34 optimal weight: 5.9990 chunk 3 optimal weight: 0.1980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 76 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.132311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.111740 restraints weight = 28092.581| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 2.96 r_work: 0.3553 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.4585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13403 Z= 0.130 Angle : 0.597 10.659 18282 Z= 0.298 Chirality : 0.042 0.179 2065 Planarity : 0.004 0.042 2402 Dihedral : 4.104 17.759 1959 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 3.99 % Allowed : 22.17 % Favored : 73.84 % 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: -0.61 (0.20), residues: 1782 helix: 1.45 (0.20), residues: 730 sheet: -1.59 (0.32), residues: 248 loop : -1.81 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 352 TYR 0.010 0.001 TYR C 59 PHE 0.020 0.001 PHE A 456 TRP 0.012 0.001 TRP A 291 HIS 0.004 0.001 HIS A 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (13382) covalent geometry : angle 0.59592 / 0.30 (18240) SS BOND : bond 0.00220 / 0.12 ( 21) SS BOND : angle 0.96287 / 0.64 ( 42) hydrogen bonds : bond 0.03370 / 2.31 ( 623) hydrogen bonds : angle 4.20269 / 2.96 ( 1803) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 256 time to evaluate : 0.478 Fit side-chains REVERT: A 140 ILE cc_start: 0.8992 (OUTLIER) cc_final: 0.8742 (pt) REVERT: A 149 ILE cc_start: 0.8963 (pt) cc_final: 0.8590 (pt) REVERT: A 180 TYR cc_start: 0.8112 (m-10) cc_final: 0.7873 (m-10) REVERT: A 193 LYS cc_start: 0.8606 (mtmt) cc_final: 0.8265 (mtmm) REVERT: A 197 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7886 (mt-10) REVERT: A 273 GLU cc_start: 0.8142 (pm20) cc_final: 0.7894 (pm20) REVERT: A 277 GLU cc_start: 0.8509 (mm-30) cc_final: 0.8241 (mm-30) REVERT: A 318 GLU cc_start: 0.7419 (pm20) cc_final: 0.7183 (pm20) REVERT: A 350 GLU cc_start: 0.8313 (mt-10) cc_final: 0.8020 (mt-10) REVERT: A 388 MET cc_start: 0.8664 (tpp) cc_final: 0.8341 (tpp) REVERT: A 631 VAL cc_start: 0.1435 (OUTLIER) cc_final: 0.1114 (t) REVERT: A 772 ILE cc_start: 0.7848 (tp) cc_final: 0.7610 (pt) REVERT: B 144 TYR cc_start: 0.9161 (m-80) cc_final: 0.8900 (m-80) REVERT: B 146 ASP cc_start: 0.8258 (OUTLIER) cc_final: 0.7960 (p0) REVERT: B 180 TYR cc_start: 0.8266 (m-10) cc_final: 0.7901 (m-10) REVERT: B 245 MET cc_start: 0.8064 (tpp) cc_final: 0.7248 (tpt) REVERT: B 273 GLU cc_start: 0.8042 (pm20) cc_final: 0.7690 (pm20) REVERT: B 277 GLU cc_start: 0.8392 (mm-30) cc_final: 0.7938 (mm-30) REVERT: B 350 GLU cc_start: 0.8398 (mt-10) cc_final: 0.8097 (mt-10) REVERT: B 392 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8875 (mt) REVERT: B 410 MET cc_start: 0.8104 (mmp) cc_final: 0.7384 (mmt) REVERT: B 619 MET cc_start: 0.5727 (tpt) cc_final: 0.5355 (mmp) REVERT: B 756 PHE cc_start: 0.8073 (p90) cc_final: 0.7486 (p90) REVERT: C 100 LYS cc_start: 0.9196 (tmtt) cc_final: 0.8965 (tptt) REVERT: D 3 GLN cc_start: 0.8300 (OUTLIER) cc_final: 0.7878 (pm20) REVERT: D 110 GLN cc_start: 0.8241 (mp10) cc_final: 0.7975 (mp10) outliers start: 50 outliers final: 36 residues processed: 286 average time/residue: 0.1091 time to fit residues: 45.8849 Evaluate side-chains 280 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 239 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 400 CYS Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 519 CYS Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 749 THR Chi-restraints excluded: chain A residue 781 TYR Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 274 ASP Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 400 CYS Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 745 TYR Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain D residue 3 GLN Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 115 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 88 optimal weight: 6.9990 chunk 126 optimal weight: 0.6980 chunk 129 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 124 optimal weight: 4.9990 chunk 139 optimal weight: 9.9990 chunk 96 optimal weight: 7.9990 chunk 90 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 89 optimal weight: 0.7980 chunk 110 optimal weight: 3.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 76 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.128809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.108463 restraints weight = 27849.069| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 2.86 r_work: 0.3507 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3387 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.4936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 13403 Z= 0.221 Angle : 0.640 9.904 18282 Z= 0.328 Chirality : 0.044 0.174 2065 Planarity : 0.004 0.044 2402 Dihedral : 4.333 17.580 1959 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 3.99 % Allowed : 22.73 % Favored : 73.29 % 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: -0.70 (0.20), residues: 1782 helix: 1.39 (0.20), residues: 732 sheet: -1.62 (0.32), residues: 248 loop : -1.89 (0.21), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 264 TYR 0.014 0.002 TYR C 101 PHE 0.025 0.002 PHE A 456 TRP 0.014 0.001 TRP A 297 HIS 0.004 0.001 HIS A 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.22 (13382) covalent geometry : angle 0.63771 / 0.33 (18240) SS BOND : bond 0.00332 / 0.24 ( 21) SS BOND : angle 1.37061 / 0.89 ( 42) hydrogen bonds : bond 0.03833 / 2.63 ( 623) hydrogen bonds : angle 4.30674 / 3.02 ( 1803) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 242 time to evaluate : 0.493 Fit side-chains revert: symmetry clash REVERT: A 140 ILE cc_start: 0.9118 (OUTLIER) cc_final: 0.8846 (pt) REVERT: A 149 ILE cc_start: 0.9105 (pt) cc_final: 0.8757 (pt) REVERT: A 193 LYS cc_start: 0.8711 (mtmt) cc_final: 0.8358 (mtmm) REVERT: A 197 GLU cc_start: 0.8452 (mt-10) cc_final: 0.8185 (mt-10) REVERT: A 218 GLU cc_start: 0.7858 (mp0) cc_final: 0.7639 (mp0) REVERT: A 273 GLU cc_start: 0.8413 (pm20) cc_final: 0.8161 (pm20) REVERT: A 277 GLU cc_start: 0.8718 (mm-30) cc_final: 0.8435 (mm-30) REVERT: A 350 GLU cc_start: 0.8526 (mt-10) cc_final: 0.8229 (mt-10) REVERT: A 388 MET cc_start: 0.8955 (tpp) cc_final: 0.8592 (tpp) REVERT: A 417 ARG cc_start: 0.8573 (ttt-90) cc_final: 0.8312 (mtp85) REVERT: A 631 VAL cc_start: 0.2017 (OUTLIER) cc_final: 0.1625 (t) REVERT: A 772 ILE cc_start: 0.7942 (tp) cc_final: 0.7658 (pt) REVERT: B 49 ASP cc_start: 0.8644 (m-30) cc_final: 0.8376 (t0) REVERT: B 112 ARG cc_start: 0.5749 (tpm170) cc_final: 0.5540 (tpp-160) REVERT: B 146 ASP cc_start: 0.8526 (OUTLIER) cc_final: 0.8213 (p0) REVERT: B 180 TYR cc_start: 0.8525 (m-10) cc_final: 0.7982 (m-10) REVERT: B 227 GLU cc_start: 0.8552 (mm-30) cc_final: 0.8271 (mp0) REVERT: B 245 MET cc_start: 0.8390 (tpp) cc_final: 0.7672 (tpt) REVERT: B 273 GLU cc_start: 0.8338 (pm20) cc_final: 0.8016 (pm20) REVERT: B 277 GLU cc_start: 0.8692 (mm-30) cc_final: 0.8220 (mm-30) REVERT: B 350 GLU cc_start: 0.8660 (mt-10) cc_final: 0.8380 (mt-10) REVERT: B 392 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.8976 (mt) REVERT: B 410 MET cc_start: 0.8293 (mmp) cc_final: 0.7671 (mmt) REVERT: B 466 TYR cc_start: 0.8369 (m-80) cc_final: 0.8072 (m-10) REVERT: B 619 MET cc_start: 0.5993 (tpt) cc_final: 0.5517 (mmp) REVERT: B 728 MET cc_start: 0.8751 (ttt) cc_final: 0.8482 (tmm) REVERT: B 756 PHE cc_start: 0.8191 (p90) cc_final: 0.7630 (p90) REVERT: C 46 GLU cc_start: 0.8156 (mp0) cc_final: 0.7588 (mp0) REVERT: C 100 LYS cc_start: 0.9345 (tmtt) cc_final: 0.9108 (tptt) REVERT: D 3 GLN cc_start: 0.8576 (OUTLIER) cc_final: 0.7977 (pm20) REVERT: D 110 GLN cc_start: 0.8515 (mp10) cc_final: 0.8275 (mp10) outliers start: 50 outliers final: 40 residues processed: 273 average time/residue: 0.1193 time to fit residues: 47.0823 Evaluate side-chains 281 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 236 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 400 CYS Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 519 CYS Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 749 THR Chi-restraints excluded: chain A residue 781 TYR Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 274 ASP Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 400 CYS Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 745 TYR Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain D residue 3 GLN Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 34 MET Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 83 ASN Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 115 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 154 optimal weight: 3.9990 chunk 66 optimal weight: 9.9990 chunk 50 optimal weight: 0.8980 chunk 120 optimal weight: 0.9990 chunk 153 optimal weight: 7.9990 chunk 101 optimal weight: 0.6980 chunk 78 optimal weight: 0.9980 chunk 141 optimal weight: 9.9990 chunk 175 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 76 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.131265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.110895 restraints weight = 28019.145| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 2.92 r_work: 0.3531 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.4844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13403 Z= 0.138 Angle : 0.603 10.830 18282 Z= 0.303 Chirality : 0.042 0.171 2065 Planarity : 0.004 0.041 2402 Dihedral : 4.133 18.136 1959 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 3.51 % Allowed : 22.65 % Favored : 73.84 % 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: -0.59 (0.20), residues: 1782 helix: 1.58 (0.20), residues: 718 sheet: -1.60 (0.32), residues: 246 loop : -1.85 (0.21), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 264 TYR 0.015 0.001 TYR A 180 PHE 0.019 0.001 PHE A 456 TRP 0.009 0.001 TRP B 291 HIS 0.004 0.001 HIS A 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (13382) covalent geometry : angle 0.60209 / 0.30 (18240) SS BOND : bond 0.00195 / 0.12 ( 21) SS BOND : angle 0.98672 / 0.66 ( 42) hydrogen bonds : bond 0.03433 / 2.36 ( 623) hydrogen bonds : angle 4.20253 / 2.95 ( 1803) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 256 time to evaluate : 0.504 Fit side-chains REVERT: A 140 ILE cc_start: 0.9003 (OUTLIER) cc_final: 0.8746 (pt) REVERT: A 149 ILE cc_start: 0.8941 (pt) cc_final: 0.8576 (pt) REVERT: A 193 LYS cc_start: 0.8612 (mtmt) cc_final: 0.8256 (mtmm) REVERT: A 197 GLU cc_start: 0.8182 (mt-10) cc_final: 0.7897 (mt-10) REVERT: A 273 GLU cc_start: 0.8177 (pm20) cc_final: 0.7951 (pm20) REVERT: A 277 GLU cc_start: 0.8486 (mm-30) cc_final: 0.8212 (mm-30) REVERT: A 318 GLU cc_start: 0.7225 (pm20) cc_final: 0.6953 (pm20) REVERT: A 350 GLU cc_start: 0.8341 (mt-10) cc_final: 0.8047 (mt-10) REVERT: A 388 MET cc_start: 0.8696 (tpp) cc_final: 0.8367 (tpp) REVERT: A 631 VAL cc_start: 0.1692 (OUTLIER) cc_final: 0.1313 (t) REVERT: A 772 ILE cc_start: 0.7857 (tp) cc_final: 0.7596 (pt) REVERT: B 49 ASP cc_start: 0.8397 (m-30) cc_final: 0.8086 (t0) REVERT: B 112 ARG cc_start: 0.5674 (tpm170) cc_final: 0.5471 (tpp-160) REVERT: B 144 TYR cc_start: 0.9166 (m-80) cc_final: 0.8892 (m-80) REVERT: B 146 ASP cc_start: 0.8251 (OUTLIER) cc_final: 0.7949 (p0) REVERT: B 180 TYR cc_start: 0.8281 (m-10) cc_final: 0.7956 (m-10) REVERT: B 218 GLU cc_start: 0.8014 (mm-30) cc_final: 0.7776 (mm-30) REVERT: B 227 GLU cc_start: 0.8161 (mm-30) cc_final: 0.7931 (mp0) REVERT: B 240 LYS cc_start: 0.8640 (mttm) cc_final: 0.8281 (mtmm) REVERT: B 273 GLU cc_start: 0.8066 (pm20) cc_final: 0.7745 (pm20) REVERT: B 277 GLU cc_start: 0.8436 (mm-30) cc_final: 0.7973 (mm-30) REVERT: B 350 GLU cc_start: 0.8413 (mt-10) cc_final: 0.8129 (mt-10) REVERT: B 392 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8874 (mt) REVERT: B 410 MET cc_start: 0.8021 (mmp) cc_final: 0.7556 (mmt) REVERT: B 619 MET cc_start: 0.5913 (tpt) cc_final: 0.5674 (mmp) REVERT: B 728 MET cc_start: 0.8664 (ttt) cc_final: 0.8428 (tmm) REVERT: B 756 PHE cc_start: 0.8082 (p90) cc_final: 0.7547 (p90) REVERT: C 100 LYS cc_start: 0.9196 (tmtt) cc_final: 0.8954 (tptt) REVERT: D 3 GLN cc_start: 0.8343 (OUTLIER) cc_final: 0.7840 (pm20) REVERT: D 110 GLN cc_start: 0.8272 (mp10) cc_final: 0.7999 (mp10) outliers start: 44 outliers final: 35 residues processed: 282 average time/residue: 0.1130 time to fit residues: 46.2715 Evaluate side-chains 288 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 248 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 400 CYS Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 519 CYS Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 749 THR Chi-restraints excluded: chain A residue 781 TYR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 274 ASP Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 400 CYS Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 745 TYR Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain D residue 3 GLN Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 34 MET Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 83 ASN Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 115 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 122 optimal weight: 3.9990 chunk 142 optimal weight: 10.0000 chunk 17 optimal weight: 5.9990 chunk 54 optimal weight: 10.0000 chunk 2 optimal weight: 0.7980 chunk 67 optimal weight: 0.1980 chunk 1 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 171 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 63 optimal weight: 9.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 76 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.130059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.109705 restraints weight = 28248.329| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 2.90 r_work: 0.3525 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3404 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.4948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 13403 Z= 0.175 Angle : 0.621 10.938 18282 Z= 0.315 Chirality : 0.043 0.171 2065 Planarity : 0.004 0.045 2402 Dihedral : 4.187 18.026 1959 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 3.67 % Allowed : 23.29 % Favored : 73.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.20), residues: 1782 helix: 1.57 (0.20), residues: 716 sheet: -1.58 (0.32), residues: 246 loop : -1.91 (0.21), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 264 TYR 0.018 0.001 TYR A 180 PHE 0.022 0.002 PHE A 456 TRP 0.011 0.001 TRP A 297 HIS 0.004 0.001 HIS A 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.17 (13382) covalent geometry : angle 0.61924 / 0.31 (18240) SS BOND : bond 0.00240 / 0.17 ( 21) SS BOND : angle 1.13735 / 0.74 ( 42) hydrogen bonds : bond 0.03590 / 2.46 ( 623) hydrogen bonds : angle 4.24842 / 2.98 ( 1803) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 247 time to evaluate : 0.524 Fit side-chains REVERT: A 140 ILE cc_start: 0.9097 (OUTLIER) cc_final: 0.8822 (pt) REVERT: A 149 ILE cc_start: 0.9087 (pt) cc_final: 0.8731 (pt) REVERT: A 193 LYS cc_start: 0.8729 (mtmt) cc_final: 0.8365 (mtmm) REVERT: A 197 GLU cc_start: 0.8512 (mt-10) cc_final: 0.8239 (mt-10) REVERT: A 218 GLU cc_start: 0.7786 (mp0) cc_final: 0.7509 (mp0) REVERT: A 273 GLU cc_start: 0.8430 (pm20) cc_final: 0.8197 (pm20) REVERT: A 277 GLU cc_start: 0.8762 (mm-30) cc_final: 0.8491 (mm-30) REVERT: A 350 GLU cc_start: 0.8528 (mt-10) cc_final: 0.8234 (mt-10) REVERT: A 388 MET cc_start: 0.8941 (tpp) cc_final: 0.8619 (tpp) REVERT: A 631 VAL cc_start: 0.1910 (OUTLIER) cc_final: 0.1586 (t) REVERT: A 745 TYR cc_start: 0.6216 (OUTLIER) cc_final: 0.4755 (t80) REVERT: A 772 ILE cc_start: 0.7955 (tp) cc_final: 0.7658 (pt) REVERT: B 49 ASP cc_start: 0.8632 (m-30) cc_final: 0.8336 (t0) REVERT: B 112 ARG cc_start: 0.5683 (tpm170) cc_final: 0.5478 (tpp-160) REVERT: B 146 ASP cc_start: 0.8553 (OUTLIER) cc_final: 0.8244 (p0) REVERT: B 180 TYR cc_start: 0.8495 (m-10) cc_final: 0.8047 (m-10) REVERT: B 227 GLU cc_start: 0.8504 (mm-30) cc_final: 0.8251 (mp0) REVERT: B 245 MET cc_start: 0.8339 (tpt) cc_final: 0.7887 (tpt) REVERT: B 273 GLU cc_start: 0.8312 (pm20) cc_final: 0.7979 (pm20) REVERT: B 277 GLU cc_start: 0.8739 (mm-30) cc_final: 0.8285 (mm-30) REVERT: B 350 GLU cc_start: 0.8658 (mt-10) cc_final: 0.8392 (mt-10) REVERT: B 392 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.8980 (mt) REVERT: B 410 MET cc_start: 0.8163 (mmp) cc_final: 0.7730 (mmt) REVERT: B 619 MET cc_start: 0.6084 (tpt) cc_final: 0.5677 (mmp) REVERT: B 728 MET cc_start: 0.8765 (ttt) cc_final: 0.8473 (tmm) REVERT: B 756 PHE cc_start: 0.8184 (p90) cc_final: 0.7648 (p90) REVERT: C 46 GLU cc_start: 0.8214 (mp0) cc_final: 0.7717 (mp0) REVERT: C 100 LYS cc_start: 0.9347 (tmtt) cc_final: 0.9118 (tptt) REVERT: D 3 GLN cc_start: 0.8482 (OUTLIER) cc_final: 0.7928 (pm20) REVERT: D 110 GLN cc_start: 0.8530 (mp10) cc_final: 0.8279 (mp10) outliers start: 46 outliers final: 36 residues processed: 275 average time/residue: 0.1061 time to fit residues: 42.2180 Evaluate side-chains 285 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 243 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 400 CYS Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 519 CYS Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 745 TYR Chi-restraints excluded: chain A residue 749 THR Chi-restraints excluded: chain A residue 781 TYR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 274 ASP Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 400 CYS Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 745 TYR Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain D residue 3 GLN Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 83 ASN Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 116 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 48 optimal weight: 0.8980 chunk 148 optimal weight: 10.0000 chunk 109 optimal weight: 1.9990 chunk 144 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 133 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 157 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 89 optimal weight: 0.3980 chunk 122 optimal weight: 4.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 76 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.130860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.110571 restraints weight = 27978.462| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 2.93 r_work: 0.3525 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.4963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13403 Z= 0.147 Angle : 0.607 11.044 18282 Z= 0.306 Chirality : 0.042 0.152 2065 Planarity : 0.004 0.041 2402 Dihedral : 4.119 18.218 1959 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 3.51 % Allowed : 23.68 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.20), residues: 1782 helix: 1.58 (0.20), residues: 720 sheet: -1.57 (0.32), residues: 246 loop : -1.89 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 417 TYR 0.017 0.001 TYR A 180 PHE 0.021 0.001 PHE A 456 TRP 0.010 0.001 TRP A 291 HIS 0.005 0.001 HIS B 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 (13382) covalent geometry : angle 0.60570 / 0.31 (18240) SS BOND : bond 0.00200 / 0.13 ( 21) SS BOND : angle 1.00656 / 0.66 ( 42) hydrogen bonds : bond 0.03440 / 2.36 ( 623) hydrogen bonds : angle 4.18976 / 2.94 ( 1803) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3059.19 seconds wall clock time: 53 minutes 5.33 seconds (3185.33 seconds total)