Starting phenix.real_space_refine on Tue Dec 31 06:22:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7epb_31236/12_2024/7epb_31236.cif Found real_map, /net/cci-nas-00/data/ceres_data/7epb_31236/12_2024/7epb_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7epb_31236/12_2024/7epb_31236.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7epb_31236/12_2024/7epb_31236.map" model { file = "/net/cci-nas-00/data/ceres_data/7epb_31236/12_2024/7epb_31236.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7epb_31236/12_2024/7epb_31236.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.198 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: {'GLN:plan1': 3, 'HIS:plan': 3, 'TYR:plan': 6, 'ASN:plan1': 3, 'TRP:plan': 3, 'ASP:plan': 3, 'PHE:plan': 13, 'GLU:plan': 4, 'ARG:plan': 9} 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: {'GLN:plan1': 3, 'HIS:plan': 3, 'TYR:plan': 7, 'ASN:plan1': 3, 'TRP:plan': 3, 'ASP:plan': 3, 'PHE:plan': 10, 'GLU:plan': 5, 'ARG:plan': 9} 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: 7.98, per 1000 atoms: 0.61 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: 3.19 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 1.41 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: 4.45 Time building geometry restraints manager: 3.66 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: 7286 17.89 - 35.78: 571 35.78 - 53.67: 134 53.67 - 71.55: 14 71.55 - 89.44: 21 Dihedral angle restraints: 8026 sinusoidal: 2861 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 8023 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 817 or resid 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 817 or resid 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: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 0.530 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 31.660 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.060 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 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 13382 Z= 0.252 Angle : 0.619 34.483 18240 Z= 0.297 Chirality : 0.058 1.294 2065 Planarity : 0.003 0.041 2402 Dihedral : 13.843 89.443 4643 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.005 0.000 TRP B 297 HIS 0.002 0.000 HIS D 104 PHE 0.018 0.001 PHE A 456 TYR 0.011 0.001 TYR A 787 ARG 0.004 0.000 ARG B 229 *********************** 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 : 1.386 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: 0.8164 (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: 0.7454 (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: 0.2279 time to fit residues: 91.4704 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 : 1.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 10.0000 chunk 133 optimal weight: 0.7980 chunk 74 optimal weight: 0.0570 chunk 45 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 chunk 71 optimal weight: 0.4980 chunk 137 optimal weight: 5.9990 chunk 53 optimal weight: 9.9990 chunk 83 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 159 optimal weight: 0.0980 overall best weight: 0.4900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 HIS B 790 GLN ** D 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 GLN D 39 GLN D 76 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 13382 Z= 0.150 Angle : 0.530 13.319 18240 Z= 0.262 Chirality : 0.041 0.201 2065 Planarity : 0.003 0.041 2402 Dihedral : 4.213 53.879 1999 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 1.36 % Allowed : 13.80 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.19), residues: 1782 helix: 1.05 (0.19), residues: 730 sheet: -1.11 (0.33), residues: 246 loop : -1.90 (0.19), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 291 HIS 0.003 0.001 HIS D 104 PHE 0.037 0.001 PHE A 456 TYR 0.010 0.001 TYR D 79 ARG 0.004 0.000 ARG A 243 *********************** 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 267 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 250 time to evaluate : 1.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 ILE cc_start: 0.8981 (pt) cc_final: 0.8490 (pt) REVERT: A 150 GLN cc_start: 0.8486 (mm-40) cc_final: 0.8209 (mm110) REVERT: A 350 GLU cc_start: 0.7941 (mt-10) cc_final: 0.7594 (mt-10) REVERT: A 414 ASN cc_start: 0.7518 (p0) cc_final: 0.7281 (p0) REVERT: B 144 TYR cc_start: 0.8967 (m-80) cc_final: 0.8685 (m-80) REVERT: B 193 LYS cc_start: 0.8175 (mmmm) cc_final: 0.7730 (mmmm) REVERT: B 342 ASN cc_start: 0.8011 (t0) cc_final: 0.7798 (t0) REVERT: B 718 THR cc_start: 0.4956 (p) cc_final: 0.3729 (m) REVERT: C 38 ARG cc_start: 0.7704 (ptm160) cc_final: 0.7249 (ptm160) REVERT: C 46 GLU cc_start: 0.7713 (mp0) cc_final: 0.7256 (mp0) REVERT: C 100 LYS cc_start: 0.8762 (tmtt) cc_final: 0.8525 (tptt) outliers start: 17 outliers final: 11 residues processed: 258 average time/residue: 0.2520 time to fit residues: 95.3974 Evaluate side-chains 238 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 227 time to evaluate : 1.451 ------------------------------------------------------------------------------- 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 749 THR Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 396 HIS Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain D residue 39 GLN 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 88 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 133 optimal weight: 0.8980 chunk 108 optimal weight: 0.0670 chunk 44 optimal weight: 3.9990 chunk 160 optimal weight: 4.9990 chunk 172 optimal weight: 4.9990 chunk 142 optimal weight: 7.9990 chunk 158 optimal weight: 0.9990 chunk 54 optimal weight: 20.0000 chunk 128 optimal weight: 20.0000 overall best weight: 1.5924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN B 101 GLN C 76 ASN ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 13382 Z= 0.292 Angle : 0.593 7.188 18240 Z= 0.310 Chirality : 0.043 0.171 2065 Planarity : 0.004 0.046 2402 Dihedral : 3.963 20.218 1999 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.71 % Allowed : 16.19 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.20), residues: 1782 helix: 1.40 (0.20), residues: 716 sheet: -1.09 (0.33), residues: 260 loop : -1.81 (0.20), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 297 HIS 0.005 0.001 HIS B 396 PHE 0.042 0.002 PHE A 456 TYR 0.014 0.002 TYR D 101 ARG 0.007 0.001 ARG D 38 *********************** 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 306 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 272 time to evaluate : 1.590 Fit side-chains REVERT: A 149 ILE cc_start: 0.8900 (pt) cc_final: 0.8531 (pt) REVERT: A 193 LYS cc_start: 0.8358 (mtmt) cc_final: 0.7960 (mtmm) REVERT: A 197 GLU cc_start: 0.7755 (mt-10) cc_final: 0.7371 (mt-10) REVERT: A 277 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7568 (mm-30) REVERT: A 350 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7702 (mt-10) REVERT: A 388 MET cc_start: 0.8147 (tpp) cc_final: 0.7778 (tpp) REVERT: A 396 HIS cc_start: 0.7118 (t70) cc_final: 0.6862 (t-90) REVERT: A 414 ASN cc_start: 0.7941 (p0) cc_final: 0.7713 (p0) REVERT: B 49 ASP cc_start: 0.7926 (OUTLIER) cc_final: 0.7662 (t0) REVERT: B 146 ASP cc_start: 0.7769 (OUTLIER) cc_final: 0.7494 (p0) REVERT: B 312 GLU cc_start: 0.7679 (mm-30) cc_final: 0.7468 (mm-30) REVERT: B 342 ASN cc_start: 0.8233 (t0) cc_final: 0.8006 (t0) REVERT: B 350 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7741 (mt-10) REVERT: B 396 HIS cc_start: 0.7260 (OUTLIER) cc_final: 0.7023 (t-90) REVERT: B 619 MET cc_start: 0.4568 (tpt) cc_final: 0.4159 (mmm) REVERT: C 38 ARG cc_start: 0.7991 (ptm160) cc_final: 0.7194 (ptm160) REVERT: C 46 GLU cc_start: 0.7629 (mp0) cc_final: 0.7077 (mp0) REVERT: C 100 LYS cc_start: 0.8973 (tmtt) cc_final: 0.8765 (tptt) REVERT: C 110 GLN cc_start: 0.7729 (mm-40) cc_final: 0.7513 (mm-40) REVERT: D 110 GLN cc_start: 0.7704 (mp10) cc_final: 0.7383 (mp10) outliers start: 34 outliers final: 25 residues processed: 287 average time/residue: 0.2599 time to fit residues: 108.8454 Evaluate side-chains 270 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 242 time to evaluate : 1.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 523 ILE 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 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 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 2 VAL Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 76 ASN Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 76 ASN Chi-restraints excluded: chain D residue 106 THR 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 158 optimal weight: 0.9980 chunk 120 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 160 optimal weight: 4.9990 chunk 170 optimal weight: 0.9990 chunk 152 optimal weight: 5.9990 chunk 45 optimal weight: 0.7980 chunk 141 optimal weight: 9.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 150 GLN C 76 ASN D 76 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 13382 Z= 0.243 Angle : 0.570 10.662 18240 Z= 0.291 Chirality : 0.042 0.157 2065 Planarity : 0.004 0.041 2402 Dihedral : 3.847 16.156 1999 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 3.27 % Allowed : 18.34 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.20), residues: 1782 helix: 1.53 (0.20), residues: 716 sheet: -1.15 (0.32), residues: 260 loop : -1.79 (0.20), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 297 HIS 0.004 0.001 HIS B 97 PHE 0.031 0.002 PHE A 456 TYR 0.013 0.001 TYR D 99 ARG 0.008 0.000 ARG A 276 *********************** 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 296 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 255 time to evaluate : 1.435 Fit side-chains REVERT: A 149 ILE cc_start: 0.8872 (pt) cc_final: 0.8527 (pt) REVERT: A 193 LYS cc_start: 0.8343 (mtmt) cc_final: 0.7977 (mtmm) REVERT: A 197 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7460 (mt-10) REVERT: A 277 GLU cc_start: 0.7858 (mm-30) cc_final: 0.7539 (mm-30) REVERT: A 350 GLU cc_start: 0.8025 (mt-10) cc_final: 0.7710 (mt-10) REVERT: A 388 MET cc_start: 0.8147 (tpp) cc_final: 0.7786 (tpp) REVERT: A 396 HIS cc_start: 0.7067 (t70) cc_final: 0.6852 (t-90) REVERT: A 414 ASN cc_start: 0.7977 (p0) cc_final: 0.7749 (p0) REVERT: B 146 ASP cc_start: 0.7786 (OUTLIER) cc_final: 0.7528 (p0) REVERT: B 342 ASN cc_start: 0.8224 (t0) cc_final: 0.8004 (t0) REVERT: B 350 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7745 (mt-10) REVERT: B 392 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8500 (mt) REVERT: B 619 MET cc_start: 0.4664 (tpt) cc_final: 0.4118 (mmm) REVERT: C 38 ARG cc_start: 0.7967 (ptm160) cc_final: 0.7089 (ptm160) REVERT: C 46 GLU cc_start: 0.7577 (mp0) cc_final: 0.7017 (mp0) REVERT: C 100 LYS cc_start: 0.8968 (tmtt) cc_final: 0.8763 (tptt) REVERT: D 76 ASN cc_start: 0.7290 (OUTLIER) cc_final: 0.6855 (p0) REVERT: D 110 GLN cc_start: 0.7732 (mp10) cc_final: 0.7295 (mp10) outliers start: 41 outliers final: 29 residues processed: 276 average time/residue: 0.2602 time to fit residues: 103.8823 Evaluate side-chains 268 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 236 time to evaluate : 1.463 ------------------------------------------------------------------------------- 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 272 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 749 THR Chi-restraints excluded: chain A residue 781 TYR Chi-restraints excluded: chain A residue 809 LEU 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 292 VAL Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 400 CYS 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 115 THR Chi-restraints excluded: chain D residue 34 MET Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 76 ASN 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 96 optimal weight: 6.9990 chunk 2 optimal weight: 0.9990 chunk 126 optimal weight: 0.0980 chunk 70 optimal weight: 3.9990 chunk 145 optimal weight: 8.9990 chunk 117 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 86 optimal weight: 9.9990 chunk 152 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 57 optimal weight: 6.9990 overall best weight: 2.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 150 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.3910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 13382 Z= 0.334 Angle : 0.615 9.323 18240 Z= 0.322 Chirality : 0.044 0.220 2065 Planarity : 0.004 0.040 2402 Dihedral : 4.136 15.912 1999 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 3.59 % Allowed : 19.22 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.20), residues: 1782 helix: 1.43 (0.20), residues: 726 sheet: -1.33 (0.33), residues: 248 loop : -1.89 (0.20), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 297 HIS 0.004 0.001 HIS A 97 PHE 0.024 0.002 PHE A 456 TYR 0.013 0.002 TYR D 99 ARG 0.007 0.001 ARG A 264 *********************** 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 305 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 260 time to evaluate : 1.571 Fit side-chains REVERT: A 149 ILE cc_start: 0.8876 (pt) cc_final: 0.8551 (pt) REVERT: A 193 LYS cc_start: 0.8440 (mtmt) cc_final: 0.8119 (mtmm) REVERT: A 197 GLU cc_start: 0.7761 (mt-10) cc_final: 0.7514 (mt-10) REVERT: A 273 GLU cc_start: 0.7692 (pm20) cc_final: 0.7487 (pm20) REVERT: A 277 GLU cc_start: 0.7936 (mm-30) cc_final: 0.7580 (mm-30) REVERT: A 350 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7747 (mt-10) REVERT: A 388 MET cc_start: 0.8182 (tpp) cc_final: 0.7844 (tpp) REVERT: A 414 ASN cc_start: 0.8048 (p0) cc_final: 0.7802 (p0) REVERT: A 631 VAL cc_start: 0.2087 (OUTLIER) cc_final: 0.1809 (t) REVERT: A 639 LEU cc_start: 0.8183 (mt) cc_final: 0.7861 (pt) REVERT: A 728 MET cc_start: 0.8158 (tpp) cc_final: 0.7869 (tmm) REVERT: B 146 ASP cc_start: 0.7791 (OUTLIER) cc_final: 0.7566 (p0) REVERT: B 342 ASN cc_start: 0.8311 (t0) cc_final: 0.8097 (t0) REVERT: B 350 GLU cc_start: 0.8059 (mt-10) cc_final: 0.7735 (mt-10) REVERT: B 392 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8631 (mt) REVERT: B 619 MET cc_start: 0.5125 (tpt) cc_final: 0.4543 (mtp) REVERT: B 756 PHE cc_start: 0.7947 (p90) cc_final: 0.7489 (p90) REVERT: C 34 MET cc_start: 0.7655 (mtp) cc_final: 0.7403 (mtp) REVERT: C 38 ARG cc_start: 0.7969 (ptm160) cc_final: 0.6927 (ptm160) REVERT: C 46 GLU cc_start: 0.7528 (mp0) cc_final: 0.6970 (mp0) REVERT: C 76 ASN cc_start: 0.7760 (p0) cc_final: 0.7425 (p0) REVERT: C 100 LYS cc_start: 0.9017 (tmtt) cc_final: 0.8774 (tptt) REVERT: D 110 GLN cc_start: 0.7732 (mp10) cc_final: 0.7503 (mp10) outliers start: 45 outliers final: 34 residues processed: 287 average time/residue: 0.2604 time to fit residues: 107.6293 Evaluate side-chains 286 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 249 time to evaluate : 1.409 ------------------------------------------------------------------------------- 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 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 631 VAL 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 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 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 68 THR Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 34 MET Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 83 ASN Chi-restraints excluded: chain D residue 103 THR 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 153 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 99 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 170 optimal weight: 0.9980 chunk 141 optimal weight: 10.0000 chunk 78 optimal weight: 0.5980 chunk 14 optimal weight: 4.9990 chunk 56 optimal weight: 0.8980 chunk 89 optimal weight: 0.5980 chunk 164 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.3923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13382 Z= 0.194 Angle : 0.578 10.951 18240 Z= 0.292 Chirality : 0.042 0.182 2065 Planarity : 0.004 0.041 2402 Dihedral : 3.942 16.120 1999 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 3.59 % Allowed : 19.62 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.20), residues: 1782 helix: 1.64 (0.20), residues: 720 sheet: -1.38 (0.32), residues: 246 loop : -1.78 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 291 HIS 0.003 0.001 HIS B 97 PHE 0.018 0.001 PHE A 456 TYR 0.013 0.001 TYR D 59 ARG 0.006 0.000 ARG B 276 *********************** 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 307 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 262 time to evaluate : 1.523 Fit side-chains REVERT: A 149 ILE cc_start: 0.8848 (pt) cc_final: 0.8613 (pt) REVERT: A 193 LYS cc_start: 0.8390 (mtmt) cc_final: 0.8065 (mtmm) REVERT: A 197 GLU cc_start: 0.7714 (mt-10) cc_final: 0.7457 (mt-10) REVERT: A 245 MET cc_start: 0.7639 (tpt) cc_final: 0.7087 (tpt) REVERT: A 277 GLU cc_start: 0.7881 (mm-30) cc_final: 0.7531 (mm-30) REVERT: A 350 GLU cc_start: 0.8034 (mt-10) cc_final: 0.7729 (mt-10) REVERT: A 388 MET cc_start: 0.8163 (tpp) cc_final: 0.7858 (tpp) REVERT: A 414 ASN cc_start: 0.7921 (p0) cc_final: 0.7706 (p0) REVERT: A 619 MET cc_start: 0.6313 (mmm) cc_final: 0.6070 (mmm) REVERT: A 631 VAL cc_start: 0.1827 (OUTLIER) cc_final: 0.1552 (t) REVERT: A 639 LEU cc_start: 0.8125 (mt) cc_final: 0.7827 (pt) REVERT: B 146 ASP cc_start: 0.7773 (OUTLIER) cc_final: 0.7544 (p0) REVERT: B 227 GLU cc_start: 0.7932 (mm-30) cc_final: 0.7614 (mp0) REVERT: B 350 GLU cc_start: 0.8017 (mt-10) cc_final: 0.7702 (mt-10) REVERT: B 392 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8595 (mt) REVERT: B 619 MET cc_start: 0.4967 (tpt) cc_final: 0.4499 (mtp) REVERT: B 756 PHE cc_start: 0.7945 (p90) cc_final: 0.7473 (p90) REVERT: C 34 MET cc_start: 0.7592 (mtp) cc_final: 0.7339 (mtp) REVERT: C 38 ARG cc_start: 0.7937 (ptm160) cc_final: 0.6876 (ptm160) REVERT: C 46 GLU cc_start: 0.7532 (mp0) cc_final: 0.7053 (mp0) REVERT: C 76 ASN cc_start: 0.7685 (p0) cc_final: 0.7354 (p0) REVERT: C 86 LYS cc_start: 0.8908 (mppt) cc_final: 0.8516 (mmtm) REVERT: C 100 LYS cc_start: 0.8963 (tmtt) cc_final: 0.8707 (tptt) REVERT: C 108 TRP cc_start: 0.8772 (m100) cc_final: 0.8465 (m100) REVERT: D 110 GLN cc_start: 0.7721 (mp10) cc_final: 0.7490 (mp10) outliers start: 45 outliers final: 31 residues processed: 288 average time/residue: 0.2633 time to fit residues: 108.7123 Evaluate side-chains 285 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 251 time to evaluate : 1.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 90 ASP 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 300 LEU Chi-restraints excluded: chain A residue 400 CYS Chi-restraints excluded: chain A residue 517 VAL 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 781 TYR Chi-restraints excluded: chain A residue 809 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 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 34 MET Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 86 LYS Chi-restraints excluded: chain D residue 115 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 19 optimal weight: 4.9990 chunk 97 optimal weight: 4.9990 chunk 124 optimal weight: 6.9990 chunk 96 optimal weight: 5.9990 chunk 143 optimal weight: 9.9990 chunk 95 optimal weight: 2.9990 chunk 169 optimal weight: 0.0980 chunk 106 optimal weight: 8.9990 chunk 103 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 104 optimal weight: 0.6980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.4199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13382 Z= 0.252 Angle : 0.603 10.367 18240 Z= 0.308 Chirality : 0.043 0.179 2065 Planarity : 0.004 0.042 2402 Dihedral : 4.061 16.311 1999 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 3.67 % Allowed : 20.57 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.20), residues: 1782 helix: 1.65 (0.20), residues: 718 sheet: -1.48 (0.32), residues: 246 loop : -1.78 (0.21), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 297 HIS 0.003 0.001 HIS A 97 PHE 0.022 0.002 PHE A 456 TYR 0.011 0.001 TYR D 99 ARG 0.008 0.001 ARG B 264 *********************** 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 302 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 256 time to evaluate : 1.512 Fit side-chains REVERT: A 95 ASP cc_start: 0.7813 (m-30) cc_final: 0.7027 (m-30) REVERT: A 140 ILE cc_start: 0.8935 (OUTLIER) cc_final: 0.8673 (pt) REVERT: A 146 ASP cc_start: 0.7866 (p0) cc_final: 0.7655 (p0) REVERT: A 149 ILE cc_start: 0.8947 (pt) cc_final: 0.8480 (pt) REVERT: A 193 LYS cc_start: 0.8402 (mtmt) cc_final: 0.8077 (mtmm) REVERT: A 197 GLU cc_start: 0.7752 (mt-10) cc_final: 0.7501 (mt-10) REVERT: A 215 ASP cc_start: 0.6604 (p0) cc_final: 0.6258 (p0) REVERT: A 243 ARG cc_start: 0.7934 (mmm160) cc_final: 0.7542 (mmm160) REVERT: A 245 MET cc_start: 0.7726 (tpt) cc_final: 0.7247 (tpt) REVERT: A 273 GLU cc_start: 0.7824 (pm20) cc_final: 0.7425 (pm20) REVERT: A 277 GLU cc_start: 0.7918 (mm-30) cc_final: 0.7565 (mm-30) REVERT: A 350 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7725 (mt-10) REVERT: A 388 MET cc_start: 0.8188 (tpp) cc_final: 0.7864 (tpp) REVERT: A 631 VAL cc_start: 0.1751 (OUTLIER) cc_final: 0.1443 (t) REVERT: A 639 LEU cc_start: 0.8189 (mt) cc_final: 0.7868 (pt) REVERT: B 146 ASP cc_start: 0.7770 (OUTLIER) cc_final: 0.7534 (p0) REVERT: B 274 ASP cc_start: 0.7945 (t0) cc_final: 0.7605 (t0) REVERT: B 350 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7738 (mt-10) REVERT: B 392 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8757 (mt) REVERT: B 410 MET cc_start: 0.7740 (mmp) cc_final: 0.7356 (mmt) REVERT: B 756 PHE cc_start: 0.8006 (p90) cc_final: 0.7525 (p90) REVERT: C 38 ARG cc_start: 0.7964 (ptm160) cc_final: 0.6844 (ptm160) REVERT: C 46 GLU cc_start: 0.7549 (mp0) cc_final: 0.7072 (mp0) REVERT: C 76 ASN cc_start: 0.7783 (p0) cc_final: 0.7444 (p0) REVERT: C 100 LYS cc_start: 0.8961 (tmtt) cc_final: 0.8696 (tptt) REVERT: D 76 ASN cc_start: 0.7640 (p0) cc_final: 0.7403 (p0) REVERT: D 110 GLN cc_start: 0.7724 (mp10) cc_final: 0.7487 (mp10) outliers start: 46 outliers final: 36 residues processed: 285 average time/residue: 0.2577 time to fit residues: 105.3442 Evaluate side-chains 286 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 246 time to evaluate : 1.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 90 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 517 VAL 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 781 TYR Chi-restraints excluded: chain A residue 809 LEU 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 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 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 34 MET Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 83 ASN Chi-restraints excluded: chain D residue 86 LYS Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 117 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 67 optimal weight: 0.0770 chunk 101 optimal weight: 0.9980 chunk 51 optimal weight: 10.0000 chunk 33 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 115 optimal weight: 0.4980 chunk 83 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 133 optimal weight: 7.9990 chunk 154 optimal weight: 3.9990 overall best weight: 0.8740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.4255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13382 Z= 0.200 Angle : 0.602 10.876 18240 Z= 0.304 Chirality : 0.042 0.161 2065 Planarity : 0.004 0.042 2402 Dihedral : 3.979 16.664 1999 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 3.43 % Allowed : 21.85 % Favored : 74.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.20), residues: 1782 helix: 1.70 (0.20), residues: 718 sheet: -1.47 (0.32), residues: 246 loop : -1.77 (0.21), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 291 HIS 0.004 0.001 HIS A 97 PHE 0.021 0.001 PHE A 456 TYR 0.011 0.001 TYR D 99 ARG 0.005 0.000 ARG B 264 *********************** 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 294 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 251 time to evaluate : 1.499 Fit side-chains REVERT: A 95 ASP cc_start: 0.7810 (m-30) cc_final: 0.6946 (m-30) REVERT: A 144 TYR cc_start: 0.9001 (m-80) cc_final: 0.8789 (m-80) REVERT: A 146 ASP cc_start: 0.7908 (p0) cc_final: 0.7665 (p0) REVERT: A 149 ILE cc_start: 0.8897 (pt) cc_final: 0.8395 (pt) REVERT: A 180 TYR cc_start: 0.7917 (m-10) cc_final: 0.7478 (m-10) REVERT: A 193 LYS cc_start: 0.8401 (mtmt) cc_final: 0.8073 (mtmm) REVERT: A 197 GLU cc_start: 0.7708 (mt-10) cc_final: 0.7427 (mt-10) REVERT: A 215 ASP cc_start: 0.6843 (p0) cc_final: 0.6480 (p0) REVERT: A 245 MET cc_start: 0.7592 (tpt) cc_final: 0.7108 (tpt) REVERT: A 273 GLU cc_start: 0.7776 (pm20) cc_final: 0.7426 (pm20) REVERT: A 277 GLU cc_start: 0.7902 (mm-30) cc_final: 0.7561 (mm-30) REVERT: A 350 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7724 (mt-10) REVERT: A 388 MET cc_start: 0.8165 (tpp) cc_final: 0.7858 (tpp) REVERT: A 631 VAL cc_start: 0.1674 (OUTLIER) cc_final: 0.1365 (t) REVERT: A 639 LEU cc_start: 0.8144 (mt) cc_final: 0.7931 (pt) REVERT: B 144 TYR cc_start: 0.8998 (m-80) cc_final: 0.8744 (m-80) REVERT: B 146 ASP cc_start: 0.7772 (OUTLIER) cc_final: 0.7543 (p0) REVERT: B 180 TYR cc_start: 0.7932 (m-10) cc_final: 0.7587 (m-10) REVERT: B 277 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7615 (mm-30) REVERT: B 315 ILE cc_start: 0.9424 (mt) cc_final: 0.9221 (mm) REVERT: B 350 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7734 (mt-10) REVERT: B 410 MET cc_start: 0.7692 (mmp) cc_final: 0.7326 (mmt) REVERT: B 756 PHE cc_start: 0.7922 (p90) cc_final: 0.7447 (p90) REVERT: C 38 ARG cc_start: 0.7937 (ptm160) cc_final: 0.7605 (ptm160) REVERT: C 86 LYS cc_start: 0.8812 (mppt) cc_final: 0.8549 (mmtm) REVERT: C 100 LYS cc_start: 0.8933 (tmtt) cc_final: 0.8673 (tptt) REVERT: D 110 GLN cc_start: 0.7728 (mp10) cc_final: 0.7492 (mp10) outliers start: 43 outliers final: 35 residues processed: 276 average time/residue: 0.2558 time to fit residues: 102.2796 Evaluate side-chains 276 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 239 time to evaluate : 1.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 90 ASP 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 395 MET Chi-restraints excluded: chain A residue 400 CYS 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 632 CYS Chi-restraints excluded: chain A residue 749 THR Chi-restraints excluded: chain A residue 781 TYR 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 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 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 2 VAL Chi-restraints excluded: chain D residue 34 MET Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 80 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 162 optimal weight: 2.9990 chunk 148 optimal weight: 0.7980 chunk 158 optimal weight: 0.7980 chunk 95 optimal weight: 2.9990 chunk 68 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 142 optimal weight: 9.9990 chunk 149 optimal weight: 0.9990 chunk 157 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.4420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13382 Z= 0.228 Angle : 0.607 10.905 18240 Z= 0.309 Chirality : 0.043 0.165 2065 Planarity : 0.004 0.042 2402 Dihedral : 4.039 16.936 1999 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 3.43 % Allowed : 21.61 % Favored : 74.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.20), residues: 1782 helix: 1.72 (0.20), residues: 720 sheet: -1.49 (0.32), residues: 246 loop : -1.80 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 108 HIS 0.004 0.001 HIS A 97 PHE 0.023 0.002 PHE A 456 TYR 0.010 0.001 TYR D 99 ARG 0.011 0.001 ARG B 352 *********************** 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 290 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 247 time to evaluate : 1.450 Fit side-chains REVERT: A 95 ASP cc_start: 0.7844 (m-30) cc_final: 0.7558 (m-30) REVERT: A 149 ILE cc_start: 0.8919 (pt) cc_final: 0.8509 (pt) REVERT: A 180 TYR cc_start: 0.7937 (m-10) cc_final: 0.7167 (m-10) REVERT: A 193 LYS cc_start: 0.8439 (mtmt) cc_final: 0.8116 (mtmm) REVERT: A 197 GLU cc_start: 0.7724 (mt-10) cc_final: 0.7453 (mt-10) REVERT: A 245 MET cc_start: 0.7561 (tpt) cc_final: 0.7178 (tpt) REVERT: A 273 GLU cc_start: 0.7800 (pm20) cc_final: 0.7355 (pm20) REVERT: A 277 GLU cc_start: 0.7915 (mm-30) cc_final: 0.7335 (mm-30) REVERT: A 350 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7737 (mt-10) REVERT: A 388 MET cc_start: 0.8162 (tpp) cc_final: 0.7862 (tpp) REVERT: A 619 MET cc_start: 0.6535 (mmm) cc_final: 0.6329 (mmm) REVERT: A 631 VAL cc_start: 0.2078 (OUTLIER) cc_final: 0.1748 (t) REVERT: A 639 LEU cc_start: 0.8184 (mt) cc_final: 0.7929 (pt) REVERT: B 146 ASP cc_start: 0.7775 (OUTLIER) cc_final: 0.7531 (p0) REVERT: B 180 TYR cc_start: 0.7938 (m-10) cc_final: 0.7539 (m-10) REVERT: B 245 MET cc_start: 0.7715 (tpt) cc_final: 0.7368 (tpt) REVERT: B 350 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7716 (mt-10) REVERT: B 392 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8785 (mt) REVERT: B 410 MET cc_start: 0.7693 (mmp) cc_final: 0.6943 (mmt) REVERT: B 756 PHE cc_start: 0.8004 (p90) cc_final: 0.7501 (p90) REVERT: C 38 ARG cc_start: 0.7929 (ptm160) cc_final: 0.6904 (ptm160) REVERT: C 46 GLU cc_start: 0.7525 (mp0) cc_final: 0.7030 (mp0) REVERT: C 66 ARG cc_start: 0.5823 (ptt180) cc_final: 0.5329 (ptt180) REVERT: C 100 LYS cc_start: 0.8921 (tmtt) cc_final: 0.8653 (tptt) REVERT: D 110 GLN cc_start: 0.7743 (mp10) cc_final: 0.7495 (mp10) outliers start: 43 outliers final: 38 residues processed: 274 average time/residue: 0.2512 time to fit residues: 99.6685 Evaluate side-chains 284 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 243 time to evaluate : 1.427 ------------------------------------------------------------------------------- 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 78 LEU Chi-restraints excluded: chain A residue 90 ASP 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 781 TYR 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 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 2 VAL Chi-restraints excluded: chain D residue 34 MET Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 83 ASN Chi-restraints excluded: chain D residue 86 LYS Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 117 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 167 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 79 optimal weight: 0.6980 chunk 116 optimal weight: 0.5980 chunk 175 optimal weight: 4.9990 chunk 161 optimal weight: 0.9980 chunk 139 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 chunk 85 optimal weight: 0.5980 chunk 110 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.4392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13382 Z= 0.198 Angle : 0.618 14.055 18240 Z= 0.311 Chirality : 0.042 0.164 2065 Planarity : 0.004 0.042 2402 Dihedral : 3.994 16.990 1999 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 3.35 % Allowed : 22.17 % Favored : 74.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.20), residues: 1782 helix: 1.75 (0.20), residues: 720 sheet: -1.48 (0.32), residues: 246 loop : -1.78 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 291 HIS 0.004 0.001 HIS A 97 PHE 0.024 0.001 PHE A 456 TYR 0.010 0.001 TYR D 99 ARG 0.008 0.000 ARG A 352 ********************** 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 287 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 245 time to evaluate : 1.568 Fit side-chains REVERT: A 29 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7544 (pp20) REVERT: A 95 ASP cc_start: 0.7823 (m-30) cc_final: 0.7524 (m-30) REVERT: A 149 ILE cc_start: 0.8917 (pt) cc_final: 0.8508 (pt) REVERT: A 193 LYS cc_start: 0.8418 (mtmt) cc_final: 0.8083 (mtmm) REVERT: A 197 GLU cc_start: 0.7713 (mt-10) cc_final: 0.7435 (mt-10) REVERT: A 245 MET cc_start: 0.7584 (tpt) cc_final: 0.7202 (tpt) REVERT: A 273 GLU cc_start: 0.7762 (pm20) cc_final: 0.7469 (pm20) REVERT: A 277 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7562 (mm-30) REVERT: A 318 GLU cc_start: 0.6849 (pm20) cc_final: 0.6567 (pm20) REVERT: A 350 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7727 (mt-10) REVERT: A 388 MET cc_start: 0.8102 (tpp) cc_final: 0.7808 (tpp) REVERT: A 631 VAL cc_start: 0.1884 (OUTLIER) cc_final: 0.1553 (t) REVERT: A 639 LEU cc_start: 0.8135 (mt) cc_final: 0.7895 (pt) REVERT: B 49 ASP cc_start: 0.7842 (m-30) cc_final: 0.7576 (t0) REVERT: B 144 TYR cc_start: 0.9003 (m-80) cc_final: 0.8751 (m-80) REVERT: B 146 ASP cc_start: 0.7760 (OUTLIER) cc_final: 0.7539 (p0) REVERT: B 180 TYR cc_start: 0.7874 (m-10) cc_final: 0.7529 (m-10) REVERT: B 240 LYS cc_start: 0.8145 (mttm) cc_final: 0.7938 (mtmm) REVERT: B 245 MET cc_start: 0.7737 (tpt) cc_final: 0.7293 (tpt) REVERT: B 277 GLU cc_start: 0.7816 (mm-30) cc_final: 0.7472 (mm-30) REVERT: B 350 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7723 (mt-10) REVERT: B 392 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8783 (mt) REVERT: B 410 MET cc_start: 0.7671 (mmp) cc_final: 0.6978 (mmt) REVERT: B 756 PHE cc_start: 0.8018 (p90) cc_final: 0.7534 (p90) REVERT: C 46 GLU cc_start: 0.7541 (mp0) cc_final: 0.7084 (mp0) REVERT: C 100 LYS cc_start: 0.8898 (tmtt) cc_final: 0.8665 (tptt) REVERT: D 3 GLN cc_start: 0.7835 (pm20) cc_final: 0.7614 (pm20) REVERT: D 110 GLN cc_start: 0.7720 (mp10) cc_final: 0.7452 (mp10) outliers start: 42 outliers final: 35 residues processed: 270 average time/residue: 0.2598 time to fit residues: 101.5645 Evaluate side-chains 277 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 238 time to evaluate : 1.545 ------------------------------------------------------------------------------- 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 78 LEU Chi-restraints excluded: chain A residue 90 ASP 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 781 TYR 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 292 VAL Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 509 VAL 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 2 VAL Chi-restraints excluded: chain D residue 34 MET Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 83 ASN Chi-restraints excluded: chain D residue 86 LYS Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 117 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 9.9990 chunk 42 optimal weight: 0.5980 chunk 128 optimal weight: 7.9990 chunk 20 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 139 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 143 optimal weight: 0.0170 chunk 17 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 overall best weight: 0.9020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 76 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.132504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.112301 restraints weight = 27611.459| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 2.93 r_work: 0.3567 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.4489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13382 Z= 0.205 Angle : 0.602 11.369 18240 Z= 0.306 Chirality : 0.042 0.157 2065 Planarity : 0.004 0.042 2402 Dihedral : 3.990 18.844 1999 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 3.35 % Allowed : 22.57 % Favored : 74.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.21), residues: 1782 helix: 1.84 (0.20), residues: 716 sheet: -1.43 (0.32), residues: 258 loop : -1.80 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 291 HIS 0.004 0.001 HIS A 97 PHE 0.025 0.001 PHE A 456 TYR 0.013 0.001 TYR B 466 ARG 0.008 0.000 ARG B 352 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2849.45 seconds wall clock time: 52 minutes 48.73 seconds (3168.73 seconds total)