Starting phenix.real_space_refine on Wed Mar 4 16:52:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7epb_31236/03_2026/7epb_31236.cif Found real_map, /net/cci-nas-00/data/ceres_data/7epb_31236/03_2026/7epb_31236.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7epb_31236/03_2026/7epb_31236.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7epb_31236/03_2026/7epb_31236.map" model { file = "/net/cci-nas-00/data/ceres_data/7epb_31236/03_2026/7epb_31236.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7epb_31236/03_2026/7epb_31236.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.198 sd= 0.783 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2352 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 84 5.16 5 C 8214 2.51 5 N 2344 2.21 5 O 2462 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 89 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13104 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 779, 5632 Classifications: {'peptide': 779} Incomplete info: {'truncation_to_alanine': 107} Link IDs: {'PTRANS': 37, 'TRANS': 741} Chain breaks: 1 Unresolved non-hydrogen bonds: 444 Unresolved non-hydrogen angles: 577 Unresolved non-hydrogen dihedrals: 382 Unresolved non-hydrogen chiralities: 46 Planarities with less than four sites: {'ARG:plan': 9, 'HIS:plan': 3, 'GLU:plan': 4, 'ASP:plan': 3, 'PHE:plan': 13, 'GLN:plan1': 3, 'TYR:plan': 6, 'TRP:plan': 3, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 253 Chain: "B" Number of atoms: 5638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 779, 5638 Classifications: {'peptide': 779} Incomplete info: {'truncation_to_alanine': 106} Link IDs: {'PTRANS': 37, 'TRANS': 741} Chain breaks: 1 Unresolved non-hydrogen bonds: 436 Unresolved non-hydrogen angles: 566 Unresolved non-hydrogen dihedrals: 374 Unresolved non-hydrogen chiralities: 45 Planarities with less than four sites: {'ARG:plan': 9, 'HIS:plan': 3, 'GLU:plan': 5, 'ASP:plan': 3, 'PHE:plan': 10, 'GLN:plan1': 3, 'TYR:plan': 7, 'TRP:plan': 3, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 246 Chain: "C" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 902 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 115} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 906 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 2, 'TRANS': 115} Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'40F': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'40F': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.15, per 1000 atoms: 0.24 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: 0.98 Conformation dependent library (CDL) restraints added in 519.3 milliseconds 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3320 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 13 sheets defined 41.8% alpha, 11.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 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: 2.07 Time building geometry restraints manager: 1.31 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 901)) selection = (chain 'B' and (resid 22 through 571 or (resid 572 through 575 and (name N or na \ me CA or name C or name O or name CB )) or resid 576 through 623 or (resid 624 t \ hrough 626 and (name N or name CA or name C or name O or name CB )) or resid 627 \ through 642 or (resid 643 through 644 and (name N or name CA or name C or name \ O or name CB )) or resid 645 through 756 or (resid 757 through 759 and (name N o \ r name CA or name C or name O or name CB )) or resid 760 through 770 or (resid 7 \ 71 and (name N or name CA or name C or name O or name CB )) or resid 772 through \ 775 or (resid 776 and (name N or name CA or name C or name O or name CB )) or r \ esid 777 through 779 or (resid 780 through 781 and (name N or name CA or name C \ or name O or name CB )) or resid 782 through 901)) } ncs_group { reference = chain 'C' selection = (chain 'D' and (resid 1 through 5 or (resid 6 and (name N or name CA or name C o \ r name O or name CB )) or resid 7 through 118)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 12.750 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.040 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.760 ------------------------------------------------------------------------------- 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 13403 Z= 0.192 Angle : 0.619 34.483 18282 Z= 0.297 Chirality : 0.058 1.294 2065 Planarity : 0.003 0.041 2402 Dihedral : 13.843 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.18), residues: 1782 helix: 0.17 (0.18), residues: 722 sheet: -1.23 (0.32), residues: 242 loop : -2.25 (0.18), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 229 TYR 0.011 0.001 TYR A 787 PHE 0.018 0.001 PHE A 456 TRP 0.005 0.000 TRP B 297 HIS 0.002 0.000 HIS D 104 Details of bonding type rmsd covalent geometry : bond 0.00379 (13382) covalent geometry : angle 0.61862 (18240) SS BOND : bond 0.00163 ( 21) SS BOND : angle 0.65148 ( 42) hydrogen bonds : bond 0.13524 ( 623) hydrogen bonds : angle 5.46082 ( 1803) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 269 time to evaluate : 0.488 Fit side-chains REVERT: A 149 ILE cc_start: 0.8899 (pt) cc_final: 0.8664 (pt) REVERT: A 150 GLN cc_start: 0.8443 (mm-40) cc_final: 0.8165 (mm110) REVERT: A 251 GLU cc_start: 0.7655 (mt-10) cc_final: 0.7412 (mt-10) REVERT: A 414 ASN cc_start: 0.7330 (p0) cc_final: 0.7073 (p0) REVERT: A 725 ASP cc_start: 0.4939 (m-30) cc_final: 0.4425 (m-30) REVERT: B 149 ILE cc_start: 0.8956 (pt) cc_final: 0.8672 (pt) REVERT: B 189 PHE cc_start: 0.7856 (m-80) cc_final: 0.7638 (m-80) REVERT: B 229 ARG cc_start: 0.7729 (mtm-85) cc_final: 0.7452 (mtt180) REVERT: B 251 GLU cc_start: 0.7916 (mt-10) cc_final: 0.7685 (mt-10) REVERT: C 45 ARG cc_start: 0.7546 (ptp90) cc_final: 0.7103 (ptt180) REVERT: C 46 GLU cc_start: 0.7513 (mp0) cc_final: 0.7058 (mp0) outliers start: 1 outliers final: 0 residues processed: 270 average time/residue: 0.1005 time to fit residues: 41.1120 Evaluate side-chains 233 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 233 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.1980 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 10.0000 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 HIS B 101 GLN B 790 GLN D 1 GLN ** D 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 GLN ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 76 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.142796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.122526 restraints weight = 28834.203| |-----------------------------------------------------------------------------| r_work (start): 0.3809 rms_B_bonded: 3.08 r_work: 0.3711 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13403 Z= 0.160 Angle : 0.575 11.786 18282 Z= 0.292 Chirality : 0.042 0.220 2065 Planarity : 0.004 0.040 2402 Dihedral : 4.402 49.296 1999 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 1.91 % Allowed : 13.88 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.20), residues: 1782 helix: 1.03 (0.20), residues: 728 sheet: -1.09 (0.33), residues: 260 loop : -1.85 (0.20), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 243 TYR 0.013 0.001 TYR C 99 PHE 0.039 0.002 PHE A 456 TRP 0.013 0.001 TRP B 297 HIS 0.004 0.001 HIS D 104 Details of bonding type rmsd covalent geometry : bond 0.00345 (13382) covalent geometry : angle 0.57439 (18240) SS BOND : bond 0.00270 ( 21) SS BOND : angle 0.85442 ( 42) hydrogen bonds : bond 0.03260 ( 623) hydrogen bonds : angle 4.17435 ( 1803) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 252 time to evaluate : 0.458 Fit side-chains revert: symmetry clash REVERT: A 149 ILE cc_start: 0.9075 (pt) cc_final: 0.8615 (pt) REVERT: A 277 GLU cc_start: 0.8181 (mm-30) cc_final: 0.7841 (mm-30) REVERT: A 350 GLU cc_start: 0.8314 (mt-10) cc_final: 0.7966 (mt-10) REVERT: A 396 HIS cc_start: 0.7200 (t70) cc_final: 0.6925 (t-90) REVERT: A 414 ASN cc_start: 0.8040 (p0) cc_final: 0.7742 (p0) REVERT: B 25 VAL cc_start: 0.8762 (t) cc_final: 0.8374 (p) REVERT: B 146 ASP cc_start: 0.8193 (p0) cc_final: 0.7701 (p0) REVERT: B 277 GLU cc_start: 0.7916 (mm-30) cc_final: 0.7711 (mm-30) REVERT: B 317 ILE cc_start: 0.9279 (mt) cc_final: 0.9036 (mt) REVERT: B 342 ASN cc_start: 0.8367 (t0) cc_final: 0.8164 (t0) REVERT: C 38 ARG cc_start: 0.8275 (ptm160) cc_final: 0.7600 (ptm160) REVERT: C 46 GLU cc_start: 0.8049 (mp0) cc_final: 0.7483 (mp0) REVERT: C 72 ASP cc_start: 0.7555 (p0) cc_final: 0.7353 (p0) REVERT: C 100 LYS cc_start: 0.9137 (tmtt) cc_final: 0.8907 (tptt) REVERT: D 76 ASN cc_start: 0.7808 (OUTLIER) cc_final: 0.7508 (p0) REVERT: D 110 GLN cc_start: 0.8201 (mp10) cc_final: 0.7874 (mp10) outliers start: 24 outliers final: 16 residues processed: 261 average time/residue: 0.1047 time to fit residues: 40.5597 Evaluate side-chains 254 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 237 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 749 THR Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 396 HIS Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 115 THR 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 115 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 44 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 12 optimal weight: 0.8980 chunk 63 optimal weight: 10.0000 chunk 105 optimal weight: 0.0020 chunk 9 optimal weight: 20.0000 chunk 50 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 128 optimal weight: 20.0000 chunk 54 optimal weight: 20.0000 overall best weight: 2.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN A 150 GLN A 338 ASN D 1 GLN ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.131554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.110526 restraints weight = 28515.121| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 3.02 r_work: 0.3528 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3406 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.3753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 13403 Z= 0.303 Angle : 0.674 6.489 18282 Z= 0.359 Chirality : 0.046 0.184 2065 Planarity : 0.005 0.045 2402 Dihedral : 4.541 27.355 1999 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 3.35 % Allowed : 16.83 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.20), residues: 1782 helix: 1.06 (0.20), residues: 726 sheet: -1.26 (0.33), residues: 248 loop : -1.92 (0.20), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 243 TYR 0.016 0.002 TYR D 99 PHE 0.045 0.002 PHE A 456 TRP 0.021 0.002 TRP C 108 HIS 0.007 0.001 HIS B 396 Details of bonding type rmsd covalent geometry : bond 0.00641 (13382) covalent geometry : angle 0.67028 (18240) SS BOND : bond 0.00508 ( 21) SS BOND : angle 1.56363 ( 42) hydrogen bonds : bond 0.04256 ( 623) hydrogen bonds : angle 4.52530 ( 1803) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 269 time to evaluate : 0.505 Fit side-chains REVERT: A 149 ILE cc_start: 0.9178 (pt) cc_final: 0.8791 (pt) REVERT: A 193 LYS cc_start: 0.8656 (mtmt) cc_final: 0.8317 (mtmm) REVERT: A 197 GLU cc_start: 0.8416 (mt-10) cc_final: 0.8118 (mt-10) REVERT: A 274 ASP cc_start: 0.8373 (t0) cc_final: 0.8139 (t0) REVERT: A 277 GLU cc_start: 0.8596 (mm-30) cc_final: 0.8270 (mm-30) REVERT: A 350 GLU cc_start: 0.8565 (mt-10) cc_final: 0.8234 (mt-10) REVERT: A 388 MET cc_start: 0.8941 (tpp) cc_final: 0.8547 (tpp) REVERT: A 399 LEU cc_start: 0.9114 (mt) cc_final: 0.8885 (mp) REVERT: A 414 ASN cc_start: 0.8416 (p0) cc_final: 0.8133 (p0) REVERT: A 417 ARG cc_start: 0.8387 (ttt90) cc_final: 0.8125 (ttt-90) REVERT: A 619 MET cc_start: 0.6467 (mmm) cc_final: 0.6260 (mmm) REVERT: A 728 MET cc_start: 0.8468 (tpp) cc_final: 0.8201 (tmm) REVERT: B 49 ASP cc_start: 0.8658 (OUTLIER) cc_final: 0.8424 (t0) REVERT: B 146 ASP cc_start: 0.8514 (OUTLIER) cc_final: 0.8258 (p0) REVERT: B 149 ILE cc_start: 0.9067 (pt) cc_final: 0.8700 (mt) REVERT: B 277 GLU cc_start: 0.8471 (mm-30) cc_final: 0.8017 (mm-30) REVERT: B 317 ILE cc_start: 0.9330 (mt) cc_final: 0.9120 (mt) REVERT: B 350 GLU cc_start: 0.8724 (mt-10) cc_final: 0.8396 (mt-10) REVERT: B 392 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8821 (mt) REVERT: B 396 HIS cc_start: 0.8353 (OUTLIER) cc_final: 0.7874 (t-90) REVERT: B 619 MET cc_start: 0.5658 (tpt) cc_final: 0.4774 (mmm) REVERT: B 756 PHE cc_start: 0.8138 (p90) cc_final: 0.7484 (p90) REVERT: C 27 ARG cc_start: 0.7360 (tpp80) cc_final: 0.7121 (mmp80) REVERT: C 38 ARG cc_start: 0.8486 (ptm160) cc_final: 0.8210 (ptm160) REVERT: C 100 LYS cc_start: 0.9333 (tmtt) cc_final: 0.9099 (tptt) REVERT: D 110 GLN cc_start: 0.8456 (mp10) cc_final: 0.8104 (mp10) outliers start: 42 outliers final: 27 residues processed: 291 average time/residue: 0.1147 time to fit residues: 48.7322 Evaluate side-chains 278 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 247 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 400 CYS Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 749 THR Chi-restraints excluded: chain A residue 781 TYR Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 365 HIS Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 396 HIS Chi-restraints excluded: chain B residue 400 CYS Chi-restraints excluded: chain B residue 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 85 LEU Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 83 ASN Chi-restraints excluded: chain D residue 115 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 2 optimal weight: 0.7980 chunk 53 optimal weight: 0.6980 chunk 125 optimal weight: 0.7980 chunk 94 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 143 optimal weight: 0.0370 chunk 123 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 66 optimal weight: 0.0980 chunk 47 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 GLN B 150 GLN C 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.136114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.115406 restraints weight = 28298.782| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 3.03 r_work: 0.3590 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.3569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13403 Z= 0.116 Angle : 0.561 10.382 18282 Z= 0.283 Chirality : 0.042 0.219 2065 Planarity : 0.004 0.045 2402 Dihedral : 3.988 21.294 1999 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 3.19 % Allowed : 19.14 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.20), residues: 1782 helix: 1.50 (0.20), residues: 716 sheet: -1.32 (0.33), residues: 248 loop : -1.78 (0.21), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 243 TYR 0.011 0.001 TYR D 99 PHE 0.024 0.001 PHE A 456 TRP 0.011 0.001 TRP A 291 HIS 0.004 0.001 HIS B 97 Details of bonding type rmsd covalent geometry : bond 0.00254 (13382) covalent geometry : angle 0.56055 (18240) SS BOND : bond 0.00345 ( 21) SS BOND : angle 0.82129 ( 42) hydrogen bonds : bond 0.03246 ( 623) hydrogen bonds : angle 4.14930 ( 1803) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 280 time to evaluate : 0.529 Fit side-chains REVERT: A 146 ASP cc_start: 0.8147 (p0) cc_final: 0.7947 (p0) REVERT: A 149 ILE cc_start: 0.8974 (pt) cc_final: 0.8557 (pt) REVERT: A 193 LYS cc_start: 0.8535 (mtmt) cc_final: 0.8277 (mtmm) REVERT: A 245 MET cc_start: 0.8012 (tpp) cc_final: 0.7681 (tpt) REVERT: A 274 ASP cc_start: 0.8136 (t0) cc_final: 0.7850 (t0) REVERT: A 350 GLU cc_start: 0.8337 (mt-10) cc_final: 0.8022 (mt-10) REVERT: A 388 MET cc_start: 0.8601 (tpp) cc_final: 0.8275 (tpp) REVERT: A 414 ASN cc_start: 0.8133 (p0) cc_final: 0.7793 (p0) REVERT: B 146 ASP cc_start: 0.8313 (OUTLIER) cc_final: 0.7954 (p0) REVERT: B 238 SER cc_start: 0.9290 (m) cc_final: 0.8999 (p) REVERT: B 273 GLU cc_start: 0.7845 (pm20) cc_final: 0.7457 (pm20) REVERT: B 277 GLU cc_start: 0.8384 (mm-30) cc_final: 0.7889 (mm-30) REVERT: B 342 ASN cc_start: 0.8478 (t0) cc_final: 0.8270 (t0) REVERT: B 350 GLU cc_start: 0.8468 (mt-10) cc_final: 0.8142 (mt-10) REVERT: B 392 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8641 (mt) REVERT: B 396 HIS cc_start: 0.7938 (OUTLIER) cc_final: 0.7636 (t-90) REVERT: B 619 MET cc_start: 0.5551 (tpt) cc_final: 0.4901 (mtp) REVERT: C 38 ARG cc_start: 0.8296 (ptm160) cc_final: 0.7397 (ptm160) REVERT: C 46 GLU cc_start: 0.7917 (mp0) cc_final: 0.7408 (mp0) REVERT: C 100 LYS cc_start: 0.9199 (tmtt) cc_final: 0.8976 (tptt) REVERT: D 3 GLN cc_start: 0.7996 (pm20) cc_final: 0.7776 (pm20) REVERT: D 110 GLN cc_start: 0.8251 (mp10) cc_final: 0.7921 (mp10) outliers start: 40 outliers final: 28 residues processed: 304 average time/residue: 0.1143 time to fit residues: 50.3419 Evaluate side-chains 283 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 252 time to evaluate : 0.445 ------------------------------------------------------------------------------- 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 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 139 VAL Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 396 HIS Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 115 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 145 optimal weight: 0.1980 chunk 135 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 9 optimal weight: 10.0000 chunk 87 optimal weight: 0.7980 chunk 131 optimal weight: 0.6980 chunk 133 optimal weight: 2.9990 chunk 121 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 35 optimal weight: 0.2980 chunk 94 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.136618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.116064 restraints weight = 28633.696| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 3.04 r_work: 0.3607 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.3642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13403 Z= 0.114 Angle : 0.548 10.216 18282 Z= 0.276 Chirality : 0.041 0.165 2065 Planarity : 0.004 0.040 2402 Dihedral : 3.792 15.972 1999 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 3.11 % Allowed : 20.41 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.20), residues: 1782 helix: 1.66 (0.20), residues: 716 sheet: -1.33 (0.32), residues: 256 loop : -1.73 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 276 TYR 0.012 0.001 TYR D 59 PHE 0.018 0.001 PHE A 456 TRP 0.010 0.001 TRP A 291 HIS 0.004 0.001 HIS B 97 Details of bonding type rmsd covalent geometry : bond 0.00251 (13382) covalent geometry : angle 0.54727 (18240) SS BOND : bond 0.00233 ( 21) SS BOND : angle 0.77076 ( 42) hydrogen bonds : bond 0.03143 ( 623) hydrogen bonds : angle 4.05873 ( 1803) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 265 time to evaluate : 0.489 Fit side-chains REVERT: A 149 ILE cc_start: 0.8963 (pt) cc_final: 0.8570 (pt) REVERT: A 193 LYS cc_start: 0.8533 (mtmt) cc_final: 0.8290 (mtmm) REVERT: A 274 ASP cc_start: 0.8109 (t0) cc_final: 0.7882 (t0) REVERT: A 350 GLU cc_start: 0.8347 (mt-10) cc_final: 0.8028 (mt-10) REVERT: A 388 MET cc_start: 0.8559 (tpp) cc_final: 0.8221 (tpp) REVERT: A 414 ASN cc_start: 0.8142 (p0) cc_final: 0.7854 (p0) REVERT: A 631 VAL cc_start: 0.1944 (OUTLIER) cc_final: 0.1667 (t) REVERT: A 639 LEU cc_start: 0.8307 (mt) cc_final: 0.7881 (pt) REVERT: B 146 ASP cc_start: 0.8243 (OUTLIER) cc_final: 0.7947 (p0) REVERT: B 273 GLU cc_start: 0.7830 (pm20) cc_final: 0.7530 (pm20) REVERT: B 277 GLU cc_start: 0.8421 (mm-30) cc_final: 0.7960 (mm-30) REVERT: B 350 GLU cc_start: 0.8454 (mt-10) cc_final: 0.8164 (mt-10) REVERT: B 392 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8635 (mt) REVERT: B 619 MET cc_start: 0.5447 (tpt) cc_final: 0.4833 (mtp) REVERT: B 756 PHE cc_start: 0.8195 (p90) cc_final: 0.7664 (p90) REVERT: C 38 ARG cc_start: 0.8306 (ptm160) cc_final: 0.7406 (ptm160) REVERT: C 46 GLU cc_start: 0.7978 (mp0) cc_final: 0.7497 (mp0) REVERT: C 100 LYS cc_start: 0.9192 (tmtt) cc_final: 0.8944 (tptt) REVERT: C 108 TRP cc_start: 0.8885 (m100) cc_final: 0.8605 (m100) REVERT: D 110 GLN cc_start: 0.8253 (mp10) cc_final: 0.7793 (mp10) outliers start: 39 outliers final: 30 residues processed: 288 average time/residue: 0.1157 time to fit residues: 48.8452 Evaluate side-chains 276 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 243 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 400 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 139 VAL Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain 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 105 ASN Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 83 ASN Chi-restraints excluded: chain D residue 115 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 127 optimal weight: 0.2980 chunk 57 optimal weight: 4.9990 chunk 145 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 105 optimal weight: 0.0000 chunk 47 optimal weight: 0.9980 chunk 92 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 123 optimal weight: 0.7980 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 150 GLN D 76 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.136935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.116364 restraints weight = 28447.004| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 3.03 r_work: 0.3613 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.3735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13403 Z= 0.114 Angle : 0.556 10.691 18282 Z= 0.279 Chirality : 0.041 0.164 2065 Planarity : 0.004 0.042 2402 Dihedral : 3.722 16.157 1999 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 3.51 % Allowed : 20.81 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.20), residues: 1782 helix: 1.75 (0.20), residues: 716 sheet: -1.30 (0.32), residues: 256 loop : -1.67 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 264 TYR 0.010 0.001 TYR D 99 PHE 0.021 0.001 PHE A 456 TRP 0.009 0.001 TRP A 291 HIS 0.003 0.001 HIS B 97 Details of bonding type rmsd covalent geometry : bond 0.00253 (13382) covalent geometry : angle 0.55575 (18240) SS BOND : bond 0.00157 ( 21) SS BOND : angle 0.72586 ( 42) hydrogen bonds : bond 0.03072 ( 623) hydrogen bonds : angle 4.02158 ( 1803) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 257 time to evaluate : 0.524 Fit side-chains REVERT: A 25 VAL cc_start: 0.9211 (t) cc_final: 0.9008 (p) REVERT: A 149 ILE cc_start: 0.8971 (pt) cc_final: 0.8578 (pt) REVERT: A 193 LYS cc_start: 0.8553 (mtmt) cc_final: 0.8303 (mtmm) REVERT: A 245 MET cc_start: 0.7912 (tpp) cc_final: 0.7581 (tpt) REVERT: A 273 GLU cc_start: 0.8017 (pm20) cc_final: 0.7786 (pm20) REVERT: A 274 ASP cc_start: 0.8209 (t0) cc_final: 0.7891 (t0) REVERT: A 318 GLU cc_start: 0.7408 (pm20) cc_final: 0.7169 (pm20) REVERT: A 350 GLU cc_start: 0.8307 (mt-10) cc_final: 0.8012 (mt-10) REVERT: A 388 MET cc_start: 0.8564 (tpp) cc_final: 0.8246 (tpp) REVERT: A 411 ARG cc_start: 0.7382 (mmt-90) cc_final: 0.7181 (mmt-90) REVERT: A 414 ASN cc_start: 0.8097 (p0) cc_final: 0.7860 (p0) REVERT: A 631 VAL cc_start: 0.2023 (OUTLIER) cc_final: 0.1735 (t) REVERT: A 639 LEU cc_start: 0.8289 (mt) cc_final: 0.7970 (pt) REVERT: B 146 ASP cc_start: 0.8247 (OUTLIER) cc_final: 0.7959 (p0) REVERT: B 245 MET cc_start: 0.8108 (tpp) cc_final: 0.7324 (tpt) REVERT: B 273 GLU cc_start: 0.7841 (pm20) cc_final: 0.7580 (pm20) REVERT: B 277 GLU cc_start: 0.8392 (mm-30) cc_final: 0.7928 (mm-30) REVERT: B 350 GLU cc_start: 0.8454 (mt-10) cc_final: 0.8163 (mt-10) REVERT: B 392 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8673 (mt) REVERT: B 619 MET cc_start: 0.5406 (tpt) cc_final: 0.4754 (mtp) REVERT: B 756 PHE cc_start: 0.8224 (p90) cc_final: 0.7699 (p90) REVERT: C 38 ARG cc_start: 0.8306 (ptm160) cc_final: 0.7382 (ptm160) REVERT: C 46 GLU cc_start: 0.8004 (mp0) cc_final: 0.7497 (mp0) REVERT: C 100 LYS cc_start: 0.9167 (tmtt) cc_final: 0.8937 (tptt) REVERT: C 108 TRP cc_start: 0.8880 (m100) cc_final: 0.8571 (m100) REVERT: D 110 GLN cc_start: 0.8277 (mp10) cc_final: 0.7835 (mp10) outliers start: 44 outliers final: 33 residues processed: 283 average time/residue: 0.1074 time to fit residues: 44.9020 Evaluate side-chains 278 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 242 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 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 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 292 VAL Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 400 CYS 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 105 ASN Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 34 MET Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 83 ASN 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 7 optimal weight: 0.9990 chunk 101 optimal weight: 0.9980 chunk 51 optimal weight: 5.9990 chunk 134 optimal weight: 8.9990 chunk 175 optimal weight: 5.9990 chunk 162 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 117 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 150 GLN D 76 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.132602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.112037 restraints weight = 28128.672| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 2.99 r_work: 0.3554 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.4160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 13403 Z= 0.174 Angle : 0.592 10.838 18282 Z= 0.303 Chirality : 0.042 0.158 2065 Planarity : 0.004 0.048 2402 Dihedral : 3.966 15.987 1999 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 3.51 % Allowed : 21.61 % Favored : 74.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.20), residues: 1782 helix: 1.69 (0.20), residues: 716 sheet: -1.36 (0.32), residues: 256 loop : -1.67 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 243 TYR 0.009 0.001 TYR D 99 PHE 0.022 0.002 PHE A 456 TRP 0.011 0.001 TRP B 297 HIS 0.004 0.001 HIS A 97 Details of bonding type rmsd covalent geometry : bond 0.00374 (13382) covalent geometry : angle 0.59052 (18240) SS BOND : bond 0.00276 ( 21) SS BOND : angle 1.11226 ( 42) hydrogen bonds : bond 0.03453 ( 623) hydrogen bonds : angle 4.14703 ( 1803) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 250 time to evaluate : 0.335 Fit side-chains REVERT: A 140 ILE cc_start: 0.9043 (OUTLIER) cc_final: 0.8782 (pt) REVERT: A 149 ILE cc_start: 0.8954 (pt) cc_final: 0.8528 (pt) REVERT: A 193 LYS cc_start: 0.8569 (mtmt) cc_final: 0.8225 (mtmm) REVERT: A 197 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7849 (mt-10) REVERT: A 245 MET cc_start: 0.7928 (tpp) cc_final: 0.7074 (tpt) REVERT: A 273 GLU cc_start: 0.8097 (pm20) cc_final: 0.7851 (pm20) REVERT: A 350 GLU cc_start: 0.8290 (mt-10) cc_final: 0.7991 (mt-10) REVERT: A 388 MET cc_start: 0.8614 (tpp) cc_final: 0.8246 (tpp) REVERT: A 414 ASN cc_start: 0.8080 (p0) cc_final: 0.7844 (p0) REVERT: A 631 VAL cc_start: 0.1786 (OUTLIER) cc_final: 0.1486 (t) REVERT: A 639 LEU cc_start: 0.8331 (mt) cc_final: 0.8073 (pt) REVERT: B 146 ASP cc_start: 0.8251 (OUTLIER) cc_final: 0.7929 (p0) REVERT: B 245 MET cc_start: 0.8127 (tpp) cc_final: 0.7356 (tpt) REVERT: B 273 GLU cc_start: 0.8044 (pm20) cc_final: 0.7688 (pm20) REVERT: B 274 ASP cc_start: 0.8279 (t0) cc_final: 0.7851 (t0) REVERT: B 277 GLU cc_start: 0.8441 (mm-30) cc_final: 0.7958 (mm-30) REVERT: B 350 GLU cc_start: 0.8454 (mt-10) cc_final: 0.8126 (mt-10) REVERT: B 392 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8765 (mt) REVERT: B 619 MET cc_start: 0.5458 (tpt) cc_final: 0.5002 (mmp) REVERT: B 756 PHE cc_start: 0.8157 (p90) cc_final: 0.7660 (p90) REVERT: C 38 ARG cc_start: 0.8344 (ptm160) cc_final: 0.7463 (ptm160) REVERT: C 46 GLU cc_start: 0.8022 (mp0) cc_final: 0.7502 (mp0) REVERT: C 100 LYS cc_start: 0.9176 (tmtt) cc_final: 0.8923 (tptt) REVERT: D 101 TYR cc_start: 0.8072 (t80) cc_final: 0.7762 (t80) REVERT: D 110 GLN cc_start: 0.8223 (mp10) cc_final: 0.7912 (mp10) outliers start: 44 outliers final: 36 residues processed: 277 average time/residue: 0.1088 time to fit residues: 43.8384 Evaluate side-chains 280 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 240 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 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 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 33 VAL Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 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 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 105 ASN Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 34 MET Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 83 ASN Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 115 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 88 optimal weight: 8.9990 chunk 126 optimal weight: 0.6980 chunk 129 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 139 optimal weight: 9.9990 chunk 96 optimal weight: 7.9990 chunk 90 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 89 optimal weight: 0.9990 chunk 110 optimal weight: 0.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- 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 = 0.3980 r_free = 0.3980 target = 0.131655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.111148 restraints weight = 27876.871| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 2.91 r_work: 0.3539 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3420 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.4468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13403 Z= 0.186 Angle : 0.613 12.098 18282 Z= 0.311 Chirality : 0.043 0.230 2065 Planarity : 0.004 0.042 2402 Dihedral : 4.098 16.716 1999 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 3.83 % Allowed : 22.01 % Favored : 74.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.20), residues: 1782 helix: 1.64 (0.20), residues: 718 sheet: -1.57 (0.32), residues: 246 loop : -1.67 (0.21), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 243 TYR 0.011 0.001 TYR D 59 PHE 0.021 0.002 PHE A 456 TRP 0.012 0.001 TRP B 297 HIS 0.004 0.001 HIS A 97 Details of bonding type rmsd covalent geometry : bond 0.00404 (13382) covalent geometry : angle 0.61123 (18240) SS BOND : bond 0.00258 ( 21) SS BOND : angle 1.11650 ( 42) hydrogen bonds : bond 0.03503 ( 623) hydrogen bonds : angle 4.21602 ( 1803) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 250 time to evaluate : 0.420 Fit side-chains REVERT: A 140 ILE cc_start: 0.9105 (OUTLIER) cc_final: 0.8853 (pt) REVERT: A 149 ILE cc_start: 0.9099 (pt) cc_final: 0.8740 (pt) REVERT: A 180 TYR cc_start: 0.8406 (m-10) cc_final: 0.7927 (m-10) REVERT: A 193 LYS cc_start: 0.8690 (mtmt) cc_final: 0.8353 (mtmm) REVERT: A 197 GLU cc_start: 0.8467 (mt-10) cc_final: 0.8185 (mt-10) REVERT: A 245 MET cc_start: 0.8216 (tpp) cc_final: 0.7414 (tpt) REVERT: A 273 GLU cc_start: 0.8351 (pm20) cc_final: 0.8131 (pm20) REVERT: A 350 GLU cc_start: 0.8486 (mt-10) cc_final: 0.8198 (mt-10) REVERT: A 388 MET cc_start: 0.8857 (tpp) cc_final: 0.8513 (tpp) REVERT: A 619 MET cc_start: 0.7095 (mmm) cc_final: 0.6840 (mmm) REVERT: A 631 VAL cc_start: 0.1575 (OUTLIER) cc_final: 0.1254 (t) REVERT: B 49 ASP cc_start: 0.8667 (m-30) cc_final: 0.8366 (t0) REVERT: B 146 ASP cc_start: 0.8575 (OUTLIER) cc_final: 0.8281 (p0) REVERT: B 227 GLU cc_start: 0.8499 (mm-30) cc_final: 0.8250 (mp0) REVERT: B 245 MET cc_start: 0.8377 (tpp) cc_final: 0.7721 (tpt) REVERT: B 273 GLU cc_start: 0.8275 (pm20) cc_final: 0.7966 (pm20) REVERT: B 277 GLU cc_start: 0.8728 (mm-30) cc_final: 0.8263 (mm-30) REVERT: B 350 GLU cc_start: 0.8649 (mt-10) cc_final: 0.8367 (mt-10) REVERT: B 410 MET cc_start: 0.8208 (mmp) cc_final: 0.7462 (mmt) REVERT: B 619 MET cc_start: 0.5705 (tpt) cc_final: 0.5198 (mmp) REVERT: B 756 PHE cc_start: 0.8259 (p90) cc_final: 0.7757 (p90) REVERT: C 38 ARG cc_start: 0.8524 (ptm160) cc_final: 0.7641 (ptm160) REVERT: C 46 GLU cc_start: 0.8160 (mp0) cc_final: 0.7659 (mp0) REVERT: C 100 LYS cc_start: 0.9305 (tmtt) cc_final: 0.9068 (tptt) REVERT: C 108 TRP cc_start: 0.9023 (m100) cc_final: 0.8767 (m100) REVERT: D 3 GLN cc_start: 0.8228 (pm20) cc_final: 0.8024 (pm20) REVERT: D 101 TYR cc_start: 0.8234 (t80) cc_final: 0.7912 (t80) REVERT: D 110 GLN cc_start: 0.8484 (mp10) cc_final: 0.8170 (mp10) outliers start: 48 outliers final: 39 residues processed: 280 average time/residue: 0.1126 time to fit residues: 46.2072 Evaluate side-chains 280 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 238 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 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 33 VAL Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 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 519 CYS 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 69 ILE Chi-restraints excluded: chain C residue 105 ASN Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 83 ASN Chi-restraints excluded: chain D residue 115 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 154 optimal weight: 6.9990 chunk 66 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 120 optimal weight: 0.7980 chunk 153 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 141 optimal weight: 10.0000 chunk 175 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 76 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.130330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.109915 restraints weight = 28035.565| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 2.89 r_work: 0.3512 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3391 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.4756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13403 Z= 0.207 Angle : 0.633 10.253 18282 Z= 0.323 Chirality : 0.044 0.228 2065 Planarity : 0.004 0.042 2402 Dihedral : 4.268 16.816 1999 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 3.83 % Allowed : 21.85 % Favored : 74.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.20), residues: 1782 helix: 1.58 (0.20), residues: 720 sheet: -1.59 (0.32), residues: 244 loop : -1.76 (0.21), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 352 TYR 0.010 0.002 TYR A 528 PHE 0.024 0.002 PHE A 456 TRP 0.016 0.001 TRP B 297 HIS 0.004 0.001 HIS A 97 Details of bonding type rmsd covalent geometry : bond 0.00446 (13382) covalent geometry : angle 0.63124 (18240) SS BOND : bond 0.00292 ( 21) SS BOND : angle 1.19325 ( 42) hydrogen bonds : bond 0.03679 ( 623) hydrogen bonds : angle 4.30749 ( 1803) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 251 time to evaluate : 0.474 Fit side-chains REVERT: A 140 ILE cc_start: 0.9121 (OUTLIER) cc_final: 0.8861 (pt) REVERT: A 149 ILE cc_start: 0.9122 (pt) cc_final: 0.8735 (pt) REVERT: A 180 TYR cc_start: 0.8446 (m-10) cc_final: 0.7971 (m-10) REVERT: A 193 LYS cc_start: 0.8715 (mtmt) cc_final: 0.8391 (mtmm) REVERT: A 197 GLU cc_start: 0.8487 (mt-10) cc_final: 0.8221 (mt-10) REVERT: A 218 GLU cc_start: 0.7866 (mp0) cc_final: 0.7570 (mp0) REVERT: A 245 MET cc_start: 0.8212 (tpp) cc_final: 0.7387 (tpt) REVERT: A 350 GLU cc_start: 0.8539 (mt-10) cc_final: 0.8235 (mt-10) REVERT: A 388 MET cc_start: 0.8885 (tpp) cc_final: 0.8529 (tpp) REVERT: A 631 VAL cc_start: 0.1892 (OUTLIER) cc_final: 0.1656 (t) REVERT: A 639 LEU cc_start: 0.8417 (mt) cc_final: 0.7948 (pt) REVERT: B 49 ASP cc_start: 0.8599 (m-30) cc_final: 0.8298 (t0) REVERT: B 146 ASP cc_start: 0.8599 (OUTLIER) cc_final: 0.8274 (p0) REVERT: B 180 TYR cc_start: 0.8448 (m-10) cc_final: 0.7997 (m-10) REVERT: B 227 GLU cc_start: 0.8544 (mm-30) cc_final: 0.8276 (mp0) REVERT: B 245 MET cc_start: 0.8403 (tpp) cc_final: 0.7741 (tpt) REVERT: B 273 GLU cc_start: 0.8330 (pm20) cc_final: 0.8016 (pm20) REVERT: B 277 GLU cc_start: 0.8765 (mm-30) cc_final: 0.8301 (mm-30) REVERT: B 350 GLU cc_start: 0.8685 (mt-10) cc_final: 0.8415 (mt-10) REVERT: B 392 LEU cc_start: 0.9270 (OUTLIER) cc_final: 0.8999 (mt) REVERT: B 410 MET cc_start: 0.8217 (mmp) cc_final: 0.7454 (mmt) REVERT: B 619 MET cc_start: 0.5880 (tpt) cc_final: 0.5375 (mmp) REVERT: B 756 PHE cc_start: 0.8327 (p90) cc_final: 0.7807 (p90) REVERT: C 38 ARG cc_start: 0.8540 (ptm160) cc_final: 0.7678 (ptm160) REVERT: C 46 GLU cc_start: 0.8204 (mp0) cc_final: 0.7714 (mp0) REVERT: C 100 LYS cc_start: 0.9325 (tmtt) cc_final: 0.9090 (tptt) REVERT: C 108 TRP cc_start: 0.9002 (m100) cc_final: 0.8774 (m100) REVERT: D 3 GLN cc_start: 0.8398 (pm20) cc_final: 0.8107 (pm20) REVERT: D 101 TYR cc_start: 0.8221 (t80) cc_final: 0.7842 (t80) REVERT: D 110 GLN cc_start: 0.8465 (mp10) cc_final: 0.8171 (mp10) outliers start: 48 outliers final: 37 residues processed: 282 average time/residue: 0.1052 time to fit residues: 43.6084 Evaluate side-chains 283 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 242 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 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 749 THR Chi-restraints excluded: chain A residue 781 TYR Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 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 519 CYS 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 69 ILE Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 83 ASN Chi-restraints excluded: chain D residue 115 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 122 optimal weight: 0.9980 chunk 142 optimal weight: 10.0000 chunk 17 optimal weight: 3.9990 chunk 54 optimal weight: 9.9990 chunk 2 optimal weight: 0.7980 chunk 67 optimal weight: 0.0060 chunk 1 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 171 optimal weight: 0.5980 chunk 53 optimal weight: 4.9990 chunk 63 optimal weight: 10.0000 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 454 ASN D 76 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.132877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.112510 restraints weight = 28179.628| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 2.94 r_work: 0.3555 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.4654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13403 Z= 0.130 Angle : 0.624 12.161 18282 Z= 0.311 Chirality : 0.042 0.216 2065 Planarity : 0.004 0.043 2402 Dihedral : 4.073 17.792 1999 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 3.51 % Allowed : 22.41 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.20), residues: 1782 helix: 1.69 (0.20), residues: 718 sheet: -1.56 (0.32), residues: 244 loop : -1.74 (0.21), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 243 TYR 0.011 0.001 TYR C 59 PHE 0.018 0.001 PHE A 456 TRP 0.010 0.001 TRP A 291 HIS 0.004 0.001 HIS A 97 Details of bonding type rmsd covalent geometry : bond 0.00290 (13382) covalent geometry : angle 0.62310 (18240) SS BOND : bond 0.00248 ( 21) SS BOND : angle 0.86321 ( 42) hydrogen bonds : bond 0.03312 ( 623) hydrogen bonds : angle 4.17308 ( 1803) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 262 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 140 ILE cc_start: 0.9003 (OUTLIER) cc_final: 0.8748 (pt) REVERT: A 149 ILE cc_start: 0.8956 (pt) cc_final: 0.8581 (pt) REVERT: A 180 TYR cc_start: 0.8227 (m-10) cc_final: 0.7960 (m-10) REVERT: A 193 LYS cc_start: 0.8527 (mtmt) cc_final: 0.8206 (mtmm) REVERT: A 197 GLU cc_start: 0.8154 (mt-10) cc_final: 0.7860 (mt-10) REVERT: A 218 GLU cc_start: 0.7391 (mp0) cc_final: 0.7142 (mp0) REVERT: A 243 ARG cc_start: 0.8060 (mmm160) cc_final: 0.7340 (mmm160) REVERT: A 245 MET cc_start: 0.7861 (tpp) cc_final: 0.6866 (tpt) REVERT: A 350 GLU cc_start: 0.8307 (mt-10) cc_final: 0.7999 (mt-10) REVERT: A 388 MET cc_start: 0.8622 (tpp) cc_final: 0.8293 (tpp) REVERT: A 631 VAL cc_start: 0.1561 (OUTLIER) cc_final: 0.1198 (t) REVERT: A 639 LEU cc_start: 0.8329 (mt) cc_final: 0.7948 (pt) REVERT: B 49 ASP cc_start: 0.8335 (m-30) cc_final: 0.8021 (t0) REVERT: B 146 ASP cc_start: 0.8262 (OUTLIER) cc_final: 0.7880 (p0) REVERT: B 180 TYR cc_start: 0.8214 (m-10) cc_final: 0.7779 (m-10) REVERT: B 227 GLU cc_start: 0.8209 (mm-30) cc_final: 0.7970 (mp0) REVERT: B 245 MET cc_start: 0.8146 (tpp) cc_final: 0.7356 (tpt) REVERT: B 271 ARG cc_start: 0.8018 (mtt180) cc_final: 0.7375 (mtt-85) REVERT: B 273 GLU cc_start: 0.8061 (pm20) cc_final: 0.7755 (pm20) REVERT: B 277 GLU cc_start: 0.8476 (mm-30) cc_final: 0.8026 (mm-30) REVERT: B 350 GLU cc_start: 0.8416 (mt-10) cc_final: 0.8148 (mt-10) REVERT: B 392 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8887 (mt) REVERT: B 410 MET cc_start: 0.7948 (mmp) cc_final: 0.7197 (mmt) REVERT: B 619 MET cc_start: 0.5539 (tpt) cc_final: 0.5290 (mmp) REVERT: B 756 PHE cc_start: 0.8176 (p90) cc_final: 0.7791 (p90) REVERT: C 46 GLU cc_start: 0.8010 (mp0) cc_final: 0.7546 (mp0) REVERT: C 100 LYS cc_start: 0.9173 (tmtt) cc_final: 0.8917 (tptt) REVERT: D 3 GLN cc_start: 0.8152 (pm20) cc_final: 0.7942 (pm20) REVERT: D 110 GLN cc_start: 0.8234 (mp10) cc_final: 0.7902 (mp10) outliers start: 44 outliers final: 34 residues processed: 289 average time/residue: 0.1172 time to fit residues: 48.7535 Evaluate side-chains 283 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 245 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 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 519 CYS Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 749 THR Chi-restraints excluded: chain A residue 781 TYR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 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 519 CYS Chi-restraints excluded: chain B residue 745 TYR Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 83 ASN Chi-restraints excluded: chain D residue 115 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 48 optimal weight: 0.4980 chunk 148 optimal weight: 9.9990 chunk 109 optimal weight: 0.9990 chunk 144 optimal weight: 1.9990 chunk 47 optimal weight: 6.9990 chunk 133 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 157 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 122 optimal weight: 0.7980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 HIS B 150 GLN D 76 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.131827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.111483 restraints weight = 28035.430| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 2.90 r_work: 0.3550 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3430 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.4728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13403 Z= 0.146 Angle : 0.623 10.834 18282 Z= 0.313 Chirality : 0.043 0.211 2065 Planarity : 0.004 0.062 2402 Dihedral : 4.083 21.484 1999 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 3.19 % Allowed : 23.13 % Favored : 73.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.20), residues: 1782 helix: 1.67 (0.20), residues: 718 sheet: -1.57 (0.32), residues: 244 loop : -1.78 (0.21), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 264 TYR 0.017 0.001 TYR B 466 PHE 0.022 0.002 PHE A 456 TRP 0.009 0.001 TRP B 291 HIS 0.004 0.001 HIS A 97 Details of bonding type rmsd covalent geometry : bond 0.00325 (13382) covalent geometry : angle 0.62182 (18240) SS BOND : bond 0.00210 ( 21) SS BOND : angle 0.91428 ( 42) hydrogen bonds : bond 0.03406 ( 623) hydrogen bonds : angle 4.17155 ( 1803) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3222.88 seconds wall clock time: 55 minutes 46.60 seconds (3346.60 seconds total)