Starting phenix.real_space_refine on Fri Jul 3 06:31:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qcm_18330/07_2026/8qcm_18330.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qcm_18330/07_2026/8qcm_18330.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8qcm_18330/07_2026/8qcm_18330.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qcm_18330/07_2026/8qcm_18330.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8qcm_18330/07_2026/8qcm_18330.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qcm_18330/07_2026/8qcm_18330.map" } resolution = 2.39 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= 0.002 sd= 0.064 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 68 5.16 5 C 8192 2.51 5 N 2042 2.21 5 O 2351 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12653 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 4406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 566, 4406 Classifications: {'peptide': 566} Link IDs: {'PTRANS': 18, 'TRANS': 547} Chain breaks: 3 Chain: "C" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 822 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 928 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain: "E" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 822 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "F" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 928 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain: "B" Number of atoms: 4406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 566, 4406 Classifications: {'peptide': 566} Link IDs: {'PTRANS': 18, 'TRANS': 547} Chain breaks: 3 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 116 Unusual residues: {'CLR': 3, 'V0U': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 116 Unusual residues: {'CLR': 3, 'V0U': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Time building chain proxies: 2.42, per 1000 atoms: 0.19 Number of scatterers: 12653 At special positions: 0 Unit cell: (100.32, 99.66, 146.52, 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 68 16.00 O 2351 8.00 N 2042 7.00 C 8192 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 592 " - pdb=" SG CYS A 608 " distance=2.03 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS B 603 " distance=1.06 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.05 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.05 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.05 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.05 Simple disulfide: pdb=" SG CYS B 592 " - pdb=" SG CYS B 608 " 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 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG X 1 " - " NAG X 2 " Time building additional restraints: 1.02 Conformation dependent library (CDL) restraints added in 486.4 milliseconds 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2896 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 16 sheets defined 48.5% alpha, 21.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 85 through 95 Processing helix chain 'A' and resid 116 through 121 Processing helix chain 'A' and resid 135 through 148 Processing helix chain 'A' and resid 153 through 169 Processing helix chain 'A' and resid 170 through 174 removed outlier: 3.578A pdb=" N ALA A 174 " --> pdb=" O ASP A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 201 removed outlier: 3.574A pdb=" N GLU A 199 " --> pdb=" O SER A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 234 removed outlier: 3.969A pdb=" N GLN A 234 " --> pdb=" O ARG A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 251 Processing helix chain 'A' and resid 269 through 271 No H-bonds generated for 'chain 'A' and resid 269 through 271' Processing helix chain 'A' and resid 272 through 281 Processing helix chain 'A' and resid 289 through 300 Processing helix chain 'A' and resid 329 through 338 Processing helix chain 'A' and resid 339 through 353 removed outlier: 3.546A pdb=" N LYS A 343 " --> pdb=" O SER A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 391 Processing helix chain 'A' and resid 392 through 413 Processing helix chain 'A' and resid 421 through 440 Processing helix chain 'A' and resid 441 through 444 Processing helix chain 'A' and resid 445 through 450 removed outlier: 3.981A pdb=" N VAL A 449 " --> pdb=" O VAL A 445 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL A 450 " --> pdb=" O GLU A 446 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 445 through 450' Processing helix chain 'A' and resid 451 through 461 Processing helix chain 'A' and resid 465 through 477 Processing helix chain 'A' and resid 477 through 482 removed outlier: 3.775A pdb=" N MET A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 498 removed outlier: 3.533A pdb=" N ILE A 487 " --> pdb=" O MET A 483 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N PHE A 495 " --> pdb=" O CYS A 491 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N MET A 496 " --> pdb=" O ILE A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 529 Processing helix chain 'A' and resid 534 through 551 Processing helix chain 'A' and resid 557 through 561 removed outlier: 3.643A pdb=" N ILE A 561 " --> pdb=" O LEU A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 567 removed outlier: 4.226A pdb=" N TRP A 567 " --> pdb=" O SER A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 571 Processing helix chain 'A' and resid 572 through 587 removed outlier: 3.643A pdb=" N TYR A 576 " --> pdb=" O SER A 572 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY A 577 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU A 587 " --> pdb=" O HIS A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 617 Processing helix chain 'A' and resid 623 through 650 removed outlier: 5.136A pdb=" N ASN A 629 " --> pdb=" O GLY A 625 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N HIS A 630 " --> pdb=" O LEU A 626 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 83 Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.550A pdb=" N THR D 91 " --> pdb=" O PRO D 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 83 Processing helix chain 'F' and resid 87 through 91 removed outlier: 3.549A pdb=" N THR F 91 " --> pdb=" O PRO F 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 95 Processing helix chain 'B' and resid 116 through 121 Processing helix chain 'B' and resid 135 through 148 Processing helix chain 'B' and resid 153 through 169 Processing helix chain 'B' and resid 170 through 174 removed outlier: 3.578A pdb=" N ALA B 174 " --> pdb=" O ASP B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 201 removed outlier: 3.576A pdb=" N GLU B 199 " --> pdb=" O SER B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 234 removed outlier: 3.969A pdb=" N GLN B 234 " --> pdb=" O ARG B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 251 Processing helix chain 'B' and resid 269 through 271 No H-bonds generated for 'chain 'B' and resid 269 through 271' Processing helix chain 'B' and resid 272 through 281 Processing helix chain 'B' and resid 289 through 300 Processing helix chain 'B' and resid 329 through 338 Processing helix chain 'B' and resid 339 through 353 removed outlier: 3.547A pdb=" N LYS B 343 " --> pdb=" O SER B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 391 Processing helix chain 'B' and resid 392 through 413 Processing helix chain 'B' and resid 421 through 440 Processing helix chain 'B' and resid 441 through 444 Processing helix chain 'B' and resid 445 through 450 removed outlier: 3.981A pdb=" N VAL B 449 " --> pdb=" O VAL B 445 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL B 450 " --> pdb=" O GLU B 446 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 445 through 450' Processing helix chain 'B' and resid 451 through 461 Processing helix chain 'B' and resid 465 through 477 Processing helix chain 'B' and resid 477 through 482 removed outlier: 3.776A pdb=" N MET B 481 " --> pdb=" O ASP B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 498 removed outlier: 3.534A pdb=" N ILE B 487 " --> pdb=" O MET B 483 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N PHE B 495 " --> pdb=" O CYS B 491 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N MET B 496 " --> pdb=" O ILE B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 529 Processing helix chain 'B' and resid 534 through 551 Processing helix chain 'B' and resid 557 through 561 removed outlier: 3.644A pdb=" N ILE B 561 " --> pdb=" O LEU B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 567 removed outlier: 4.226A pdb=" N TRP B 567 " --> pdb=" O SER B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 571 Processing helix chain 'B' and resid 572 through 587 removed outlier: 3.644A pdb=" N TYR B 576 " --> pdb=" O SER B 572 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY B 577 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU B 587 " --> pdb=" O HIS B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 617 Processing helix chain 'B' and resid 623 through 650 removed outlier: 5.136A pdb=" N ASN B 629 " --> pdb=" O GLY B 625 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N HIS B 630 " --> pdb=" O LEU B 626 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 62 through 71 removed outlier: 6.543A pdb=" N ILE A 63 " --> pdb=" O ARG A 45 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N ARG A 45 " --> pdb=" O ILE A 63 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N SER A 65 " --> pdb=" O CYS A 43 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N CYS A 43 " --> pdb=" O SER A 65 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N ILE A 67 " --> pdb=" O ASN A 41 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 122 through 124 removed outlier: 6.148A pdb=" N LEU A 207 " --> pdb=" O ILE A 239 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N SER A 241 " --> pdb=" O LEU A 207 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N LEU A 209 " --> pdb=" O SER A 241 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N GLY A 74 " --> pdb=" O ILE A 238 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N PHE A 240 " --> pdb=" O GLY A 74 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N ASN A 76 " --> pdb=" O PHE A 240 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N LEU A 75 " --> pdb=" O SER A 255 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N THR A 257 " --> pdb=" O LEU A 75 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ALA A 77 " --> pdb=" O THR A 257 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N LEU A 259 " --> pdb=" O ALA A 77 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N LEU A 79 " --> pdb=" O LEU A 259 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ALA A 260 " --> pdb=" O LEU A 264 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N LEU A 264 " --> pdb=" O ALA A 260 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 4 through 6 removed outlier: 3.566A pdb=" N ASP C 70 " --> pdb=" O SER C 67 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 10 through 13 removed outlier: 6.360A pdb=" N PHE C 11 " --> pdb=" O GLU C 105 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N LEU C 33 " --> pdb=" O SER C 49 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N SER C 49 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 10 through 13 removed outlier: 6.360A pdb=" N PHE C 11 " --> pdb=" O GLU C 105 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N THR C 97 " --> pdb=" O GLN C 90 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AA7, first strand: chain 'D' and resid 11 through 12 removed outlier: 6.162A pdb=" N TRP D 35 " --> pdb=" O TYR D 51 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N TYR D 51 " --> pdb=" O TRP D 35 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N TRP D 37 " --> pdb=" O MET D 49 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS D 45 " --> pdb=" O PHE D 41 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 11 through 12 removed outlier: 4.133A pdb=" N TYR D 108 " --> pdb=" O THR D 98 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 4 through 6 removed outlier: 3.566A pdb=" N ASP E 70 " --> pdb=" O SER E 67 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.360A pdb=" N PHE E 11 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N LEU E 33 " --> pdb=" O SER E 49 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N SER E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.360A pdb=" N PHE E 11 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N THR E 97 " --> pdb=" O GLN E 90 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AB4, first strand: chain 'F' and resid 11 through 12 removed outlier: 6.162A pdb=" N TRP F 35 " --> pdb=" O TYR F 51 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N TYR F 51 " --> pdb=" O TRP F 35 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N TRP F 37 " --> pdb=" O MET F 49 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LYS F 45 " --> pdb=" O PHE F 41 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 11 through 12 removed outlier: 4.133A pdb=" N TYR F 108 " --> pdb=" O THR F 98 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 62 through 71 removed outlier: 6.543A pdb=" N ILE B 63 " --> pdb=" O ARG B 45 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N ARG B 45 " --> pdb=" O ILE B 63 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N SER B 65 " --> pdb=" O CYS B 43 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N CYS B 43 " --> pdb=" O SER B 65 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N ILE B 67 " --> pdb=" O ASN B 41 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 122 through 124 removed outlier: 6.148A pdb=" N LEU B 207 " --> pdb=" O ILE B 239 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N SER B 241 " --> pdb=" O LEU B 207 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N LEU B 209 " --> pdb=" O SER B 241 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE B 238 " --> pdb=" O GLY B 74 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N LEU B 75 " --> pdb=" O SER B 255 " (cutoff:3.500A) removed outlier: 8.336A pdb=" N THR B 257 " --> pdb=" O LEU B 75 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ALA B 77 " --> pdb=" O THR B 257 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N LEU B 259 " --> pdb=" O ALA B 77 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N LEU B 79 " --> pdb=" O LEU B 259 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ALA B 260 " --> pdb=" O LEU B 264 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N LEU B 264 " --> pdb=" O ALA B 260 " (cutoff:3.500A) 675 hydrogen bonds defined for protein. 1887 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: 2.26 Time building geometry restraints manager: 1.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1938 1.31 - 1.44: 3602 1.44 - 1.57: 7232 1.57 - 1.70: 22 1.70 - 1.82: 106 Bond restraints: 12900 Sorted by residual: bond pdb=" C05 V0U A 701 " pdb=" C06 V0U A 701 " ideal model delta sigma weight residual 1.446 1.339 0.107 2.00e-02 2.50e+03 2.84e+01 bond pdb=" C05 V0U B 701 " pdb=" C06 V0U B 701 " ideal model delta sigma weight residual 1.446 1.341 0.105 2.00e-02 2.50e+03 2.77e+01 bond pdb=" C01 V0U B 701 " pdb=" O02 V0U B 701 " ideal model delta sigma weight residual 1.454 1.362 0.092 2.00e-02 2.50e+03 2.12e+01 bond pdb=" C01 V0U A 701 " pdb=" O02 V0U A 701 " ideal model delta sigma weight residual 1.454 1.362 0.092 2.00e-02 2.50e+03 2.10e+01 bond pdb=" C20 V0U B 701 " pdb=" N22 V0U B 701 " ideal model delta sigma weight residual 1.377 1.463 -0.086 2.00e-02 2.50e+03 1.85e+01 ... (remaining 12895 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 16928 1.74 - 3.47: 467 3.47 - 5.21: 88 5.21 - 6.94: 33 6.94 - 8.68: 8 Bond angle restraints: 17524 Sorted by residual: angle pdb=" N ASP D 32 " pdb=" CA ASP D 32 " pdb=" C ASP D 32 " ideal model delta sigma weight residual 110.80 118.89 -8.09 2.13e+00 2.20e-01 1.44e+01 angle pdb=" N ASP F 32 " pdb=" CA ASP F 32 " pdb=" C ASP F 32 " ideal model delta sigma weight residual 110.80 118.88 -8.08 2.13e+00 2.20e-01 1.44e+01 angle pdb=" N LEU A 558 " pdb=" CA LEU A 558 " pdb=" C LEU A 558 " ideal model delta sigma weight residual 112.34 117.24 -4.90 1.30e+00 5.92e-01 1.42e+01 angle pdb=" N LEU B 558 " pdb=" CA LEU B 558 " pdb=" C LEU B 558 " ideal model delta sigma weight residual 112.34 117.20 -4.86 1.30e+00 5.92e-01 1.40e+01 angle pdb=" C ASN B 557 " pdb=" N LEU B 558 " pdb=" CA LEU B 558 " ideal model delta sigma weight residual 120.63 126.08 -5.45 1.61e+00 3.86e-01 1.14e+01 ... (remaining 17519 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 7451 17.75 - 35.51: 402 35.51 - 53.26: 79 53.26 - 71.01: 13 71.01 - 88.77: 8 Dihedral angle restraints: 7953 sinusoidal: 3417 harmonic: 4536 Sorted by residual: dihedral pdb=" CB CYS A 603 " pdb=" SG CYS A 603 " pdb=" SG CYS B 603 " pdb=" CB CYS B 603 " ideal model delta sinusoidal sigma weight residual 93.00 24.72 68.28 1 1.00e+01 1.00e-02 6.05e+01 dihedral pdb=" CA ASP D 32 " pdb=" C ASP D 32 " pdb=" N TYR D 33 " pdb=" CA TYR D 33 " ideal model delta harmonic sigma weight residual -180.00 -153.99 -26.01 0 5.00e+00 4.00e-02 2.71e+01 dihedral pdb=" CA ASP F 32 " pdb=" C ASP F 32 " pdb=" N TYR F 33 " pdb=" CA TYR F 33 " ideal model delta harmonic sigma weight residual -180.00 -154.05 -25.95 0 5.00e+00 4.00e-02 2.69e+01 ... (remaining 7950 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1729 0.067 - 0.134: 245 0.134 - 0.202: 21 0.202 - 0.269: 15 0.269 - 0.336: 6 Chirality restraints: 2016 Sorted by residual: chirality pdb=" C17 CLR B 703 " pdb=" C13 CLR B 703 " pdb=" C16 CLR B 703 " pdb=" C20 CLR B 703 " both_signs ideal model delta sigma weight residual False 2.55 2.89 -0.34 2.00e-01 2.50e+01 2.82e+00 chirality pdb=" C17 CLR A 702 " pdb=" C13 CLR A 702 " pdb=" C16 CLR A 702 " pdb=" C20 CLR A 702 " both_signs ideal model delta sigma weight residual False 2.55 2.89 -0.34 2.00e-01 2.50e+01 2.81e+00 chirality pdb=" C17 CLR B 702 " pdb=" C13 CLR B 702 " pdb=" C16 CLR B 702 " pdb=" C20 CLR B 702 " both_signs ideal model delta sigma weight residual False 2.55 2.88 -0.32 2.00e-01 2.50e+01 2.61e+00 ... (remaining 2013 not shown) Planarity restraints: 2144 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 35 " 0.020 2.00e-02 2.50e+03 1.01e-02 2.54e+00 pdb=" CG TRP D 35 " -0.023 2.00e-02 2.50e+03 pdb=" CD1 TRP D 35 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TRP D 35 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP D 35 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP D 35 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP D 35 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 35 " 0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 35 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP D 35 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 35 " -0.019 2.00e-02 2.50e+03 9.92e-03 2.46e+00 pdb=" CG TRP F 35 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 TRP F 35 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 TRP F 35 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP F 35 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP F 35 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP F 35 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 35 " -0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 35 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP F 35 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS B 500 " -0.025 5.00e-02 4.00e+02 3.83e-02 2.35e+00 pdb=" N PRO B 501 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO B 501 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 501 " -0.021 5.00e-02 4.00e+02 ... (remaining 2141 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 821 2.73 - 3.27: 12058 3.27 - 3.82: 20210 3.82 - 4.36: 25465 4.36 - 4.90: 43942 Nonbonded interactions: 102496 Sorted by model distance: nonbonded pdb=" NZ LYS B 616 " pdb=" O HOH B 801 " model vdw 2.188 3.120 nonbonded pdb=" O LEU B 377 " pdb=" OG SER B 381 " model vdw 2.193 3.040 nonbonded pdb=" O LEU A 377 " pdb=" OG SER A 381 " model vdw 2.193 3.040 nonbonded pdb=" N ASP B 98 " pdb=" OD1 ASP B 98 " model vdw 2.203 3.120 nonbonded pdb=" N ASP A 98 " pdb=" OD1 ASP A 98 " model vdw 2.203 3.120 ... (remaining 102491 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'X' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.040 Set scattering table: 0.010 Process input model: 11.240 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 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:9.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8857 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 : 0.012 0.970 12909 Z= 0.556 Angle : 0.795 31.259 17544 Z= 0.398 Chirality : 0.054 0.336 2016 Planarity : 0.004 0.038 2144 Dihedral : 11.720 88.768 5036 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 1.19 % Allowed : 5.19 % Favored : 93.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.21), residues: 1558 helix: 1.71 (0.20), residues: 678 sheet: 0.02 (0.29), residues: 282 loop : -1.42 (0.23), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 575 TYR 0.014 0.002 TYR D 95 PHE 0.023 0.002 PHE A 432 TRP 0.023 0.002 TRP D 35 HIS 0.005 0.001 HIS A 630 Details of bonding type rmsd/Z covalent geometry : bond 0.00811 / 0.36 (12900) covalent geometry : angle 0.74595 / 0.38 (17524) SS BOND : bond 0.36671 / 20.38 ( 7) SS BOND : angle 9.51966 / 5.10 ( 14) hydrogen bonds : bond 0.16189 / 11.09 ( 661) hydrogen bonds : angle 5.61132 / 4.06 ( 1887) link_BETA1-4 : bond 0.00226 / 0.14 ( 2) link_BETA1-4 : angle 3.07660 / 1.53 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 237 time to evaluate : 0.460 Fit side-chains revert: symmetry clash REVERT: A 125 VAL cc_start: 0.8628 (t) cc_final: 0.8320 (m) REVERT: A 176 SER cc_start: 0.8856 (m) cc_final: 0.8543 (p) REVERT: A 177 LYS cc_start: 0.7902 (mttm) cc_final: 0.7467 (mtpt) REVERT: A 263 ARG cc_start: 0.6745 (mtp85) cc_final: 0.6523 (tpp-160) REVERT: B 396 ILE cc_start: 0.8300 (mm) cc_final: 0.7986 (mt) outliers start: 16 outliers final: 9 residues processed: 249 average time/residue: 0.5113 time to fit residues: 139.2981 Evaluate side-chains 172 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 163 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 242 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 20.0000 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 162 ASN B 66 ASN B 76 ASN B 162 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.147351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.085358 restraints weight = 14326.352| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 1.92 r_work: 0.2808 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2688 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8853 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 12909 Z= 0.193 Angle : 0.624 7.207 17544 Z= 0.327 Chirality : 0.043 0.170 2016 Planarity : 0.004 0.043 2144 Dihedral : 6.992 50.983 2260 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.11 % Allowed : 9.85 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.21), residues: 1558 helix: 2.01 (0.20), residues: 690 sheet: 0.26 (0.30), residues: 274 loop : -1.34 (0.23), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 18 TYR 0.015 0.002 TYR A 336 PHE 0.020 0.002 PHE A 432 TRP 0.021 0.002 TRP F 35 HIS 0.004 0.001 HIS B 630 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.19 (12900) covalent geometry : angle 0.62161 / 0.33 (17524) SS BOND : bond 0.00924 / 0.70 ( 7) SS BOND : angle 1.57762 / 1.02 ( 14) hydrogen bonds : bond 0.05681 / 3.87 ( 661) hydrogen bonds : angle 4.35478 / 3.09 ( 1887) link_BETA1-4 : bond 0.00291 / 0.18 ( 2) link_BETA1-4 : angle 1.88268 / 0.98 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 182 time to evaluate : 0.480 Fit side-chains REVERT: A 125 VAL cc_start: 0.8537 (OUTLIER) cc_final: 0.8200 (m) REVERT: A 176 SER cc_start: 0.8576 (m) cc_final: 0.8017 (p) REVERT: A 177 LYS cc_start: 0.7729 (mttm) cc_final: 0.7117 (mtpt) REVERT: A 251 LYS cc_start: 0.7742 (ptmm) cc_final: 0.7538 (mtmm) REVERT: A 344 GLU cc_start: 0.7864 (mt-10) cc_final: 0.7559 (tp30) REVERT: A 426 ARG cc_start: 0.9133 (OUTLIER) cc_final: 0.8197 (mtt90) REVERT: C 61 ARG cc_start: 0.8395 (mtm110) cc_final: 0.8195 (mtm110) REVERT: F 84 ARG cc_start: 0.8389 (ptp90) cc_final: 0.8023 (ptt-90) REVERT: B 125 VAL cc_start: 0.8418 (OUTLIER) cc_final: 0.7998 (m) REVERT: B 190 GLU cc_start: 0.7500 (mt-10) cc_final: 0.7265 (mt-10) REVERT: B 426 ARG cc_start: 0.9153 (OUTLIER) cc_final: 0.8190 (mtt90) REVERT: B 531 GLN cc_start: 0.8304 (OUTLIER) cc_final: 0.7688 (mt0) outliers start: 42 outliers final: 22 residues processed: 204 average time/residue: 0.5384 time to fit residues: 120.0345 Evaluate side-chains 194 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 167 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ASN Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain A residue 426 ARG Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 76 LYS Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 426 ARG Chi-restraints excluded: chain B residue 531 GLN Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 652 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 90 optimal weight: 1.9990 chunk 134 optimal weight: 4.9990 chunk 125 optimal weight: 8.9990 chunk 21 optimal weight: 0.4980 chunk 9 optimal weight: 0.9990 chunk 127 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 30 optimal weight: 8.9990 chunk 51 optimal weight: 0.6980 chunk 131 optimal weight: 0.6980 chunk 119 optimal weight: 7.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 ASN A 120 ASN A 162 ASN B 40 HIS B 162 ASN B 596 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.149570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.087864 restraints weight = 14527.582| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 1.94 r_work: 0.2844 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12909 Z= 0.114 Angle : 0.536 6.394 17544 Z= 0.279 Chirality : 0.039 0.155 2016 Planarity : 0.004 0.048 2144 Dihedral : 6.383 55.239 2253 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.15 % Allowed : 12.74 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.22), residues: 1558 helix: 2.29 (0.20), residues: 690 sheet: 0.41 (0.31), residues: 276 loop : -1.13 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 18 TYR 0.013 0.001 TYR F 95 PHE 0.016 0.001 PHE B 432 TRP 0.017 0.001 TRP F 35 HIS 0.007 0.001 HIS B 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (12900) covalent geometry : angle 0.53392 / 0.28 (17524) SS BOND : bond 0.00560 / 0.42 ( 7) SS BOND : angle 1.09362 / 0.72 ( 14) hydrogen bonds : bond 0.04291 / 2.91 ( 661) hydrogen bonds : angle 4.05415 / 2.87 ( 1887) link_BETA1-4 : bond 0.00235 / 0.15 ( 2) link_BETA1-4 : angle 2.20248 / 1.14 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 182 time to evaluate : 0.477 Fit side-chains revert: symmetry clash REVERT: A 125 VAL cc_start: 0.8525 (OUTLIER) cc_final: 0.8220 (m) REVERT: A 177 LYS cc_start: 0.7648 (mttm) cc_final: 0.7023 (mtpt) REVERT: A 251 LYS cc_start: 0.7849 (ptmm) cc_final: 0.7647 (mtmm) REVERT: A 344 GLU cc_start: 0.7851 (mt-10) cc_final: 0.7539 (tp30) REVERT: C 61 ARG cc_start: 0.8352 (mtm110) cc_final: 0.8149 (mtm110) REVERT: D 3 GLN cc_start: 0.8258 (OUTLIER) cc_final: 0.7562 (mp10) REVERT: E 81 GLU cc_start: 0.7991 (pm20) cc_final: 0.7776 (pm20) REVERT: E 82 ASP cc_start: 0.8645 (m-30) cc_final: 0.8432 (m-30) REVERT: F 3 GLN cc_start: 0.7939 (mm-40) cc_final: 0.7459 (mm-40) REVERT: B 125 VAL cc_start: 0.8371 (OUTLIER) cc_final: 0.7995 (m) REVERT: B 236 ARG cc_start: 0.7502 (ttm-80) cc_final: 0.7232 (ttm-80) REVERT: B 251 LYS cc_start: 0.7902 (ptpp) cc_final: 0.7575 (pttt) REVERT: B 426 ARG cc_start: 0.9103 (OUTLIER) cc_final: 0.8068 (mtt90) REVERT: B 531 GLN cc_start: 0.8227 (OUTLIER) cc_final: 0.7578 (mt0) outliers start: 29 outliers final: 9 residues processed: 194 average time/residue: 0.5176 time to fit residues: 109.8282 Evaluate side-chains 178 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 164 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ASN Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 3 GLN Chi-restraints excluded: chain D residue 76 LYS Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 426 ARG Chi-restraints excluded: chain B residue 531 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 70 optimal weight: 4.9990 chunk 61 optimal weight: 10.0000 chunk 128 optimal weight: 0.2980 chunk 139 optimal weight: 0.3980 chunk 34 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 145 optimal weight: 5.9990 chunk 120 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 55 optimal weight: 5.9990 chunk 143 optimal weight: 0.6980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 120 ASN A 158 ASN A 350 HIS B 40 HIS B 162 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.149140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.087370 restraints weight = 14506.353| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 1.93 r_work: 0.2835 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12909 Z= 0.125 Angle : 0.542 6.606 17544 Z= 0.281 Chirality : 0.040 0.152 2016 Planarity : 0.004 0.049 2144 Dihedral : 6.003 58.276 2249 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.52 % Allowed : 13.56 % Favored : 83.93 % 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: 1.18 (0.22), residues: 1558 helix: 2.33 (0.20), residues: 692 sheet: 0.53 (0.31), residues: 276 loop : -1.01 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 18 TYR 0.013 0.001 TYR F 95 PHE 0.017 0.001 PHE B 432 TRP 0.019 0.001 TRP F 35 HIS 0.007 0.001 HIS B 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.12 (12900) covalent geometry : angle 0.53949 / 0.28 (17524) SS BOND : bond 0.00828 / 0.58 ( 7) SS BOND : angle 1.25255 / 0.89 ( 14) hydrogen bonds : bond 0.04209 / 2.85 ( 661) hydrogen bonds : angle 3.95487 / 2.80 ( 1887) link_BETA1-4 : bond 0.00188 / 0.12 ( 2) link_BETA1-4 : angle 2.22642 / 1.17 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 171 time to evaluate : 0.539 Fit side-chains revert: symmetry clash REVERT: A 125 VAL cc_start: 0.8553 (OUTLIER) cc_final: 0.8280 (m) REVERT: A 158 ASN cc_start: 0.8144 (m-40) cc_final: 0.7899 (m110) REVERT: A 177 LYS cc_start: 0.7594 (mttm) cc_final: 0.6959 (mtpt) REVERT: A 251 LYS cc_start: 0.7868 (ptmm) cc_final: 0.7592 (mtmm) REVERT: A 344 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7540 (tp30) REVERT: A 426 ARG cc_start: 0.9109 (OUTLIER) cc_final: 0.8354 (mtt90) REVERT: A 451 GLU cc_start: 0.8392 (mt-10) cc_final: 0.8134 (mt-10) REVERT: C 61 ARG cc_start: 0.8355 (mtm110) cc_final: 0.8037 (mtm110) REVERT: C 81 GLU cc_start: 0.8145 (pt0) cc_final: 0.7530 (pm20) REVERT: D 3 GLN cc_start: 0.8264 (OUTLIER) cc_final: 0.7539 (mp10) REVERT: E 81 GLU cc_start: 0.7969 (pm20) cc_final: 0.7650 (pm20) REVERT: E 82 ASP cc_start: 0.8580 (m-30) cc_final: 0.8260 (m-30) REVERT: F 3 GLN cc_start: 0.7958 (mm-40) cc_final: 0.7546 (mp10) REVERT: B 125 VAL cc_start: 0.8392 (OUTLIER) cc_final: 0.8034 (m) REVERT: B 190 GLU cc_start: 0.7523 (mt-10) cc_final: 0.7319 (mt-10) REVERT: B 236 ARG cc_start: 0.7467 (ttm-80) cc_final: 0.7141 (ttm-80) REVERT: B 251 LYS cc_start: 0.7898 (ptpp) cc_final: 0.7588 (pttt) REVERT: B 531 GLN cc_start: 0.8218 (OUTLIER) cc_final: 0.7584 (mt0) outliers start: 34 outliers final: 14 residues processed: 192 average time/residue: 0.5062 time to fit residues: 106.4925 Evaluate side-chains 180 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 161 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain A residue 426 ARG Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 3 GLN Chi-restraints excluded: chain D residue 76 LYS Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 531 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 21 optimal weight: 20.0000 chunk 123 optimal weight: 10.0000 chunk 112 optimal weight: 8.9990 chunk 15 optimal weight: 4.9990 chunk 119 optimal weight: 9.9990 chunk 141 optimal weight: 6.9990 chunk 99 optimal weight: 9.9990 chunk 105 optimal weight: 4.9990 chunk 116 optimal weight: 4.9990 chunk 24 optimal weight: 9.9990 chunk 128 optimal weight: 0.0030 overall best weight: 4.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 120 ASN A 162 ASN B 162 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.145275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.083069 restraints weight = 14457.219| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 1.91 r_work: 0.2766 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2647 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8882 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.065 12909 Z= 0.315 Angle : 0.706 8.380 17544 Z= 0.367 Chirality : 0.048 0.219 2016 Planarity : 0.005 0.063 2144 Dihedral : 6.336 51.621 2249 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 3.19 % Allowed : 13.33 % Favored : 83.48 % 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: 0.76 (0.21), residues: 1558 helix: 2.08 (0.20), residues: 678 sheet: 0.34 (0.31), residues: 276 loop : -1.29 (0.23), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 18 TYR 0.023 0.003 TYR B 342 PHE 0.026 0.003 PHE A 432 TRP 0.023 0.003 TRP F 35 HIS 0.006 0.002 HIS B 630 Details of bonding type rmsd/Z covalent geometry : bond 0.00776 / 0.32 (12900) covalent geometry : angle 0.70246 / 0.37 (17524) SS BOND : bond 0.01362 / 1.04 ( 7) SS BOND : angle 2.33763 / 1.65 ( 14) hydrogen bonds : bond 0.06000 / 4.06 ( 661) hydrogen bonds : angle 4.23046 / 3.01 ( 1887) link_BETA1-4 : bond 0.00393 / 0.22 ( 2) link_BETA1-4 : angle 2.19991 / 1.19 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 166 time to evaluate : 0.473 Fit side-chains revert: symmetry clash REVERT: A 125 VAL cc_start: 0.8547 (OUTLIER) cc_final: 0.8238 (m) REVERT: A 158 ASN cc_start: 0.8253 (m-40) cc_final: 0.7974 (m110) REVERT: A 177 LYS cc_start: 0.7639 (mttm) cc_final: 0.7051 (mtpt) REVERT: A 426 ARG cc_start: 0.9190 (OUTLIER) cc_final: 0.8390 (mtt90) REVERT: C 61 ARG cc_start: 0.8417 (mtm110) cc_final: 0.8068 (mtm110) REVERT: C 81 GLU cc_start: 0.8196 (pt0) cc_final: 0.7576 (pm20) REVERT: D 3 GLN cc_start: 0.8372 (OUTLIER) cc_final: 0.7588 (mp10) REVERT: E 81 GLU cc_start: 0.7987 (pm20) cc_final: 0.7689 (pm20) REVERT: E 82 ASP cc_start: 0.8602 (m-30) cc_final: 0.8335 (m-30) REVERT: F 3 GLN cc_start: 0.8085 (mm-40) cc_final: 0.7608 (mp10) REVERT: B 42 ILE cc_start: 0.7406 (OUTLIER) cc_final: 0.6944 (mp) REVERT: B 71 MET cc_start: 0.7841 (OUTLIER) cc_final: 0.6631 (mtt) REVERT: B 125 VAL cc_start: 0.8430 (OUTLIER) cc_final: 0.8014 (m) REVERT: B 190 GLU cc_start: 0.7565 (mt-10) cc_final: 0.7352 (mt-10) REVERT: B 236 ARG cc_start: 0.7523 (ttm-80) cc_final: 0.7205 (ttm-80) REVERT: B 426 ARG cc_start: 0.9203 (OUTLIER) cc_final: 0.8361 (mtt180) REVERT: B 531 GLN cc_start: 0.8316 (OUTLIER) cc_final: 0.7748 (mt0) outliers start: 43 outliers final: 22 residues processed: 189 average time/residue: 0.4996 time to fit residues: 103.3800 Evaluate side-chains 188 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 158 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain A residue 426 ARG Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 3 GLN Chi-restraints excluded: chain D residue 76 LYS Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 426 ARG Chi-restraints excluded: chain B residue 531 GLN Chi-restraints excluded: chain B residue 598 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 85 optimal weight: 5.9990 chunk 57 optimal weight: 10.0000 chunk 130 optimal weight: 0.7980 chunk 83 optimal weight: 6.9990 chunk 78 optimal weight: 9.9990 chunk 36 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 137 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 120 ASN A 162 ASN B 66 ASN B 162 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.149126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.087520 restraints weight = 14406.649| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 1.92 r_work: 0.2840 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2722 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12909 Z= 0.114 Angle : 0.540 7.900 17544 Z= 0.279 Chirality : 0.039 0.154 2016 Planarity : 0.004 0.049 2144 Dihedral : 5.895 52.444 2249 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.07 % Allowed : 15.48 % Favored : 82.44 % 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: 1.16 (0.22), residues: 1558 helix: 2.46 (0.20), residues: 676 sheet: 0.42 (0.31), residues: 276 loop : -1.08 (0.24), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 18 TYR 0.025 0.001 TYR B 342 PHE 0.017 0.001 PHE B 432 TRP 0.018 0.001 TRP F 35 HIS 0.003 0.001 HIS A 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (12900) covalent geometry : angle 0.53822 / 0.28 (17524) SS BOND : bond 0.00514 / 0.39 ( 7) SS BOND : angle 0.98813 / 0.68 ( 14) hydrogen bonds : bond 0.04118 / 2.78 ( 661) hydrogen bonds : angle 3.97497 / 2.82 ( 1887) link_BETA1-4 : bond 0.00334 / 0.21 ( 2) link_BETA1-4 : angle 2.39868 / 1.24 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 173 time to evaluate : 0.500 Fit side-chains revert: symmetry clash REVERT: A 125 VAL cc_start: 0.8535 (OUTLIER) cc_final: 0.8286 (m) REVERT: A 158 ASN cc_start: 0.8290 (m-40) cc_final: 0.7968 (m110) REVERT: A 177 LYS cc_start: 0.7558 (mttm) cc_final: 0.6937 (mtpt) REVERT: A 251 LYS cc_start: 0.7894 (ptmm) cc_final: 0.7611 (mtmm) REVERT: A 263 ARG cc_start: 0.6828 (mmt90) cc_final: 0.6470 (mmt180) REVERT: A 344 GLU cc_start: 0.7981 (mm-30) cc_final: 0.7775 (tp30) REVERT: A 426 ARG cc_start: 0.9094 (OUTLIER) cc_final: 0.8292 (mtt90) REVERT: C 61 ARG cc_start: 0.8360 (mtm110) cc_final: 0.8128 (mtm110) REVERT: D 3 GLN cc_start: 0.8260 (OUTLIER) cc_final: 0.7509 (mp10) REVERT: E 81 GLU cc_start: 0.7931 (pm20) cc_final: 0.7621 (pm20) REVERT: E 82 ASP cc_start: 0.8538 (m-30) cc_final: 0.8296 (m-30) REVERT: F 3 GLN cc_start: 0.7941 (mm-40) cc_final: 0.7520 (mp10) REVERT: B 71 MET cc_start: 0.7791 (OUTLIER) cc_final: 0.6455 (mtt) REVERT: B 125 VAL cc_start: 0.8380 (OUTLIER) cc_final: 0.8010 (m) REVERT: B 190 GLU cc_start: 0.7534 (mt-10) cc_final: 0.7325 (mt-10) REVERT: B 236 ARG cc_start: 0.7459 (ttm-80) cc_final: 0.7156 (ttm-80) REVERT: B 251 LYS cc_start: 0.7829 (ptpp) cc_final: 0.7532 (pttm) REVERT: B 426 ARG cc_start: 0.9110 (OUTLIER) cc_final: 0.8115 (mtt90) REVERT: B 531 GLN cc_start: 0.8231 (OUTLIER) cc_final: 0.7641 (mt0) outliers start: 28 outliers final: 13 residues processed: 187 average time/residue: 0.5203 time to fit residues: 106.2084 Evaluate side-chains 183 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 163 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 426 ARG Chi-restraints excluded: chain A residue 481 MET Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 3 GLN Chi-restraints excluded: chain D residue 76 LYS Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 426 ARG Chi-restraints excluded: chain B residue 531 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 109 optimal weight: 10.0000 chunk 93 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 118 optimal weight: 1.9990 chunk 135 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 0.9990 chunk 79 optimal weight: 6.9990 chunk 7 optimal weight: 7.9990 chunk 117 optimal weight: 0.8980 chunk 66 optimal weight: 7.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 120 ASN A 126 GLN A 162 ASN B 162 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.147215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.085236 restraints weight = 14364.505| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 1.91 r_work: 0.2804 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2686 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8856 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12909 Z= 0.183 Angle : 0.604 7.863 17544 Z= 0.313 Chirality : 0.042 0.173 2016 Planarity : 0.004 0.048 2144 Dihedral : 5.890 50.470 2249 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.74 % Allowed : 15.04 % Favored : 82.22 % 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: 1.06 (0.21), residues: 1558 helix: 2.36 (0.20), residues: 676 sheet: 0.39 (0.31), residues: 276 loop : -1.11 (0.24), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 18 TYR 0.024 0.002 TYR B 342 PHE 0.021 0.002 PHE A 432 TRP 0.021 0.002 TRP F 35 HIS 0.004 0.001 HIS A 583 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.18 (12900) covalent geometry : angle 0.60029 / 0.31 (17524) SS BOND : bond 0.01048 / 0.81 ( 7) SS BOND : angle 1.89434 / 1.20 ( 14) hydrogen bonds : bond 0.04847 / 3.28 ( 661) hydrogen bonds : angle 4.03712 / 2.87 ( 1887) link_BETA1-4 : bond 0.00286 / 0.16 ( 2) link_BETA1-4 : angle 2.31432 / 1.24 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 160 time to evaluate : 0.520 Fit side-chains revert: symmetry clash REVERT: A 125 VAL cc_start: 0.8569 (OUTLIER) cc_final: 0.8316 (m) REVERT: A 158 ASN cc_start: 0.8312 (m-40) cc_final: 0.7992 (m110) REVERT: A 177 LYS cc_start: 0.7554 (mttm) cc_final: 0.6933 (mtpt) REVERT: A 251 LYS cc_start: 0.7917 (ptmm) cc_final: 0.7614 (mtmm) REVERT: A 263 ARG cc_start: 0.6850 (mmt90) cc_final: 0.6494 (mmt180) REVERT: A 344 GLU cc_start: 0.7983 (mm-30) cc_final: 0.7780 (tp30) REVERT: A 426 ARG cc_start: 0.9143 (OUTLIER) cc_final: 0.8337 (mtt90) REVERT: C 61 ARG cc_start: 0.8391 (mtm110) cc_final: 0.8053 (mtm110) REVERT: C 81 GLU cc_start: 0.8158 (pt0) cc_final: 0.7569 (pm20) REVERT: D 3 GLN cc_start: 0.8312 (OUTLIER) cc_final: 0.7551 (mp10) REVERT: E 61 ARG cc_start: 0.8219 (mtm-85) cc_final: 0.7759 (ptt90) REVERT: E 81 GLU cc_start: 0.7943 (pm20) cc_final: 0.7587 (pm20) REVERT: E 82 ASP cc_start: 0.8564 (m-30) cc_final: 0.8361 (m-30) REVERT: F 3 GLN cc_start: 0.8014 (mm-40) cc_final: 0.7587 (mp10) REVERT: B 71 MET cc_start: 0.7794 (OUTLIER) cc_final: 0.6552 (mtt) REVERT: B 125 VAL cc_start: 0.8411 (OUTLIER) cc_final: 0.8035 (m) REVERT: B 190 GLU cc_start: 0.7586 (mt-10) cc_final: 0.7352 (mt-10) REVERT: B 251 LYS cc_start: 0.7823 (ptpp) cc_final: 0.7529 (pttm) REVERT: B 426 ARG cc_start: 0.9167 (OUTLIER) cc_final: 0.8310 (mtt90) REVERT: B 531 GLN cc_start: 0.8270 (OUTLIER) cc_final: 0.7686 (mt0) outliers start: 37 outliers final: 21 residues processed: 178 average time/residue: 0.5586 time to fit residues: 108.4758 Evaluate side-chains 184 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 156 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain A residue 426 ARG Chi-restraints excluded: chain A residue 481 MET Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 3 GLN Chi-restraints excluded: chain D residue 76 LYS Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 426 ARG Chi-restraints excluded: chain B residue 531 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 131 optimal weight: 0.9990 chunk 147 optimal weight: 0.9990 chunk 72 optimal weight: 4.9990 chunk 144 optimal weight: 0.0370 chunk 55 optimal weight: 4.9990 chunk 26 optimal weight: 10.0000 chunk 123 optimal weight: 6.9990 chunk 142 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 84 optimal weight: 8.9990 chunk 126 optimal weight: 8.9990 overall best weight: 1.3664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 120 ASN A 162 ASN B 162 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.148552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.086821 restraints weight = 14340.662| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 1.92 r_work: 0.2830 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2713 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8834 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12909 Z= 0.130 Angle : 0.557 8.248 17544 Z= 0.288 Chirality : 0.040 0.150 2016 Planarity : 0.004 0.053 2144 Dihedral : 5.726 51.696 2249 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.15 % Allowed : 15.78 % Favored : 82.07 % 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: 1.22 (0.22), residues: 1558 helix: 2.46 (0.20), residues: 676 sheet: 0.48 (0.31), residues: 276 loop : -0.99 (0.25), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 18 TYR 0.024 0.002 TYR B 342 PHE 0.018 0.001 PHE A 432 TRP 0.019 0.001 TRP F 35 HIS 0.003 0.001 HIS A 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (12900) covalent geometry : angle 0.55410 / 0.29 (17524) SS BOND : bond 0.00760 / 0.57 ( 7) SS BOND : angle 1.28203 / 0.87 ( 14) hydrogen bonds : bond 0.04267 / 2.89 ( 661) hydrogen bonds : angle 3.96677 / 2.83 ( 1887) link_BETA1-4 : bond 0.00269 / 0.16 ( 2) link_BETA1-4 : angle 2.38108 / 1.26 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 166 time to evaluate : 0.466 Fit side-chains revert: symmetry clash REVERT: A 125 VAL cc_start: 0.8573 (OUTLIER) cc_final: 0.8320 (m) REVERT: A 152 MET cc_start: 0.7545 (mtp) cc_final: 0.7186 (ttp) REVERT: A 158 ASN cc_start: 0.8277 (m-40) cc_final: 0.7935 (m110) REVERT: A 177 LYS cc_start: 0.7530 (mttm) cc_final: 0.6909 (mtpt) REVERT: A 251 LYS cc_start: 0.7915 (ptmm) cc_final: 0.7622 (mtmm) REVERT: A 263 ARG cc_start: 0.6853 (mmt90) cc_final: 0.6452 (mmt180) REVERT: A 344 GLU cc_start: 0.8023 (mm-30) cc_final: 0.7809 (tp30) REVERT: A 426 ARG cc_start: 0.9109 (OUTLIER) cc_final: 0.8383 (mtt90) REVERT: A 451 GLU cc_start: 0.8459 (mt-10) cc_final: 0.8051 (pt0) REVERT: C 61 ARG cc_start: 0.8366 (mtm110) cc_final: 0.8122 (mtm110) REVERT: D 3 GLN cc_start: 0.8276 (OUTLIER) cc_final: 0.7525 (mp10) REVERT: E 61 ARG cc_start: 0.8158 (mtm-85) cc_final: 0.7783 (ptt90) REVERT: E 81 GLU cc_start: 0.7891 (pm20) cc_final: 0.7531 (pm20) REVERT: F 3 GLN cc_start: 0.7978 (mm-40) cc_final: 0.7564 (mp10) REVERT: B 71 MET cc_start: 0.7773 (OUTLIER) cc_final: 0.6445 (mtt) REVERT: B 125 VAL cc_start: 0.8415 (OUTLIER) cc_final: 0.8049 (m) REVERT: B 190 GLU cc_start: 0.7551 (mt-10) cc_final: 0.7321 (mt-10) REVERT: B 251 LYS cc_start: 0.7812 (ptpp) cc_final: 0.7521 (pttm) REVERT: B 426 ARG cc_start: 0.9123 (OUTLIER) cc_final: 0.8153 (mtt90) REVERT: B 531 GLN cc_start: 0.8249 (OUTLIER) cc_final: 0.7668 (mt0) outliers start: 29 outliers final: 20 residues processed: 183 average time/residue: 0.5563 time to fit residues: 111.2438 Evaluate side-chains 190 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 163 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 426 ARG Chi-restraints excluded: chain A residue 481 MET Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 3 GLN Chi-restraints excluded: chain D residue 76 LYS Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain F residue 73 ASP Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 426 ARG Chi-restraints excluded: chain B residue 531 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 5 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 151 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 76 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 147 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 chunk 139 optimal weight: 0.6980 chunk 100 optimal weight: 6.9990 chunk 47 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 120 ASN A 126 GLN A 162 ASN B 162 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.150368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.089219 restraints weight = 14461.797| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 1.92 r_work: 0.2865 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12909 Z= 0.102 Angle : 0.523 8.705 17544 Z= 0.269 Chirality : 0.039 0.147 2016 Planarity : 0.004 0.056 2144 Dihedral : 5.466 52.797 2249 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 1.85 % Allowed : 16.22 % Favored : 81.93 % 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: 1.41 (0.22), residues: 1558 helix: 2.59 (0.20), residues: 676 sheet: 0.58 (0.31), residues: 276 loop : -0.86 (0.25), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 18 TYR 0.025 0.001 TYR B 342 PHE 0.015 0.001 PHE B 432 TRP 0.020 0.001 TRP F 35 HIS 0.003 0.001 HIS A 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 (12900) covalent geometry : angle 0.52024 / 0.27 (17524) SS BOND : bond 0.00516 / 0.38 ( 7) SS BOND : angle 0.99313 / 0.63 ( 14) hydrogen bonds : bond 0.03670 / 2.49 ( 661) hydrogen bonds : angle 3.85425 / 2.75 ( 1887) link_BETA1-4 : bond 0.00241 / 0.15 ( 2) link_BETA1-4 : angle 2.48089 / 1.30 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 175 time to evaluate : 0.466 Fit side-chains revert: symmetry clash REVERT: A 125 VAL cc_start: 0.8573 (OUTLIER) cc_final: 0.8363 (m) REVERT: A 152 MET cc_start: 0.7454 (mtp) cc_final: 0.7163 (ttp) REVERT: A 158 ASN cc_start: 0.8268 (m-40) cc_final: 0.7922 (m110) REVERT: A 177 LYS cc_start: 0.7475 (mttm) cc_final: 0.6945 (mtpt) REVERT: A 251 LYS cc_start: 0.7914 (ptmm) cc_final: 0.7630 (mtmm) REVERT: A 263 ARG cc_start: 0.6877 (mmt90) cc_final: 0.6552 (mmt180) REVERT: A 344 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7741 (tp30) REVERT: A 426 ARG cc_start: 0.9079 (OUTLIER) cc_final: 0.8297 (mtt90) REVERT: A 451 GLU cc_start: 0.8445 (mt-10) cc_final: 0.8050 (pt0) REVERT: A 475 LEU cc_start: 0.8540 (tt) cc_final: 0.8159 (mp) REVERT: D 3 GLN cc_start: 0.8242 (OUTLIER) cc_final: 0.7504 (mp10) REVERT: D 111 GLN cc_start: 0.8760 (tp40) cc_final: 0.8119 (pm20) REVERT: E 61 ARG cc_start: 0.8161 (mtm-85) cc_final: 0.7887 (ptt90) REVERT: E 81 GLU cc_start: 0.7879 (pm20) cc_final: 0.7530 (pm20) REVERT: F 3 GLN cc_start: 0.7962 (mm-40) cc_final: 0.7547 (mp10) REVERT: B 71 MET cc_start: 0.7727 (OUTLIER) cc_final: 0.6418 (mtt) REVERT: B 120 ASN cc_start: 0.7857 (m110) cc_final: 0.7178 (t0) REVERT: B 125 VAL cc_start: 0.8419 (OUTLIER) cc_final: 0.8067 (m) REVERT: B 190 GLU cc_start: 0.7566 (mt-10) cc_final: 0.7341 (mt-10) REVERT: B 251 LYS cc_start: 0.7800 (ptpp) cc_final: 0.7512 (pttm) REVERT: B 426 ARG cc_start: 0.9087 (OUTLIER) cc_final: 0.8196 (mtt180) outliers start: 25 outliers final: 16 residues processed: 188 average time/residue: 0.4950 time to fit residues: 102.2165 Evaluate side-chains 189 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 167 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ASN Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain A residue 426 ARG Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 3 GLN Chi-restraints excluded: chain D residue 76 LYS Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain F residue 73 ASP Chi-restraints excluded: chain F residue 76 LYS Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 426 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 128 optimal weight: 6.9990 chunk 57 optimal weight: 10.0000 chunk 59 optimal weight: 4.9990 chunk 58 optimal weight: 0.7980 chunk 44 optimal weight: 7.9990 chunk 68 optimal weight: 6.9990 chunk 98 optimal weight: 20.0000 chunk 94 optimal weight: 3.9990 chunk 139 optimal weight: 0.9980 chunk 113 optimal weight: 0.3980 chunk 11 optimal weight: 9.9990 overall best weight: 2.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 120 ASN A 126 GLN A 162 ASN B 162 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.147597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.085573 restraints weight = 14358.821| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 1.92 r_work: 0.2807 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2688 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8851 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12909 Z= 0.177 Angle : 0.608 9.587 17544 Z= 0.313 Chirality : 0.042 0.169 2016 Planarity : 0.004 0.060 2144 Dihedral : 5.676 50.666 2249 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.70 % Allowed : 16.59 % Favored : 81.70 % 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: 1.18 (0.22), residues: 1558 helix: 2.41 (0.20), residues: 676 sheet: 0.50 (0.32), residues: 274 loop : -1.00 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 18 TYR 0.024 0.002 TYR B 342 PHE 0.021 0.002 PHE A 432 TRP 0.018 0.002 TRP F 35 HIS 0.004 0.001 HIS A 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.18 (12900) covalent geometry : angle 0.60446 / 0.31 (17524) SS BOND : bond 0.01015 / 0.78 ( 7) SS BOND : angle 1.77354 / 1.16 ( 14) hydrogen bonds : bond 0.04776 / 3.23 ( 661) hydrogen bonds : angle 4.00175 / 2.85 ( 1887) link_BETA1-4 : bond 0.00240 / 0.14 ( 2) link_BETA1-4 : angle 2.25889 / 1.23 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 164 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 LEU cc_start: 0.7591 (mt) cc_final: 0.7326 (mm) REVERT: A 125 VAL cc_start: 0.8580 (OUTLIER) cc_final: 0.8346 (m) REVERT: A 152 MET cc_start: 0.7536 (mtp) cc_final: 0.7216 (ttp) REVERT: A 158 ASN cc_start: 0.8253 (m-40) cc_final: 0.7923 (m110) REVERT: A 177 LYS cc_start: 0.7503 (mttm) cc_final: 0.6964 (mtpt) REVERT: A 263 ARG cc_start: 0.6890 (mmt90) cc_final: 0.6573 (mmt180) REVERT: A 426 ARG cc_start: 0.9149 (OUTLIER) cc_final: 0.8323 (mtt90) REVERT: A 451 GLU cc_start: 0.8474 (mt-10) cc_final: 0.8079 (pt0) REVERT: C 61 ARG cc_start: 0.8340 (mtm110) cc_final: 0.8116 (mtm110) REVERT: C 81 GLU cc_start: 0.8146 (pt0) cc_final: 0.7578 (pm20) REVERT: D 3 GLN cc_start: 0.8311 (OUTLIER) cc_final: 0.7554 (mp10) REVERT: D 111 GLN cc_start: 0.8796 (tp40) cc_final: 0.8122 (pm20) REVERT: E 61 ARG cc_start: 0.8200 (mtm-85) cc_final: 0.7924 (ptt90) REVERT: E 81 GLU cc_start: 0.7908 (pm20) cc_final: 0.7575 (pm20) REVERT: F 3 GLN cc_start: 0.8030 (mm-40) cc_final: 0.7637 (mp10) REVERT: B 45 ARG cc_start: 0.6472 (mtm-85) cc_final: 0.6235 (mtm-85) REVERT: B 71 MET cc_start: 0.7752 (OUTLIER) cc_final: 0.6442 (mtt) REVERT: B 125 VAL cc_start: 0.8439 (OUTLIER) cc_final: 0.8069 (m) REVERT: B 190 GLU cc_start: 0.7555 (mt-10) cc_final: 0.7328 (mt-10) REVERT: B 251 LYS cc_start: 0.7800 (ptpp) cc_final: 0.7520 (pttm) REVERT: B 426 ARG cc_start: 0.9164 (OUTLIER) cc_final: 0.8301 (mtt90) outliers start: 23 outliers final: 15 residues processed: 178 average time/residue: 0.5297 time to fit residues: 103.1333 Evaluate side-chains 180 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 159 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ASN Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain A residue 426 ARG Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 3 GLN Chi-restraints excluded: chain D residue 76 LYS Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 426 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 24 optimal weight: 9.9990 chunk 36 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 96 optimal weight: 2.9990 chunk 126 optimal weight: 7.9990 chunk 92 optimal weight: 1.9990 chunk 115 optimal weight: 10.0000 chunk 80 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 106 optimal weight: 9.9990 chunk 139 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 120 ASN A 126 GLN A 162 ASN B 162 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.146795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.084882 restraints weight = 14485.062| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 1.92 r_work: 0.2797 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2679 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8860 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 12909 Z= 0.198 Angle : 0.622 9.506 17544 Z= 0.321 Chirality : 0.043 0.174 2016 Planarity : 0.004 0.059 2144 Dihedral : 5.820 50.291 2249 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 2.00 % Allowed : 16.30 % Favored : 81.70 % 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: 1.02 (0.21), residues: 1558 helix: 2.32 (0.20), residues: 676 sheet: 0.40 (0.31), residues: 274 loop : -1.13 (0.24), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 18 TYR 0.025 0.002 TYR B 342 PHE 0.021 0.002 PHE A 432 TRP 0.018 0.002 TRP F 35 HIS 0.004 0.001 HIS B 630 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.20 (12900) covalent geometry : angle 0.61874 / 0.32 (17524) SS BOND : bond 0.01068 / 0.82 ( 7) SS BOND : angle 1.67991 / 1.14 ( 14) hydrogen bonds : bond 0.04973 / 3.36 ( 661) hydrogen bonds : angle 4.03331 / 2.87 ( 1887) link_BETA1-4 : bond 0.00301 / 0.18 ( 2) link_BETA1-4 : angle 2.26331 / 1.21 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5825.16 seconds wall clock time: 99 minutes 42.92 seconds (5982.92 seconds total)