Starting phenix.real_space_refine on Fri Jul 3 05:55:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pxo_18003/07_2026/8pxo_18003.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pxo_18003/07_2026/8pxo_18003.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8pxo_18003/07_2026/8pxo_18003.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pxo_18003/07_2026/8pxo_18003.map" model { file = "/net/cci-nas-00/data/ceres_data/8pxo_18003/07_2026/8pxo_18003.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pxo_18003/07_2026/8pxo_18003.cif" } resolution = 3.0 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= 0.000 sd= 0.002 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 8140 2.51 5 N 2041 2.21 5 O 2293 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12542 Number of models: 1 Model: "" Number of chains: 10 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: 4405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 566, 4405 Classifications: {'peptide': 566} Link IDs: {'PTRANS': 18, 'TRANS': 547} Chain breaks: 3 Chain: "A" Number of atoms: 4397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 565, 4397 Classifications: {'peptide': 565} Link IDs: {'PTRANS': 18, 'TRANS': 546} 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: "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: "B" Number of atoms: 128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 128 Unusual residues: {'CLR': 2, 'I3T': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'CLR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.11, per 1000 atoms: 0.25 Number of scatterers: 12542 At special positions: 0 Unit cell: (100.98, 103.62, 145.86, 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 2293 8.00 N 2041 7.00 C 8140 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.04 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.04 Simple disulfide: pdb=" SG CYS B 592 " - pdb=" SG CYS B 608 " distance=2.03 Simple disulfide: pdb=" SG CYS B 603 " - pdb=" SG CYS A 603 " distance=2.03 Simple disulfide: pdb=" SG CYS A 592 " - pdb=" SG CYS A 608 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.04 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: 1.14 Conformation dependent library (CDL) restraints added in 601.7 milliseconds 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2894 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 18 sheets defined 48.8% alpha, 19.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.667A pdb=" N THR D 91 " --> pdb=" O PRO D 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 91 removed outlier: 3.667A 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 98 through 102 removed outlier: 3.563A pdb=" N GLY B 101 " --> pdb=" O ASP B 98 " (cutoff:3.500A) 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: 3.563A pdb=" N ALA B 174 " --> pdb=" O ASP B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 201 removed outlier: 3.891A pdb=" N GLU B 199 " --> pdb=" O SER B 195 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE B 201 " --> pdb=" O GLY B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 234 removed outlier: 3.954A pdb=" N GLN B 234 " --> pdb=" O ARG B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 253 removed outlier: 3.692A pdb=" N PHE B 253 " --> pdb=" O ILE B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 281 removed outlier: 4.386A pdb=" N LEU B 274 " --> pdb=" O ALA B 270 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLY B 275 " --> pdb=" O GLN B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 300 Processing helix chain 'B' and resid 329 through 339 Processing helix chain 'B' and resid 339 through 354 removed outlier: 3.586A pdb=" N LYS B 343 " --> pdb=" O SER B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 390 removed outlier: 3.841A pdb=" N GLN B 376 " --> pdb=" O SER B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 413 removed outlier: 4.202A pdb=" N SER B 395 " --> pdb=" O ASN B 391 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN B 398 " --> pdb=" O ALA B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 441 removed outlier: 4.232A pdb=" N ILE B 423 " --> pdb=" O ASP B 419 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N GLN B 424 " --> pdb=" O SER B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 444 No H-bonds generated for 'chain 'B' and resid 442 through 444' Processing helix chain 'B' and resid 445 through 451 removed outlier: 3.786A pdb=" N VAL B 449 " --> pdb=" O VAL B 445 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLU B 451 " --> pdb=" O LEU B 447 " (cutoff:3.500A) 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 498 removed outlier: 3.646A pdb=" N MET B 481 " --> pdb=" O ASP B 477 " (cutoff:3.500A) Proline residue: B 485 - end of helix removed outlier: 4.383A pdb=" N PHE B 495 " --> pdb=" O CYS B 491 " (cutoff:3.500A) removed outlier: 3.777A 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 533 through 551 removed outlier: 4.339A pdb=" N ALA B 537 " --> pdb=" O VAL B 533 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE B 550 " --> pdb=" O VAL B 546 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N PHE B 551 " --> pdb=" O PHE B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 567 removed outlier: 4.418A 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: 3.819A pdb=" N TYR B 576 " --> pdb=" O SER B 572 " (cutoff:3.500A) removed outlier: 3.806A 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: 5.233A pdb=" N ASN B 629 " --> pdb=" O GLY B 625 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N HIS B 630 " --> pdb=" O LEU B 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 95 Processing helix chain 'A' and resid 98 through 102 removed outlier: 3.563A pdb=" N GLY A 101 " --> pdb=" O ASP A 98 " (cutoff:3.500A) 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: 3.562A pdb=" N ALA A 174 " --> pdb=" O ASP A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 201 removed outlier: 3.890A pdb=" N GLU A 199 " --> pdb=" O SER A 195 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE A 201 " --> pdb=" O GLY A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 234 removed outlier: 3.954A pdb=" N GLN A 234 " --> pdb=" O ARG A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 253 removed outlier: 3.693A pdb=" N PHE A 253 " --> pdb=" O ILE A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 281 removed outlier: 4.386A pdb=" N LEU A 274 " --> pdb=" O ALA A 270 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLY A 275 " --> pdb=" O GLN A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 300 Processing helix chain 'A' and resid 329 through 339 Processing helix chain 'A' and resid 339 through 354 removed outlier: 3.586A pdb=" N LYS A 343 " --> pdb=" O SER A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 390 removed outlier: 3.842A pdb=" N GLN A 376 " --> pdb=" O SER A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 413 removed outlier: 4.201A pdb=" N SER A 395 " --> pdb=" O ASN A 391 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN A 398 " --> pdb=" O ALA A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 441 removed outlier: 4.232A pdb=" N ILE A 423 " --> pdb=" O ASP A 419 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N GLN A 424 " --> pdb=" O SER A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 444 No H-bonds generated for 'chain 'A' and resid 442 through 444' Processing helix chain 'A' and resid 445 through 451 removed outlier: 3.787A pdb=" N VAL A 449 " --> pdb=" O VAL A 445 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLU A 451 " --> pdb=" O LEU A 447 " (cutoff:3.500A) 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 498 removed outlier: 3.646A pdb=" N MET A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) Proline residue: A 485 - end of helix removed outlier: 4.383A pdb=" N PHE A 495 " --> pdb=" O CYS A 491 " (cutoff:3.500A) removed outlier: 3.777A 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 533 through 551 removed outlier: 4.340A pdb=" N ALA A 537 " --> pdb=" O VAL A 533 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE A 550 " --> pdb=" O VAL A 546 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N PHE A 551 " --> pdb=" O PHE A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 567 removed outlier: 4.417A 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: 3.820A pdb=" N TYR A 576 " --> pdb=" O SER A 572 " (cutoff:3.500A) removed outlier: 3.806A 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: 5.234A pdb=" N ASN A 629 " --> pdb=" O GLY A 625 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N HIS A 630 " --> pdb=" O LEU A 626 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 3 through 7 removed outlier: 3.665A pdb=" N THR D 71 " --> pdb=" O PHE D 80 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 58 through 60 removed outlier: 3.811A pdb=" N LYS D 45 " --> pdb=" O PHE D 41 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N TRP D 37 " --> pdb=" O MET D 49 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N TYR D 51 " --> pdb=" O TRP D 35 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N TRP D 35 " --> pdb=" O TYR D 51 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N TYR D 108 " --> pdb=" O THR D 98 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 58 through 60 removed outlier: 3.811A pdb=" N LYS D 45 " --> pdb=" O PHE D 41 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N TRP D 37 " --> pdb=" O MET D 49 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N TYR D 51 " --> pdb=" O TRP D 35 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N TRP D 35 " --> pdb=" O TYR D 51 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 4 through 5 removed outlier: 3.810A pdb=" N ASP E 70 " --> pdb=" O SER E 67 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 53 through 54 removed outlier: 6.530A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N SER E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LEU E 33 " --> pdb=" O SER E 49 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N THR E 97 " --> pdb=" O GLN E 90 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 53 through 54 removed outlier: 6.530A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N SER E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LEU E 33 " --> pdb=" O SER E 49 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR E 86 " --> pdb=" O THR E 102 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 3 through 7 removed outlier: 3.665A pdb=" N THR F 71 " --> pdb=" O PHE F 80 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 58 through 60 removed outlier: 3.811A pdb=" N LYS F 45 " --> pdb=" O PHE F 41 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N TRP F 37 " --> pdb=" O MET F 49 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N TYR F 51 " --> pdb=" O TRP F 35 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N TRP F 35 " --> pdb=" O TYR F 51 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N TYR F 108 " --> pdb=" O THR F 98 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 58 through 60 removed outlier: 3.811A pdb=" N LYS F 45 " --> pdb=" O PHE F 41 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N TRP F 37 " --> pdb=" O MET F 49 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N TYR F 51 " --> pdb=" O TRP F 35 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N TRP F 35 " --> pdb=" O TYR F 51 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 64 through 71 removed outlier: 6.703A pdb=" N SER B 65 " --> pdb=" O CYS B 43 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N CYS B 43 " --> pdb=" O SER B 65 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ILE B 67 " --> pdb=" O ASN B 41 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASP B 105 " --> pdb=" O HIS B 40 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 74 through 75 removed outlier: 5.604A pdb=" N GLY B 74 " --> pdb=" O ILE B 238 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N PHE B 240 " --> pdb=" O GLY B 74 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N LEU B 207 " --> pdb=" O ILE B 239 " (cutoff:3.500A) removed outlier: 8.406A pdb=" N SER B 241 " --> pdb=" O LEU B 207 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N LEU B 209 " --> pdb=" O SER B 241 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N GLY B 122 " --> pdb=" O PHE B 208 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N ASP B 210 " --> pdb=" O GLY B 122 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N VAL B 124 " --> pdb=" O ASP B 210 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 256 through 260 removed outlier: 3.854A pdb=" N PHE B 266 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N ALA B 260 " --> pdb=" O LEU B 264 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N LEU B 264 " --> pdb=" O ALA B 260 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 64 through 71 removed outlier: 6.703A pdb=" N SER A 65 " --> pdb=" O CYS A 43 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N CYS A 43 " --> pdb=" O SER A 65 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N ILE A 67 " --> pdb=" O ASN A 41 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP A 105 " --> pdb=" O HIS A 40 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 74 through 75 removed outlier: 5.603A pdb=" N GLY A 74 " --> pdb=" O ILE A 238 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N PHE A 240 " --> pdb=" O GLY A 74 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N LEU A 207 " --> pdb=" O ILE A 239 " (cutoff:3.500A) removed outlier: 8.406A pdb=" N SER A 241 " --> pdb=" O LEU A 207 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N LEU A 209 " --> pdb=" O SER A 241 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N GLY A 122 " --> pdb=" O PHE A 208 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N ASP A 210 " --> pdb=" O GLY A 122 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N VAL A 124 " --> pdb=" O ASP A 210 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 256 through 260 removed outlier: 3.853A pdb=" N PHE A 266 " --> pdb=" O LEU A 258 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ALA A 260 " --> pdb=" O LEU A 264 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N LEU A 264 " --> pdb=" O ALA A 260 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 4 through 5 removed outlier: 3.810A pdb=" N ASP C 70 " --> pdb=" O SER C 67 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 53 through 54 removed outlier: 6.530A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N SER C 49 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N LEU C 33 " --> pdb=" O SER C 49 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N THR C 97 " --> pdb=" O GLN C 90 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 53 through 54 removed outlier: 6.530A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N SER C 49 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N LEU C 33 " --> pdb=" O SER C 49 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TYR C 86 " --> pdb=" O THR C 102 " (cutoff:3.500A) 680 hydrogen bonds defined for protein. 1908 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: 2.03 Time building geometry restraints manager: 1.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3863 1.34 - 1.46: 3280 1.46 - 1.58: 5578 1.58 - 1.70: 11 1.70 - 1.82: 106 Bond restraints: 12838 Sorted by residual: bond pdb=" C16 I3T B 704 " pdb=" O03 I3T B 704 " ideal model delta sigma weight residual 1.219 1.301 -0.082 2.00e-02 2.50e+03 1.68e+01 bond pdb=" C22 I3T B 703 " pdb=" O02 I3T B 703 " ideal model delta sigma weight residual 1.220 1.302 -0.082 2.00e-02 2.50e+03 1.68e+01 bond pdb=" C22 I3T B 704 " pdb=" O02 I3T B 704 " ideal model delta sigma weight residual 1.220 1.302 -0.082 2.00e-02 2.50e+03 1.67e+01 bond pdb=" C16 I3T B 703 " pdb=" O03 I3T B 703 " ideal model delta sigma weight residual 1.219 1.301 -0.082 2.00e-02 2.50e+03 1.67e+01 bond pdb=" C07 I3T B 703 " pdb=" C09 I3T B 703 " ideal model delta sigma weight residual 1.484 1.557 -0.073 2.00e-02 2.50e+03 1.33e+01 ... (remaining 12833 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 16921 1.79 - 3.58: 404 3.58 - 5.37: 76 5.37 - 7.15: 25 7.15 - 8.94: 3 Bond angle restraints: 17429 Sorted by residual: angle pdb=" OG1 THR B 220 " pdb=" CB THR B 220 " pdb=" CG2 THR B 220 " ideal model delta sigma weight residual 109.30 115.06 -5.76 2.00e+00 2.50e-01 8.29e+00 angle pdb=" OG1 THR A 220 " pdb=" CB THR A 220 " pdb=" CG2 THR A 220 " ideal model delta sigma weight residual 109.30 115.05 -5.75 2.00e+00 2.50e-01 8.26e+00 angle pdb=" OG1 THR D 23 " pdb=" CB THR D 23 " pdb=" CG2 THR D 23 " ideal model delta sigma weight residual 109.30 114.82 -5.52 2.00e+00 2.50e-01 7.61e+00 angle pdb=" OG1 THR F 23 " pdb=" CB THR F 23 " pdb=" CG2 THR F 23 " ideal model delta sigma weight residual 109.30 114.81 -5.51 2.00e+00 2.50e-01 7.60e+00 angle pdb=" CA LEU B 587 " pdb=" CB LEU B 587 " pdb=" CG LEU B 587 " ideal model delta sigma weight residual 116.30 125.24 -8.94 3.50e+00 8.16e-02 6.53e+00 ... (remaining 17424 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.00: 7240 16.00 - 32.01: 477 32.01 - 48.01: 79 48.01 - 64.01: 34 64.01 - 80.02: 4 Dihedral angle restraints: 7834 sinusoidal: 3301 harmonic: 4533 Sorted by residual: dihedral pdb=" CA GLY F 43 " pdb=" C GLY F 43 " pdb=" N LYS F 44 " pdb=" CA LYS F 44 " ideal model delta harmonic sigma weight residual -180.00 -158.10 -21.90 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" CA GLY D 43 " pdb=" C GLY D 43 " pdb=" N LYS D 44 " pdb=" CA LYS D 44 " ideal model delta harmonic sigma weight residual -180.00 -158.14 -21.86 0 5.00e+00 4.00e-02 1.91e+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 -159.10 -20.90 0 5.00e+00 4.00e-02 1.75e+01 ... (remaining 7831 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.143: 1970 0.143 - 0.287: 21 0.287 - 0.430: 4 0.430 - 0.574: 4 0.574 - 0.717: 2 Chirality restraints: 2001 Sorted by residual: chirality pdb=" CG LEU A 405 " pdb=" CB LEU A 405 " pdb=" CD1 LEU A 405 " pdb=" CD2 LEU A 405 " both_signs ideal model delta sigma weight residual False -2.59 -1.87 -0.72 2.00e-01 2.50e+01 1.29e+01 chirality pdb=" CG LEU B 405 " pdb=" CB LEU B 405 " pdb=" CD1 LEU B 405 " pdb=" CD2 LEU B 405 " both_signs ideal model delta sigma weight residual False -2.59 -1.87 -0.72 2.00e-01 2.50e+01 1.28e+01 chirality pdb=" CB THR F 23 " pdb=" CA THR F 23 " pdb=" OG1 THR F 23 " pdb=" CG2 THR F 23 " both_signs ideal model delta sigma weight residual False 2.55 2.02 0.53 2.00e-01 2.50e+01 7.04e+00 ... (remaining 1998 not shown) Planarity restraints: 2142 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C09 I3T B 703 " 0.105 2.00e-02 2.50e+03 1.13e-01 1.90e+02 pdb=" C10 I3T B 703 " 0.078 2.00e-02 2.50e+03 pdb=" C22 I3T B 703 " -0.049 2.00e-02 2.50e+03 pdb=" C23 I3T B 703 " 0.058 2.00e-02 2.50e+03 pdb=" N02 I3T B 703 " -0.228 2.00e-02 2.50e+03 pdb=" O02 I3T B 703 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C09 I3T B 704 " -0.092 2.00e-02 2.50e+03 1.03e-01 1.58e+02 pdb=" C10 I3T B 704 " -0.075 2.00e-02 2.50e+03 pdb=" C22 I3T B 704 " 0.044 2.00e-02 2.50e+03 pdb=" C23 I3T B 704 " -0.050 2.00e-02 2.50e+03 pdb=" N02 I3T B 704 " 0.208 2.00e-02 2.50e+03 pdb=" O02 I3T B 704 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 I3T B 703 " -0.011 2.00e-02 2.50e+03 3.35e-02 1.40e+01 pdb=" C16 I3T B 703 " -0.008 2.00e-02 2.50e+03 pdb=" C23 I3T B 703 " 0.040 2.00e-02 2.50e+03 pdb=" N03 I3T B 703 " -0.053 2.00e-02 2.50e+03 pdb=" O03 I3T B 703 " 0.033 2.00e-02 2.50e+03 ... (remaining 2139 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2730 2.78 - 3.31: 11987 3.31 - 3.84: 19710 3.84 - 4.37: 23784 4.37 - 4.90: 42940 Nonbonded interactions: 101151 Sorted by model distance: nonbonded pdb=" NH1 ARG A 137 " pdb=" OD1 ASN A 162 " model vdw 2.253 3.120 nonbonded pdb=" NH1 ARG B 137 " pdb=" OD1 ASN B 162 " model vdw 2.253 3.120 nonbonded pdb=" O ARG D 84 " pdb=" OG SER D 85 " model vdw 2.259 3.040 nonbonded pdb=" O ARG F 84 " pdb=" OG SER F 85 " model vdw 2.259 3.040 nonbonded pdb=" NH2 ARG B 160 " pdb=" OD2 ASP B 203 " model vdw 2.260 3.120 ... (remaining 101146 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 35 through 300 or resid 328 through 702)) } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'X' } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.240 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: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.650 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 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 : 0.010 0.082 12847 Z= 0.421 Angle : 0.713 8.942 17449 Z= 0.346 Chirality : 0.060 0.717 2001 Planarity : 0.005 0.113 2142 Dihedral : 11.487 80.019 4919 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 1.04 % Allowed : 4.15 % Favored : 94.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.21), residues: 1557 helix: 1.80 (0.20), residues: 671 sheet: -0.95 (0.32), residues: 250 loop : -1.47 (0.23), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 575 TYR 0.015 0.002 TYR D 51 PHE 0.014 0.002 PHE D 79 TRP 0.011 0.001 TRP F 35 HIS 0.004 0.001 HIS B 40 Details of bonding type rmsd/Z covalent geometry : bond 0.01032 / 0.42 (12838) covalent geometry : angle 0.71055 / 0.35 (17429) SS BOND : bond 0.00779 / 0.34 ( 7) SS BOND : angle 1.29508 / 0.71 ( 14) hydrogen bonds : bond 0.15895 / 10.43 ( 630) hydrogen bonds : angle 6.63320 / 4.60 ( 1908) link_BETA1-4 : bond 0.00607 / 0.32 ( 2) link_BETA1-4 : angle 3.09165 / 1.53 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 262 time to evaluate : 0.343 Fit side-chains revert: symmetry clash REVERT: D 5 GLN cc_start: 0.7778 (tp40) cc_final: 0.7543 (tp40) REVERT: E 3 VAL cc_start: 0.9034 (m) cc_final: 0.8824 (t) REVERT: E 107 ARG cc_start: 0.6957 (mtm110) cc_final: 0.5453 (tpm170) REVERT: C 3 VAL cc_start: 0.9049 (m) cc_final: 0.8825 (t) REVERT: C 18 ARG cc_start: 0.7437 (ttt-90) cc_final: 0.7083 (ttt180) REVERT: C 107 ARG cc_start: 0.6937 (mtm110) cc_final: 0.5366 (tpm170) outliers start: 14 outliers final: 1 residues processed: 272 average time/residue: 0.5674 time to fit residues: 167.8570 Evaluate side-chains 158 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 157 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 5 GLN E 42 ASN F 5 GLN F 111 GLN B 109 ASN B 391 ASN B 601 ASN B 617 GLN A 109 ASN A 391 ASN A 424 GLN C 42 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.135474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.104737 restraints weight = 17183.060| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 2.24 r_work: 0.3100 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12847 Z= 0.134 Angle : 0.582 6.990 17449 Z= 0.301 Chirality : 0.042 0.165 2001 Planarity : 0.004 0.037 2142 Dihedral : 6.102 53.687 2135 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.04 % Allowed : 12.45 % Favored : 84.51 % 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: 0.64 (0.22), residues: 1557 helix: 2.30 (0.20), residues: 677 sheet: -0.74 (0.30), residues: 284 loop : -1.20 (0.24), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 230 TYR 0.013 0.001 TYR B 336 PHE 0.015 0.001 PHE D 79 TRP 0.011 0.001 TRP D 35 HIS 0.005 0.001 HIS A 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (12838) covalent geometry : angle 0.57941 / 0.30 (17429) SS BOND : bond 0.00551 / 0.33 ( 7) SS BOND : angle 1.37553 / 0.79 ( 14) hydrogen bonds : bond 0.04542 / 2.91 ( 630) hydrogen bonds : angle 4.47453 / 3.13 ( 1908) link_BETA1-4 : bond 0.00825 / 0.40 ( 2) link_BETA1-4 : angle 2.16486 / 1.04 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 188 time to evaluate : 0.361 Fit side-chains revert: symmetry clash REVERT: D 82 GLN cc_start: 0.8780 (OUTLIER) cc_final: 0.8318 (tt0) REVERT: D 89 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.8339 (tt0) REVERT: E 3 VAL cc_start: 0.9183 (m) cc_final: 0.8961 (t) REVERT: E 61 ARG cc_start: 0.8315 (mtm110) cc_final: 0.8028 (mtm110) REVERT: E 74 SER cc_start: 0.8909 (OUTLIER) cc_final: 0.8622 (p) REVERT: E 107 ARG cc_start: 0.6614 (mtm110) cc_final: 0.5013 (tpm170) REVERT: B 163 ARG cc_start: 0.7982 (ttp-110) cc_final: 0.7617 (ttp80) REVERT: B 523 MET cc_start: 0.8941 (OUTLIER) cc_final: 0.8568 (ttt) REVERT: A 163 ARG cc_start: 0.7963 (ttp-110) cc_final: 0.7533 (ttp80) REVERT: A 278 GLU cc_start: 0.6209 (mm-30) cc_final: 0.5659 (mt-10) REVERT: A 348 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7547 (tt0) REVERT: C 3 VAL cc_start: 0.9160 (m) cc_final: 0.8926 (t) REVERT: C 18 ARG cc_start: 0.7533 (ttt-90) cc_final: 0.7230 (ttt180) REVERT: C 74 SER cc_start: 0.8916 (OUTLIER) cc_final: 0.8568 (p) REVERT: C 107 ARG cc_start: 0.6687 (mtm110) cc_final: 0.4991 (tpm170) outliers start: 41 outliers final: 9 residues processed: 212 average time/residue: 0.4927 time to fit residues: 114.3237 Evaluate side-chains 163 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 148 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 82 GLN Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain E residue 42 ASN Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 523 MET Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 42 ASN Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 74 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 16 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 78 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 7 optimal weight: 0.0770 chunk 147 optimal weight: 3.9990 chunk 101 optimal weight: 10.0000 chunk 105 optimal weight: 9.9990 chunk 25 optimal weight: 3.9990 overall best weight: 1.5944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 601 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.131381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.096677 restraints weight = 17502.522| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 2.13 r_work: 0.3036 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12847 Z= 0.176 Angle : 0.581 7.732 17449 Z= 0.297 Chirality : 0.043 0.167 2001 Planarity : 0.004 0.036 2142 Dihedral : 5.941 58.371 2133 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.56 % Allowed : 13.71 % Favored : 82.73 % 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: 0.67 (0.22), residues: 1557 helix: 2.21 (0.20), residues: 678 sheet: -0.50 (0.30), residues: 284 loop : -1.18 (0.24), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 45 TYR 0.014 0.001 TYR B 336 PHE 0.016 0.002 PHE F 79 TRP 0.010 0.001 TRP A 379 HIS 0.006 0.001 HIS A 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.18 (12838) covalent geometry : angle 0.57849 / 0.30 (17429) SS BOND : bond 0.00817 / 0.50 ( 7) SS BOND : angle 1.37805 / 0.74 ( 14) hydrogen bonds : bond 0.04636 / 2.99 ( 630) hydrogen bonds : angle 4.23393 / 2.95 ( 1908) link_BETA1-4 : bond 0.00209 / 0.10 ( 2) link_BETA1-4 : angle 2.05871 / 1.03 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 161 time to evaluate : 0.413 Fit side-chains revert: symmetry clash REVERT: D 89 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.8344 (tt0) REVERT: E 3 VAL cc_start: 0.9193 (m) cc_final: 0.8969 (t) REVERT: E 74 SER cc_start: 0.8914 (OUTLIER) cc_final: 0.8630 (p) REVERT: E 107 ARG cc_start: 0.6668 (mtm110) cc_final: 0.5039 (tpm170) REVERT: F 82 GLN cc_start: 0.8779 (OUTLIER) cc_final: 0.8493 (tt0) REVERT: B 163 ARG cc_start: 0.7966 (ttp-110) cc_final: 0.7520 (ttp80) REVERT: A 163 ARG cc_start: 0.7972 (ttp-110) cc_final: 0.7513 (ttp80) REVERT: A 278 GLU cc_start: 0.6124 (mm-30) cc_final: 0.5639 (mt-10) REVERT: C 3 VAL cc_start: 0.9201 (m) cc_final: 0.8975 (t) REVERT: C 74 SER cc_start: 0.8926 (OUTLIER) cc_final: 0.8578 (p) REVERT: C 107 ARG cc_start: 0.6658 (mtm110) cc_final: 0.5010 (tpm170) outliers start: 48 outliers final: 12 residues processed: 190 average time/residue: 0.4848 time to fit residues: 101.4205 Evaluate side-chains 159 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 143 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain F residue 82 GLN Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 251 LYS Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 74 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 109 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 102 optimal weight: 6.9990 chunk 89 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 104 optimal weight: 2.9990 chunk 143 optimal weight: 0.8980 chunk 96 optimal weight: 0.0670 chunk 147 optimal weight: 2.9990 chunk 150 optimal weight: 6.9990 chunk 117 optimal weight: 3.9990 overall best weight: 1.3722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 40 GLN E 38 GLN F 40 GLN B 437 GLN A 437 GLN C 38 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.130553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.097476 restraints weight = 17442.182| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 2.33 r_work: 0.3025 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12847 Z= 0.156 Angle : 0.557 7.980 17449 Z= 0.286 Chirality : 0.041 0.158 2001 Planarity : 0.004 0.031 2142 Dihedral : 5.655 59.909 2133 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.89 % Allowed : 14.60 % Favored : 82.51 % 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: 0.79 (0.21), residues: 1557 helix: 2.31 (0.20), residues: 668 sheet: -0.41 (0.30), residues: 284 loop : -1.08 (0.24), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 45 TYR 0.012 0.001 TYR B 336 PHE 0.019 0.001 PHE A 294 TRP 0.011 0.001 TRP A 379 HIS 0.006 0.001 HIS A 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 (12838) covalent geometry : angle 0.55469 / 0.29 (17429) SS BOND : bond 0.00618 / 0.35 ( 7) SS BOND : angle 1.00398 / 0.54 ( 14) hydrogen bonds : bond 0.04305 / 2.79 ( 630) hydrogen bonds : angle 4.07402 / 2.85 ( 1908) link_BETA1-4 : bond 0.00174 / 0.08 ( 2) link_BETA1-4 : angle 2.28797 / 1.17 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 147 time to evaluate : 0.475 Fit side-chains revert: symmetry clash REVERT: D 2 VAL cc_start: 0.7877 (t) cc_final: 0.7676 (p) REVERT: D 89 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.8366 (tt0) REVERT: E 3 VAL cc_start: 0.9200 (m) cc_final: 0.8986 (t) REVERT: E 11 PHE cc_start: 0.8152 (OUTLIER) cc_final: 0.7929 (m-80) REVERT: E 74 SER cc_start: 0.8978 (OUTLIER) cc_final: 0.8692 (p) REVERT: E 107 ARG cc_start: 0.6670 (mtm110) cc_final: 0.5091 (tpm170) REVERT: B 66 ASN cc_start: 0.8531 (t0) cc_final: 0.8273 (t0) REVERT: B 163 ARG cc_start: 0.7951 (ttp-110) cc_final: 0.7169 (ttp80) REVERT: B 166 GLN cc_start: 0.7760 (mt0) cc_final: 0.7531 (pp30) REVERT: B 523 MET cc_start: 0.9083 (OUTLIER) cc_final: 0.8748 (ttt) REVERT: A 163 ARG cc_start: 0.7953 (ttp-110) cc_final: 0.7150 (ttp80) REVERT: A 166 GLN cc_start: 0.7824 (mt0) cc_final: 0.7599 (pp30) REVERT: A 278 GLU cc_start: 0.6099 (mm-30) cc_final: 0.5630 (mt-10) REVERT: A 483 MET cc_start: 0.7796 (ttp) cc_final: 0.7312 (mtt) REVERT: C 3 VAL cc_start: 0.9213 (m) cc_final: 0.8995 (t) REVERT: C 11 PHE cc_start: 0.8137 (OUTLIER) cc_final: 0.7901 (m-80) REVERT: C 74 SER cc_start: 0.8936 (OUTLIER) cc_final: 0.8594 (p) outliers start: 39 outliers final: 16 residues processed: 174 average time/residue: 0.4667 time to fit residues: 89.7733 Evaluate side-chains 157 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 135 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 76 LYS Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 11 PHE Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain F residue 76 LYS Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 523 MET Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 11 PHE Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 74 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 60 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 1 optimal weight: 5.9990 chunk 152 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 56 optimal weight: 9.9990 chunk 133 optimal weight: 0.6980 chunk 89 optimal weight: 0.4980 chunk 63 optimal weight: 0.5980 chunk 135 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.131845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.096872 restraints weight = 17479.506| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.18 r_work: 0.3040 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 12847 Z= 0.106 Angle : 0.504 6.513 17449 Z= 0.258 Chirality : 0.039 0.146 2001 Planarity : 0.003 0.030 2142 Dihedral : 5.380 59.994 2133 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.89 % Allowed : 15.05 % Favored : 82.06 % 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: 1.00 (0.22), residues: 1557 helix: 2.44 (0.20), residues: 670 sheet: -0.29 (0.30), residues: 284 loop : -0.93 (0.25), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 45 TYR 0.011 0.001 TYR A 336 PHE 0.014 0.001 PHE F 79 TRP 0.012 0.001 TRP F 35 HIS 0.004 0.001 HIS B 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (12838) covalent geometry : angle 0.50195 / 0.26 (17429) SS BOND : bond 0.00282 / 0.11 ( 7) SS BOND : angle 0.68777 / 0.37 ( 14) hydrogen bonds : bond 0.03676 / 2.39 ( 630) hydrogen bonds : angle 3.90779 / 2.74 ( 1908) link_BETA1-4 : bond 0.00073 / 0.03 ( 2) link_BETA1-4 : angle 2.47429 / 1.23 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 145 time to evaluate : 0.517 Fit side-chains revert: symmetry clash REVERT: D 89 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.8303 (tt0) REVERT: E 3 VAL cc_start: 0.9201 (m) cc_final: 0.8995 (t) REVERT: E 11 PHE cc_start: 0.8168 (OUTLIER) cc_final: 0.7951 (m-80) REVERT: E 15 LEU cc_start: 0.7999 (mp) cc_final: 0.7436 (tt) REVERT: E 18 ARG cc_start: 0.7367 (ttt-90) cc_final: 0.6996 (ttt180) REVERT: E 74 SER cc_start: 0.8981 (OUTLIER) cc_final: 0.8666 (p) REVERT: E 107 ARG cc_start: 0.6672 (mtm110) cc_final: 0.5120 (tpm170) REVERT: B 66 ASN cc_start: 0.8492 (t0) cc_final: 0.8241 (t0) REVERT: B 163 ARG cc_start: 0.7938 (ttp-110) cc_final: 0.7122 (ttp80) REVERT: B 166 GLN cc_start: 0.7774 (mt0) cc_final: 0.7555 (pp30) REVERT: B 483 MET cc_start: 0.7765 (ttp) cc_final: 0.7278 (mtt) REVERT: A 163 ARG cc_start: 0.7987 (ttp-110) cc_final: 0.7173 (ttp80) REVERT: A 166 GLN cc_start: 0.7819 (mt0) cc_final: 0.7608 (pp30) REVERT: A 207 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8599 (tp) REVERT: A 278 GLU cc_start: 0.6036 (mm-30) cc_final: 0.5515 (mt-10) REVERT: A 483 MET cc_start: 0.7804 (ttp) cc_final: 0.7329 (mtt) REVERT: C 3 VAL cc_start: 0.9186 (m) cc_final: 0.8980 (t) REVERT: C 11 PHE cc_start: 0.8168 (OUTLIER) cc_final: 0.7925 (m-80) REVERT: C 74 SER cc_start: 0.8944 (OUTLIER) cc_final: 0.8652 (p) outliers start: 39 outliers final: 20 residues processed: 172 average time/residue: 0.4895 time to fit residues: 92.9388 Evaluate side-chains 163 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 137 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 76 LYS Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain E residue 11 PHE Chi-restraints excluded: chain E residue 42 ASN Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain F residue 76 LYS Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain C residue 11 PHE Chi-restraints excluded: chain C residue 42 ASN Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 74 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 58 optimal weight: 6.9990 chunk 149 optimal weight: 5.9990 chunk 133 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 142 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 99 optimal weight: 10.0000 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 387 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.127397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.092537 restraints weight = 17582.312| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 2.12 r_work: 0.2982 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8850 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 12847 Z= 0.235 Angle : 0.617 8.962 17449 Z= 0.315 Chirality : 0.044 0.193 2001 Planarity : 0.004 0.033 2142 Dihedral : 5.822 53.918 2133 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 3.93 % Allowed : 14.46 % Favored : 81.62 % 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: 0.71 (0.21), residues: 1557 helix: 2.12 (0.20), residues: 673 sheet: -0.24 (0.31), residues: 282 loop : -1.09 (0.24), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 45 TYR 0.014 0.002 TYR D 51 PHE 0.018 0.002 PHE F 79 TRP 0.010 0.002 TRP D 35 HIS 0.007 0.001 HIS B 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00563 / 0.23 (12838) covalent geometry : angle 0.61327 / 0.31 (17429) SS BOND : bond 0.00666 / 0.30 ( 7) SS BOND : angle 1.67277 / 0.92 ( 14) hydrogen bonds : bond 0.05003 / 3.24 ( 630) hydrogen bonds : angle 4.15064 / 2.89 ( 1908) link_BETA1-4 : bond 0.00198 / 0.10 ( 2) link_BETA1-4 : angle 2.60232 / 1.32 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 150 time to evaluate : 0.395 Fit side-chains revert: symmetry clash REVERT: D 89 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.8245 (tt0) REVERT: E 18 ARG cc_start: 0.7430 (ttt-90) cc_final: 0.7095 (ttt180) REVERT: E 74 SER cc_start: 0.8948 (OUTLIER) cc_final: 0.8679 (p) REVERT: E 107 ARG cc_start: 0.6718 (mtm110) cc_final: 0.5136 (tpm170) REVERT: B 66 ASN cc_start: 0.8497 (t0) cc_final: 0.8248 (t0) REVERT: B 163 ARG cc_start: 0.7914 (ttp-110) cc_final: 0.7114 (ttp80) REVERT: B 246 ARG cc_start: 0.6972 (mtt180) cc_final: 0.6566 (mtm-85) REVERT: A 163 ARG cc_start: 0.7953 (ttp-110) cc_final: 0.7170 (ttp80) REVERT: A 278 GLU cc_start: 0.6145 (mm-30) cc_final: 0.5677 (mt-10) REVERT: A 292 ASP cc_start: 0.7229 (m-30) cc_final: 0.6834 (t70) REVERT: C 74 SER cc_start: 0.8931 (OUTLIER) cc_final: 0.8677 (p) REVERT: C 107 ARG cc_start: 0.6695 (mtm110) cc_final: 0.5092 (tpm170) outliers start: 53 outliers final: 24 residues processed: 189 average time/residue: 0.4688 time to fit residues: 97.8859 Evaluate side-chains 172 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 145 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 76 LYS Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain F residue 76 LYS Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 620 ASP Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 620 ASP Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 74 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 18 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 139 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 112 optimal weight: 9.9990 chunk 41 optimal weight: 3.9990 chunk 116 optimal weight: 0.7980 chunk 1 optimal weight: 0.0470 chunk 26 optimal weight: 0.9980 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.130235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.095702 restraints weight = 17505.996| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 2.11 r_work: 0.3032 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.3384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 12847 Z= 0.108 Angle : 0.511 6.705 17449 Z= 0.262 Chirality : 0.039 0.149 2001 Planarity : 0.003 0.031 2142 Dihedral : 5.387 55.081 2133 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.74 % Allowed : 16.23 % Favored : 81.02 % 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: 0.94 (0.22), residues: 1557 helix: 2.37 (0.20), residues: 670 sheet: -0.27 (0.30), residues: 286 loop : -0.95 (0.25), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 45 TYR 0.010 0.001 TYR C 91 PHE 0.013 0.001 PHE D 79 TRP 0.013 0.001 TRP D 35 HIS 0.005 0.001 HIS A 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 (12838) covalent geometry : angle 0.50826 / 0.26 (17429) SS BOND : bond 0.00259 / 0.11 ( 7) SS BOND : angle 0.63796 / 0.35 ( 14) hydrogen bonds : bond 0.03777 / 2.46 ( 630) hydrogen bonds : angle 3.91819 / 2.73 ( 1908) link_BETA1-4 : bond 0.00264 / 0.14 ( 2) link_BETA1-4 : angle 2.75652 / 1.38 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 142 time to evaluate : 0.504 Fit side-chains revert: symmetry clash REVERT: D 89 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.8230 (tt0) REVERT: E 18 ARG cc_start: 0.7542 (ttt-90) cc_final: 0.7018 (ttt180) REVERT: E 74 SER cc_start: 0.8968 (OUTLIER) cc_final: 0.8652 (p) REVERT: E 107 ARG cc_start: 0.6645 (mtm110) cc_final: 0.5124 (tpm170) REVERT: B 66 ASN cc_start: 0.8482 (t0) cc_final: 0.8235 (t0) REVERT: B 163 ARG cc_start: 0.7906 (ttp-110) cc_final: 0.7225 (ttp80) REVERT: A 163 ARG cc_start: 0.7905 (ttp-110) cc_final: 0.7234 (ttp80) REVERT: A 278 GLU cc_start: 0.6118 (mm-30) cc_final: 0.5557 (mt-10) REVERT: A 483 MET cc_start: 0.7776 (ttp) cc_final: 0.7304 (mtt) REVERT: C 3 VAL cc_start: 0.9209 (m) cc_final: 0.9007 (t) REVERT: C 74 SER cc_start: 0.8960 (OUTLIER) cc_final: 0.8672 (p) REVERT: C 107 ARG cc_start: 0.6605 (mtm110) cc_final: 0.5073 (tpm170) outliers start: 37 outliers final: 20 residues processed: 170 average time/residue: 0.5462 time to fit residues: 101.9240 Evaluate side-chains 156 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 133 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 76 LYS Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain F residue 76 LYS Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 620 ASP Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 620 ASP Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 74 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 99 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 142 optimal weight: 4.9990 chunk 113 optimal weight: 9.9990 chunk 137 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 117 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.126685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.096465 restraints weight = 17486.138| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 2.33 r_work: 0.2971 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8884 moved from start: 0.3461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 12847 Z= 0.258 Angle : 0.640 8.858 17449 Z= 0.327 Chirality : 0.044 0.191 2001 Planarity : 0.004 0.034 2142 Dihedral : 5.845 50.087 2133 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.11 % Allowed : 15.79 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.21), residues: 1557 helix: 2.02 (0.20), residues: 673 sheet: -0.26 (0.31), residues: 282 loop : -1.17 (0.24), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 193 TYR 0.015 0.002 TYR D 51 PHE 0.021 0.002 PHE A 294 TRP 0.010 0.002 TRP F 109 HIS 0.007 0.001 HIS B 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00622 / 0.26 (12838) covalent geometry : angle 0.63618 / 0.33 (17429) SS BOND : bond 0.00660 / 0.31 ( 7) SS BOND : angle 1.71742 / 0.96 ( 14) hydrogen bonds : bond 0.05076 / 3.29 ( 630) hydrogen bonds : angle 4.15536 / 2.89 ( 1908) link_BETA1-4 : bond 0.00414 / 0.21 ( 2) link_BETA1-4 : angle 2.72901 / 1.38 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 143 time to evaluate : 0.498 Fit side-chains revert: symmetry clash REVERT: D 89 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.8254 (tt0) REVERT: E 18 ARG cc_start: 0.7594 (ttt-90) cc_final: 0.7094 (ttt180) REVERT: E 74 SER cc_start: 0.8911 (OUTLIER) cc_final: 0.8701 (p) REVERT: E 107 ARG cc_start: 0.6813 (mtm110) cc_final: 0.5252 (tpm170) REVERT: B 163 ARG cc_start: 0.7905 (ttp-110) cc_final: 0.7271 (ttp80) REVERT: B 172 LYS cc_start: 0.8220 (mttt) cc_final: 0.8008 (pttm) REVERT: B 272 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7425 (mm-30) REVERT: A 163 ARG cc_start: 0.7914 (ttp-110) cc_final: 0.7259 (ttp80) REVERT: A 278 GLU cc_start: 0.6150 (mm-30) cc_final: 0.5668 (mt-10) REVERT: A 533 VAL cc_start: 0.6699 (OUTLIER) cc_final: 0.6470 (p) REVERT: C 107 ARG cc_start: 0.6768 (mtm110) cc_final: 0.5189 (tpm170) outliers start: 42 outliers final: 26 residues processed: 174 average time/residue: 0.5349 time to fit residues: 102.2911 Evaluate side-chains 168 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 138 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 76 LYS Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain F residue 76 LYS Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 620 ASP Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 85 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 33 optimal weight: 3.9990 chunk 78 optimal weight: 0.7980 chunk 98 optimal weight: 6.9990 chunk 32 optimal weight: 0.9990 chunk 112 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 102 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 42 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.128010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.092602 restraints weight = 17692.554| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 2.16 r_work: 0.2985 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.3555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 12847 Z= 0.200 Angle : 0.588 7.868 17449 Z= 0.301 Chirality : 0.042 0.154 2001 Planarity : 0.004 0.031 2142 Dihedral : 5.755 48.127 2133 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.89 % Allowed : 16.75 % Favored : 80.36 % 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: 0.60 (0.21), residues: 1557 helix: 2.02 (0.20), residues: 672 sheet: -0.26 (0.31), residues: 282 loop : -1.17 (0.24), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 246 TYR 0.012 0.002 TYR F 51 PHE 0.020 0.002 PHE A 294 TRP 0.011 0.001 TRP D 35 HIS 0.006 0.001 HIS A 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.20 (12838) covalent geometry : angle 0.58531 / 0.30 (17429) SS BOND : bond 0.00501 / 0.24 ( 7) SS BOND : angle 1.25710 / 0.70 ( 14) hydrogen bonds : bond 0.04658 / 3.02 ( 630) hydrogen bonds : angle 4.09751 / 2.84 ( 1908) link_BETA1-4 : bond 0.00219 / 0.11 ( 2) link_BETA1-4 : angle 2.77634 / 1.40 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 134 time to evaluate : 0.512 Fit side-chains revert: symmetry clash REVERT: D 89 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.8273 (tt0) REVERT: E 18 ARG cc_start: 0.7588 (ttt-90) cc_final: 0.7109 (ttt180) REVERT: E 74 SER cc_start: 0.8961 (OUTLIER) cc_final: 0.8664 (p) REVERT: E 107 ARG cc_start: 0.6766 (mtm110) cc_final: 0.5206 (tpm170) REVERT: B 163 ARG cc_start: 0.7860 (ttp-110) cc_final: 0.7157 (ttp80) REVERT: B 172 LYS cc_start: 0.8299 (mttt) cc_final: 0.8025 (pttm) REVERT: A 163 ARG cc_start: 0.7839 (ttp-110) cc_final: 0.7174 (ttp80) REVERT: A 172 LYS cc_start: 0.8272 (mttt) cc_final: 0.7998 (pttm) REVERT: A 278 GLU cc_start: 0.6120 (mm-30) cc_final: 0.5631 (mt-10) REVERT: A 533 VAL cc_start: 0.6705 (OUTLIER) cc_final: 0.6464 (p) REVERT: C 3 VAL cc_start: 0.9145 (OUTLIER) cc_final: 0.8930 (t) REVERT: C 107 ARG cc_start: 0.6751 (mtm110) cc_final: 0.5182 (tpm170) outliers start: 39 outliers final: 28 residues processed: 162 average time/residue: 0.5355 time to fit residues: 95.0405 Evaluate side-chains 166 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 134 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 76 LYS Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain F residue 76 LYS Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 620 ASP Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 620 ASP Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 85 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 126 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 105 optimal weight: 10.0000 chunk 70 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 135 optimal weight: 3.9990 chunk 56 optimal weight: 10.0000 chunk 35 optimal weight: 9.9990 chunk 79 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 243 HIS ** A 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.126612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.091206 restraints weight = 17840.497| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 2.16 r_work: 0.2958 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 12847 Z= 0.257 Angle : 0.648 8.939 17449 Z= 0.331 Chirality : 0.044 0.185 2001 Planarity : 0.004 0.031 2142 Dihedral : 5.982 43.489 2133 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.89 % Allowed : 16.90 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.21), residues: 1557 helix: 1.82 (0.19), residues: 673 sheet: -0.25 (0.31), residues: 280 loop : -1.30 (0.24), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 246 TYR 0.014 0.002 TYR D 51 PHE 0.021 0.002 PHE A 294 TRP 0.011 0.002 TRP F 35 HIS 0.008 0.001 HIS A 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00619 / 0.26 (12838) covalent geometry : angle 0.64467 / 0.33 (17429) SS BOND : bond 0.00620 / 0.30 ( 7) SS BOND : angle 1.61575 / 0.90 ( 14) hydrogen bonds : bond 0.05155 / 3.34 ( 630) hydrogen bonds : angle 4.22228 / 2.92 ( 1908) link_BETA1-4 : bond 0.00255 / 0.13 ( 2) link_BETA1-4 : angle 2.80971 / 1.42 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 135 time to evaluate : 0.519 Fit side-chains revert: symmetry clash REVERT: D 89 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.8287 (tt0) REVERT: E 18 ARG cc_start: 0.7584 (ttt-90) cc_final: 0.7096 (ttt180) REVERT: E 74 SER cc_start: 0.8949 (OUTLIER) cc_final: 0.8680 (p) REVERT: E 107 ARG cc_start: 0.6867 (mtm110) cc_final: 0.5321 (tpm170) REVERT: B 163 ARG cc_start: 0.7881 (ttp-110) cc_final: 0.7286 (ttp80) REVERT: B 172 LYS cc_start: 0.8297 (mttt) cc_final: 0.8046 (pttm) REVERT: B 533 VAL cc_start: 0.6709 (OUTLIER) cc_final: 0.6487 (p) REVERT: A 125 VAL cc_start: 0.9000 (t) cc_final: 0.8697 (m) REVERT: A 163 ARG cc_start: 0.7846 (ttp-110) cc_final: 0.7137 (ttp80) REVERT: A 172 LYS cc_start: 0.8268 (mttt) cc_final: 0.8046 (pttm) REVERT: A 278 GLU cc_start: 0.6159 (mm-30) cc_final: 0.5653 (mt-10) REVERT: A 533 VAL cc_start: 0.6727 (OUTLIER) cc_final: 0.6495 (p) REVERT: C 17 ASP cc_start: 0.7701 (t70) cc_final: 0.7257 (t0) REVERT: C 107 ARG cc_start: 0.6831 (mtm110) cc_final: 0.5283 (tpm170) outliers start: 39 outliers final: 30 residues processed: 164 average time/residue: 0.5441 time to fit residues: 98.0461 Evaluate side-chains 166 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 132 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 76 LYS Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 620 ASP Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 620 ASP Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 85 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 72 optimal weight: 0.9980 chunk 97 optimal weight: 5.9990 chunk 137 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 145 optimal weight: 2.9990 chunk 131 optimal weight: 4.9990 chunk 32 optimal weight: 0.5980 chunk 147 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 11 optimal weight: 0.0020 chunk 124 optimal weight: 0.9980 overall best weight: 0.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 243 HIS C 42 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.130005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.096009 restraints weight = 17779.318| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 2.40 r_work: 0.3007 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.3667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12847 Z= 0.118 Angle : 0.541 7.365 17449 Z= 0.275 Chirality : 0.039 0.142 2001 Planarity : 0.003 0.031 2142 Dihedral : 5.390 43.549 2133 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.37 % Allowed : 17.57 % Favored : 80.06 % 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: 0.77 (0.22), residues: 1557 helix: 2.20 (0.20), residues: 672 sheet: -0.24 (0.31), residues: 282 loop : -1.07 (0.24), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 246 TYR 0.010 0.001 TYR C 91 PHE 0.023 0.001 PHE A 294 TRP 0.015 0.001 TRP D 35 HIS 0.005 0.001 HIS A 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (12838) covalent geometry : angle 0.53789 / 0.27 (17429) SS BOND : bond 0.00275 / 0.13 ( 7) SS BOND : angle 0.62730 / 0.35 ( 14) hydrogen bonds : bond 0.03864 / 2.52 ( 630) hydrogen bonds : angle 3.96619 / 2.75 ( 1908) link_BETA1-4 : bond 0.00163 / 0.08 ( 2) link_BETA1-4 : angle 2.87755 / 1.46 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4256.52 seconds wall clock time: 73 minutes 24.32 seconds (4404.32 seconds total)