Starting phenix.real_space_refine on Mon Mar 18 10:03:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s8c_24893/03_2024/7s8c_24893.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s8c_24893/03_2024/7s8c_24893.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s8c_24893/03_2024/7s8c_24893.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s8c_24893/03_2024/7s8c_24893.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s8c_24893/03_2024/7s8c_24893.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s8c_24893/03_2024/7s8c_24893.pdb" } resolution = 2.85 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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: 7 Type Number sf(0) Gaussians Ca 1 9.91 5 P 4 5.49 5 S 160 5.16 5 Cl 13 4.86 5 C 13472 2.51 5 N 3336 2.21 5 O 3576 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 33": "NH1" <-> "NH2" Residue "A ARG 43": "NH1" <-> "NH2" Residue "A ARG 75": "NH1" <-> "NH2" Residue "A ARG 139": "NH1" <-> "NH2" Residue "A ARG 140": "NH1" <-> "NH2" Residue "A ARG 153": "NH1" <-> "NH2" Residue "A ARG 180": "NH1" <-> "NH2" Residue "A ARG 224": "NH1" <-> "NH2" Residue "A ARG 355": "NH1" <-> "NH2" Residue "A ARG 385": "NH1" <-> "NH2" Residue "A ARG 492": "NH1" <-> "NH2" Residue "A ARG 584": "NH1" <-> "NH2" Residue "A ARG 594": "NH1" <-> "NH2" Residue "A ARG 606": "NH1" <-> "NH2" Residue "A ARG 610": "NH1" <-> "NH2" Residue "A ARG 615": "NH1" <-> "NH2" Residue "A ARG 628": "NH1" <-> "NH2" Residue "B ARG 33": "NH1" <-> "NH2" Residue "B ARG 43": "NH1" <-> "NH2" Residue "B ARG 75": "NH1" <-> "NH2" Residue "B ARG 139": "NH1" <-> "NH2" Residue "B ARG 140": "NH1" <-> "NH2" Residue "B ARG 153": "NH1" <-> "NH2" Residue "B ARG 180": "NH1" <-> "NH2" Residue "B ARG 224": "NH1" <-> "NH2" Residue "B ARG 355": "NH1" <-> "NH2" Residue "B ARG 385": "NH1" <-> "NH2" Residue "B ARG 492": "NH1" <-> "NH2" Residue "B ARG 584": "NH1" <-> "NH2" Residue "B ARG 594": "NH1" <-> "NH2" Residue "B ARG 606": "NH1" <-> "NH2" Residue "B ARG 610": "NH1" <-> "NH2" Residue "B ARG 615": "NH1" <-> "NH2" Residue "B ARG 628": "NH1" <-> "NH2" Residue "C ARG 33": "NH1" <-> "NH2" Residue "C ARG 43": "NH1" <-> "NH2" Residue "C ARG 75": "NH1" <-> "NH2" Residue "C ARG 139": "NH1" <-> "NH2" Residue "C ARG 140": "NH1" <-> "NH2" Residue "C ARG 153": "NH1" <-> "NH2" Residue "C ARG 180": "NH1" <-> "NH2" Residue "C ARG 224": "NH1" <-> "NH2" Residue "C ARG 355": "NH1" <-> "NH2" Residue "C ARG 385": "NH1" <-> "NH2" Residue "C ARG 492": "NH1" <-> "NH2" Residue "C ARG 584": "NH1" <-> "NH2" Residue "C ARG 594": "NH1" <-> "NH2" Residue "C ARG 606": "NH1" <-> "NH2" Residue "C ARG 610": "NH1" <-> "NH2" Residue "C ARG 615": "NH1" <-> "NH2" Residue "C ARG 628": "NH1" <-> "NH2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D ARG 43": "NH1" <-> "NH2" Residue "D ARG 75": "NH1" <-> "NH2" Residue "D ARG 139": "NH1" <-> "NH2" Residue "D ARG 140": "NH1" <-> "NH2" Residue "D ARG 153": "NH1" <-> "NH2" Residue "D ARG 180": "NH1" <-> "NH2" Residue "D ARG 224": "NH1" <-> "NH2" Residue "D ARG 355": "NH1" <-> "NH2" Residue "D ARG 385": "NH1" <-> "NH2" Residue "D ARG 492": "NH1" <-> "NH2" Residue "D ARG 584": "NH1" <-> "NH2" Residue "D ARG 594": "NH1" <-> "NH2" Residue "D ARG 606": "NH1" <-> "NH2" Residue "D ARG 610": "NH1" <-> "NH2" Residue "D ARG 615": "NH1" <-> "NH2" Residue "D ARG 628": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 20562 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4912 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 26, 'TRANS': 585} Chain: "B" Number of atoms: 4912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4912 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 26, 'TRANS': 585} Chain: "C" Number of atoms: 4912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4912 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 26, 'TRANS': 585} Chain: "D" Number of atoms: 4912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4912 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 26, 'TRANS': 585} Chain: "A" Number of atoms: 230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 230 Unusual residues: {' CA': 1, ' CL': 1, 'ECL': 1, 'POV': 4, 'Y01': 3} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 109 Unresolved non-hydrogen angles: 134 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'POV:plan-3': 2, 'POV:plan-2': 2, 'POV:plan-1': 2} Unresolved non-hydrogen planarities: 22 Chain: "B" Number of atoms: 228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 228 Unusual residues: {'ECL': 1, 'POV': 4, 'Y01': 3} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 109 Unresolved non-hydrogen angles: 134 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'POV:plan-3': 2, 'POV:plan-2': 2, 'POV:plan-1': 2} Unresolved non-hydrogen planarities: 22 Chain: "C" Number of atoms: 228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 228 Unusual residues: {'ECL': 1, 'POV': 4, 'Y01': 3} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 109 Unresolved non-hydrogen angles: 134 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'POV:plan-3': 2, 'POV:plan-2': 2, 'POV:plan-1': 2} Unresolved non-hydrogen planarities: 22 Chain: "D" Number of atoms: 228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 228 Unusual residues: {'ECL': 1, 'POV': 4, 'Y01': 3} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 109 Unresolved non-hydrogen angles: 134 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'POV:plan-3': 2, 'POV:plan-2': 2, 'POV:plan-1': 2} Unresolved non-hydrogen planarities: 22 Time building chain proxies: 11.41, per 1000 atoms: 0.55 Number of scatterers: 20562 At special positions: 0 Unit cell: (130.624, 130.624, 122.304, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 1 19.99 Cl 13 17.00 S 160 16.00 P 4 15.00 O 3576 8.00 N 3336 7.00 C 13472 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.72 Conformation dependent library (CDL) restraints added in 3.7 seconds 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4624 Finding SS restraints... Secondary structure from input PDB file: 128 helices and 8 sheets defined 66.1% alpha, 3.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.31 Creating SS restraints... Processing helix chain 'A' and resid 27 through 46 removed outlier: 3.557A pdb=" N GLN A 41 " --> pdb=" O ASN A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 55 removed outlier: 3.554A pdb=" N ALA A 52 " --> pdb=" O PRO A 48 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASP A 55 " --> pdb=" O LEU A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 68 removed outlier: 3.572A pdb=" N LYS A 63 " --> pdb=" O GLN A 59 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU A 64 " --> pdb=" O ALA A 60 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU A 65 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLU A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 89 Processing helix chain 'A' and resid 91 through 102 removed outlier: 3.759A pdb=" N VAL A 97 " --> pdb=" O GLU A 93 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU A 98 " --> pdb=" O ALA A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.825A pdb=" N GLU A 108 " --> pdb=" O LEU A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.552A pdb=" N ILE A 123 " --> pdb=" O THR A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 138 Processing helix chain 'A' and resid 149 through 153 Processing helix chain 'A' and resid 165 through 173 Processing helix chain 'A' and resid 175 through 184 removed outlier: 3.624A pdb=" N ARG A 180 " --> pdb=" O GLU A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 removed outlier: 3.754A pdb=" N ILE A 204 " --> pdb=" O LEU A 200 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU A 205 " --> pdb=" O HIS A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 222 removed outlier: 3.514A pdb=" N GLN A 214 " --> pdb=" O THR A 210 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 235 removed outlier: 3.670A pdb=" N VAL A 235 " --> pdb=" O LEU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 250 Processing helix chain 'A' and resid 252 through 261 removed outlier: 3.506A pdb=" N GLN A 261 " --> pdb=" O GLN A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 298 Processing helix chain 'A' and resid 302 through 310 Processing helix chain 'A' and resid 312 through 324 Processing helix chain 'A' and resid 326 through 349 removed outlier: 3.634A pdb=" N LEU A 332 " --> pdb=" O TYR A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 377 removed outlier: 4.107A pdb=" N TYR A 377 " --> pdb=" O LEU A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 403 removed outlier: 3.746A pdb=" N ILE A 384 " --> pdb=" O PRO A 380 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG A 385 " --> pdb=" O LYS A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 409 removed outlier: 3.632A pdb=" N PHE A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 419 Processing helix chain 'A' and resid 424 through 445 Processing helix chain 'A' and resid 450 through 464 Processing helix chain 'A' and resid 465 through 470 removed outlier: 3.580A pdb=" N ALA A 469 " --> pdb=" O MET A 466 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG A 470 " --> pdb=" O TYR A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 488 removed outlier: 3.539A pdb=" N ILE A 480 " --> pdb=" O GLY A 476 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N MET A 481 " --> pdb=" O PRO A 477 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE A 482 " --> pdb=" O PHE A 478 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN A 483 " --> pdb=" O THR A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 512 removed outlier: 3.717A pdb=" N LEU A 496 " --> pdb=" O ARG A 492 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER A 506 " --> pdb=" O LEU A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 538 Processing helix chain 'A' and resid 552 through 580 removed outlier: 4.014A pdb=" N SER A 556 " --> pdb=" O PRO A 552 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE A 557 " --> pdb=" O PHE A 553 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU A 574 " --> pdb=" O MET A 570 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N MET A 578 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASP A 580 " --> pdb=" O ALA A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 608 removed outlier: 3.927A pdb=" N ASP A 590 " --> pdb=" O ALA A 586 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU A 591 " --> pdb=" O HIS A 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 46 removed outlier: 3.557A pdb=" N GLN B 41 " --> pdb=" O ASN B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 55 removed outlier: 3.555A pdb=" N ALA B 52 " --> pdb=" O PRO B 48 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASP B 55 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 68 removed outlier: 3.572A pdb=" N LYS B 63 " --> pdb=" O GLN B 59 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU B 64 " --> pdb=" O ALA B 60 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU B 65 " --> pdb=" O LEU B 61 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLU B 68 " --> pdb=" O LEU B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 89 Processing helix chain 'B' and resid 91 through 102 removed outlier: 3.759A pdb=" N VAL B 97 " --> pdb=" O GLU B 93 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU B 98 " --> pdb=" O ALA B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 108 removed outlier: 3.825A pdb=" N GLU B 108 " --> pdb=" O LEU B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 127 removed outlier: 3.551A pdb=" N ILE B 123 " --> pdb=" O THR B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 138 Processing helix chain 'B' and resid 149 through 153 Processing helix chain 'B' and resid 165 through 173 Processing helix chain 'B' and resid 175 through 184 removed outlier: 3.624A pdb=" N ARG B 180 " --> pdb=" O GLU B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 205 removed outlier: 3.754A pdb=" N ILE B 204 " --> pdb=" O LEU B 200 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU B 205 " --> pdb=" O HIS B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 222 removed outlier: 3.513A pdb=" N GLN B 214 " --> pdb=" O THR B 210 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 235 removed outlier: 3.670A pdb=" N VAL B 235 " --> pdb=" O LEU B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 250 Processing helix chain 'B' and resid 252 through 261 removed outlier: 3.506A pdb=" N GLN B 261 " --> pdb=" O GLN B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 298 Processing helix chain 'B' and resid 302 through 310 Processing helix chain 'B' and resid 312 through 324 Processing helix chain 'B' and resid 326 through 349 removed outlier: 3.634A pdb=" N LEU B 332 " --> pdb=" O TYR B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 377 removed outlier: 4.107A pdb=" N TYR B 377 " --> pdb=" O LEU B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 403 removed outlier: 3.746A pdb=" N ILE B 384 " --> pdb=" O PRO B 380 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG B 385 " --> pdb=" O LYS B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 409 removed outlier: 3.632A pdb=" N PHE B 408 " --> pdb=" O VAL B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 419 Processing helix chain 'B' and resid 424 through 445 Processing helix chain 'B' and resid 450 through 464 Processing helix chain 'B' and resid 465 through 470 removed outlier: 3.581A pdb=" N ALA B 469 " --> pdb=" O MET B 466 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG B 470 " --> pdb=" O TYR B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 488 removed outlier: 3.538A pdb=" N ILE B 480 " --> pdb=" O GLY B 476 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N MET B 481 " --> pdb=" O PRO B 477 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE B 482 " --> pdb=" O PHE B 478 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN B 483 " --> pdb=" O THR B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 512 removed outlier: 3.718A pdb=" N LEU B 496 " --> pdb=" O ARG B 492 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER B 506 " --> pdb=" O LEU B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 538 Processing helix chain 'B' and resid 552 through 580 removed outlier: 4.014A pdb=" N SER B 556 " --> pdb=" O PRO B 552 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE B 557 " --> pdb=" O PHE B 553 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU B 574 " --> pdb=" O MET B 570 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N MET B 578 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASP B 580 " --> pdb=" O ALA B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 608 removed outlier: 3.927A pdb=" N ASP B 590 " --> pdb=" O ALA B 586 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU B 591 " --> pdb=" O HIS B 587 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 46 removed outlier: 3.557A pdb=" N GLN C 41 " --> pdb=" O ASN C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 55 removed outlier: 3.554A pdb=" N ALA C 52 " --> pdb=" O PRO C 48 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASP C 55 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 68 removed outlier: 3.573A pdb=" N LYS C 63 " --> pdb=" O GLN C 59 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU C 64 " --> pdb=" O ALA C 60 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU C 65 " --> pdb=" O LEU C 61 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLU C 68 " --> pdb=" O LEU C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 91 through 102 removed outlier: 3.759A pdb=" N VAL C 97 " --> pdb=" O GLU C 93 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU C 98 " --> pdb=" O ALA C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 108 removed outlier: 3.825A pdb=" N GLU C 108 " --> pdb=" O LEU C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 127 removed outlier: 3.551A pdb=" N ILE C 123 " --> pdb=" O THR C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 138 Processing helix chain 'C' and resid 149 through 153 Processing helix chain 'C' and resid 165 through 173 Processing helix chain 'C' and resid 175 through 184 removed outlier: 3.624A pdb=" N ARG C 180 " --> pdb=" O GLU C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 205 removed outlier: 3.754A pdb=" N ILE C 204 " --> pdb=" O LEU C 200 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU C 205 " --> pdb=" O HIS C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 222 removed outlier: 3.514A pdb=" N GLN C 214 " --> pdb=" O THR C 210 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TYR C 222 " --> pdb=" O LEU C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 235 removed outlier: 3.671A pdb=" N VAL C 235 " --> pdb=" O LEU C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 250 Processing helix chain 'C' and resid 252 through 261 removed outlier: 3.506A pdb=" N GLN C 261 " --> pdb=" O GLN C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 298 Processing helix chain 'C' and resid 302 through 310 Processing helix chain 'C' and resid 312 through 324 Processing helix chain 'C' and resid 326 through 349 removed outlier: 3.634A pdb=" N LEU C 332 " --> pdb=" O TYR C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 377 removed outlier: 4.107A pdb=" N TYR C 377 " --> pdb=" O LEU C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 403 removed outlier: 3.747A pdb=" N ILE C 384 " --> pdb=" O PRO C 380 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG C 385 " --> pdb=" O LYS C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 409 removed outlier: 3.632A pdb=" N PHE C 408 " --> pdb=" O VAL C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 419 Processing helix chain 'C' and resid 424 through 445 Processing helix chain 'C' and resid 450 through 464 Processing helix chain 'C' and resid 465 through 470 removed outlier: 3.581A pdb=" N ALA C 469 " --> pdb=" O MET C 466 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG C 470 " --> pdb=" O TYR C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 488 removed outlier: 3.539A pdb=" N ILE C 480 " --> pdb=" O GLY C 476 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N MET C 481 " --> pdb=" O PRO C 477 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE C 482 " --> pdb=" O PHE C 478 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN C 483 " --> pdb=" O THR C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 512 removed outlier: 3.717A pdb=" N LEU C 496 " --> pdb=" O ARG C 492 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER C 506 " --> pdb=" O LEU C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 538 Processing helix chain 'C' and resid 552 through 580 removed outlier: 4.014A pdb=" N SER C 556 " --> pdb=" O PRO C 552 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE C 557 " --> pdb=" O PHE C 553 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU C 574 " --> pdb=" O MET C 570 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N MET C 578 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASP C 580 " --> pdb=" O ALA C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 585 through 608 removed outlier: 3.927A pdb=" N ASP C 590 " --> pdb=" O ALA C 586 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU C 591 " --> pdb=" O HIS C 587 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 46 removed outlier: 3.558A pdb=" N GLN D 41 " --> pdb=" O ASN D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 55 removed outlier: 3.554A pdb=" N ALA D 52 " --> pdb=" O PRO D 48 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASP D 55 " --> pdb=" O LEU D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 68 removed outlier: 3.572A pdb=" N LYS D 63 " --> pdb=" O GLN D 59 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU D 64 " --> pdb=" O ALA D 60 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU D 65 " --> pdb=" O LEU D 61 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLU D 68 " --> pdb=" O LEU D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 89 Processing helix chain 'D' and resid 91 through 102 removed outlier: 3.759A pdb=" N VAL D 97 " --> pdb=" O GLU D 93 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU D 98 " --> pdb=" O ALA D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 108 removed outlier: 3.825A pdb=" N GLU D 108 " --> pdb=" O LEU D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 127 removed outlier: 3.551A pdb=" N ILE D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 138 Processing helix chain 'D' and resid 149 through 153 Processing helix chain 'D' and resid 165 through 173 Processing helix chain 'D' and resid 175 through 184 removed outlier: 3.624A pdb=" N ARG D 180 " --> pdb=" O GLU D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 removed outlier: 3.754A pdb=" N ILE D 204 " --> pdb=" O LEU D 200 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU D 205 " --> pdb=" O HIS D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 222 removed outlier: 3.514A pdb=" N GLN D 214 " --> pdb=" O THR D 210 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR D 222 " --> pdb=" O LEU D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 235 removed outlier: 3.670A pdb=" N VAL D 235 " --> pdb=" O LEU D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 250 Processing helix chain 'D' and resid 252 through 261 removed outlier: 3.505A pdb=" N GLN D 261 " --> pdb=" O GLN D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 298 Processing helix chain 'D' and resid 302 through 310 Processing helix chain 'D' and resid 312 through 324 Processing helix chain 'D' and resid 326 through 349 removed outlier: 3.635A pdb=" N LEU D 332 " --> pdb=" O TYR D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 377 removed outlier: 4.107A pdb=" N TYR D 377 " --> pdb=" O LEU D 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 403 removed outlier: 3.746A pdb=" N ILE D 384 " --> pdb=" O PRO D 380 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG D 385 " --> pdb=" O LYS D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 409 removed outlier: 3.633A pdb=" N PHE D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 419 Processing helix chain 'D' and resid 424 through 445 Processing helix chain 'D' and resid 450 through 464 Processing helix chain 'D' and resid 465 through 470 removed outlier: 3.580A pdb=" N ALA D 469 " --> pdb=" O MET D 466 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG D 470 " --> pdb=" O TYR D 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 488 removed outlier: 3.539A pdb=" N ILE D 480 " --> pdb=" O GLY D 476 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N MET D 481 " --> pdb=" O PRO D 477 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE D 482 " --> pdb=" O PHE D 478 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN D 483 " --> pdb=" O THR D 479 " (cutoff:3.500A) Processing helix chain 'D' and resid 488 through 512 removed outlier: 3.717A pdb=" N LEU D 496 " --> pdb=" O ARG D 492 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER D 506 " --> pdb=" O LEU D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 538 Processing helix chain 'D' and resid 552 through 580 removed outlier: 4.014A pdb=" N SER D 556 " --> pdb=" O PRO D 552 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE D 557 " --> pdb=" O PHE D 553 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU D 574 " --> pdb=" O MET D 570 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N MET D 578 " --> pdb=" O LEU D 574 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASP D 580 " --> pdb=" O ALA D 576 " (cutoff:3.500A) Processing helix chain 'D' and resid 585 through 608 removed outlier: 3.928A pdb=" N ASP D 590 " --> pdb=" O ALA D 586 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU D 591 " --> pdb=" O HIS D 587 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 264 through 270 removed outlier: 6.740A pdb=" N SER A 275 " --> pdb=" O GLN A 267 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N THR A 269 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LEU A 273 " --> pdb=" O THR A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 352 through 354 Processing sheet with id=AA3, first strand: chain 'B' and resid 264 through 270 removed outlier: 6.740A pdb=" N SER B 275 " --> pdb=" O GLN B 267 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N THR B 269 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LEU B 273 " --> pdb=" O THR B 269 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 352 through 354 Processing sheet with id=AA5, first strand: chain 'C' and resid 264 through 270 removed outlier: 6.740A pdb=" N SER C 275 " --> pdb=" O GLN C 267 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N THR C 269 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LEU C 273 " --> pdb=" O THR C 269 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 352 through 354 Processing sheet with id=AA7, first strand: chain 'D' and resid 264 through 270 removed outlier: 6.741A pdb=" N SER D 275 " --> pdb=" O GLN D 267 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N THR D 269 " --> pdb=" O LEU D 273 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LEU D 273 " --> pdb=" O THR D 269 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 352 through 354 1025 hydrogen bonds defined for protein. 2919 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: 5.71 Time building geometry restraints manager: 8.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 3196 1.31 - 1.44: 5552 1.44 - 1.56: 12000 1.56 - 1.69: 8 1.69 - 1.81: 284 Bond restraints: 21040 Sorted by residual: bond pdb=" C29 POV C 707 " pdb="C210 POV C 707 " ideal model delta sigma weight residual 1.333 1.554 -0.221 2.00e-02 2.50e+03 1.22e+02 bond pdb=" C29 POV D 708 " pdb="C210 POV D 708 " ideal model delta sigma weight residual 1.333 1.554 -0.221 2.00e-02 2.50e+03 1.22e+02 bond pdb=" C29 POV B 707 " pdb="C210 POV B 707 " ideal model delta sigma weight residual 1.333 1.553 -0.220 2.00e-02 2.50e+03 1.21e+02 bond pdb=" C29 POV A 707 " pdb="C210 POV A 707 " ideal model delta sigma weight residual 1.333 1.553 -0.220 2.00e-02 2.50e+03 1.21e+02 bond pdb=" C21 POV A 707 " pdb=" O21 POV A 707 " ideal model delta sigma weight residual 1.330 1.415 -0.085 2.00e-02 2.50e+03 1.82e+01 ... (remaining 21035 not shown) Histogram of bond angle deviations from ideal: 99.08 - 106.13: 577 106.13 - 113.18: 11479 113.18 - 120.22: 7931 120.22 - 127.27: 8273 127.27 - 134.31: 244 Bond angle restraints: 28504 Sorted by residual: angle pdb=" C28 POV B 707 " pdb=" C29 POV B 707 " pdb="C210 POV B 707 " ideal model delta sigma weight residual 127.79 111.74 16.05 3.00e+00 1.11e-01 2.86e+01 angle pdb=" C ASN C 546 " pdb=" N TYR C 547 " pdb=" CA TYR C 547 " ideal model delta sigma weight residual 121.54 131.67 -10.13 1.91e+00 2.74e-01 2.81e+01 angle pdb=" C ASN B 546 " pdb=" N TYR B 547 " pdb=" CA TYR B 547 " ideal model delta sigma weight residual 121.54 131.67 -10.13 1.91e+00 2.74e-01 2.81e+01 angle pdb=" C ASN D 546 " pdb=" N TYR D 547 " pdb=" CA TYR D 547 " ideal model delta sigma weight residual 121.54 131.64 -10.10 1.91e+00 2.74e-01 2.79e+01 angle pdb=" C ASN A 546 " pdb=" N TYR A 547 " pdb=" CA TYR A 547 " ideal model delta sigma weight residual 121.54 131.62 -10.08 1.91e+00 2.74e-01 2.79e+01 ... (remaining 28499 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.19: 12702 28.19 - 56.38: 436 56.38 - 84.57: 80 84.57 - 112.76: 6 112.76 - 140.95: 12 Dihedral angle restraints: 13236 sinusoidal: 6076 harmonic: 7160 Sorted by residual: dihedral pdb=" CA MET C 466 " pdb=" C MET C 466 " pdb=" N TYR C 467 " pdb=" CA TYR C 467 " ideal model delta harmonic sigma weight residual 180.00 155.98 24.02 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" CA MET A 466 " pdb=" C MET A 466 " pdb=" N TYR A 467 " pdb=" CA TYR A 467 " ideal model delta harmonic sigma weight residual 180.00 155.99 24.01 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" CA MET B 466 " pdb=" C MET B 466 " pdb=" N TYR B 467 " pdb=" CA TYR B 467 " ideal model delta harmonic sigma weight residual 180.00 156.00 24.00 0 5.00e+00 4.00e-02 2.30e+01 ... (remaining 13233 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 2509 0.064 - 0.128: 568 0.128 - 0.192: 92 0.192 - 0.256: 15 0.256 - 0.319: 16 Chirality restraints: 3200 Sorted by residual: chirality pdb=" CG LEU D 308 " pdb=" CB LEU D 308 " pdb=" CD1 LEU D 308 " pdb=" CD2 LEU D 308 " both_signs ideal model delta sigma weight residual False -2.59 -2.27 -0.32 2.00e-01 2.50e+01 2.55e+00 chirality pdb=" CG LEU C 308 " pdb=" CB LEU C 308 " pdb=" CD1 LEU C 308 " pdb=" CD2 LEU C 308 " both_signs ideal model delta sigma weight residual False -2.59 -2.27 -0.32 2.00e-01 2.50e+01 2.55e+00 chirality pdb=" CG LEU B 308 " pdb=" CB LEU B 308 " pdb=" CD1 LEU B 308 " pdb=" CD2 LEU B 308 " both_signs ideal model delta sigma weight residual False -2.59 -2.27 -0.32 2.00e-01 2.50e+01 2.52e+00 ... (remaining 3197 not shown) Planarity restraints: 3512 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C28 POV D 708 " 0.222 2.00e-02 2.50e+03 2.21e-01 4.88e+02 pdb=" C29 POV D 708 " -0.225 2.00e-02 2.50e+03 pdb="C210 POV D 708 " -0.217 2.00e-02 2.50e+03 pdb="C211 POV D 708 " 0.220 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV B 707 " -0.210 2.00e-02 2.50e+03 2.11e-01 4.45e+02 pdb=" C29 POV B 707 " 0.207 2.00e-02 2.50e+03 pdb="C210 POV B 707 " 0.214 2.00e-02 2.50e+03 pdb="C211 POV B 707 " -0.212 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV A 707 " -0.204 2.00e-02 2.50e+03 2.04e-01 4.18e+02 pdb=" C29 POV A 707 " 0.204 2.00e-02 2.50e+03 pdb="C210 POV A 707 " 0.204 2.00e-02 2.50e+03 pdb="C211 POV A 707 " -0.204 2.00e-02 2.50e+03 ... (remaining 3509 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 3754 2.76 - 3.29: 18688 3.29 - 3.83: 34462 3.83 - 4.36: 43855 4.36 - 4.90: 72202 Nonbonded interactions: 172961 Sorted by model distance: nonbonded pdb=" O MET B 577 " pdb=" OG1 THR B 581 " model vdw 2.221 2.440 nonbonded pdb=" O MET D 577 " pdb=" OG1 THR D 581 " model vdw 2.222 2.440 nonbonded pdb=" O MET C 577 " pdb=" OG1 THR C 581 " model vdw 2.222 2.440 nonbonded pdb=" O MET A 577 " pdb=" OG1 THR A 581 " model vdw 2.222 2.440 nonbonded pdb=" O11 POV A 706 " pdb=" O21 POV A 706 " model vdw 2.342 2.432 ... (remaining 172956 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 638 or resid 703 through 704 or (resid 706 and \ (name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C3 \ 7 or name C38 or name C39 or name C310 or name C311 or name C312 or name C313)) \ or resid 707)) selection = (chain 'B' and (resid 27 through 638 or resid 703 through 704 or (resid 706 and \ (name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C3 \ 7 or name C38 or name C39 or name C310 or name C311 or name C312 or name C313)) \ or resid 707)) selection = (chain 'C' and (resid 27 through 638 or resid 703 through 704 or (resid 706 and \ (name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C3 \ 7 or name C38 or name C39 or name C310 or name C311 or name C312 or name C313)) \ or resid 707)) selection = (chain 'D' and (resid 27 through 638 or resid 703 through 704 or resid 706 or (r \ esid 707 and (name C2 or name C21 or name C22 or name C23 or name C24 or name C2 \ 5 or name C26 or name C27 or name C28 or name C29 or name O21 or name O22 or nam \ e C210 or name C211 or name C212 or name C213 or name C214 or name C215 or name \ C216)))) } 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=0.45 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.800 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: 0.020 Extract box with map and model: 4.630 Check model and map are aligned: 0.310 Set scattering table: 0.190 Process input model: 53.610 Find NCS groups from input model: 1.560 Set up NCS constraints: 0.130 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:11.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 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 0.221 21040 Z= 0.666 Angle : 1.187 16.050 28504 Z= 0.606 Chirality : 0.059 0.319 3200 Planarity : 0.011 0.221 3512 Dihedral : 14.480 140.949 8612 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.75 % Allowed : 3.77 % Favored : 95.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.72 (0.12), residues: 2440 helix: -3.68 (0.08), residues: 1468 sheet: -1.73 (0.45), residues: 124 loop : -1.82 (0.19), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.004 TRP C 629 HIS 0.016 0.003 HIS D 426 PHE 0.027 0.004 PHE A 169 TYR 0.023 0.004 TYR C 216 ARG 0.014 0.002 ARG D 33 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 550 time to evaluate : 2.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7279 (tp40) cc_final: 0.6933 (tp-100) REVERT: A 41 GLN cc_start: 0.8288 (mm-40) cc_final: 0.7979 (mp-120) REVERT: A 99 MET cc_start: 0.6109 (mtm) cc_final: 0.5812 (mtm) REVERT: A 178 ILE cc_start: 0.8167 (mt) cc_final: 0.7905 (mt) REVERT: B 31 GLN cc_start: 0.7278 (tp40) cc_final: 0.7009 (tp-100) REVERT: B 41 GLN cc_start: 0.8306 (mm-40) cc_final: 0.7962 (mp-120) REVERT: B 99 MET cc_start: 0.6113 (mtm) cc_final: 0.5840 (mtm) REVERT: B 178 ILE cc_start: 0.8143 (mt) cc_final: 0.7854 (mt) REVERT: C 31 GLN cc_start: 0.7284 (tp40) cc_final: 0.6876 (tp-100) REVERT: C 41 GLN cc_start: 0.8292 (mm-40) cc_final: 0.7982 (mp-120) REVERT: C 99 MET cc_start: 0.6062 (mtm) cc_final: 0.5770 (mtm) REVERT: C 178 ILE cc_start: 0.8135 (mt) cc_final: 0.7874 (mt) REVERT: C 591 GLU cc_start: 0.6990 (tt0) cc_final: 0.6782 (tt0) REVERT: D 31 GLN cc_start: 0.7298 (tp40) cc_final: 0.6897 (tp-100) REVERT: D 41 GLN cc_start: 0.8293 (mm-40) cc_final: 0.7973 (mp-120) REVERT: D 99 MET cc_start: 0.6100 (mtm) cc_final: 0.5803 (mtm) REVERT: D 178 ILE cc_start: 0.8155 (mt) cc_final: 0.7888 (mt) REVERT: D 481 MET cc_start: 0.6427 (ttm) cc_final: 0.6136 (tpp) outliers start: 16 outliers final: 0 residues processed: 562 average time/residue: 1.3672 time to fit residues: 862.4454 Evaluate side-chains 399 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 399 time to evaluate : 2.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 206 optimal weight: 0.5980 chunk 184 optimal weight: 7.9990 chunk 102 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 191 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 116 optimal weight: 5.9990 chunk 142 optimal weight: 2.9990 chunk 221 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN A 122 HIS ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 265 HIS A 358 ASN A 369 GLN A 572 ASN ** A 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 GLN B 74 GLN B 91 ASN B 122 HIS ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 HIS B 358 ASN B 369 GLN ** B 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 ASN C 122 HIS ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 HIS C 358 ASN C 369 GLN D 91 ASN D 122 HIS ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 265 HIS D 358 ASN D 369 GLN ** D 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21040 Z= 0.208 Angle : 0.627 7.667 28504 Z= 0.317 Chirality : 0.040 0.200 3200 Planarity : 0.005 0.038 3512 Dihedral : 14.771 117.921 3888 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 4.66 % Allowed : 12.24 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.15), residues: 2440 helix: -1.05 (0.12), residues: 1464 sheet: -1.20 (0.46), residues: 124 loop : -1.08 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 593 HIS 0.008 0.002 HIS B 225 PHE 0.013 0.002 PHE B 531 TYR 0.010 0.002 TYR D 467 ARG 0.008 0.001 ARG D 492 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 390 time to evaluate : 2.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.6919 (tp40) cc_final: 0.6700 (tp-100) REVERT: A 41 GLN cc_start: 0.8176 (mm-40) cc_final: 0.7915 (mp-120) REVERT: A 78 MET cc_start: 0.7252 (OUTLIER) cc_final: 0.6533 (mtp) REVERT: A 90 ASP cc_start: 0.6929 (OUTLIER) cc_final: 0.6342 (t0) REVERT: A 96 MET cc_start: 0.7089 (mmt) cc_final: 0.6780 (mmm) REVERT: A 99 MET cc_start: 0.6453 (mtm) cc_final: 0.6209 (mtm) REVERT: A 133 VAL cc_start: 0.7646 (p) cc_final: 0.7253 (t) REVERT: A 225 HIS cc_start: 0.4208 (p90) cc_final: 0.3797 (p90) REVERT: A 260 MET cc_start: 0.7929 (tpt) cc_final: 0.7703 (tpt) REVERT: A 300 LYS cc_start: 0.7845 (mppt) cc_final: 0.7531 (mmmm) REVERT: A 403 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.6574 (mp0) REVERT: A 481 MET cc_start: 0.6140 (tpp) cc_final: 0.5935 (tpp) REVERT: A 590 ASP cc_start: 0.7104 (OUTLIER) cc_final: 0.6840 (m-30) REVERT: B 31 GLN cc_start: 0.6864 (tp40) cc_final: 0.6649 (tp-100) REVERT: B 41 GLN cc_start: 0.8158 (mm-40) cc_final: 0.7878 (mp-120) REVERT: B 90 ASP cc_start: 0.6923 (OUTLIER) cc_final: 0.6319 (t0) REVERT: B 99 MET cc_start: 0.6470 (mtm) cc_final: 0.6143 (mtm) REVERT: B 133 VAL cc_start: 0.7637 (p) cc_final: 0.7268 (t) REVERT: B 225 HIS cc_start: 0.4260 (OUTLIER) cc_final: 0.3806 (p90) REVERT: B 300 LYS cc_start: 0.7820 (mppt) cc_final: 0.7507 (mmmm) REVERT: B 403 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.6542 (mp0) REVERT: B 481 MET cc_start: 0.6170 (tpp) cc_final: 0.5967 (tpp) REVERT: B 484 LYS cc_start: 0.7405 (OUTLIER) cc_final: 0.6984 (ttmm) REVERT: B 590 ASP cc_start: 0.7066 (OUTLIER) cc_final: 0.6754 (m-30) REVERT: C 31 GLN cc_start: 0.6827 (tp40) cc_final: 0.6594 (tp-100) REVERT: C 78 MET cc_start: 0.7240 (OUTLIER) cc_final: 0.6521 (mtp) REVERT: C 90 ASP cc_start: 0.6947 (OUTLIER) cc_final: 0.6367 (t0) REVERT: C 96 MET cc_start: 0.7094 (mmt) cc_final: 0.6767 (mmm) REVERT: C 99 MET cc_start: 0.6417 (mtm) cc_final: 0.6163 (mtm) REVERT: C 133 VAL cc_start: 0.7629 (p) cc_final: 0.7239 (t) REVERT: C 225 HIS cc_start: 0.4240 (p90) cc_final: 0.3808 (p90) REVERT: C 260 MET cc_start: 0.7973 (tpt) cc_final: 0.7728 (tpt) REVERT: C 300 LYS cc_start: 0.7840 (mppt) cc_final: 0.7521 (mmmm) REVERT: C 403 GLU cc_start: 0.7482 (OUTLIER) cc_final: 0.6546 (mp0) REVERT: C 440 MET cc_start: 0.7355 (OUTLIER) cc_final: 0.6793 (tpp) REVERT: C 590 ASP cc_start: 0.7196 (OUTLIER) cc_final: 0.6921 (m-30) REVERT: D 31 GLN cc_start: 0.6826 (tp40) cc_final: 0.6587 (tp-100) REVERT: D 90 ASP cc_start: 0.6931 (OUTLIER) cc_final: 0.6361 (t0) REVERT: D 96 MET cc_start: 0.7094 (mmt) cc_final: 0.6779 (mmm) REVERT: D 99 MET cc_start: 0.6450 (mtm) cc_final: 0.6208 (mtm) REVERT: D 133 VAL cc_start: 0.7654 (p) cc_final: 0.7251 (t) REVERT: D 225 HIS cc_start: 0.4255 (p90) cc_final: 0.3838 (p90) REVERT: D 260 MET cc_start: 0.7998 (tpt) cc_final: 0.7757 (tpt) REVERT: D 300 LYS cc_start: 0.7839 (mppt) cc_final: 0.7528 (mmmm) REVERT: D 403 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.6560 (mp0) REVERT: D 484 LYS cc_start: 0.7446 (OUTLIER) cc_final: 0.6948 (ttmm) REVERT: D 577 MET cc_start: 0.5454 (mtp) cc_final: 0.5241 (mtp) outliers start: 99 outliers final: 34 residues processed: 444 average time/residue: 1.3199 time to fit residues: 661.7621 Evaluate side-chains 386 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 335 time to evaluate : 2.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 484 LYS Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain B residue 484 LYS Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain B residue 588 GLU Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain C residue 78 MET Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 255 MET Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 403 GLU Chi-restraints excluded: chain C residue 440 MET Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 403 GLU Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 484 LYS Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 588 GLU Chi-restraints excluded: chain D residue 590 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 123 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 184 optimal weight: 5.9990 chunk 150 optimal weight: 0.9980 chunk 61 optimal weight: 5.9990 chunk 221 optimal weight: 20.0000 chunk 239 optimal weight: 2.9990 chunk 197 optimal weight: 0.9990 chunk 220 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 178 optimal weight: 3.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 HIS ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 265 HIS ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 426 HIS ** A 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 HIS ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 HIS ** B 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 HIS C 40 GLN C 165 HIS ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 HIS ** C 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 426 HIS ** C 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 GLN D 165 HIS ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 265 HIS ** D 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 426 HIS ** D 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 21040 Z= 0.200 Angle : 0.604 9.307 28504 Z= 0.300 Chirality : 0.040 0.193 3200 Planarity : 0.004 0.032 3512 Dihedral : 13.990 115.478 3888 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 4.33 % Allowed : 15.49 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.16), residues: 2440 helix: 0.18 (0.13), residues: 1476 sheet: -0.90 (0.49), residues: 124 loop : -0.81 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 593 HIS 0.008 0.001 HIS A 265 PHE 0.014 0.002 PHE D 478 TYR 0.010 0.002 TYR B 89 ARG 0.006 0.001 ARG C 134 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 344 time to evaluate : 2.445 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 GLN cc_start: 0.8167 (mm-40) cc_final: 0.7866 (mp-120) REVERT: A 78 MET cc_start: 0.7258 (OUTLIER) cc_final: 0.6760 (mtp) REVERT: A 90 ASP cc_start: 0.6847 (OUTLIER) cc_final: 0.6488 (t0) REVERT: A 99 MET cc_start: 0.6452 (mtm) cc_final: 0.6181 (mtm) REVERT: A 133 VAL cc_start: 0.7683 (p) cc_final: 0.7296 (t) REVERT: A 137 LEU cc_start: 0.7677 (OUTLIER) cc_final: 0.7441 (mm) REVERT: A 300 LYS cc_start: 0.7843 (mppt) cc_final: 0.7559 (mmmm) REVERT: A 403 GLU cc_start: 0.7413 (OUTLIER) cc_final: 0.6639 (mp0) REVERT: A 410 MET cc_start: 0.3707 (tmm) cc_final: 0.3106 (mmm) REVERT: A 484 LYS cc_start: 0.7354 (OUTLIER) cc_final: 0.6949 (ttmm) REVERT: A 590 ASP cc_start: 0.7092 (OUTLIER) cc_final: 0.6855 (m-30) REVERT: B 80 GLU cc_start: 0.6428 (mp0) cc_final: 0.6106 (mp0) REVERT: B 90 ASP cc_start: 0.6817 (OUTLIER) cc_final: 0.6460 (t0) REVERT: B 96 MET cc_start: 0.6861 (mmm) cc_final: 0.6490 (mmm) REVERT: B 99 MET cc_start: 0.6466 (mtm) cc_final: 0.6209 (mtm) REVERT: B 130 MET cc_start: 0.6642 (mmm) cc_final: 0.6334 (mmm) REVERT: B 133 VAL cc_start: 0.7669 (p) cc_final: 0.7304 (t) REVERT: B 300 LYS cc_start: 0.7849 (mppt) cc_final: 0.7579 (mmmm) REVERT: B 403 GLU cc_start: 0.7419 (OUTLIER) cc_final: 0.6635 (mp0) REVERT: B 410 MET cc_start: 0.3736 (tmm) cc_final: 0.3154 (mmm) REVERT: B 484 LYS cc_start: 0.7346 (OUTLIER) cc_final: 0.6945 (ttmm) REVERT: B 578 MET cc_start: 0.6620 (ttm) cc_final: 0.6336 (ttm) REVERT: B 590 ASP cc_start: 0.7105 (OUTLIER) cc_final: 0.6799 (m-30) REVERT: B 592 LEU cc_start: 0.7780 (mt) cc_final: 0.7570 (mp) REVERT: C 80 GLU cc_start: 0.6399 (mp0) cc_final: 0.6072 (mp0) REVERT: C 90 ASP cc_start: 0.6863 (OUTLIER) cc_final: 0.6506 (t0) REVERT: C 96 MET cc_start: 0.7084 (mmt) cc_final: 0.6673 (mmm) REVERT: C 99 MET cc_start: 0.6444 (mtm) cc_final: 0.6201 (mtm) REVERT: C 133 VAL cc_start: 0.7609 (p) cc_final: 0.7261 (t) REVERT: C 137 LEU cc_start: 0.7657 (OUTLIER) cc_final: 0.7423 (mm) REVERT: C 300 LYS cc_start: 0.7850 (mppt) cc_final: 0.7554 (mmmm) REVERT: C 403 GLU cc_start: 0.7441 (OUTLIER) cc_final: 0.6669 (mp0) REVERT: C 484 LYS cc_start: 0.7298 (OUTLIER) cc_final: 0.6968 (ttmm) REVERT: C 590 ASP cc_start: 0.7071 (OUTLIER) cc_final: 0.6814 (m-30) REVERT: D 80 GLU cc_start: 0.6397 (mp0) cc_final: 0.6072 (mp0) REVERT: D 90 ASP cc_start: 0.6864 (OUTLIER) cc_final: 0.6512 (t0) REVERT: D 96 MET cc_start: 0.7063 (mmt) cc_final: 0.6664 (mmm) REVERT: D 99 MET cc_start: 0.6442 (mtm) cc_final: 0.6205 (mtm) REVERT: D 133 VAL cc_start: 0.7682 (p) cc_final: 0.7293 (t) REVERT: D 137 LEU cc_start: 0.7669 (OUTLIER) cc_final: 0.7442 (mm) REVERT: D 300 LYS cc_start: 0.7846 (mppt) cc_final: 0.7559 (mmmm) REVERT: D 403 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.6629 (mp0) REVERT: D 410 MET cc_start: 0.3865 (tmm) cc_final: 0.3160 (mmm) REVERT: D 484 LYS cc_start: 0.7264 (OUTLIER) cc_final: 0.6802 (ttmm) REVERT: D 578 MET cc_start: 0.6524 (ttm) cc_final: 0.6192 (ttm) REVERT: D 590 ASP cc_start: 0.7109 (OUTLIER) cc_final: 0.6856 (m-30) outliers start: 92 outliers final: 29 residues processed: 395 average time/residue: 1.3338 time to fit residues: 593.2538 Evaluate side-chains 371 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 322 time to evaluate : 2.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 484 LYS Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 588 GLU Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 484 LYS Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 255 MET Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 403 GLU Chi-restraints excluded: chain C residue 484 LYS Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 574 LEU Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 403 GLU Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 484 LYS Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 574 LEU Chi-restraints excluded: chain D residue 588 GLU Chi-restraints excluded: chain D residue 590 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 219 optimal weight: 1.9990 chunk 166 optimal weight: 2.9990 chunk 115 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 chunk 105 optimal weight: 5.9990 chunk 149 optimal weight: 0.9990 chunk 222 optimal weight: 3.9990 chunk 235 optimal weight: 4.9990 chunk 116 optimal weight: 2.9990 chunk 211 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 HIS A 265 HIS ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 369 GLN A 426 HIS B 41 GLN B 201 HIS B 265 HIS ** B 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 369 GLN B 426 HIS C 201 HIS C 265 HIS ** C 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 426 HIS ** C 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 201 HIS D 265 HIS ** D 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 369 GLN D 426 HIS ** D 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 21040 Z= 0.273 Angle : 0.647 9.634 28504 Z= 0.320 Chirality : 0.042 0.194 3200 Planarity : 0.004 0.032 3512 Dihedral : 13.821 114.338 3888 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 4.57 % Allowed : 17.09 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.17), residues: 2440 helix: 0.55 (0.13), residues: 1468 sheet: -1.05 (0.47), residues: 124 loop : -0.65 (0.22), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 593 HIS 0.008 0.002 HIS A 265 PHE 0.014 0.002 PHE C 478 TYR 0.012 0.002 TYR D 89 ARG 0.005 0.001 ARG B 33 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 329 time to evaluate : 2.450 Fit side-chains revert: symmetry clash REVERT: A 41 GLN cc_start: 0.8246 (mm-40) cc_final: 0.8005 (mm110) REVERT: A 80 GLU cc_start: 0.6396 (mp0) cc_final: 0.6087 (mp0) REVERT: A 90 ASP cc_start: 0.6811 (OUTLIER) cc_final: 0.6326 (t0) REVERT: A 96 MET cc_start: 0.6825 (mmm) cc_final: 0.6537 (mmm) REVERT: A 99 MET cc_start: 0.6427 (mtm) cc_final: 0.6165 (mtm) REVERT: A 137 LEU cc_start: 0.7685 (OUTLIER) cc_final: 0.7437 (mm) REVERT: A 294 GLU cc_start: 0.6993 (mp0) cc_final: 0.6720 (mp0) REVERT: A 386 LEU cc_start: 0.8078 (tp) cc_final: 0.7861 (tp) REVERT: A 403 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.6603 (mp0) REVERT: A 410 MET cc_start: 0.3997 (tmm) cc_final: 0.3271 (mmm) REVERT: A 590 ASP cc_start: 0.7155 (OUTLIER) cc_final: 0.6950 (m-30) REVERT: B 80 GLU cc_start: 0.6474 (mp0) cc_final: 0.6118 (mp0) REVERT: B 90 ASP cc_start: 0.6812 (OUTLIER) cc_final: 0.6322 (t0) REVERT: B 96 MET cc_start: 0.6969 (mmm) cc_final: 0.6645 (mmm) REVERT: B 99 MET cc_start: 0.6384 (mtm) cc_final: 0.6087 (mtm) REVERT: B 386 LEU cc_start: 0.8108 (tp) cc_final: 0.7878 (tp) REVERT: B 403 GLU cc_start: 0.7453 (OUTLIER) cc_final: 0.6679 (mp0) REVERT: B 410 MET cc_start: 0.3982 (tmm) cc_final: 0.3320 (mmm) REVERT: B 578 MET cc_start: 0.6661 (ttm) cc_final: 0.6237 (ttm) REVERT: B 590 ASP cc_start: 0.7145 (OUTLIER) cc_final: 0.6829 (m-30) REVERT: B 592 LEU cc_start: 0.7991 (mt) cc_final: 0.7750 (mp) REVERT: C 80 GLU cc_start: 0.6507 (mp0) cc_final: 0.6174 (mp0) REVERT: C 90 ASP cc_start: 0.6888 (OUTLIER) cc_final: 0.6386 (t0) REVERT: C 99 MET cc_start: 0.6366 (mtm) cc_final: 0.6117 (mtm) REVERT: C 137 LEU cc_start: 0.7665 (OUTLIER) cc_final: 0.7415 (mm) REVERT: C 386 LEU cc_start: 0.8093 (tp) cc_final: 0.7859 (tp) REVERT: C 403 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.6751 (mp0) REVERT: C 410 MET cc_start: 0.3370 (ttp) cc_final: 0.3130 (mmt) REVERT: C 590 ASP cc_start: 0.7144 (OUTLIER) cc_final: 0.6863 (m-30) REVERT: D 80 GLU cc_start: 0.6517 (mp0) cc_final: 0.6189 (mp0) REVERT: D 90 ASP cc_start: 0.6873 (OUTLIER) cc_final: 0.6377 (t0) REVERT: D 99 MET cc_start: 0.6374 (mtm) cc_final: 0.6129 (mtm) REVERT: D 137 LEU cc_start: 0.7683 (OUTLIER) cc_final: 0.7433 (mm) REVERT: D 294 GLU cc_start: 0.7010 (mp0) cc_final: 0.6731 (mp0) REVERT: D 345 MET cc_start: 0.7600 (OUTLIER) cc_final: 0.7238 (mtt) REVERT: D 386 LEU cc_start: 0.8066 (tp) cc_final: 0.7844 (tp) REVERT: D 403 GLU cc_start: 0.7436 (OUTLIER) cc_final: 0.6624 (mp0) REVERT: D 410 MET cc_start: 0.4000 (tmm) cc_final: 0.3346 (mmm) REVERT: D 590 ASP cc_start: 0.7162 (OUTLIER) cc_final: 0.6923 (m-30) outliers start: 97 outliers final: 30 residues processed: 383 average time/residue: 1.2720 time to fit residues: 552.1953 Evaluate side-chains 358 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 312 time to evaluate : 2.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain B residue 484 LYS Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 255 MET Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 403 GLU Chi-restraints excluded: chain C residue 484 LYS Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 588 GLU Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 340 ILE Chi-restraints excluded: chain D residue 345 MET Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 403 GLU Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain D residue 592 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 196 optimal weight: 0.0770 chunk 133 optimal weight: 4.9990 chunk 3 optimal weight: 7.9990 chunk 175 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 201 optimal weight: 1.9990 chunk 163 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 120 optimal weight: 6.9990 chunk 211 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 overall best weight: 1.3744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 HIS ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 426 HIS B 41 GLN B 265 HIS ** B 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 HIS C 265 HIS ** C 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 426 HIS D 265 HIS ** D 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 426 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 21040 Z= 0.218 Angle : 0.608 8.932 28504 Z= 0.299 Chirality : 0.040 0.190 3200 Planarity : 0.004 0.033 3512 Dihedral : 13.112 109.333 3888 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 4.80 % Allowed : 17.98 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.17), residues: 2440 helix: 0.87 (0.13), residues: 1468 sheet: -1.04 (0.47), residues: 124 loop : -0.63 (0.22), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 593 HIS 0.008 0.001 HIS B 265 PHE 0.014 0.002 PHE B 478 TYR 0.010 0.002 TYR B 524 ARG 0.006 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 323 time to evaluate : 2.304 Fit side-chains REVERT: A 41 GLN cc_start: 0.8191 (mm-40) cc_final: 0.7971 (mm110) REVERT: A 80 GLU cc_start: 0.6482 (mp0) cc_final: 0.6186 (mp0) REVERT: A 90 ASP cc_start: 0.6824 (OUTLIER) cc_final: 0.6347 (t0) REVERT: A 96 MET cc_start: 0.6804 (mmm) cc_final: 0.6568 (mmm) REVERT: A 99 MET cc_start: 0.6428 (mtm) cc_final: 0.6202 (mtm) REVERT: A 137 LEU cc_start: 0.7680 (OUTLIER) cc_final: 0.7434 (mm) REVERT: A 294 GLU cc_start: 0.6999 (mp0) cc_final: 0.6736 (mp0) REVERT: A 300 LYS cc_start: 0.7908 (mppt) cc_final: 0.7619 (mmmm) REVERT: A 345 MET cc_start: 0.7558 (OUTLIER) cc_final: 0.7176 (mtt) REVERT: A 403 GLU cc_start: 0.7451 (OUTLIER) cc_final: 0.6710 (mp0) REVERT: A 410 MET cc_start: 0.4047 (tmm) cc_final: 0.3422 (mmt) REVERT: A 484 LYS cc_start: 0.7223 (OUTLIER) cc_final: 0.6777 (ttmm) REVERT: A 590 ASP cc_start: 0.7073 (OUTLIER) cc_final: 0.6771 (m-30) REVERT: A 594 ARG cc_start: 0.7760 (mtm-85) cc_final: 0.7552 (mtm-85) REVERT: B 80 GLU cc_start: 0.6544 (OUTLIER) cc_final: 0.6218 (mp0) REVERT: B 90 ASP cc_start: 0.6832 (OUTLIER) cc_final: 0.6324 (t0) REVERT: B 96 MET cc_start: 0.6797 (mmm) cc_final: 0.6542 (mmm) REVERT: B 99 MET cc_start: 0.6591 (mtm) cc_final: 0.6275 (mtm) REVERT: B 300 LYS cc_start: 0.7900 (mppt) cc_final: 0.7606 (mmmm) REVERT: B 345 MET cc_start: 0.7595 (OUTLIER) cc_final: 0.7304 (mtt) REVERT: B 386 LEU cc_start: 0.8065 (tp) cc_final: 0.7858 (tp) REVERT: B 403 GLU cc_start: 0.7460 (OUTLIER) cc_final: 0.6711 (mp0) REVERT: B 410 MET cc_start: 0.4063 (tmm) cc_final: 0.3360 (mmm) REVERT: B 578 MET cc_start: 0.6620 (ttm) cc_final: 0.6154 (ttm) REVERT: B 590 ASP cc_start: 0.7129 (OUTLIER) cc_final: 0.6762 (m-30) REVERT: B 592 LEU cc_start: 0.7931 (mt) cc_final: 0.7663 (mp) REVERT: C 80 GLU cc_start: 0.6614 (OUTLIER) cc_final: 0.6293 (mp0) REVERT: C 90 ASP cc_start: 0.6821 (OUTLIER) cc_final: 0.6353 (t0) REVERT: C 96 MET cc_start: 0.6695 (mmm) cc_final: 0.6390 (mmm) REVERT: C 99 MET cc_start: 0.6396 (mtm) cc_final: 0.6174 (mtm) REVERT: C 137 LEU cc_start: 0.7664 (OUTLIER) cc_final: 0.7414 (mm) REVERT: C 300 LYS cc_start: 0.7927 (mppt) cc_final: 0.7626 (mmmm) REVERT: C 345 MET cc_start: 0.7552 (OUTLIER) cc_final: 0.7171 (mtt) REVERT: C 386 LEU cc_start: 0.8048 (tp) cc_final: 0.7840 (tp) REVERT: C 403 GLU cc_start: 0.7444 (OUTLIER) cc_final: 0.6697 (mp0) REVERT: C 590 ASP cc_start: 0.7136 (OUTLIER) cc_final: 0.6813 (m-30) REVERT: C 594 ARG cc_start: 0.7787 (mtm-85) cc_final: 0.7585 (mtm-85) REVERT: D 80 GLU cc_start: 0.6650 (OUTLIER) cc_final: 0.6338 (mp0) REVERT: D 90 ASP cc_start: 0.6817 (OUTLIER) cc_final: 0.6350 (t0) REVERT: D 96 MET cc_start: 0.6694 (mmm) cc_final: 0.6395 (mmm) REVERT: D 99 MET cc_start: 0.6406 (mtm) cc_final: 0.6183 (mtm) REVERT: D 137 LEU cc_start: 0.7678 (OUTLIER) cc_final: 0.7432 (mm) REVERT: D 294 GLU cc_start: 0.7003 (mp0) cc_final: 0.6741 (mp0) REVERT: D 300 LYS cc_start: 0.7908 (mppt) cc_final: 0.7621 (mmmm) REVERT: D 345 MET cc_start: 0.7582 (OUTLIER) cc_final: 0.7201 (mtt) REVERT: D 403 GLU cc_start: 0.7444 (OUTLIER) cc_final: 0.6709 (mp0) REVERT: D 410 MET cc_start: 0.4044 (tmm) cc_final: 0.3412 (mmt) REVERT: D 590 ASP cc_start: 0.7108 (OUTLIER) cc_final: 0.6758 (m-30) outliers start: 102 outliers final: 33 residues processed: 384 average time/residue: 1.3378 time to fit residues: 578.2222 Evaluate side-chains 361 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 305 time to evaluate : 2.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ASP Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 484 LYS Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 588 GLU Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain B residue 484 LYS Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain C residue 69 ASP Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 255 MET Chi-restraints excluded: chain C residue 305 ARG Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 403 GLU Chi-restraints excluded: chain C residue 484 LYS Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain D residue 69 ASP Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 345 MET Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 403 GLU Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 590 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 79 optimal weight: 2.9990 chunk 212 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 chunk 138 optimal weight: 10.0000 chunk 58 optimal weight: 0.7980 chunk 236 optimal weight: 2.9990 chunk 195 optimal weight: 7.9990 chunk 109 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 78 optimal weight: 1.9990 chunk 123 optimal weight: 8.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 HIS ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 426 HIS B 265 HIS ** B 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 HIS C 265 HIS ** C 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 426 HIS ** C 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 265 HIS ** D 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 426 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 21040 Z= 0.189 Angle : 0.584 14.467 28504 Z= 0.286 Chirality : 0.040 0.191 3200 Planarity : 0.003 0.032 3512 Dihedral : 12.597 105.197 3888 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 4.90 % Allowed : 18.36 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.17), residues: 2440 helix: 1.11 (0.14), residues: 1460 sheet: -1.00 (0.47), residues: 124 loop : -0.41 (0.22), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 593 HIS 0.009 0.001 HIS B 265 PHE 0.013 0.001 PHE D 478 TYR 0.010 0.001 TYR A 524 ARG 0.004 0.000 ARG B 594 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 314 time to evaluate : 2.443 Fit side-chains REVERT: A 35 GLU cc_start: 0.7099 (mt-10) cc_final: 0.6686 (mp0) REVERT: A 41 GLN cc_start: 0.8174 (mm-40) cc_final: 0.7968 (mm110) REVERT: A 80 GLU cc_start: 0.6517 (mp0) cc_final: 0.6261 (mp0) REVERT: A 90 ASP cc_start: 0.6819 (OUTLIER) cc_final: 0.6313 (t0) REVERT: A 99 MET cc_start: 0.6633 (mtm) cc_final: 0.6384 (mtm) REVERT: A 137 LEU cc_start: 0.7698 (OUTLIER) cc_final: 0.7443 (mm) REVERT: A 210 THR cc_start: 0.7763 (m) cc_final: 0.7509 (t) REVERT: A 294 GLU cc_start: 0.7019 (mp0) cc_final: 0.6729 (mp0) REVERT: A 300 LYS cc_start: 0.7877 (mppt) cc_final: 0.7595 (mmmm) REVERT: A 345 MET cc_start: 0.7568 (OUTLIER) cc_final: 0.7194 (mtt) REVERT: A 381 LYS cc_start: 0.6813 (ttmt) cc_final: 0.6259 (mmpt) REVERT: A 410 MET cc_start: 0.4133 (tmm) cc_final: 0.3523 (mmt) REVERT: A 590 ASP cc_start: 0.7023 (OUTLIER) cc_final: 0.6793 (m-30) REVERT: A 594 ARG cc_start: 0.7784 (mtm-85) cc_final: 0.7561 (mtm-85) REVERT: B 35 GLU cc_start: 0.7095 (mt-10) cc_final: 0.6680 (mp0) REVERT: B 80 GLU cc_start: 0.6495 (OUTLIER) cc_final: 0.6155 (mp0) REVERT: B 90 ASP cc_start: 0.6818 (OUTLIER) cc_final: 0.6311 (t0) REVERT: B 99 MET cc_start: 0.6522 (mtm) cc_final: 0.6203 (mtm) REVERT: B 294 GLU cc_start: 0.6995 (mp0) cc_final: 0.6602 (mp0) REVERT: B 345 MET cc_start: 0.7571 (OUTLIER) cc_final: 0.7276 (mtt) REVERT: B 381 LYS cc_start: 0.6982 (ttmt) cc_final: 0.6309 (mmpt) REVERT: B 403 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.6754 (mp0) REVERT: B 410 MET cc_start: 0.4113 (tmm) cc_final: 0.3467 (mmt) REVERT: B 481 MET cc_start: 0.5841 (mmt) cc_final: 0.5619 (mmp) REVERT: B 590 ASP cc_start: 0.6988 (OUTLIER) cc_final: 0.6757 (m-30) REVERT: C 35 GLU cc_start: 0.7071 (mt-10) cc_final: 0.6683 (mp0) REVERT: C 80 GLU cc_start: 0.6598 (OUTLIER) cc_final: 0.6272 (mp0) REVERT: C 90 ASP cc_start: 0.6801 (OUTLIER) cc_final: 0.6330 (t0) REVERT: C 96 MET cc_start: 0.6739 (mmm) cc_final: 0.6502 (mmm) REVERT: C 99 MET cc_start: 0.6390 (mtm) cc_final: 0.6112 (mtm) REVERT: C 137 LEU cc_start: 0.7682 (OUTLIER) cc_final: 0.7425 (mm) REVERT: C 300 LYS cc_start: 0.7939 (mppt) cc_final: 0.7615 (mmmm) REVERT: C 305 ARG cc_start: 0.7212 (OUTLIER) cc_final: 0.6971 (ttm170) REVERT: C 345 MET cc_start: 0.7538 (OUTLIER) cc_final: 0.7164 (mtt) REVERT: C 381 LYS cc_start: 0.7006 (ttmt) cc_final: 0.6309 (mmpt) REVERT: C 403 GLU cc_start: 0.7440 (OUTLIER) cc_final: 0.6799 (mp0) REVERT: C 410 MET cc_start: 0.4083 (tmm) cc_final: 0.3430 (mmt) REVERT: C 519 GLU cc_start: 0.6981 (OUTLIER) cc_final: 0.6657 (mt-10) REVERT: C 590 ASP cc_start: 0.7062 (OUTLIER) cc_final: 0.6852 (m-30) REVERT: C 594 ARG cc_start: 0.7820 (mtm-85) cc_final: 0.7585 (mtm-85) REVERT: D 35 GLU cc_start: 0.7081 (mt-10) cc_final: 0.6703 (mp0) REVERT: D 80 GLU cc_start: 0.6562 (OUTLIER) cc_final: 0.6242 (mp0) REVERT: D 90 ASP cc_start: 0.6794 (OUTLIER) cc_final: 0.6326 (t0) REVERT: D 96 MET cc_start: 0.6733 (mmm) cc_final: 0.6506 (mmm) REVERT: D 99 MET cc_start: 0.6404 (mtm) cc_final: 0.6125 (mtm) REVERT: D 137 LEU cc_start: 0.7697 (OUTLIER) cc_final: 0.7441 (mm) REVERT: D 210 THR cc_start: 0.7755 (m) cc_final: 0.7507 (t) REVERT: D 294 GLU cc_start: 0.7023 (mp0) cc_final: 0.6732 (mp0) REVERT: D 300 LYS cc_start: 0.7887 (mppt) cc_final: 0.7595 (mmmm) REVERT: D 345 MET cc_start: 0.7565 (OUTLIER) cc_final: 0.7183 (mtt) REVERT: D 410 MET cc_start: 0.4124 (tmm) cc_final: 0.3509 (mmt) REVERT: D 590 ASP cc_start: 0.7033 (OUTLIER) cc_final: 0.6810 (m-30) outliers start: 104 outliers final: 40 residues processed: 384 average time/residue: 1.3382 time to fit residues: 581.2201 Evaluate side-chains 360 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 298 time to evaluate : 2.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ASP Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain B residue 484 LYS Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain C residue 69 ASP Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 255 MET Chi-restraints excluded: chain C residue 305 ARG Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 403 GLU Chi-restraints excluded: chain C residue 484 LYS Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 519 GLU Chi-restraints excluded: chain C residue 588 GLU Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain D residue 69 ASP Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 340 ILE Chi-restraints excluded: chain D residue 345 MET Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 588 GLU Chi-restraints excluded: chain D residue 590 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 227 optimal weight: 0.8980 chunk 26 optimal weight: 9.9990 chunk 134 optimal weight: 3.9990 chunk 172 optimal weight: 1.9990 chunk 133 optimal weight: 0.3980 chunk 198 optimal weight: 0.3980 chunk 131 optimal weight: 5.9990 chunk 235 optimal weight: 4.9990 chunk 147 optimal weight: 4.9990 chunk 143 optimal weight: 0.7980 chunk 108 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 HIS ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 426 HIS B 265 HIS ** B 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 HIS C 265 HIS ** C 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 426 HIS D 265 HIS ** D 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 426 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.3412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 21040 Z= 0.173 Angle : 0.571 11.056 28504 Z= 0.280 Chirality : 0.039 0.188 3200 Planarity : 0.003 0.032 3512 Dihedral : 12.158 101.743 3888 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 4.33 % Allowed : 18.97 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.17), residues: 2440 helix: 1.27 (0.14), residues: 1460 sheet: -0.97 (0.47), residues: 124 loop : -0.35 (0.22), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 593 HIS 0.009 0.001 HIS A 265 PHE 0.013 0.001 PHE B 478 TYR 0.010 0.001 TYR A 524 ARG 0.007 0.000 ARG D 589 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 312 time to evaluate : 2.125 Fit side-chains REVERT: A 35 GLU cc_start: 0.7072 (mt-10) cc_final: 0.6682 (mp0) REVERT: A 41 GLN cc_start: 0.8163 (mm-40) cc_final: 0.7951 (mm110) REVERT: A 90 ASP cc_start: 0.6785 (OUTLIER) cc_final: 0.6304 (t0) REVERT: A 137 LEU cc_start: 0.7698 (OUTLIER) cc_final: 0.7434 (mm) REVERT: A 139 ARG cc_start: 0.6707 (mmt90) cc_final: 0.6500 (mmt90) REVERT: A 210 THR cc_start: 0.7726 (m) cc_final: 0.7430 (t) REVERT: A 294 GLU cc_start: 0.7028 (mp0) cc_final: 0.6738 (mp0) REVERT: A 345 MET cc_start: 0.7569 (OUTLIER) cc_final: 0.7197 (mtt) REVERT: A 381 LYS cc_start: 0.6928 (ttmt) cc_final: 0.6348 (mmpt) REVERT: A 403 GLU cc_start: 0.7427 (OUTLIER) cc_final: 0.6766 (mp0) REVERT: A 410 MET cc_start: 0.4078 (tmm) cc_final: 0.3480 (mmt) REVERT: A 594 ARG cc_start: 0.7819 (mtm-85) cc_final: 0.7593 (mtm-85) REVERT: B 35 GLU cc_start: 0.7074 (mt-10) cc_final: 0.6679 (mp0) REVERT: B 80 GLU cc_start: 0.6545 (OUTLIER) cc_final: 0.6218 (mp0) REVERT: B 90 ASP cc_start: 0.6724 (OUTLIER) cc_final: 0.6212 (t0) REVERT: B 99 MET cc_start: 0.6503 (mtm) cc_final: 0.6239 (mtm) REVERT: B 210 THR cc_start: 0.7723 (m) cc_final: 0.7423 (t) REVERT: B 294 GLU cc_start: 0.7038 (mp0) cc_final: 0.6660 (mp0) REVERT: B 300 LYS cc_start: 0.7959 (mppt) cc_final: 0.7613 (mmmm) REVERT: B 345 MET cc_start: 0.7560 (OUTLIER) cc_final: 0.7249 (mtt) REVERT: B 381 LYS cc_start: 0.7062 (ttmt) cc_final: 0.6373 (mmpt) REVERT: B 410 MET cc_start: 0.4095 (tmm) cc_final: 0.3488 (mmt) REVERT: B 590 ASP cc_start: 0.6962 (OUTLIER) cc_final: 0.6756 (m-30) REVERT: C 35 GLU cc_start: 0.7028 (mt-10) cc_final: 0.6659 (mp0) REVERT: C 80 GLU cc_start: 0.6564 (OUTLIER) cc_final: 0.6220 (mp0) REVERT: C 90 ASP cc_start: 0.6805 (OUTLIER) cc_final: 0.6317 (t0) REVERT: C 99 MET cc_start: 0.6541 (mtm) cc_final: 0.6328 (mtm) REVERT: C 137 LEU cc_start: 0.7682 (OUTLIER) cc_final: 0.7429 (mm) REVERT: C 210 THR cc_start: 0.7725 (m) cc_final: 0.7435 (t) REVERT: C 300 LYS cc_start: 0.7939 (mppt) cc_final: 0.7579 (mmmm) REVERT: C 345 MET cc_start: 0.7572 (OUTLIER) cc_final: 0.7197 (mtt) REVERT: C 381 LYS cc_start: 0.7081 (ttmt) cc_final: 0.6364 (mmpt) REVERT: C 410 MET cc_start: 0.4025 (tmm) cc_final: 0.3412 (mmt) REVERT: C 594 ARG cc_start: 0.7836 (mtm-85) cc_final: 0.7606 (mtm-85) REVERT: D 35 GLU cc_start: 0.7046 (mt-10) cc_final: 0.6682 (mp0) REVERT: D 80 GLU cc_start: 0.6569 (OUTLIER) cc_final: 0.6224 (mp0) REVERT: D 90 ASP cc_start: 0.6801 (OUTLIER) cc_final: 0.6315 (t0) REVERT: D 99 MET cc_start: 0.6567 (mtm) cc_final: 0.6352 (mtm) REVERT: D 137 LEU cc_start: 0.7698 (OUTLIER) cc_final: 0.7449 (mm) REVERT: D 210 THR cc_start: 0.7719 (m) cc_final: 0.7427 (t) REVERT: D 294 GLU cc_start: 0.7031 (mp0) cc_final: 0.6740 (mp0) REVERT: D 345 MET cc_start: 0.7559 (OUTLIER) cc_final: 0.7175 (mtt) REVERT: D 403 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.6763 (mp0) REVERT: D 410 MET cc_start: 0.4078 (tmm) cc_final: 0.3470 (mmt) outliers start: 92 outliers final: 33 residues processed: 374 average time/residue: 1.3396 time to fit residues: 564.6135 Evaluate side-chains 343 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 293 time to evaluate : 2.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ASP Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 305 ARG Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 484 LYS Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain C residue 69 ASP Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 255 MET Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 484 LYS Chi-restraints excluded: chain D residue 69 ASP Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 340 ILE Chi-restraints excluded: chain D residue 345 MET Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 403 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 145 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 chunk 140 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 chunk 160 optimal weight: 3.9990 chunk 116 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 184 optimal weight: 7.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 HIS ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 426 HIS ** A 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 HIS ** B 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 HIS B 582 HIS C 265 HIS ** C 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 426 HIS ** C 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 265 HIS ** D 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 426 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 21040 Z= 0.227 Angle : 0.628 12.917 28504 Z= 0.306 Chirality : 0.041 0.210 3200 Planarity : 0.004 0.033 3512 Dihedral : 12.245 102.512 3888 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 4.05 % Allowed : 19.54 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.17), residues: 2440 helix: 1.19 (0.14), residues: 1464 sheet: -1.03 (0.47), residues: 124 loop : -0.33 (0.23), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 593 HIS 0.016 0.002 HIS B 582 PHE 0.014 0.002 PHE A 478 TYR 0.011 0.002 TYR B 89 ARG 0.003 0.001 ARG D 594 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 298 time to evaluate : 2.330 Fit side-chains revert: symmetry clash REVERT: A 41 GLN cc_start: 0.8188 (mm-40) cc_final: 0.7964 (mm110) REVERT: A 80 GLU cc_start: 0.6473 (mp0) cc_final: 0.5844 (pm20) REVERT: A 90 ASP cc_start: 0.6785 (OUTLIER) cc_final: 0.6313 (t0) REVERT: A 96 MET cc_start: 0.6608 (mmm) cc_final: 0.6281 (mmm) REVERT: A 137 LEU cc_start: 0.7712 (OUTLIER) cc_final: 0.7428 (mm) REVERT: A 210 THR cc_start: 0.7760 (m) cc_final: 0.7467 (t) REVERT: A 294 GLU cc_start: 0.7023 (mp0) cc_final: 0.6717 (mp0) REVERT: A 300 LYS cc_start: 0.8005 (mppt) cc_final: 0.7591 (mmmm) REVERT: A 345 MET cc_start: 0.7599 (OUTLIER) cc_final: 0.7242 (mtt) REVERT: A 381 LYS cc_start: 0.6818 (ttmt) cc_final: 0.6270 (mmpt) REVERT: A 403 GLU cc_start: 0.7432 (OUTLIER) cc_final: 0.6775 (mp0) REVERT: A 410 MET cc_start: 0.4108 (tmm) cc_final: 0.3374 (mmm) REVERT: B 35 GLU cc_start: 0.7076 (mt-10) cc_final: 0.6661 (mp0) REVERT: B 80 GLU cc_start: 0.6513 (OUTLIER) cc_final: 0.6200 (mp0) REVERT: B 90 ASP cc_start: 0.6699 (OUTLIER) cc_final: 0.6224 (t0) REVERT: B 96 MET cc_start: 0.7090 (mmt) cc_final: 0.6707 (mmm) REVERT: B 210 THR cc_start: 0.7759 (m) cc_final: 0.7459 (t) REVERT: B 294 GLU cc_start: 0.7041 (mp0) cc_final: 0.6619 (mp0) REVERT: B 381 LYS cc_start: 0.7087 (ttmt) cc_final: 0.6377 (mmpt) REVERT: B 403 GLU cc_start: 0.7444 (OUTLIER) cc_final: 0.6774 (mp0) REVERT: B 410 MET cc_start: 0.4087 (tmm) cc_final: 0.3338 (mmm) REVERT: B 590 ASP cc_start: 0.7010 (t70) cc_final: 0.6783 (m-30) REVERT: B 592 LEU cc_start: 0.7740 (mt) cc_final: 0.7461 (mp) REVERT: C 80 GLU cc_start: 0.6547 (OUTLIER) cc_final: 0.6234 (mp0) REVERT: C 90 ASP cc_start: 0.6837 (OUTLIER) cc_final: 0.6339 (t0) REVERT: C 99 MET cc_start: 0.6568 (mtm) cc_final: 0.6351 (mtm) REVERT: C 137 LEU cc_start: 0.7691 (OUTLIER) cc_final: 0.7422 (mm) REVERT: C 139 ARG cc_start: 0.6714 (mmt90) cc_final: 0.6464 (mmt90) REVERT: C 210 THR cc_start: 0.7728 (m) cc_final: 0.7428 (t) REVERT: C 345 MET cc_start: 0.7601 (OUTLIER) cc_final: 0.7240 (mtt) REVERT: C 381 LYS cc_start: 0.7088 (ttmt) cc_final: 0.6344 (mmpt) REVERT: C 403 GLU cc_start: 0.7441 (OUTLIER) cc_final: 0.6781 (mp0) REVERT: C 410 MET cc_start: 0.3975 (tmm) cc_final: 0.3334 (mmt) REVERT: C 594 ARG cc_start: 0.7841 (mtm-85) cc_final: 0.7633 (mtm-85) REVERT: D 80 GLU cc_start: 0.6512 (OUTLIER) cc_final: 0.6208 (mp0) REVERT: D 90 ASP cc_start: 0.6832 (OUTLIER) cc_final: 0.6335 (t0) REVERT: D 99 MET cc_start: 0.6566 (mtm) cc_final: 0.6364 (mtm) REVERT: D 137 LEU cc_start: 0.7703 (OUTLIER) cc_final: 0.7441 (mm) REVERT: D 139 ARG cc_start: 0.6715 (mmt90) cc_final: 0.6488 (mmt90) REVERT: D 210 THR cc_start: 0.7728 (m) cc_final: 0.7431 (t) REVERT: D 294 GLU cc_start: 0.7027 (mp0) cc_final: 0.6716 (mp0) REVERT: D 300 LYS cc_start: 0.8003 (mppt) cc_final: 0.7587 (mmmm) REVERT: D 345 MET cc_start: 0.7602 (OUTLIER) cc_final: 0.7230 (mtt) REVERT: D 403 GLU cc_start: 0.7427 (OUTLIER) cc_final: 0.6772 (mp0) REVERT: D 410 MET cc_start: 0.4104 (tmm) cc_final: 0.3367 (mmm) REVERT: D 574 LEU cc_start: 0.7808 (OUTLIER) cc_final: 0.7571 (tt) outliers start: 86 outliers final: 44 residues processed: 362 average time/residue: 1.3588 time to fit residues: 555.1688 Evaluate side-chains 353 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 291 time to evaluate : 2.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 69 ASP Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 305 ARG Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain B residue 484 LYS Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 588 GLU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 69 ASP Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 255 MET Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 403 GLU Chi-restraints excluded: chain C residue 484 LYS Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 588 GLU Chi-restraints excluded: chain D residue 69 ASP Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 255 MET Chi-restraints excluded: chain D residue 340 ILE Chi-restraints excluded: chain D residue 345 MET Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 403 GLU Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 574 LEU Chi-restraints excluded: chain D residue 592 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 213 optimal weight: 1.9990 chunk 225 optimal weight: 0.6980 chunk 205 optimal weight: 3.9990 chunk 219 optimal weight: 0.9990 chunk 131 optimal weight: 6.9990 chunk 95 optimal weight: 4.9990 chunk 172 optimal weight: 0.5980 chunk 67 optimal weight: 4.9990 chunk 198 optimal weight: 0.9990 chunk 207 optimal weight: 2.9990 chunk 218 optimal weight: 5.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 HIS ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 426 HIS A 572 ASN ** A 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 HIS ** B 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 HIS C 265 HIS ** C 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 426 HIS D 265 HIS ** D 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 426 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.3507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 21040 Z= 0.186 Angle : 0.603 12.053 28504 Z= 0.293 Chirality : 0.040 0.220 3200 Planarity : 0.004 0.033 3512 Dihedral : 11.958 100.884 3888 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 4.00 % Allowed : 20.43 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.17), residues: 2440 helix: 1.26 (0.14), residues: 1464 sheet: -0.93 (0.48), residues: 124 loop : -0.25 (0.23), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 593 HIS 0.010 0.001 HIS C 265 PHE 0.013 0.001 PHE C 478 TYR 0.010 0.001 TYR A 524 ARG 0.005 0.000 ARG B 589 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 283 time to evaluate : 2.295 Fit side-chains REVERT: A 35 GLU cc_start: 0.7088 (mt-10) cc_final: 0.6657 (mp0) REVERT: A 41 GLN cc_start: 0.8188 (mm-40) cc_final: 0.7980 (mm110) REVERT: A 80 GLU cc_start: 0.6452 (mp0) cc_final: 0.5936 (pm20) REVERT: A 90 ASP cc_start: 0.6765 (OUTLIER) cc_final: 0.6307 (t0) REVERT: A 96 MET cc_start: 0.6616 (mmm) cc_final: 0.6328 (mmm) REVERT: A 137 LEU cc_start: 0.7706 (OUTLIER) cc_final: 0.7443 (mm) REVERT: A 210 THR cc_start: 0.7665 (m) cc_final: 0.7382 (t) REVERT: A 294 GLU cc_start: 0.7016 (mp0) cc_final: 0.6724 (mp0) REVERT: A 345 MET cc_start: 0.7568 (OUTLIER) cc_final: 0.7194 (mtt) REVERT: A 381 LYS cc_start: 0.6933 (ttmt) cc_final: 0.6352 (mmpt) REVERT: A 403 GLU cc_start: 0.7430 (OUTLIER) cc_final: 0.6808 (mp0) REVERT: A 410 MET cc_start: 0.3994 (tmm) cc_final: 0.3439 (mmt) REVERT: B 35 GLU cc_start: 0.7077 (mt-10) cc_final: 0.6665 (mp0) REVERT: B 80 GLU cc_start: 0.6561 (OUTLIER) cc_final: 0.6241 (mp0) REVERT: B 90 ASP cc_start: 0.6754 (OUTLIER) cc_final: 0.6259 (t0) REVERT: B 210 THR cc_start: 0.7663 (m) cc_final: 0.7380 (t) REVERT: B 294 GLU cc_start: 0.7051 (mp0) cc_final: 0.6649 (mp0) REVERT: B 300 LYS cc_start: 0.8001 (mppt) cc_final: 0.7599 (mmmm) REVERT: B 345 MET cc_start: 0.7578 (OUTLIER) cc_final: 0.7266 (mtt) REVERT: B 403 GLU cc_start: 0.7441 (OUTLIER) cc_final: 0.6806 (mp0) REVERT: B 410 MET cc_start: 0.4039 (tmm) cc_final: 0.3351 (mmm) REVERT: C 35 GLU cc_start: 0.7083 (mt-10) cc_final: 0.6657 (mp0) REVERT: C 80 GLU cc_start: 0.6559 (OUTLIER) cc_final: 0.6240 (mp0) REVERT: C 90 ASP cc_start: 0.6811 (OUTLIER) cc_final: 0.6333 (t0) REVERT: C 96 MET cc_start: 0.6633 (mmm) cc_final: 0.6247 (mmm) REVERT: C 99 MET cc_start: 0.6567 (mtm) cc_final: 0.6283 (mtm) REVERT: C 137 LEU cc_start: 0.7686 (OUTLIER) cc_final: 0.7427 (mm) REVERT: C 300 LYS cc_start: 0.7934 (mppt) cc_final: 0.7608 (mmmm) REVERT: C 345 MET cc_start: 0.7566 (OUTLIER) cc_final: 0.7188 (mtt) REVERT: C 403 GLU cc_start: 0.7444 (OUTLIER) cc_final: 0.6815 (mp0) REVERT: C 410 MET cc_start: 0.4026 (tmm) cc_final: 0.3371 (mmt) REVERT: C 594 ARG cc_start: 0.7816 (mtm-85) cc_final: 0.7613 (mtm-85) REVERT: D 35 GLU cc_start: 0.7082 (mt-10) cc_final: 0.6669 (mp0) REVERT: D 80 GLU cc_start: 0.6474 (OUTLIER) cc_final: 0.6164 (mp0) REVERT: D 90 ASP cc_start: 0.6807 (OUTLIER) cc_final: 0.6332 (t0) REVERT: D 96 MET cc_start: 0.6617 (mmm) cc_final: 0.6231 (mmm) REVERT: D 99 MET cc_start: 0.6568 (mtm) cc_final: 0.6286 (mtm) REVERT: D 137 LEU cc_start: 0.7702 (OUTLIER) cc_final: 0.7441 (mm) REVERT: D 294 GLU cc_start: 0.7019 (mp0) cc_final: 0.6725 (mp0) REVERT: D 345 MET cc_start: 0.7571 (OUTLIER) cc_final: 0.7189 (mtt) REVERT: D 403 GLU cc_start: 0.7428 (OUTLIER) cc_final: 0.6808 (mp0) REVERT: D 410 MET cc_start: 0.4087 (tmm) cc_final: 0.3483 (mmt) REVERT: D 574 LEU cc_start: 0.7787 (OUTLIER) cc_final: 0.7575 (tt) outliers start: 85 outliers final: 43 residues processed: 348 average time/residue: 1.3271 time to fit residues: 521.9250 Evaluate side-chains 343 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 281 time to evaluate : 2.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 69 ASP Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 305 ARG Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain B residue 484 LYS Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 69 ASP Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 255 MET Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 403 GLU Chi-restraints excluded: chain C residue 484 LYS Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 69 ASP Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 157 CYS Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 340 ILE Chi-restraints excluded: chain D residue 345 MET Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 403 GLU Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 574 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 143 optimal weight: 0.9990 chunk 231 optimal weight: 1.9990 chunk 141 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 chunk 161 optimal weight: 0.9980 chunk 243 optimal weight: 2.9990 chunk 223 optimal weight: 1.9990 chunk 193 optimal weight: 5.9990 chunk 20 optimal weight: 0.7980 chunk 149 optimal weight: 0.7980 chunk 118 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 HIS ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 HIS ** B 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 HIS ** C 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 265 HIS ** D 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.3570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 21040 Z= 0.178 Angle : 0.605 15.086 28504 Z= 0.292 Chirality : 0.040 0.239 3200 Planarity : 0.004 0.032 3512 Dihedral : 11.798 99.562 3888 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.77 % Allowed : 20.62 % Favored : 75.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.17), residues: 2440 helix: 1.30 (0.14), residues: 1464 sheet: -0.86 (0.48), residues: 124 loop : -0.17 (0.23), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 593 HIS 0.011 0.002 HIS B 582 PHE 0.015 0.001 PHE D 478 TYR 0.010 0.001 TYR A 524 ARG 0.004 0.000 ARG A 594 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 290 time to evaluate : 2.288 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.7156 (mt-10) cc_final: 0.6646 (mp0) REVERT: A 80 GLU cc_start: 0.6464 (mp0) cc_final: 0.5983 (pm20) REVERT: A 90 ASP cc_start: 0.6760 (OUTLIER) cc_final: 0.6297 (t0) REVERT: A 96 MET cc_start: 0.6621 (mmm) cc_final: 0.6287 (mmm) REVERT: A 137 LEU cc_start: 0.7707 (OUTLIER) cc_final: 0.7443 (mm) REVERT: A 210 THR cc_start: 0.7717 (m) cc_final: 0.7512 (t) REVERT: A 294 GLU cc_start: 0.7015 (mp0) cc_final: 0.6718 (mp0) REVERT: A 300 LYS cc_start: 0.8012 (mppt) cc_final: 0.7611 (mmmm) REVERT: A 345 MET cc_start: 0.7559 (OUTLIER) cc_final: 0.7327 (mtt) REVERT: A 403 GLU cc_start: 0.7407 (OUTLIER) cc_final: 0.6827 (mp0) REVERT: A 410 MET cc_start: 0.4012 (tmm) cc_final: 0.3451 (mmt) REVERT: A 519 GLU cc_start: 0.6877 (OUTLIER) cc_final: 0.6591 (mp0) REVERT: B 35 GLU cc_start: 0.7066 (mt-10) cc_final: 0.6656 (mp0) REVERT: B 80 GLU cc_start: 0.6573 (OUTLIER) cc_final: 0.6243 (mp0) REVERT: B 210 THR cc_start: 0.7722 (m) cc_final: 0.7508 (t) REVERT: B 294 GLU cc_start: 0.7077 (mp0) cc_final: 0.6661 (mp0) REVERT: B 345 MET cc_start: 0.7571 (OUTLIER) cc_final: 0.7250 (mtt) REVERT: B 403 GLU cc_start: 0.7427 (OUTLIER) cc_final: 0.6830 (mp0) REVERT: B 410 MET cc_start: 0.4053 (tmm) cc_final: 0.3465 (mmt) REVERT: B 578 MET cc_start: 0.6418 (tpp) cc_final: 0.6159 (mpt) REVERT: B 592 LEU cc_start: 0.7730 (mt) cc_final: 0.7455 (mp) REVERT: C 35 GLU cc_start: 0.7145 (mt-10) cc_final: 0.6762 (mp0) REVERT: C 80 GLU cc_start: 0.6631 (OUTLIER) cc_final: 0.6304 (mp0) REVERT: C 90 ASP cc_start: 0.6800 (OUTLIER) cc_final: 0.6321 (t0) REVERT: C 96 MET cc_start: 0.6612 (mmm) cc_final: 0.6263 (mmm) REVERT: C 99 MET cc_start: 0.6648 (mtm) cc_final: 0.6361 (mtm) REVERT: C 137 LEU cc_start: 0.7691 (OUTLIER) cc_final: 0.7432 (mm) REVERT: C 210 THR cc_start: 0.7650 (t) cc_final: 0.7438 (t) REVERT: C 300 LYS cc_start: 0.7960 (mppt) cc_final: 0.7598 (mmmm) REVERT: C 345 MET cc_start: 0.7562 (OUTLIER) cc_final: 0.7331 (mtt) REVERT: C 403 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.6845 (mp0) REVERT: C 410 MET cc_start: 0.4135 (tmm) cc_final: 0.3479 (mmt) REVERT: C 592 LEU cc_start: 0.7785 (mt) cc_final: 0.7529 (mp) REVERT: D 35 GLU cc_start: 0.7150 (mt-10) cc_final: 0.6652 (mp0) REVERT: D 80 GLU cc_start: 0.6568 (OUTLIER) cc_final: 0.6258 (mp0) REVERT: D 90 ASP cc_start: 0.6798 (OUTLIER) cc_final: 0.6328 (t0) REVERT: D 96 MET cc_start: 0.6611 (mmm) cc_final: 0.6255 (mmm) REVERT: D 99 MET cc_start: 0.6643 (mtm) cc_final: 0.6359 (mtm) REVERT: D 137 LEU cc_start: 0.7701 (OUTLIER) cc_final: 0.7446 (mm) REVERT: D 210 THR cc_start: 0.7639 (t) cc_final: 0.7421 (t) REVERT: D 294 GLU cc_start: 0.7003 (mp0) cc_final: 0.6704 (mp0) REVERT: D 300 LYS cc_start: 0.8010 (mppt) cc_final: 0.7604 (mmmm) REVERT: D 345 MET cc_start: 0.7582 (OUTLIER) cc_final: 0.7192 (mtt) REVERT: D 403 GLU cc_start: 0.7406 (OUTLIER) cc_final: 0.6826 (mp0) REVERT: D 410 MET cc_start: 0.4009 (tmm) cc_final: 0.3441 (mmt) outliers start: 80 outliers final: 44 residues processed: 347 average time/residue: 1.3460 time to fit residues: 526.5915 Evaluate side-chains 347 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 285 time to evaluate : 2.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 69 ASP Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 519 GLU Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 305 ARG Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain B residue 484 LYS Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 519 GLU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 69 ASP Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 255 MET Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 403 GLU Chi-restraints excluded: chain C residue 484 LYS Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 588 GLU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 69 ASP Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 157 CYS Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 340 ILE Chi-restraints excluded: chain D residue 345 MET Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 403 GLU Chi-restraints excluded: chain D residue 499 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 153 optimal weight: 2.9990 chunk 206 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 178 optimal weight: 0.7980 chunk 28 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 193 optimal weight: 6.9990 chunk 81 optimal weight: 0.8980 chunk 199 optimal weight: 6.9990 chunk 24 optimal weight: 0.7980 chunk 35 optimal weight: 0.0060 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 GLN A 265 HIS ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 HIS ** B 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 HIS ** C 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 473 GLN C 582 HIS D 265 HIS ** D 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.156394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.124319 restraints weight = 23272.735| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 1.71 r_work: 0.3052 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3022 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3022 r_free = 0.3022 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3021 r_free = 0.3021 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3021 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.3683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 21040 Z= 0.159 Angle : 0.587 13.730 28504 Z= 0.283 Chirality : 0.040 0.267 3200 Planarity : 0.003 0.032 3512 Dihedral : 11.531 97.447 3888 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.34 % Allowed : 21.42 % Favored : 75.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.18), residues: 2440 helix: 1.40 (0.14), residues: 1456 sheet: -0.81 (0.49), residues: 124 loop : -0.06 (0.23), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 268 HIS 0.011 0.001 HIS A 265 PHE 0.017 0.001 PHE C 211 TYR 0.011 0.001 TYR A 524 ARG 0.004 0.000 ARG A 594 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8725.26 seconds wall clock time: 155 minutes 3.90 seconds (9303.90 seconds total)