Starting phenix.real_space_refine (version: 1.21rc1) on Mon Jul 10 05:22:24 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s8c_24893/07_2023/7s8c_24893.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s8c_24893/07_2023/7s8c_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_24893/07_2023/7s8c_24893.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s8c_24893/07_2023/7s8c_24893.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s8c_24893/07_2023/7s8c_24893.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s8c_24893/07_2023/7s8c_24893.pdb" } resolution = 2.85 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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-1.21rc1-5013/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: 81 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: 81 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: 81 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: 81 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: 10.25, per 1000 atoms: 0.50 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: 8.60 Conformation dependent library (CDL) restraints added in 2.8 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: 0.97 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: 6.18 Time building geometry restraints manager: 8.85 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: 12035 28.19 - 56.38: 378 56.38 - 84.57: 43 84.57 - 112.76: 4 112.76 - 140.95: 12 Dihedral angle restraints: 12472 sinusoidal: 5312 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 12469 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: 1.020 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: 5.360 Check model and map are aligned: 0.270 Set scattering table: 0.150 Process input model: 50.460 Find NCS groups from input model: 1.480 Set up NCS constraints: 0.110 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:11.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.110 ------------------------------------------------------------------------------- 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 : 14.025 140.949 7848 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 % 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 *********************** 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 : 2.422 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 outliers start: 16 outliers final: 0 residues processed: 562 average time/residue: 1.3556 time to fit residues: 857.1496 Evaluate side-chains 384 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 384 time to evaluate : 2.225 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1454 ------------------------------------------------------------------------------- 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: 1.9990 chunk 184 optimal weight: 3.9990 chunk 102 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 98 optimal weight: 4.9990 chunk 191 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 116 optimal weight: 6.9990 chunk 142 optimal weight: 2.9990 chunk 221 optimal weight: 4.9990 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 40 GLN A 91 ASN A 122 HIS A 165 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 165 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 40 GLN C 91 ASN C 122 HIS C 165 HIS ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 HIS C 358 ASN C 369 GLN C 587 HIS D 40 GLN D 91 ASN D 122 HIS D 165 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: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 21040 Z= 0.272 Angle : 0.680 8.215 28504 Z= 0.341 Chirality : 0.042 0.209 3200 Planarity : 0.005 0.040 3512 Dihedral : 14.541 120.509 3124 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer Outliers : 5.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.79 (0.15), residues: 2440 helix: -1.05 (0.12), residues: 1464 sheet: -1.25 (0.46), residues: 124 loop : -1.11 (0.20), residues: 852 *********************** 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 479 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 372 time to evaluate : 2.282 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 outliers start: 107 outliers final: 38 residues processed: 433 average time/residue: 1.3366 time to fit residues: 655.5122 Evaluate side-chains 362 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 324 time to evaluate : 2.289 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 26 residues processed: 12 average time/residue: 0.7622 time to fit residues: 14.1716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 123 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 184 optimal weight: 6.9990 chunk 150 optimal weight: 5.9990 chunk 61 optimal weight: 0.8980 chunk 221 optimal weight: 9.9990 chunk 239 optimal weight: 5.9990 chunk 197 optimal weight: 3.9990 chunk 220 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 chunk 178 optimal weight: 4.9990 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 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 HIS B 426 HIS ** B 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 HIS C 426 HIS ** C 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 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: 0.7888 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 21040 Z= 0.229 Angle : 0.631 9.418 28504 Z= 0.313 Chirality : 0.040 0.196 3200 Planarity : 0.004 0.033 3512 Dihedral : 13.561 104.773 3124 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer Outliers : 4.99 % 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: -0.49 (0.16), residues: 2440 helix: 0.16 (0.13), residues: 1480 sheet: -0.94 (0.48), residues: 124 loop : -0.91 (0.21), residues: 836 *********************** 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 430 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 324 time to evaluate : 2.381 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 106 outliers final: 29 residues processed: 384 average time/residue: 1.3403 time to fit residues: 582.5124 Evaluate side-chains 337 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 308 time to evaluate : 2.234 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 21 residues processed: 8 average time/residue: 0.7649 time to fit residues: 10.6488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 219 optimal weight: 0.9990 chunk 166 optimal weight: 1.9990 chunk 115 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 105 optimal weight: 5.9990 chunk 149 optimal weight: 1.9990 chunk 222 optimal weight: 0.8980 chunk 235 optimal weight: 1.9990 chunk 116 optimal weight: 0.7980 chunk 211 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 HIS ** B 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 HIS ** B 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 201 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: 0.7872 moved from start: 0.3097 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= 0.197 Angle : 0.590 9.537 28504 Z= 0.292 Chirality : 0.039 0.186 3200 Planarity : 0.004 0.031 3512 Dihedral : 12.458 97.604 3124 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer Outliers : 4.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.17), residues: 2440 helix: 0.64 (0.13), residues: 1472 sheet: -0.93 (0.48), residues: 124 loop : -0.71 (0.22), residues: 844 *********************** 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 411 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 324 time to evaluate : 2.299 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 87 outliers final: 29 residues processed: 372 average time/residue: 1.3162 time to fit residues: 556.2100 Evaluate side-chains 326 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 297 time to evaluate : 2.453 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 26 residues processed: 3 average time/residue: 1.1874 time to fit residues: 8.5038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 196 optimal weight: 1.9990 chunk 133 optimal weight: 0.0870 chunk 3 optimal weight: 8.9990 chunk 175 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 201 optimal weight: 5.9990 chunk 163 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 120 optimal weight: 3.9990 chunk 211 optimal weight: 1.9990 chunk 59 optimal weight: 0.0050 overall best weight: 1.2178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 265 HIS ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 426 HIS ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 HIS ** B 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 HIS B 582 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 201 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: 0.7874 moved from start: 0.3242 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= 0.201 Angle : 0.595 8.734 28504 Z= 0.292 Chirality : 0.040 0.186 3200 Planarity : 0.004 0.030 3512 Dihedral : 11.872 89.749 3124 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer Outliers : 4.05 % 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: 0.38 (0.17), residues: 2440 helix: 0.92 (0.13), residues: 1472 sheet: -0.98 (0.47), residues: 124 loop : -0.63 (0.22), residues: 844 *********************** 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 400 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 314 time to evaluate : 2.352 Fit side-chains revert: symmetry clash outliers start: 86 outliers final: 32 residues processed: 370 average time/residue: 1.3228 time to fit residues: 553.6989 Evaluate side-chains 328 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 296 time to evaluate : 2.279 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 29 residues processed: 3 average time/residue: 0.8434 time to fit residues: 6.0958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 79 optimal weight: 6.9990 chunk 212 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 138 optimal weight: 7.9990 chunk 58 optimal weight: 0.0060 chunk 236 optimal weight: 0.9980 chunk 195 optimal weight: 4.9990 chunk 109 optimal weight: 4.9990 chunk 19 optimal weight: 0.6980 chunk 78 optimal weight: 0.9980 chunk 123 optimal weight: 7.9990 overall best weight: 0.7196 ------------------------------------------------------------------------------- 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 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 ** 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: 0.7843 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 : 0.003 0.050 21040 Z= 0.163 Angle : 0.569 11.659 28504 Z= 0.278 Chirality : 0.039 0.186 3200 Planarity : 0.003 0.034 3512 Dihedral : 11.180 88.631 3124 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer Outliers : 4.05 % 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: 0.79 (0.17), residues: 2440 helix: 1.26 (0.14), residues: 1456 sheet: -0.90 (0.48), residues: 124 loop : -0.42 (0.22), residues: 860 *********************** 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 404 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 318 time to evaluate : 2.436 Fit side-chains outliers start: 86 outliers final: 35 residues processed: 370 average time/residue: 1.3552 time to fit residues: 569.4525 Evaluate side-chains 337 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 302 time to evaluate : 2.328 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 30 residues processed: 5 average time/residue: 0.6477 time to fit residues: 7.2339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 227 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 134 optimal weight: 0.0170 chunk 172 optimal weight: 0.5980 chunk 133 optimal weight: 2.9990 chunk 198 optimal weight: 0.5980 chunk 131 optimal weight: 9.9990 chunk 235 optimal weight: 0.0570 chunk 147 optimal weight: 4.9990 chunk 143 optimal weight: 6.9990 chunk 108 optimal weight: 6.9990 overall best weight: 0.8538 ------------------------------------------------------------------------------- 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 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 ** D 201 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: 0.7848 moved from start: 0.3533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 21040 Z= 0.171 Angle : 0.582 12.131 28504 Z= 0.282 Chirality : 0.040 0.191 3200 Planarity : 0.003 0.033 3512 Dihedral : 10.606 77.605 3124 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer Outliers : 3.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.18), residues: 2440 helix: 1.36 (0.14), residues: 1460 sheet: -0.93 (0.48), residues: 124 loop : -0.33 (0.23), residues: 856 *********************** 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 382 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 303 time to evaluate : 2.376 Fit side-chains outliers start: 79 outliers final: 36 residues processed: 363 average time/residue: 1.2684 time to fit residues: 523.6393 Evaluate side-chains 325 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 289 time to evaluate : 2.264 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 32 residues processed: 4 average time/residue: 0.5644 time to fit residues: 6.4609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 140 optimal weight: 7.9990 chunk 70 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 45 optimal weight: 0.5980 chunk 149 optimal weight: 0.9980 chunk 160 optimal weight: 4.9990 chunk 116 optimal weight: 4.9990 chunk 21 optimal weight: 0.4980 chunk 184 optimal weight: 7.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 261 GLN A 265 HIS ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 426 HIS ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 GLN B 265 HIS ** B 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 HIS C 91 ASN ** 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 473 GLN ** D 201 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: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.3557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 21040 Z= 0.201 Angle : 0.606 10.988 28504 Z= 0.297 Chirality : 0.040 0.207 3200 Planarity : 0.003 0.031 3512 Dihedral : 10.517 72.963 3124 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer Outliers : 3.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.91 (0.18), residues: 2440 helix: 1.31 (0.14), residues: 1464 sheet: -0.95 (0.48), residues: 124 loop : -0.28 (0.23), residues: 852 *********************** 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 372 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 295 time to evaluate : 2.299 Fit side-chains outliers start: 77 outliers final: 33 residues processed: 356 average time/residue: 1.2918 time to fit residues: 522.9123 Evaluate side-chains 321 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 288 time to evaluate : 2.242 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 32 residues processed: 1 average time/residue: 0.1782 time to fit residues: 3.4056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 213 optimal weight: 0.8980 chunk 225 optimal weight: 0.7980 chunk 205 optimal weight: 7.9990 chunk 219 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 chunk 172 optimal weight: 0.5980 chunk 67 optimal weight: 6.9990 chunk 198 optimal weight: 0.8980 chunk 207 optimal weight: 5.9990 chunk 218 optimal weight: 0.0470 overall best weight: 0.6278 ------------------------------------------------------------------------------- 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** 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 D 91 ASN D 265 HIS ** D 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.3725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 21040 Z= 0.162 Angle : 0.580 11.018 28504 Z= 0.282 Chirality : 0.040 0.197 3200 Planarity : 0.003 0.030 3512 Dihedral : 9.948 65.859 3124 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer Outliers : 3.01 % 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: 1.04 (0.18), residues: 2440 helix: 1.40 (0.14), residues: 1460 sheet: -0.88 (0.49), residues: 124 loop : -0.18 (0.23), residues: 856 *********************** 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 379 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 315 time to evaluate : 2.472 Fit side-chains outliers start: 64 outliers final: 35 residues processed: 361 average time/residue: 1.4138 time to fit residues: 578.7551 Evaluate side-chains 336 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 301 time to evaluate : 2.260 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 29 residues processed: 6 average time/residue: 0.6711 time to fit residues: 8.0330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 143 optimal weight: 0.0010 chunk 231 optimal weight: 1.9990 chunk 141 optimal weight: 0.9980 chunk 109 optimal weight: 4.9990 chunk 161 optimal weight: 10.0000 chunk 243 optimal weight: 0.6980 chunk 223 optimal weight: 0.9980 chunk 193 optimal weight: 0.7980 chunk 20 optimal weight: 4.9990 chunk 149 optimal weight: 6.9990 chunk 118 optimal weight: 6.9990 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 258 HIS A 265 HIS ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 HIS ** B 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 GLN C 265 HIS ** C 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 473 GLN D 265 HIS ** D 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.3795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 21040 Z= 0.166 Angle : 0.603 16.352 28504 Z= 0.291 Chirality : 0.040 0.243 3200 Planarity : 0.003 0.030 3512 Dihedral : 9.690 60.965 3124 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer Outliers : 2.64 % 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: 1.07 (0.18), residues: 2440 helix: 1.39 (0.14), residues: 1460 sheet: -0.94 (0.49), residues: 124 loop : -0.10 (0.23), residues: 856 ********************** 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 360 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 304 time to evaluate : 2.421 Fit side-chains outliers start: 56 outliers final: 32 residues processed: 344 average time/residue: 1.3244 time to fit residues: 516.4478 Evaluate side-chains 325 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 293 time to evaluate : 2.259 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 29 residues processed: 3 average time/residue: 0.2183 time to fit residues: 4.1820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 59 optimal weight: 0.0070 chunk 178 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 193 optimal weight: 0.7980 chunk 81 optimal weight: 6.9990 chunk 199 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 overall best weight: 0.6598 ------------------------------------------------------------------------------- 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** B 265 HIS ** B 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 258 HIS C 265 HIS ** C 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 473 GLN ** D 201 HIS ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.157321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.124976 restraints weight = 23197.612| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 1.85 r_work: 0.3051 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3042 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3042 r_free = 0.3042 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3042 r_free = 0.3042 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3042 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.3857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 21040 Z= 0.165 Angle : 0.601 11.036 28504 Z= 0.290 Chirality : 0.040 0.268 3200 Planarity : 0.003 0.030 3512 Dihedral : 9.445 58.909 3124 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer Outliers : 2.40 % 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: 1.08 (0.18), residues: 2440 helix: 1.39 (0.14), residues: 1456 sheet: -0.98 (0.49), residues: 124 loop : -0.04 (0.23), residues: 860 =============================================================================== Job complete usr+sys time: 8400.07 seconds wall clock time: 149 minutes 23.61 seconds (8963.61 seconds total)