Starting phenix.real_space_refine (version: dev) on Fri Feb 24 11:48:51 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqy_23491/02_2023/7lqy_23491_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqy_23491/02_2023/7lqy_23491.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqy_23491/02_2023/7lqy_23491_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqy_23491/02_2023/7lqy_23491_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqy_23491/02_2023/7lqy_23491_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqy_23491/02_2023/7lqy_23491.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqy_23491/02_2023/7lqy_23491.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqy_23491/02_2023/7lqy_23491_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqy_23491/02_2023/7lqy_23491_neut_updated.pdb" } resolution = 3.19 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= 0.001 sd= 0.004 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 Process input model Symmetric amino acids flipped Residue "A ARG 116": "NH1" <-> "NH2" Residue "A ARG 117": "NH1" <-> "NH2" Residue "A ARG 142": "NH1" <-> "NH2" Residue "A ARG 144": "NH1" <-> "NH2" Residue "A ARG 213": "NH1" <-> "NH2" Residue "A PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 365": "NH1" <-> "NH2" Residue "A ARG 411": "NH1" <-> "NH2" Residue "A ARG 422": "NH1" <-> "NH2" Residue "A PHE 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 434": "NH1" <-> "NH2" Residue "A ARG 476": "NH1" <-> "NH2" Residue "A ARG 581": "NH1" <-> "NH2" Residue "A TYR 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 703": "NH1" <-> "NH2" Residue "A ARG 723": "NH1" <-> "NH2" Residue "A ARG 741": "NH1" <-> "NH2" Residue "A ARG 745": "NH1" <-> "NH2" Residue "A ARG 773": "NH1" <-> "NH2" Residue "B ARG 116": "NH1" <-> "NH2" Residue "B ARG 117": "NH1" <-> "NH2" Residue "B ARG 142": "NH1" <-> "NH2" Residue "B ARG 144": "NH1" <-> "NH2" Residue "B ARG 213": "NH1" <-> "NH2" Residue "B PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 365": "NH1" <-> "NH2" Residue "B ARG 411": "NH1" <-> "NH2" Residue "B ARG 422": "NH1" <-> "NH2" Residue "B PHE 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 434": "NH1" <-> "NH2" Residue "B ARG 476": "NH1" <-> "NH2" Residue "B ARG 581": "NH1" <-> "NH2" Residue "B TYR 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 703": "NH1" <-> "NH2" Residue "B ARG 723": "NH1" <-> "NH2" Residue "B ARG 741": "NH1" <-> "NH2" Residue "B ARG 745": "NH1" <-> "NH2" Residue "B ARG 773": "NH1" <-> "NH2" Residue "C ARG 116": "NH1" <-> "NH2" Residue "C ARG 117": "NH1" <-> "NH2" Residue "C ARG 142": "NH1" <-> "NH2" Residue "C ARG 144": "NH1" <-> "NH2" Residue "C ARG 213": "NH1" <-> "NH2" Residue "C PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 365": "NH1" <-> "NH2" Residue "C ARG 411": "NH1" <-> "NH2" Residue "C ARG 422": "NH1" <-> "NH2" Residue "C PHE 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 434": "NH1" <-> "NH2" Residue "C ARG 476": "NH1" <-> "NH2" Residue "C ARG 581": "NH1" <-> "NH2" Residue "C TYR 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 703": "NH1" <-> "NH2" Residue "C ARG 723": "NH1" <-> "NH2" Residue "C ARG 741": "NH1" <-> "NH2" Residue "C ARG 745": "NH1" <-> "NH2" Residue "C ARG 773": "NH1" <-> "NH2" Residue "D ARG 116": "NH1" <-> "NH2" Residue "D ARG 117": "NH1" <-> "NH2" Residue "D ARG 142": "NH1" <-> "NH2" Residue "D ARG 144": "NH1" <-> "NH2" Residue "D ARG 213": "NH1" <-> "NH2" Residue "D PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 365": "NH1" <-> "NH2" Residue "D ARG 411": "NH1" <-> "NH2" Residue "D ARG 422": "NH1" <-> "NH2" Residue "D PHE 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 434": "NH1" <-> "NH2" Residue "D ARG 476": "NH1" <-> "NH2" Residue "D ARG 581": "NH1" <-> "NH2" Residue "D TYR 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 703": "NH1" <-> "NH2" Residue "D ARG 723": "NH1" <-> "NH2" Residue "D ARG 741": "NH1" <-> "NH2" Residue "D ARG 745": "NH1" <-> "NH2" Residue "D ARG 773": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 22954 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 659, 5320 Classifications: {'peptide': 659} Link IDs: {'PTRANS': 20, 'TRANS': 638} Chain breaks: 1 Chain: "B" Number of atoms: 5320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 659, 5320 Classifications: {'peptide': 659} Link IDs: {'PTRANS': 20, 'TRANS': 638} Chain breaks: 1 Chain: "C" Number of atoms: 5320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 659, 5320 Classifications: {'peptide': 659} Link IDs: {'PTRANS': 20, 'TRANS': 638} Chain breaks: 1 Chain: "D" Number of atoms: 5320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 659, 5320 Classifications: {'peptide': 659} Link IDs: {'PTRANS': 20, 'TRANS': 638} Chain breaks: 1 Chain: "A" Number of atoms: 420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 420 Unusual residues: {' CL': 1, ' NA': 1, 'POV': 8, 'YBG': 1} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-3': 1, 'POV:plan-2': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 418 Unusual residues: {'POV': 8, 'YBG': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-3': 1, 'POV:plan-2': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 418 Unusual residues: {'POV': 8, 'YBG': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-3': 1, 'POV:plan-2': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 418 Unusual residues: {'POV': 8, 'YBG': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-3': 1, 'POV:plan-2': 1} Unresolved non-hydrogen planarities: 7 Time building chain proxies: 12.41, per 1000 atoms: 0.54 Number of scatterers: 22954 At special positions: 0 Unit cell: (122.96, 124.02, 125.08, 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) Cl 1 17.00 S 128 16.00 P 32 15.00 Na 1 11.00 O 4128 8.00 N 3532 7.00 C 15132 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 8.34 Conformation dependent library (CDL) restraints added in 3.1 seconds 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4984 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 116 helices and 4 sheets defined 51.1% alpha, 2.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.29 Creating SS restraints... Processing helix chain 'A' and resid 116 through 124 Processing helix chain 'A' and resid 134 through 141 Processing helix chain 'A' and resid 159 through 165 Processing helix chain 'A' and resid 175 through 184 removed outlier: 3.520A pdb=" N ASP A 180 " --> pdb=" O SER A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 192 Processing helix chain 'A' and resid 206 through 212 Processing helix chain 'A' and resid 216 through 223 Processing helix chain 'A' and resid 253 through 259 removed outlier: 3.550A pdb=" N ALA A 258 " --> pdb=" O LEU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 270 removed outlier: 3.688A pdb=" N LEU A 270 " --> pdb=" O VAL A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 296 Processing helix chain 'A' and resid 301 through 321 removed outlier: 3.670A pdb=" N LYS A 305 " --> pdb=" O ALA A 301 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE A 306 " --> pdb=" O ASP A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 329 No H-bonds generated for 'chain 'A' and resid 327 through 329' Processing helix chain 'A' and resid 338 through 344 Processing helix chain 'A' and resid 348 through 354 Processing helix chain 'A' and resid 365 through 367 No H-bonds generated for 'chain 'A' and resid 365 through 367' Processing helix chain 'A' and resid 397 through 402 Processing helix chain 'A' and resid 414 through 416 No H-bonds generated for 'chain 'A' and resid 414 through 416' Processing helix chain 'A' and resid 418 through 428 removed outlier: 3.957A pdb=" N ARG A 422 " --> pdb=" O GLU A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 455 Processing helix chain 'A' and resid 471 through 498 Processing helix chain 'A' and resid 513 through 533 Processing helix chain 'A' and resid 537 through 556 removed outlier: 3.730A pdb=" N VAL A 540 " --> pdb=" O LYS A 537 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N MET A 543 " --> pdb=" O VAL A 540 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N VAL A 544 " --> pdb=" O ALA A 541 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA A 548 " --> pdb=" O PHE A 545 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N MET A 549 " --> pdb=" O SER A 546 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N TRP A 551 " --> pdb=" O ALA A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 577 removed outlier: 3.613A pdb=" N TYR A 567 " --> pdb=" O GLN A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 600 removed outlier: 3.805A pdb=" N VAL A 585 " --> pdb=" O ARG A 581 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU A 587 " --> pdb=" O MET A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 644 removed outlier: 3.505A pdb=" N LYS A 641 " --> pdb=" O LEU A 637 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N PHE A 642 " --> pdb=" O GLU A 638 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N THR A 643 " --> pdb=" O LEU A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 672 Processing helix chain 'A' and resid 676 through 690 removed outlier: 3.613A pdb=" N ASN A 689 " --> pdb=" O GLY A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 694 through 713 removed outlier: 3.539A pdb=" N SER A 713 " --> pdb=" O ASP A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 720 removed outlier: 3.853A pdb=" N ARG A 719 " --> pdb=" O LEU A 715 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS A 720 " --> pdb=" O LYS A 716 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 715 through 720' Processing helix chain 'B' and resid 116 through 124 Processing helix chain 'B' and resid 134 through 141 Processing helix chain 'B' and resid 159 through 165 Processing helix chain 'B' and resid 175 through 184 removed outlier: 3.520A pdb=" N ASP B 180 " --> pdb=" O SER B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 192 Processing helix chain 'B' and resid 206 through 212 Processing helix chain 'B' and resid 216 through 223 Processing helix chain 'B' and resid 253 through 259 removed outlier: 3.550A pdb=" N ALA B 258 " --> pdb=" O LEU B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 270 removed outlier: 3.687A pdb=" N LEU B 270 " --> pdb=" O VAL B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 296 Processing helix chain 'B' and resid 301 through 321 removed outlier: 3.670A pdb=" N LYS B 305 " --> pdb=" O ALA B 301 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE B 306 " --> pdb=" O ASP B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 329 No H-bonds generated for 'chain 'B' and resid 327 through 329' Processing helix chain 'B' and resid 338 through 344 Processing helix chain 'B' and resid 348 through 354 Processing helix chain 'B' and resid 365 through 367 No H-bonds generated for 'chain 'B' and resid 365 through 367' Processing helix chain 'B' and resid 397 through 402 Processing helix chain 'B' and resid 414 through 416 No H-bonds generated for 'chain 'B' and resid 414 through 416' Processing helix chain 'B' and resid 418 through 428 removed outlier: 3.957A pdb=" N ARG B 422 " --> pdb=" O GLU B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 455 Processing helix chain 'B' and resid 471 through 498 Processing helix chain 'B' and resid 513 through 533 Processing helix chain 'B' and resid 537 through 556 removed outlier: 3.730A pdb=" N VAL B 540 " --> pdb=" O LYS B 537 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N MET B 543 " --> pdb=" O VAL B 540 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N VAL B 544 " --> pdb=" O ALA B 541 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA B 548 " --> pdb=" O PHE B 545 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N MET B 549 " --> pdb=" O SER B 546 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N TRP B 551 " --> pdb=" O ALA B 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 577 removed outlier: 3.612A pdb=" N TYR B 567 " --> pdb=" O GLN B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 600 removed outlier: 3.805A pdb=" N VAL B 585 " --> pdb=" O ARG B 581 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU B 587 " --> pdb=" O MET B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 644 removed outlier: 3.505A pdb=" N LYS B 641 " --> pdb=" O LEU B 637 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N PHE B 642 " --> pdb=" O GLU B 638 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N THR B 643 " --> pdb=" O LEU B 639 " (cutoff:3.500A) Processing helix chain 'B' and resid 658 through 672 Processing helix chain 'B' and resid 676 through 690 removed outlier: 3.614A pdb=" N ASN B 689 " --> pdb=" O GLY B 685 " (cutoff:3.500A) Processing helix chain 'B' and resid 694 through 713 removed outlier: 3.539A pdb=" N SER B 713 " --> pdb=" O ASP B 709 " (cutoff:3.500A) Processing helix chain 'B' and resid 715 through 720 removed outlier: 3.853A pdb=" N ARG B 719 " --> pdb=" O LEU B 715 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS B 720 " --> pdb=" O LYS B 716 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 715 through 720' Processing helix chain 'C' and resid 116 through 124 Processing helix chain 'C' and resid 134 through 141 Processing helix chain 'C' and resid 159 through 165 Processing helix chain 'C' and resid 175 through 184 removed outlier: 3.519A pdb=" N ASP C 180 " --> pdb=" O SER C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 192 Processing helix chain 'C' and resid 206 through 212 Processing helix chain 'C' and resid 216 through 223 Processing helix chain 'C' and resid 253 through 259 removed outlier: 3.550A pdb=" N ALA C 258 " --> pdb=" O LEU C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 270 removed outlier: 3.687A pdb=" N LEU C 270 " --> pdb=" O VAL C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 296 Processing helix chain 'C' and resid 301 through 321 removed outlier: 3.670A pdb=" N LYS C 305 " --> pdb=" O ALA C 301 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE C 306 " --> pdb=" O ASP C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 329 No H-bonds generated for 'chain 'C' and resid 327 through 329' Processing helix chain 'C' and resid 338 through 344 Processing helix chain 'C' and resid 348 through 354 Processing helix chain 'C' and resid 365 through 367 No H-bonds generated for 'chain 'C' and resid 365 through 367' Processing helix chain 'C' and resid 397 through 402 Processing helix chain 'C' and resid 414 through 416 No H-bonds generated for 'chain 'C' and resid 414 through 416' Processing helix chain 'C' and resid 418 through 428 removed outlier: 3.956A pdb=" N ARG C 422 " --> pdb=" O GLU C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 455 Processing helix chain 'C' and resid 471 through 498 Processing helix chain 'C' and resid 513 through 533 Processing helix chain 'C' and resid 537 through 556 removed outlier: 3.730A pdb=" N VAL C 540 " --> pdb=" O LYS C 537 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N MET C 543 " --> pdb=" O VAL C 540 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N VAL C 544 " --> pdb=" O ALA C 541 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA C 548 " --> pdb=" O PHE C 545 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N MET C 549 " --> pdb=" O SER C 546 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N TRP C 551 " --> pdb=" O ALA C 548 " (cutoff:3.500A) Processing helix chain 'C' and resid 562 through 577 removed outlier: 3.612A pdb=" N TYR C 567 " --> pdb=" O GLN C 563 " (cutoff:3.500A) Processing helix chain 'C' and resid 579 through 600 removed outlier: 3.805A pdb=" N VAL C 585 " --> pdb=" O ARG C 581 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU C 587 " --> pdb=" O MET C 583 " (cutoff:3.500A) Processing helix chain 'C' and resid 632 through 644 removed outlier: 3.505A pdb=" N LYS C 641 " --> pdb=" O LEU C 637 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N PHE C 642 " --> pdb=" O GLU C 638 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N THR C 643 " --> pdb=" O LEU C 639 " (cutoff:3.500A) Processing helix chain 'C' and resid 658 through 672 Processing helix chain 'C' and resid 676 through 690 removed outlier: 3.614A pdb=" N ASN C 689 " --> pdb=" O GLY C 685 " (cutoff:3.500A) Processing helix chain 'C' and resid 694 through 713 removed outlier: 3.540A pdb=" N SER C 713 " --> pdb=" O ASP C 709 " (cutoff:3.500A) Processing helix chain 'C' and resid 715 through 720 removed outlier: 3.853A pdb=" N ARG C 719 " --> pdb=" O LEU C 715 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS C 720 " --> pdb=" O LYS C 716 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 715 through 720' Processing helix chain 'D' and resid 116 through 124 Processing helix chain 'D' and resid 134 through 141 Processing helix chain 'D' and resid 159 through 165 Processing helix chain 'D' and resid 175 through 184 removed outlier: 3.519A pdb=" N ASP D 180 " --> pdb=" O SER D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 192 Processing helix chain 'D' and resid 206 through 212 Processing helix chain 'D' and resid 216 through 223 Processing helix chain 'D' and resid 253 through 259 removed outlier: 3.551A pdb=" N ALA D 258 " --> pdb=" O LEU D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 270 removed outlier: 3.688A pdb=" N LEU D 270 " --> pdb=" O VAL D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 296 Processing helix chain 'D' and resid 301 through 321 removed outlier: 3.671A pdb=" N LYS D 305 " --> pdb=" O ALA D 301 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE D 306 " --> pdb=" O ASP D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 329 No H-bonds generated for 'chain 'D' and resid 327 through 329' Processing helix chain 'D' and resid 338 through 344 Processing helix chain 'D' and resid 348 through 354 Processing helix chain 'D' and resid 365 through 367 No H-bonds generated for 'chain 'D' and resid 365 through 367' Processing helix chain 'D' and resid 397 through 402 Processing helix chain 'D' and resid 414 through 416 No H-bonds generated for 'chain 'D' and resid 414 through 416' Processing helix chain 'D' and resid 418 through 428 removed outlier: 3.956A pdb=" N ARG D 422 " --> pdb=" O GLU D 418 " (cutoff:3.500A) Processing helix chain 'D' and resid 433 through 455 Processing helix chain 'D' and resid 471 through 498 Processing helix chain 'D' and resid 513 through 533 Processing helix chain 'D' and resid 537 through 556 removed outlier: 3.730A pdb=" N VAL D 540 " --> pdb=" O LYS D 537 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N MET D 543 " --> pdb=" O VAL D 540 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N VAL D 544 " --> pdb=" O ALA D 541 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA D 548 " --> pdb=" O PHE D 545 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N MET D 549 " --> pdb=" O SER D 546 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N TRP D 551 " --> pdb=" O ALA D 548 " (cutoff:3.500A) Processing helix chain 'D' and resid 562 through 577 removed outlier: 3.613A pdb=" N TYR D 567 " --> pdb=" O GLN D 563 " (cutoff:3.500A) Processing helix chain 'D' and resid 579 through 600 removed outlier: 3.804A pdb=" N VAL D 585 " --> pdb=" O ARG D 581 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU D 587 " --> pdb=" O MET D 583 " (cutoff:3.500A) Processing helix chain 'D' and resid 632 through 644 removed outlier: 3.506A pdb=" N LYS D 641 " --> pdb=" O LEU D 637 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N PHE D 642 " --> pdb=" O GLU D 638 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N THR D 643 " --> pdb=" O LEU D 639 " (cutoff:3.500A) Processing helix chain 'D' and resid 658 through 672 Processing helix chain 'D' and resid 676 through 690 removed outlier: 3.613A pdb=" N ASN D 689 " --> pdb=" O GLY D 685 " (cutoff:3.500A) Processing helix chain 'D' and resid 694 through 713 removed outlier: 3.539A pdb=" N SER D 713 " --> pdb=" O ASP D 709 " (cutoff:3.500A) Processing helix chain 'D' and resid 715 through 720 removed outlier: 3.853A pdb=" N ARG D 719 " --> pdb=" O LEU D 715 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS D 720 " --> pdb=" O LYS D 716 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 715 through 720' Processing sheet with id= A, first strand: chain 'A' and resid 743 through 749 removed outlier: 4.026A pdb=" N TRP A 374 " --> pdb=" O SER A 381 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N LEU A 383 " --> pdb=" O THR A 372 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N THR A 372 " --> pdb=" O LEU A 383 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ASP A 385 " --> pdb=" O LYS A 370 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LYS A 370 " --> pdb=" O ASP A 385 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 743 through 749 removed outlier: 4.027A pdb=" N TRP B 374 " --> pdb=" O SER B 381 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N LEU B 383 " --> pdb=" O THR B 372 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N THR B 372 " --> pdb=" O LEU B 383 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ASP B 385 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LYS B 370 " --> pdb=" O ASP B 385 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 743 through 749 removed outlier: 4.026A pdb=" N TRP C 374 " --> pdb=" O SER C 381 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N LEU C 383 " --> pdb=" O THR C 372 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N THR C 372 " --> pdb=" O LEU C 383 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ASP C 385 " --> pdb=" O LYS C 370 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LYS C 370 " --> pdb=" O ASP C 385 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 743 through 749 removed outlier: 4.027A pdb=" N TRP D 374 " --> pdb=" O SER D 381 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LEU D 383 " --> pdb=" O THR D 372 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N THR D 372 " --> pdb=" O LEU D 383 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ASP D 385 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LYS D 370 " --> pdb=" O ASP D 385 " (cutoff:3.500A) 848 hydrogen bonds defined for protein. 2400 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: 5.88 Time building geometry restraints manager: 9.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3452 1.31 - 1.43: 6271 1.43 - 1.56: 13349 1.56 - 1.69: 124 1.69 - 1.81: 204 Bond restraints: 23400 Sorted by residual: bond pdb=" C31 POV B 902 " pdb=" O31 POV B 902 " ideal model delta sigma weight residual 1.327 1.425 -0.098 2.00e-02 2.50e+03 2.40e+01 bond pdb=" C31 POV A 902 " pdb=" O31 POV A 902 " ideal model delta sigma weight residual 1.327 1.424 -0.097 2.00e-02 2.50e+03 2.38e+01 bond pdb=" C31 POV D 905 " pdb=" O31 POV D 905 " ideal model delta sigma weight residual 1.327 1.424 -0.097 2.00e-02 2.50e+03 2.37e+01 bond pdb=" C31 POV C 902 " pdb=" O31 POV C 902 " ideal model delta sigma weight residual 1.327 1.424 -0.097 2.00e-02 2.50e+03 2.33e+01 bond pdb=" C21 POV D 902 " pdb=" O21 POV D 902 " ideal model delta sigma weight residual 1.330 1.426 -0.096 2.00e-02 2.50e+03 2.30e+01 ... (remaining 23395 not shown) Histogram of bond angle deviations from ideal: 96.79 - 104.24: 260 104.24 - 111.69: 10336 111.69 - 119.14: 8646 119.14 - 126.59: 11820 126.59 - 134.04: 294 Bond angle restraints: 31356 Sorted by residual: angle pdb=" C10 YBG A 903 " pdb=" C1 YBG A 903 " pdb=" C2 YBG A 903 " ideal model delta sigma weight residual 152.65 120.26 32.39 3.00e+00 1.11e-01 1.17e+02 angle pdb=" C10 YBG C 903 " pdb=" C1 YBG C 903 " pdb=" C2 YBG C 903 " ideal model delta sigma weight residual 152.65 120.41 32.24 3.00e+00 1.11e-01 1.16e+02 angle pdb=" C10 YBG D 906 " pdb=" C1 YBG D 906 " pdb=" C2 YBG D 906 " ideal model delta sigma weight residual 152.65 120.42 32.23 3.00e+00 1.11e-01 1.15e+02 angle pdb=" C10 YBG B 903 " pdb=" C1 YBG B 903 " pdb=" C2 YBG B 903 " ideal model delta sigma weight residual 152.65 120.51 32.14 3.00e+00 1.11e-01 1.15e+02 angle pdb=" C ARG A 430 " pdb=" N PHE A 431 " pdb=" CA PHE A 431 " ideal model delta sigma weight residual 121.54 133.14 -11.60 1.91e+00 2.74e-01 3.69e+01 ... (remaining 31351 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.80: 13424 35.80 - 71.59: 503 71.59 - 107.39: 80 107.39 - 143.19: 41 143.19 - 178.98: 28 Dihedral angle restraints: 14076 sinusoidal: 6328 harmonic: 7748 Sorted by residual: dihedral pdb=" CA ARG A 624 " pdb=" C ARG A 624 " pdb=" N PRO A 625 " pdb=" CA PRO A 625 " ideal model delta harmonic sigma weight residual 180.00 147.28 32.72 0 5.00e+00 4.00e-02 4.28e+01 dihedral pdb=" CA ARG B 624 " pdb=" C ARG B 624 " pdb=" N PRO B 625 " pdb=" CA PRO B 625 " ideal model delta harmonic sigma weight residual 180.00 147.31 32.69 0 5.00e+00 4.00e-02 4.27e+01 dihedral pdb=" CA ARG D 624 " pdb=" C ARG D 624 " pdb=" N PRO D 625 " pdb=" CA PRO D 625 " ideal model delta harmonic sigma weight residual 180.00 147.32 32.68 0 5.00e+00 4.00e-02 4.27e+01 ... (remaining 14073 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.997: 3356 0.997 - 1.994: 0 1.994 - 2.991: 0 2.991 - 3.988: 0 3.988 - 4.985: 4 Chirality restraints: 3360 Sorted by residual: chirality pdb=" C38 YBG A 903 " pdb=" C39 YBG A 903 " pdb=" C43 YBG A 903 " pdb=" O8 YBG A 903 " both_signs ideal model delta sigma weight residual False -2.52 2.47 -4.98 2.00e-01 2.50e+01 6.21e+02 chirality pdb=" C38 YBG B 903 " pdb=" C39 YBG B 903 " pdb=" C43 YBG B 903 " pdb=" O8 YBG B 903 " both_signs ideal model delta sigma weight residual False -2.52 2.45 -4.97 2.00e-01 2.50e+01 6.18e+02 chirality pdb=" C38 YBG D 906 " pdb=" C39 YBG D 906 " pdb=" C43 YBG D 906 " pdb=" O8 YBG D 906 " both_signs ideal model delta sigma weight residual False -2.52 2.45 -4.97 2.00e-01 2.50e+01 6.17e+02 ... (remaining 3357 not shown) Planarity restraints: 3796 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG C 624 " -0.056 5.00e-02 4.00e+02 8.41e-02 1.13e+01 pdb=" N PRO C 625 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO C 625 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO C 625 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 624 " 0.056 5.00e-02 4.00e+02 8.39e-02 1.13e+01 pdb=" N PRO B 625 " -0.145 5.00e-02 4.00e+02 pdb=" CA PRO B 625 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 625 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 624 " 0.056 5.00e-02 4.00e+02 8.38e-02 1.12e+01 pdb=" N PRO A 625 " -0.145 5.00e-02 4.00e+02 pdb=" CA PRO A 625 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 625 " 0.046 5.00e-02 4.00e+02 ... (remaining 3793 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1960 2.73 - 3.27: 21823 3.27 - 3.81: 37358 3.81 - 4.36: 48562 4.36 - 4.90: 80870 Nonbonded interactions: 190573 Sorted by model distance: nonbonded pdb=" O PRO A 765 " pdb=" OH TYR B 201 " model vdw 2.186 2.440 nonbonded pdb=" O PRO C 765 " pdb=" OH TYR D 201 " model vdw 2.222 2.440 nonbonded pdb=" OH TYR A 201 " pdb=" O PRO D 765 " model vdw 2.250 2.440 nonbonded pdb=" O PRO B 765 " pdb=" OH TYR C 201 " model vdw 2.251 2.440 nonbonded pdb=" N SER B 514 " pdb=" O6 YBG B 903 " model vdw 2.342 2.520 ... (remaining 190568 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 111 through 779 or resid 901 through 902 or (resid 904 and \ (name N or name C1 or name C11 or name C12 or name C13 or name C14 or name C15 \ or name C2 or name C21 or name C22 or name C23 or name C24 or name C25 or name C \ 26 or name C27 or name C28 or name C29 or name C3 or name C31 or name C32 or nam \ e C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name O11 or \ name O12 or name O13 or name O14 or name O21 or name O22 or name O31 or name O3 \ 2 or name P or name C210 or name C211 or name C212 or name C213 or name C214 or \ name C215 or name C216 or name C217 or name C218)) or (resid 905 and (name N or \ name C1 or name C11 or name C12 or name C13 or name C14 or name C15 or name C2 o \ r name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C \ 27 or name C28 or name C29 or name C3 or name C31 or name C32 or name C33 or nam \ e C34 or name C35 or name C36 or name C37 or name C38 or name C39 or name O11 or \ name O12 or name O13 or name O14 or name O21 or name O22 or name O31 or name O3 \ 2 or name P or name C210 or name C211 or name C212 or name C213 or name C214 or \ name C215 or name C216 or name C217 or name C218 or name C310 or name C311)) or \ resid 907 through 908 or (resid 909 and (name C22 or name C23 or name C24 or nam \ e C25 or name C26 or name C27 or name C28 or name C29 or name C210 or name C211 \ or name C212 or name C213 or name C214 or name C215 or name C216 or name C217 or \ name C218)))) selection = (chain 'B' and (resid 111 through 779 or resid 901 through 902 or (resid 904 and \ (name N or name C1 or name C11 or name C12 or name C13 or name C14 or name C15 \ or name C2 or name C21 or name C22 or name C23 or name C24 or name C25 or name C \ 26 or name C27 or name C28 or name C29 or name C3 or name C31 or name C32 or nam \ e C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name O11 or \ name O12 or name O13 or name O14 or name O21 or name O22 or name O31 or name O3 \ 2 or name P or name C210 or name C211 or name C212 or name C213 or name C214 or \ name C215 or name C216 or name C217 or name C218)) or (resid 905 and (name N or \ name C1 or name C11 or name C12 or name C13 or name C14 or name C15 or name C2 o \ r name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C \ 27 or name C28 or name C29 or name C3 or name C31 or name C32 or name C33 or nam \ e C34 or name C35 or name C36 or name C37 or name C38 or name C39 or name O11 or \ name O12 or name O13 or name O14 or name O21 or name O22 or name O31 or name O3 \ 2 or name P or name C210 or name C211 or name C212 or name C213 or name C214 or \ name C215 or name C216 or name C217 or name C218 or name C310 or name C311)) or \ resid 907 through 908 or (resid 909 and (name C22 or name C23 or name C24 or nam \ e C25 or name C26 or name C27 or name C28 or name C29 or name C210 or name C211 \ or name C212 or name C213 or name C214 or name C215 or name C216 or name C217 or \ name C218)))) selection = (chain 'C' and (resid 111 through 779 or resid 901 through 902 or (resid 904 and \ (name N or name C1 or name C11 or name C12 or name C13 or name C14 or name C15 \ or name C2 or name C21 or name C22 or name C23 or name C24 or name C25 or name C \ 26 or name C27 or name C28 or name C29 or name C3 or name C31 or name C32 or nam \ e C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name O11 or \ name O12 or name O13 or name O14 or name O21 or name O22 or name O31 or name O3 \ 2 or name P or name C210 or name C211 or name C212 or name C213 or name C214 or \ name C215 or name C216 or name C217 or name C218)) or (resid 905 and (name N or \ name C1 or name C11 or name C12 or name C13 or name C14 or name C15 or name C2 o \ r name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C \ 27 or name C28 or name C29 or name C3 or name C31 or name C32 or name C33 or nam \ e C34 or name C35 or name C36 or name C37 or name C38 or name C39 or name O11 or \ name O12 or name O13 or name O14 or name O21 or name O22 or name O31 or name O3 \ 2 or name P or name C210 or name C211 or name C212 or name C213 or name C214 or \ name C215 or name C216 or name C217 or name C218 or name C310 or name C311)) or \ resid 907 through 908 or (resid 909 and (name C22 or name C23 or name C24 or nam \ e C25 or name C26 or name C27 or name C28 or name C29 or name C210 or name C211 \ or name C212 or name C213 or name C214 or name C215 or name C216 or name C217 or \ name C218)))) selection = (chain 'D' and (resid 111 through 779 or (resid 901 and (name N or name C1 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C2 \ 8 or name C29 or name C3 or name C31 or name C32 or name C33 or name C34 or name \ C35 or name C36 or name C37 or name C38 or name O11 or name O12 or name O13 or \ name O14 or name O21 or name O22 or name O31 or name O32 or name P or name C210 \ or name C211 or name C212 or name C213 or name C214 or name C215 or name C216 or \ name C217 or name C218)) or (resid 902 and (name N or name C1 or name C11 or na \ me C12 or name C13 or name C14 or name C15 or name C2 or name C21 or name C22 or \ name C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C2 \ 9 or name C3 or name C31 or name C32 or name C33 or name C34 or name C35 or name \ C36 or name C37 or name C38 or name C39 or name O11 or name O12 or name O13 or \ name O14 or name O21 or name O22 or name O31 or name O32 or name P or name C210 \ or name C211 or name C212 or name C213 or name C214 or name C215 or name C216 or \ name C217 or name C218 or name C310 or name C311)) or resid 904 through 905 or \ resid 907 through 909)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 32 5.49 5 S 128 5.16 5 Cl 1 4.86 5 Na 1 4.78 5 C 15132 2.51 5 N 3532 2.21 5 O 4128 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.690 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: 5.490 Check model and map are aligned: 0.350 Process input model: 53.720 Find NCS groups from input model: 1.680 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Set scattering table: 0.200 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 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 : 0.011 0.098 23400 Z= 0.657 Angle : 1.422 32.389 31356 Z= 0.662 Chirality : 0.179 4.985 3360 Planarity : 0.007 0.084 3796 Dihedral : 21.175 178.984 9092 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.56 % Favored : 93.28 % Rotamer Outliers : 0.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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: -5.23 (0.12), residues: 2620 helix: -4.09 (0.06), residues: 1456 sheet: -0.93 (0.60), residues: 96 loop : -2.52 (0.16), residues: 1068 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 2332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 502 time to evaluate : 2.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 5 residues processed: 510 average time/residue: 0.4040 time to fit residues: 301.9222 Evaluate side-chains 270 residues out of total 2332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 265 time to evaluate : 2.783 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2077 time to fit residues: 5.6267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 219 optimal weight: 1.9990 chunk 197 optimal weight: 10.0000 chunk 109 optimal weight: 0.6980 chunk 67 optimal weight: 6.9990 chunk 132 optimal weight: 0.9990 chunk 105 optimal weight: 0.6980 chunk 203 optimal weight: 0.7980 chunk 78 optimal weight: 10.0000 chunk 123 optimal weight: 0.6980 chunk 151 optimal weight: 0.0000 chunk 236 optimal weight: 0.6980 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 ASN A 169 ASN A 225 ASN A 230 GLN A 261 ASN A 291 HIS ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 366 HIS A 421 ASN A 697 ASN ** A 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 126 ASN B 129 GLN B 169 ASN B 225 ASN B 230 GLN B 261 ASN B 291 HIS B 312 ASN B 421 ASN B 697 ASN C 129 GLN C 166 ASN C 169 ASN C 225 ASN C 230 GLN C 261 ASN C 291 HIS C 312 ASN C 421 ASN C 697 ASN D 129 GLN D 166 ASN D 169 ASN D 225 ASN D 230 GLN D 261 ASN D 291 HIS D 312 ASN D 360 GLN D 421 ASN D 697 ASN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 23400 Z= 0.158 Angle : 0.593 12.914 31356 Z= 0.299 Chirality : 0.038 0.205 3360 Planarity : 0.005 0.050 3796 Dihedral : 25.206 179.007 4028 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer Outliers : 2.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.67 (0.14), residues: 2620 helix: -1.55 (0.11), residues: 1456 sheet: -0.03 (0.61), residues: 84 loop : -2.09 (0.17), residues: 1080 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 308 time to evaluate : 2.602 Fit side-chains revert: symmetry clash outliers start: 54 outliers final: 37 residues processed: 354 average time/residue: 0.3567 time to fit residues: 195.2606 Evaluate side-chains 282 residues out of total 2332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 245 time to evaluate : 2.425 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 0 residues processed: 37 average time/residue: 0.2146 time to fit residues: 18.3691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 131 optimal weight: 10.0000 chunk 73 optimal weight: 5.9990 chunk 196 optimal weight: 7.9990 chunk 160 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 236 optimal weight: 0.9980 chunk 255 optimal weight: 9.9990 chunk 210 optimal weight: 0.0870 chunk 234 optimal weight: 0.0050 chunk 80 optimal weight: 0.0970 chunk 189 optimal weight: 0.2980 overall best weight: 0.2970 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN ** A 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 380 HIS ** C 630 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 129 GLN D 360 GLN D 380 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.3229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 23400 Z= 0.128 Angle : 0.522 12.097 31356 Z= 0.265 Chirality : 0.036 0.145 3360 Planarity : 0.004 0.044 3796 Dihedral : 22.671 178.214 4028 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.61 % Favored : 94.24 % Rotamer Outliers : 1.89 % 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: -1.27 (0.15), residues: 2620 helix: -0.07 (0.13), residues: 1456 sheet: -0.02 (0.58), residues: 84 loop : -1.96 (0.17), residues: 1080 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 276 time to evaluate : 2.687 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 15 residues processed: 311 average time/residue: 0.3614 time to fit residues: 175.9194 Evaluate side-chains 258 residues out of total 2332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 243 time to evaluate : 2.481 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.2040 time to fit residues: 9.2326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 233 optimal weight: 6.9990 chunk 177 optimal weight: 2.9990 chunk 122 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 112 optimal weight: 3.9990 chunk 158 optimal weight: 3.9990 chunk 237 optimal weight: 4.9990 chunk 251 optimal weight: 0.9990 chunk 124 optimal weight: 5.9990 chunk 224 optimal weight: 0.1980 chunk 67 optimal weight: 7.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN A 262 GLN A 562 GLN ** A 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 562 GLN C 562 GLN ** C 630 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 129 GLN D 215 ASN D 562 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.3635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 23400 Z= 0.208 Angle : 0.548 10.834 31356 Z= 0.275 Chirality : 0.038 0.161 3360 Planarity : 0.004 0.049 3796 Dihedral : 21.490 178.691 4028 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.85 % Favored : 95.00 % Rotamer Outliers : 2.19 % 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: -0.52 (0.16), residues: 2620 helix: 0.66 (0.14), residues: 1468 sheet: -0.19 (0.55), residues: 84 loop : -1.81 (0.18), residues: 1068 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 250 time to evaluate : 2.500 Fit side-chains revert: symmetry clash outliers start: 51 outliers final: 37 residues processed: 294 average time/residue: 0.3752 time to fit residues: 170.3535 Evaluate side-chains 255 residues out of total 2332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 218 time to evaluate : 2.659 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 0 residues processed: 37 average time/residue: 0.2141 time to fit residues: 18.3545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 209 optimal weight: 6.9990 chunk 142 optimal weight: 7.9990 chunk 3 optimal weight: 8.9990 chunk 187 optimal weight: 0.9990 chunk 103 optimal weight: 6.9990 chunk 214 optimal weight: 2.9990 chunk 173 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 128 optimal weight: 7.9990 chunk 225 optimal weight: 2.9990 chunk 63 optimal weight: 9.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 654 ASN ** A 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 366 HIS B 654 ASN ** C 630 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.4167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.063 23400 Z= 0.408 Angle : 0.656 10.561 31356 Z= 0.327 Chirality : 0.044 0.278 3360 Planarity : 0.004 0.042 3796 Dihedral : 21.602 176.961 4028 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.27 % Favored : 94.58 % Rotamer Outliers : 1.46 % 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: -0.50 (0.16), residues: 2620 helix: 0.65 (0.13), residues: 1472 sheet: -0.73 (0.52), residues: 84 loop : -1.71 (0.18), residues: 1064 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 213 time to evaluate : 2.522 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 21 residues processed: 244 average time/residue: 0.3907 time to fit residues: 144.9118 Evaluate side-chains 212 residues out of total 2332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 191 time to evaluate : 2.651 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.2263 time to fit residues: 12.4425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 84 optimal weight: 3.9990 chunk 226 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 chunk 147 optimal weight: 8.9990 chunk 62 optimal weight: 0.8980 chunk 251 optimal weight: 0.9980 chunk 208 optimal weight: 0.6980 chunk 116 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 HIS ** A 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 GLN ** C 630 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.4291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 23400 Z= 0.166 Angle : 0.531 10.202 31356 Z= 0.267 Chirality : 0.038 0.194 3360 Planarity : 0.003 0.043 3796 Dihedral : 20.436 172.177 4028 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.47 % Favored : 95.42 % Rotamer Outliers : 0.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.12 (0.16), residues: 2620 helix: 1.05 (0.14), residues: 1488 sheet: -0.64 (0.52), residues: 84 loop : -1.72 (0.18), residues: 1048 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 215 time to evaluate : 2.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 8 residues processed: 226 average time/residue: 0.3948 time to fit residues: 136.4258 Evaluate side-chains 209 residues out of total 2332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 201 time to evaluate : 2.817 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2203 time to fit residues: 6.4296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 242 optimal weight: 0.5980 chunk 28 optimal weight: 7.9990 chunk 143 optimal weight: 4.9990 chunk 183 optimal weight: 3.9990 chunk 142 optimal weight: 8.9990 chunk 211 optimal weight: 7.9990 chunk 140 optimal weight: 7.9990 chunk 250 optimal weight: 0.8980 chunk 156 optimal weight: 0.0870 chunk 152 optimal weight: 0.4980 chunk 115 optimal weight: 0.9980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 767 ASN B 322 HIS ** C 630 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.4432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 23400 Z= 0.147 Angle : 0.512 10.457 31356 Z= 0.256 Chirality : 0.037 0.189 3360 Planarity : 0.003 0.040 3796 Dihedral : 19.423 171.273 4028 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.04 % Favored : 94.85 % Rotamer Outliers : 0.64 % 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: 0.15 (0.17), residues: 2620 helix: 1.29 (0.14), residues: 1496 sheet: -0.45 (0.52), residues: 84 loop : -1.68 (0.18), residues: 1040 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 217 time to evaluate : 2.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 6 residues processed: 230 average time/residue: 0.3980 time to fit residues: 139.3477 Evaluate side-chains 211 residues out of total 2332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 205 time to evaluate : 2.783 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2269 time to fit residues: 6.1596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 155 optimal weight: 2.9990 chunk 100 optimal weight: 0.6980 chunk 149 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 48 optimal weight: 0.9980 chunk 159 optimal weight: 0.9990 chunk 170 optimal weight: 3.9990 chunk 123 optimal weight: 4.9990 chunk 23 optimal weight: 0.0000 chunk 196 optimal weight: 5.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 322 HIS C 630 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.4504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 23400 Z= 0.193 Angle : 0.532 12.437 31356 Z= 0.265 Chirality : 0.038 0.210 3360 Planarity : 0.003 0.040 3796 Dihedral : 19.054 169.433 4028 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.11 % Favored : 94.81 % Rotamer Outliers : 0.64 % 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: 0.23 (0.17), residues: 2620 helix: 1.37 (0.14), residues: 1496 sheet: -0.52 (0.51), residues: 84 loop : -1.65 (0.18), residues: 1040 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 214 time to evaluate : 2.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 8 residues processed: 227 average time/residue: 0.4369 time to fit residues: 152.1718 Evaluate side-chains 214 residues out of total 2332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 206 time to evaluate : 2.550 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2116 time to fit residues: 6.7227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 227 optimal weight: 4.9990 chunk 240 optimal weight: 0.9990 chunk 219 optimal weight: 1.9990 chunk 233 optimal weight: 0.9980 chunk 140 optimal weight: 4.9990 chunk 101 optimal weight: 6.9990 chunk 183 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 211 optimal weight: 1.9990 chunk 220 optimal weight: 0.9990 chunk 232 optimal weight: 2.9990 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 322 HIS ** A 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 322 HIS C 129 GLN C 630 ASN D 322 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.4587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 23400 Z= 0.199 Angle : 0.537 13.019 31356 Z= 0.268 Chirality : 0.038 0.200 3360 Planarity : 0.003 0.039 3796 Dihedral : 18.516 165.779 4028 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.34 % Favored : 94.58 % Rotamer Outliers : 0.43 % 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: 0.29 (0.17), residues: 2620 helix: 1.38 (0.14), residues: 1500 sheet: -0.55 (0.50), residues: 84 loop : -1.58 (0.18), residues: 1036 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 214 time to evaluate : 2.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 2 residues processed: 223 average time/residue: 0.3943 time to fit residues: 134.5006 Evaluate side-chains 207 residues out of total 2332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 205 time to evaluate : 2.428 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2124 time to fit residues: 4.1105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 153 optimal weight: 5.9990 chunk 246 optimal weight: 0.3980 chunk 150 optimal weight: 0.8980 chunk 117 optimal weight: 0.8980 chunk 171 optimal weight: 1.9990 chunk 259 optimal weight: 1.9990 chunk 238 optimal weight: 3.9990 chunk 206 optimal weight: 8.9990 chunk 21 optimal weight: 0.0570 chunk 159 optimal weight: 0.7980 chunk 126 optimal weight: 6.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 767 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.4699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.049 23400 Z= 0.148 Angle : 0.515 11.974 31356 Z= 0.256 Chirality : 0.037 0.196 3360 Planarity : 0.003 0.051 3796 Dihedral : 17.678 162.436 4028 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.31 % Favored : 94.66 % Rotamer Outliers : 0.26 % 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: 2620 helix: 1.45 (0.14), residues: 1520 sheet: -0.38 (0.51), residues: 84 loop : -1.60 (0.19), residues: 1016 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 222 time to evaluate : 2.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 227 average time/residue: 0.3934 time to fit residues: 137.6757 Evaluate side-chains 218 residues out of total 2332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 215 time to evaluate : 2.373 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1987 time to fit residues: 4.4221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 163 optimal weight: 0.7980 chunk 219 optimal weight: 0.9990 chunk 63 optimal weight: 7.9990 chunk 190 optimal weight: 1.9990 chunk 30 optimal weight: 0.0980 chunk 57 optimal weight: 3.9990 chunk 206 optimal weight: 8.9990 chunk 86 optimal weight: 0.0670 chunk 212 optimal weight: 0.1980 chunk 26 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 overall best weight: 0.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.130653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.097400 restraints weight = 35411.987| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 2.39 r_work: 0.3081 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3699 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3699 r_free = 0.3699 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3684 r_free = 0.3684 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| r_final: 0.3684 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.4808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.089 23400 Z= 0.137 Angle : 0.512 12.786 31356 Z= 0.255 Chirality : 0.037 0.203 3360 Planarity : 0.003 0.045 3796 Dihedral : 16.964 158.199 4028 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.15 % Favored : 94.81 % Rotamer Outliers : 0.39 % 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: 0.47 (0.17), residues: 2620 helix: 1.53 (0.14), residues: 1520 sheet: -0.32 (0.51), residues: 84 loop : -1.58 (0.19), residues: 1016 =============================================================================== Job complete usr+sys time: 4328.60 seconds wall clock time: 79 minutes 56.61 seconds (4796.61 seconds total)