Starting phenix.real_space_refine on Mon Mar 18 01:20:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tdo_25837/03_2024/7tdo_25837_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tdo_25837/03_2024/7tdo_25837.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tdo_25837/03_2024/7tdo_25837.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tdo_25837/03_2024/7tdo_25837.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tdo_25837/03_2024/7tdo_25837_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tdo_25837/03_2024/7tdo_25837_updated.pdb" } resolution = 3.15 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.012 sd= 0.111 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: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 60 5.16 5 C 12348 2.51 5 N 3420 2.21 5 O 3732 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 471": "OE1" <-> "OE2" Residue "A GLU 506": "OE1" <-> "OE2" Residue "A GLU 548": "OE1" <-> "OE2" Residue "A GLU 556": "OE1" <-> "OE2" Residue "A GLU 570": "OE1" <-> "OE2" Residue "A GLU 590": "OE1" <-> "OE2" Residue "A GLU 596": "OE1" <-> "OE2" Residue "B GLU 471": "OE1" <-> "OE2" Residue "B GLU 506": "OE1" <-> "OE2" Residue "B GLU 548": "OE1" <-> "OE2" Residue "B GLU 556": "OE1" <-> "OE2" Residue "B GLU 570": "OE1" <-> "OE2" Residue "B GLU 590": "OE1" <-> "OE2" Residue "B GLU 596": "OE1" <-> "OE2" Residue "C GLU 471": "OE1" <-> "OE2" Residue "C GLU 506": "OE1" <-> "OE2" Residue "C GLU 548": "OE1" <-> "OE2" Residue "C GLU 556": "OE1" <-> "OE2" Residue "C GLU 570": "OE1" <-> "OE2" Residue "C GLU 590": "OE1" <-> "OE2" Residue "C GLU 596": "OE1" <-> "OE2" Residue "D GLU 471": "OE1" <-> "OE2" Residue "D GLU 506": "OE1" <-> "OE2" Residue "D GLU 548": "OE1" <-> "OE2" Residue "D GLU 556": "OE1" <-> "OE2" Residue "D GLU 570": "OE1" <-> "OE2" Residue "D GLU 590": "OE1" <-> "OE2" Residue "D GLU 596": "OE1" <-> "OE2" Residue "E GLU 471": "OE1" <-> "OE2" Residue "E GLU 506": "OE1" <-> "OE2" Residue "E GLU 548": "OE1" <-> "OE2" Residue "E GLU 556": "OE1" <-> "OE2" Residue "E GLU 570": "OE1" <-> "OE2" Residue "E GLU 590": "OE1" <-> "OE2" Residue "E GLU 596": "OE1" <-> "OE2" Residue "F GLU 471": "OE1" <-> "OE2" Residue "F GLU 506": "OE1" <-> "OE2" Residue "F GLU 548": "OE1" <-> "OE2" Residue "F GLU 556": "OE1" <-> "OE2" Residue "F GLU 570": "OE1" <-> "OE2" Residue "F GLU 590": "OE1" <-> "OE2" Residue "F GLU 596": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 19572 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3235 Classifications: {'peptide': 420} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 20, 'TRANS': 399} Chain breaks: 2 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "B" Number of atoms: 3235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3235 Classifications: {'peptide': 420} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 20, 'TRANS': 399} Chain breaks: 2 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "C" Number of atoms: 3235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3235 Classifications: {'peptide': 420} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 20, 'TRANS': 399} Chain breaks: 2 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "D" Number of atoms: 3235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3235 Classifications: {'peptide': 420} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 20, 'TRANS': 399} Chain breaks: 2 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "E" Number of atoms: 3235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3235 Classifications: {'peptide': 420} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 20, 'TRANS': 399} Chain breaks: 2 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "F" Number of atoms: 3235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3235 Classifications: {'peptide': 420} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 20, 'TRANS': 399} Chain breaks: 2 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.19, per 1000 atoms: 0.52 Number of scatterers: 19572 At special positions: 0 Unit cell: (135.472, 140.945, 90.3144, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 60 16.00 P 12 15.00 O 3732 8.00 N 3420 7.00 C 12348 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: 6.16 Conformation dependent library (CDL) restraints added in 3.5 seconds 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4656 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 102 helices and 12 sheets defined 42.4% alpha, 7.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.50 Creating SS restraints... Processing helix chain 'A' and resid 160 through 162 No H-bonds generated for 'chain 'A' and resid 160 through 162' Processing helix chain 'A' and resid 175 through 179 Processing helix chain 'A' and resid 207 through 217 removed outlier: 3.801A pdb=" N ALA A 211 " --> pdb=" O LYS A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 251 removed outlier: 3.576A pdb=" N ALA A 251 " --> pdb=" O ALA A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 265 No H-bonds generated for 'chain 'A' and resid 262 through 265' Processing helix chain 'A' and resid 282 through 293 Processing helix chain 'A' and resid 314 through 317 Processing helix chain 'A' and resid 333 through 343 removed outlier: 3.700A pdb=" N LYS A 337 " --> pdb=" O MET A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 360 Processing helix chain 'A' and resid 367 through 384 removed outlier: 4.380A pdb=" N GLU A 371 " --> pdb=" O GLY A 367 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASN A 372 " --> pdb=" O ALA A 368 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLU A 384 " --> pdb=" O LEU A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 402 removed outlier: 3.687A pdb=" N ASP A 399 " --> pdb=" O GLU A 395 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG A 400 " --> pdb=" O GLU A 396 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 433 removed outlier: 3.705A pdb=" N HIS A 427 " --> pdb=" O TYR A 423 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA A 428 " --> pdb=" O GLU A 424 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL A 429 " --> pdb=" O ALA A 425 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER A 431 " --> pdb=" O HIS A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 481 removed outlier: 3.777A pdb=" N LEU A 479 " --> pdb=" O LYS A 475 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU A 480 " --> pdb=" O LEU A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 489 removed outlier: 3.792A pdb=" N VAL A 488 " --> pdb=" O ALA A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 574 removed outlier: 3.809A pdb=" N LYS A 552 " --> pdb=" O GLU A 548 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ASP A 554 " --> pdb=" O ALA A 550 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLU A 555 " --> pdb=" O SER A 551 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU A 556 " --> pdb=" O LYS A 552 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS A 559 " --> pdb=" O GLU A 555 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR A 562 " --> pdb=" O LYS A 558 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ARG A 567 " --> pdb=" O ASN A 563 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS A 569 " --> pdb=" O TYR A 565 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLU A 570 " --> pdb=" O GLU A 566 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LYS A 574 " --> pdb=" O GLU A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 586 removed outlier: 4.215A pdb=" N ASN A 581 " --> pdb=" O LYS A 577 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ILE A 582 " --> pdb=" O GLN A 578 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL A 583 " --> pdb=" O LEU A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 601 Processing helix chain 'B' and resid 160 through 162 No H-bonds generated for 'chain 'B' and resid 160 through 162' Processing helix chain 'B' and resid 175 through 179 Processing helix chain 'B' and resid 207 through 217 removed outlier: 3.803A pdb=" N ALA B 211 " --> pdb=" O LYS B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 251 removed outlier: 3.577A pdb=" N ALA B 251 " --> pdb=" O ALA B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 265 No H-bonds generated for 'chain 'B' and resid 262 through 265' Processing helix chain 'B' and resid 282 through 293 Processing helix chain 'B' and resid 314 through 317 Processing helix chain 'B' and resid 333 through 343 removed outlier: 3.700A pdb=" N LYS B 337 " --> pdb=" O MET B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 360 Processing helix chain 'B' and resid 367 through 384 removed outlier: 4.380A pdb=" N GLU B 371 " --> pdb=" O GLY B 367 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASN B 372 " --> pdb=" O ALA B 368 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLU B 384 " --> pdb=" O LEU B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 402 removed outlier: 3.687A pdb=" N ASP B 399 " --> pdb=" O GLU B 395 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG B 400 " --> pdb=" O GLU B 396 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL B 401 " --> pdb=" O ALA B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 433 removed outlier: 3.706A pdb=" N HIS B 427 " --> pdb=" O TYR B 423 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA B 428 " --> pdb=" O GLU B 424 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL B 429 " --> pdb=" O ALA B 425 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER B 431 " --> pdb=" O HIS B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 481 removed outlier: 3.777A pdb=" N LEU B 479 " --> pdb=" O LYS B 475 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU B 480 " --> pdb=" O LEU B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 489 removed outlier: 3.792A pdb=" N VAL B 488 " --> pdb=" O ALA B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 574 removed outlier: 3.809A pdb=" N LYS B 552 " --> pdb=" O GLU B 548 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ASP B 554 " --> pdb=" O ALA B 550 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLU B 555 " --> pdb=" O SER B 551 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU B 556 " --> pdb=" O LYS B 552 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS B 559 " --> pdb=" O GLU B 555 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR B 562 " --> pdb=" O LYS B 558 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ARG B 567 " --> pdb=" O ASN B 563 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS B 569 " --> pdb=" O TYR B 565 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLU B 570 " --> pdb=" O GLU B 566 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS B 574 " --> pdb=" O GLU B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 586 removed outlier: 4.215A pdb=" N ASN B 581 " --> pdb=" O LYS B 577 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ILE B 582 " --> pdb=" O GLN B 578 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL B 583 " --> pdb=" O LEU B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 601 Processing helix chain 'C' and resid 160 through 162 No H-bonds generated for 'chain 'C' and resid 160 through 162' Processing helix chain 'C' and resid 175 through 179 Processing helix chain 'C' and resid 207 through 217 removed outlier: 3.803A pdb=" N ALA C 211 " --> pdb=" O LYS C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 251 removed outlier: 3.576A pdb=" N ALA C 251 " --> pdb=" O ALA C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 265 No H-bonds generated for 'chain 'C' and resid 262 through 265' Processing helix chain 'C' and resid 282 through 293 Processing helix chain 'C' and resid 314 through 317 Processing helix chain 'C' and resid 333 through 343 removed outlier: 3.700A pdb=" N LYS C 337 " --> pdb=" O MET C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 360 Processing helix chain 'C' and resid 367 through 384 removed outlier: 4.380A pdb=" N GLU C 371 " --> pdb=" O GLY C 367 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASN C 372 " --> pdb=" O ALA C 368 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLU C 384 " --> pdb=" O LEU C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 402 removed outlier: 3.687A pdb=" N ASP C 399 " --> pdb=" O GLU C 395 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG C 400 " --> pdb=" O GLU C 396 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL C 401 " --> pdb=" O ALA C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 433 removed outlier: 3.705A pdb=" N HIS C 427 " --> pdb=" O TYR C 423 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA C 428 " --> pdb=" O GLU C 424 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL C 429 " --> pdb=" O ALA C 425 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER C 431 " --> pdb=" O HIS C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 481 removed outlier: 3.776A pdb=" N LEU C 479 " --> pdb=" O LYS C 475 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU C 480 " --> pdb=" O LEU C 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 489 removed outlier: 3.792A pdb=" N VAL C 488 " --> pdb=" O ALA C 484 " (cutoff:3.500A) Processing helix chain 'C' and resid 547 through 574 removed outlier: 3.808A pdb=" N LYS C 552 " --> pdb=" O GLU C 548 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ASP C 554 " --> pdb=" O ALA C 550 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLU C 555 " --> pdb=" O SER C 551 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU C 556 " --> pdb=" O LYS C 552 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS C 559 " --> pdb=" O GLU C 555 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR C 562 " --> pdb=" O LYS C 558 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ARG C 567 " --> pdb=" O ASN C 563 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS C 569 " --> pdb=" O TYR C 565 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLU C 570 " --> pdb=" O GLU C 566 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS C 574 " --> pdb=" O GLU C 570 " (cutoff:3.500A) Processing helix chain 'C' and resid 577 through 586 removed outlier: 4.215A pdb=" N ASN C 581 " --> pdb=" O LYS C 577 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ILE C 582 " --> pdb=" O GLN C 578 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL C 583 " --> pdb=" O LEU C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 594 through 601 Processing helix chain 'D' and resid 160 through 162 No H-bonds generated for 'chain 'D' and resid 160 through 162' Processing helix chain 'D' and resid 175 through 179 Processing helix chain 'D' and resid 207 through 217 removed outlier: 3.802A pdb=" N ALA D 211 " --> pdb=" O LYS D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 251 removed outlier: 3.577A pdb=" N ALA D 251 " --> pdb=" O ALA D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 262 through 265 No H-bonds generated for 'chain 'D' and resid 262 through 265' Processing helix chain 'D' and resid 282 through 293 Processing helix chain 'D' and resid 314 through 317 Processing helix chain 'D' and resid 333 through 343 removed outlier: 3.700A pdb=" N LYS D 337 " --> pdb=" O MET D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 360 Processing helix chain 'D' and resid 367 through 384 removed outlier: 4.380A pdb=" N GLU D 371 " --> pdb=" O GLY D 367 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASN D 372 " --> pdb=" O ALA D 368 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLU D 384 " --> pdb=" O LEU D 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 402 removed outlier: 3.687A pdb=" N ASP D 399 " --> pdb=" O GLU D 395 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG D 400 " --> pdb=" O GLU D 396 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL D 401 " --> pdb=" O ALA D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 433 removed outlier: 3.705A pdb=" N HIS D 427 " --> pdb=" O TYR D 423 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA D 428 " --> pdb=" O GLU D 424 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL D 429 " --> pdb=" O ALA D 425 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER D 431 " --> pdb=" O HIS D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 481 removed outlier: 3.777A pdb=" N LEU D 479 " --> pdb=" O LYS D 475 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU D 480 " --> pdb=" O LEU D 476 " (cutoff:3.500A) Processing helix chain 'D' and resid 483 through 489 removed outlier: 3.792A pdb=" N VAL D 488 " --> pdb=" O ALA D 484 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 574 removed outlier: 3.809A pdb=" N LYS D 552 " --> pdb=" O GLU D 548 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ASP D 554 " --> pdb=" O ALA D 550 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLU D 555 " --> pdb=" O SER D 551 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU D 556 " --> pdb=" O LYS D 552 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS D 559 " --> pdb=" O GLU D 555 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR D 562 " --> pdb=" O LYS D 558 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ARG D 567 " --> pdb=" O ASN D 563 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS D 569 " --> pdb=" O TYR D 565 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLU D 570 " --> pdb=" O GLU D 566 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS D 574 " --> pdb=" O GLU D 570 " (cutoff:3.500A) Processing helix chain 'D' and resid 577 through 586 removed outlier: 4.215A pdb=" N ASN D 581 " --> pdb=" O LYS D 577 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ILE D 582 " --> pdb=" O GLN D 578 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL D 583 " --> pdb=" O LEU D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 594 through 601 Processing helix chain 'E' and resid 160 through 162 No H-bonds generated for 'chain 'E' and resid 160 through 162' Processing helix chain 'E' and resid 175 through 179 Processing helix chain 'E' and resid 207 through 217 removed outlier: 3.802A pdb=" N ALA E 211 " --> pdb=" O LYS E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 237 through 251 removed outlier: 3.576A pdb=" N ALA E 251 " --> pdb=" O ALA E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 262 through 265 No H-bonds generated for 'chain 'E' and resid 262 through 265' Processing helix chain 'E' and resid 282 through 293 Processing helix chain 'E' and resid 314 through 317 Processing helix chain 'E' and resid 333 through 343 removed outlier: 3.700A pdb=" N LYS E 337 " --> pdb=" O MET E 333 " (cutoff:3.500A) Processing helix chain 'E' and resid 355 through 360 Processing helix chain 'E' and resid 367 through 384 removed outlier: 4.380A pdb=" N GLU E 371 " --> pdb=" O GLY E 367 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASN E 372 " --> pdb=" O ALA E 368 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLU E 384 " --> pdb=" O LEU E 380 " (cutoff:3.500A) Processing helix chain 'E' and resid 391 through 402 removed outlier: 3.687A pdb=" N ASP E 399 " --> pdb=" O GLU E 395 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG E 400 " --> pdb=" O GLU E 396 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL E 401 " --> pdb=" O ALA E 397 " (cutoff:3.500A) Processing helix chain 'E' and resid 417 through 433 removed outlier: 3.705A pdb=" N HIS E 427 " --> pdb=" O TYR E 423 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA E 428 " --> pdb=" O GLU E 424 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL E 429 " --> pdb=" O ALA E 425 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER E 431 " --> pdb=" O HIS E 427 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 481 removed outlier: 3.777A pdb=" N LEU E 479 " --> pdb=" O LYS E 475 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU E 480 " --> pdb=" O LEU E 476 " (cutoff:3.500A) Processing helix chain 'E' and resid 483 through 489 removed outlier: 3.792A pdb=" N VAL E 488 " --> pdb=" O ALA E 484 " (cutoff:3.500A) Processing helix chain 'E' and resid 547 through 574 removed outlier: 3.809A pdb=" N LYS E 552 " --> pdb=" O GLU E 548 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ASP E 554 " --> pdb=" O ALA E 550 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLU E 555 " --> pdb=" O SER E 551 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU E 556 " --> pdb=" O LYS E 552 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS E 559 " --> pdb=" O GLU E 555 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR E 562 " --> pdb=" O LYS E 558 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ARG E 567 " --> pdb=" O ASN E 563 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS E 569 " --> pdb=" O TYR E 565 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLU E 570 " --> pdb=" O GLU E 566 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LYS E 574 " --> pdb=" O GLU E 570 " (cutoff:3.500A) Processing helix chain 'E' and resid 577 through 586 removed outlier: 4.216A pdb=" N ASN E 581 " --> pdb=" O LYS E 577 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ILE E 582 " --> pdb=" O GLN E 578 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL E 583 " --> pdb=" O LEU E 579 " (cutoff:3.500A) Processing helix chain 'E' and resid 594 through 601 Processing helix chain 'F' and resid 160 through 162 No H-bonds generated for 'chain 'F' and resid 160 through 162' Processing helix chain 'F' and resid 175 through 179 Processing helix chain 'F' and resid 207 through 217 removed outlier: 3.801A pdb=" N ALA F 211 " --> pdb=" O LYS F 207 " (cutoff:3.500A) Processing helix chain 'F' and resid 237 through 251 removed outlier: 3.576A pdb=" N ALA F 251 " --> pdb=" O ALA F 247 " (cutoff:3.500A) Processing helix chain 'F' and resid 262 through 265 No H-bonds generated for 'chain 'F' and resid 262 through 265' Processing helix chain 'F' and resid 282 through 293 Processing helix chain 'F' and resid 314 through 317 Processing helix chain 'F' and resid 333 through 343 removed outlier: 3.700A pdb=" N LYS F 337 " --> pdb=" O MET F 333 " (cutoff:3.500A) Processing helix chain 'F' and resid 355 through 360 Processing helix chain 'F' and resid 367 through 384 removed outlier: 4.380A pdb=" N GLU F 371 " --> pdb=" O GLY F 367 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASN F 372 " --> pdb=" O ALA F 368 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLU F 384 " --> pdb=" O LEU F 380 " (cutoff:3.500A) Processing helix chain 'F' and resid 391 through 402 removed outlier: 3.687A pdb=" N ASP F 399 " --> pdb=" O GLU F 395 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG F 400 " --> pdb=" O GLU F 396 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL F 401 " --> pdb=" O ALA F 397 " (cutoff:3.500A) Processing helix chain 'F' and resid 417 through 433 removed outlier: 3.705A pdb=" N HIS F 427 " --> pdb=" O TYR F 423 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA F 428 " --> pdb=" O GLU F 424 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL F 429 " --> pdb=" O ALA F 425 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER F 431 " --> pdb=" O HIS F 427 " (cutoff:3.500A) Processing helix chain 'F' and resid 475 through 481 removed outlier: 3.777A pdb=" N LEU F 479 " --> pdb=" O LYS F 475 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU F 480 " --> pdb=" O LEU F 476 " (cutoff:3.500A) Processing helix chain 'F' and resid 483 through 489 removed outlier: 3.792A pdb=" N VAL F 488 " --> pdb=" O ALA F 484 " (cutoff:3.500A) Processing helix chain 'F' and resid 547 through 574 removed outlier: 3.810A pdb=" N LYS F 552 " --> pdb=" O GLU F 548 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ASP F 554 " --> pdb=" O ALA F 550 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLU F 555 " --> pdb=" O SER F 551 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU F 556 " --> pdb=" O LYS F 552 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS F 559 " --> pdb=" O GLU F 555 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR F 562 " --> pdb=" O LYS F 558 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ARG F 567 " --> pdb=" O ASN F 563 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS F 569 " --> pdb=" O TYR F 565 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLU F 570 " --> pdb=" O GLU F 566 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LYS F 574 " --> pdb=" O GLU F 570 " (cutoff:3.500A) Processing helix chain 'F' and resid 577 through 586 removed outlier: 4.215A pdb=" N ASN F 581 " --> pdb=" O LYS F 577 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ILE F 582 " --> pdb=" O GLN F 578 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL F 583 " --> pdb=" O LEU F 579 " (cutoff:3.500A) Processing helix chain 'F' and resid 594 through 601 Processing sheet with id= A, first strand: chain 'A' and resid 324 through 327 removed outlier: 4.137A pdb=" N LYS A 324 " --> pdb=" O GLY A 196 " (cutoff:3.500A) removed outlier: 8.509A pdb=" N ILE A 197 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL A 302 " --> pdb=" O ILE A 197 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N LEU A 199 " --> pdb=" O VAL A 302 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ALA A 304 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N CYS A 255 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 8.413A pdb=" N MET A 303 " --> pdb=" O CYS A 255 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N VAL A 257 " --> pdb=" O MET A 303 " (cutoff:3.500A) removed outlier: 8.594A pdb=" N ALA A 305 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N ILE A 259 " --> pdb=" O ALA A 305 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 591 through 593 removed outlier: 7.007A pdb=" N LEU A 457 " --> pdb=" O HIS A 441 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N ILE A 443 " --> pdb=" O TYR A 455 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N TYR A 455 " --> pdb=" O ILE A 443 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 324 through 327 removed outlier: 4.136A pdb=" N LYS B 324 " --> pdb=" O GLY B 196 " (cutoff:3.500A) removed outlier: 8.509A pdb=" N ILE B 197 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL B 302 " --> pdb=" O ILE B 197 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N LEU B 199 " --> pdb=" O VAL B 302 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ALA B 304 " --> pdb=" O LEU B 199 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N CYS B 255 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 8.413A pdb=" N MET B 303 " --> pdb=" O CYS B 255 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N VAL B 257 " --> pdb=" O MET B 303 " (cutoff:3.500A) removed outlier: 8.594A pdb=" N ALA B 305 " --> pdb=" O VAL B 257 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N ILE B 259 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 591 through 593 removed outlier: 7.006A pdb=" N LEU B 457 " --> pdb=" O HIS B 441 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N ILE B 443 " --> pdb=" O TYR B 455 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N TYR B 455 " --> pdb=" O ILE B 443 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 324 through 327 removed outlier: 4.136A pdb=" N LYS C 324 " --> pdb=" O GLY C 196 " (cutoff:3.500A) removed outlier: 8.509A pdb=" N ILE C 197 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL C 302 " --> pdb=" O ILE C 197 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N LEU C 199 " --> pdb=" O VAL C 302 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ALA C 304 " --> pdb=" O LEU C 199 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N CYS C 255 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 8.413A pdb=" N MET C 303 " --> pdb=" O CYS C 255 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N VAL C 257 " --> pdb=" O MET C 303 " (cutoff:3.500A) removed outlier: 8.594A pdb=" N ALA C 305 " --> pdb=" O VAL C 257 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ILE C 259 " --> pdb=" O ALA C 305 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 591 through 593 removed outlier: 7.006A pdb=" N LEU C 457 " --> pdb=" O HIS C 441 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N ILE C 443 " --> pdb=" O TYR C 455 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N TYR C 455 " --> pdb=" O ILE C 443 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 324 through 327 removed outlier: 4.137A pdb=" N LYS D 324 " --> pdb=" O GLY D 196 " (cutoff:3.500A) removed outlier: 8.509A pdb=" N ILE D 197 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL D 302 " --> pdb=" O ILE D 197 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N LEU D 199 " --> pdb=" O VAL D 302 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ALA D 304 " --> pdb=" O LEU D 199 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N CYS D 255 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 8.413A pdb=" N MET D 303 " --> pdb=" O CYS D 255 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N VAL D 257 " --> pdb=" O MET D 303 " (cutoff:3.500A) removed outlier: 8.594A pdb=" N ALA D 305 " --> pdb=" O VAL D 257 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ILE D 259 " --> pdb=" O ALA D 305 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 591 through 593 removed outlier: 7.006A pdb=" N LEU D 457 " --> pdb=" O HIS D 441 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N ILE D 443 " --> pdb=" O TYR D 455 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N TYR D 455 " --> pdb=" O ILE D 443 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 324 through 327 removed outlier: 4.137A pdb=" N LYS E 324 " --> pdb=" O GLY E 196 " (cutoff:3.500A) removed outlier: 8.509A pdb=" N ILE E 197 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL E 302 " --> pdb=" O ILE E 197 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N LEU E 199 " --> pdb=" O VAL E 302 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ALA E 304 " --> pdb=" O LEU E 199 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N CYS E 255 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 8.412A pdb=" N MET E 303 " --> pdb=" O CYS E 255 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N VAL E 257 " --> pdb=" O MET E 303 " (cutoff:3.500A) removed outlier: 8.595A pdb=" N ALA E 305 " --> pdb=" O VAL E 257 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ILE E 259 " --> pdb=" O ALA E 305 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 591 through 593 removed outlier: 7.006A pdb=" N LEU E 457 " --> pdb=" O HIS E 441 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N ILE E 443 " --> pdb=" O TYR E 455 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N TYR E 455 " --> pdb=" O ILE E 443 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 324 through 327 removed outlier: 4.137A pdb=" N LYS F 324 " --> pdb=" O GLY F 196 " (cutoff:3.500A) removed outlier: 8.510A pdb=" N ILE F 197 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL F 302 " --> pdb=" O ILE F 197 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N LEU F 199 " --> pdb=" O VAL F 302 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ALA F 304 " --> pdb=" O LEU F 199 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N CYS F 255 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 8.413A pdb=" N MET F 303 " --> pdb=" O CYS F 255 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N VAL F 257 " --> pdb=" O MET F 303 " (cutoff:3.500A) removed outlier: 8.594A pdb=" N ALA F 305 " --> pdb=" O VAL F 257 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ILE F 259 " --> pdb=" O ALA F 305 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 591 through 593 removed outlier: 7.006A pdb=" N LEU F 457 " --> pdb=" O HIS F 441 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N ILE F 443 " --> pdb=" O TYR F 455 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N TYR F 455 " --> pdb=" O ILE F 443 " (cutoff:3.500A) 558 hydrogen bonds defined for protein. 1656 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: 4.70 Time building geometry restraints manager: 6.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6663 1.34 - 1.46: 2226 1.46 - 1.57: 10851 1.57 - 1.69: 18 1.69 - 1.80: 102 Bond restraints: 19860 Sorted by residual: bond pdb=" C4 ADP B 701 " pdb=" C5 ADP B 701 " ideal model delta sigma weight residual 1.490 1.366 0.124 2.00e-02 2.50e+03 3.86e+01 bond pdb=" C4 ADP D 701 " pdb=" C5 ADP D 701 " ideal model delta sigma weight residual 1.490 1.366 0.124 2.00e-02 2.50e+03 3.82e+01 bond pdb=" C4 ADP C 701 " pdb=" C5 ADP C 701 " ideal model delta sigma weight residual 1.490 1.367 0.123 2.00e-02 2.50e+03 3.80e+01 bond pdb=" C4 ADP A 701 " pdb=" C5 ADP A 701 " ideal model delta sigma weight residual 1.490 1.367 0.123 2.00e-02 2.50e+03 3.80e+01 bond pdb=" C4 ADP E 701 " pdb=" C5 ADP E 701 " ideal model delta sigma weight residual 1.490 1.367 0.123 2.00e-02 2.50e+03 3.76e+01 ... (remaining 19855 not shown) Histogram of bond angle deviations from ideal: 100.31 - 107.06: 578 107.06 - 113.80: 11492 113.80 - 120.55: 7876 120.55 - 127.29: 6760 127.29 - 134.04: 144 Bond angle restraints: 26850 Sorted by residual: angle pdb=" CA LEU D 173 " pdb=" CB LEU D 173 " pdb=" CG LEU D 173 " ideal model delta sigma weight residual 116.30 123.49 -7.19 3.50e+00 8.16e-02 4.22e+00 angle pdb=" CA LEU A 173 " pdb=" CB LEU A 173 " pdb=" CG LEU A 173 " ideal model delta sigma weight residual 116.30 123.47 -7.17 3.50e+00 8.16e-02 4.20e+00 angle pdb=" CA LEU C 173 " pdb=" CB LEU C 173 " pdb=" CG LEU C 173 " ideal model delta sigma weight residual 116.30 123.45 -7.15 3.50e+00 8.16e-02 4.17e+00 angle pdb=" O1B ADP C 701 " pdb=" PB ADP C 701 " pdb=" O3B ADP C 701 " ideal model delta sigma weight residual 119.90 113.78 6.12 3.00e+00 1.11e-01 4.16e+00 angle pdb=" CA LEU E 173 " pdb=" CB LEU E 173 " pdb=" CG LEU E 173 " ideal model delta sigma weight residual 116.30 123.44 -7.14 3.50e+00 8.16e-02 4.16e+00 ... (remaining 26845 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.67: 11960 31.67 - 63.35: 256 63.35 - 95.02: 12 95.02 - 126.69: 12 126.69 - 158.37: 6 Dihedral angle restraints: 12246 sinusoidal: 5046 harmonic: 7200 Sorted by residual: dihedral pdb=" C5' ADP A 701 " pdb=" O5' ADP A 701 " pdb=" PA ADP A 701 " pdb=" O2A ADP A 701 " ideal model delta sinusoidal sigma weight residual 300.00 141.64 158.37 1 2.00e+01 2.50e-03 4.63e+01 dihedral pdb=" C5' ADP D 701 " pdb=" O5' ADP D 701 " pdb=" PA ADP D 701 " pdb=" O2A ADP D 701 " ideal model delta sinusoidal sigma weight residual 300.00 141.68 158.33 1 2.00e+01 2.50e-03 4.63e+01 dihedral pdb=" C5' ADP E 701 " pdb=" O5' ADP E 701 " pdb=" PA ADP E 701 " pdb=" O2A ADP E 701 " ideal model delta sinusoidal sigma weight residual 300.00 141.68 158.33 1 2.00e+01 2.50e-03 4.63e+01 ... (remaining 12243 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1884 0.033 - 0.067: 902 0.067 - 0.100: 189 0.100 - 0.133: 121 0.133 - 0.167: 6 Chirality restraints: 3102 Sorted by residual: chirality pdb=" CB THR D 362 " pdb=" CA THR D 362 " pdb=" OG1 THR D 362 " pdb=" CG2 THR D 362 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.17 2.00e-01 2.50e+01 6.94e-01 chirality pdb=" CB THR C 362 " pdb=" CA THR C 362 " pdb=" OG1 THR C 362 " pdb=" CG2 THR C 362 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.80e-01 chirality pdb=" CB THR A 362 " pdb=" CA THR A 362 " pdb=" OG1 THR A 362 " pdb=" CG2 THR A 362 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.79e-01 ... (remaining 3099 not shown) Planarity restraints: 3492 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY E 201 " -0.034 5.00e-02 4.00e+02 5.15e-02 4.24e+00 pdb=" N PRO E 202 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO E 202 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO E 202 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY D 201 " -0.033 5.00e-02 4.00e+02 5.13e-02 4.22e+00 pdb=" N PRO D 202 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO D 202 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 202 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 201 " 0.033 5.00e-02 4.00e+02 5.13e-02 4.20e+00 pdb=" N PRO B 202 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO B 202 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 202 " 0.028 5.00e-02 4.00e+02 ... (remaining 3489 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 5292 2.81 - 3.33: 17132 3.33 - 3.85: 27452 3.85 - 4.38: 32746 4.38 - 4.90: 55875 Nonbonded interactions: 138497 Sorted by model distance: nonbonded pdb=" OG SER E 226 " pdb=" OG SER E 228 " model vdw 2.284 2.440 nonbonded pdb=" OG SER A 226 " pdb=" OG SER A 228 " model vdw 2.284 2.440 nonbonded pdb=" OG SER D 226 " pdb=" OG SER D 228 " model vdw 2.285 2.440 nonbonded pdb=" OG SER B 226 " pdb=" OG SER B 228 " model vdw 2.285 2.440 nonbonded pdb=" OG SER F 226 " pdb=" OG SER F 228 " model vdw 2.285 2.440 ... (remaining 138492 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.480 Check model and map are aligned: 0.270 Set scattering table: 0.150 Process input model: 46.720 Find NCS groups from input model: 1.170 Set up NCS constraints: 0.120 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6616 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 : 0.004 0.124 19860 Z= 0.270 Angle : 0.574 7.189 26850 Z= 0.302 Chirality : 0.043 0.167 3102 Planarity : 0.004 0.051 3492 Dihedral : 14.508 158.368 7590 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % 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: -1.16 (0.17), residues: 2484 helix: -1.16 (0.15), residues: 1170 sheet: 1.59 (0.35), residues: 198 loop : -0.59 (0.20), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 526 HIS 0.003 0.001 HIS C 458 PHE 0.004 0.001 PHE E 223 TYR 0.009 0.001 TYR D 545 ARG 0.002 0.000 ARG D 576 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 2082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 2.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.3957 time to fit residues: 98.3325 Evaluate side-chains 109 residues out of total 2082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 2.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 0.0270 chunk 191 optimal weight: 0.6980 chunk 105 optimal weight: 10.0000 chunk 65 optimal weight: 7.9990 chunk 128 optimal weight: 0.4980 chunk 102 optimal weight: 6.9990 chunk 197 optimal weight: 4.9990 chunk 76 optimal weight: 5.9990 chunk 120 optimal weight: 3.9990 chunk 147 optimal weight: 7.9990 chunk 228 optimal weight: 6.9990 overall best weight: 2.0442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6692 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19860 Z= 0.228 Angle : 0.618 15.262 26850 Z= 0.295 Chirality : 0.042 0.152 3102 Planarity : 0.004 0.047 3492 Dihedral : 9.922 147.145 2778 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 0.15 % Allowed : 5.33 % Favored : 94.53 % 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: -0.84 (0.17), residues: 2484 helix: -0.67 (0.15), residues: 1200 sheet: 1.73 (0.36), residues: 198 loop : -0.71 (0.20), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 526 HIS 0.006 0.001 HIS A 252 PHE 0.042 0.001 PHE E 246 TYR 0.007 0.001 TYR B 545 ARG 0.006 0.000 ARG B 308 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 2082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 116 time to evaluate : 2.177 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: 3 outliers final: 3 residues processed: 116 average time/residue: 0.3999 time to fit residues: 67.4207 Evaluate side-chains 108 residues out of total 2082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 105 time to evaluate : 2.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 303 MET Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain E residue 242 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 127 optimal weight: 9.9990 chunk 71 optimal weight: 4.9990 chunk 190 optimal weight: 1.9990 chunk 155 optimal weight: 4.9990 chunk 63 optimal weight: 9.9990 chunk 229 optimal weight: 0.6980 chunk 247 optimal weight: 0.7980 chunk 204 optimal weight: 6.9990 chunk 227 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 183 optimal weight: 5.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 285 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6724 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19860 Z= 0.205 Angle : 0.570 11.017 26850 Z= 0.268 Chirality : 0.042 0.138 3102 Planarity : 0.004 0.043 3492 Dihedral : 8.204 131.893 2778 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 0.10 % Allowed : 8.50 % Favored : 91.40 % 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: -0.40 (0.17), residues: 2484 helix: -0.20 (0.16), residues: 1194 sheet: 1.82 (0.36), residues: 198 loop : -0.61 (0.20), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 526 HIS 0.003 0.001 HIS E 458 PHE 0.053 0.001 PHE E 246 TYR 0.009 0.001 TYR B 423 ARG 0.006 0.000 ARG C 308 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 2082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 109 time to evaluate : 2.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 109 average time/residue: 0.4267 time to fit residues: 66.7468 Evaluate side-chains 100 residues out of total 2082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 98 time to evaluate : 2.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 303 MET Chi-restraints excluded: chain E residue 291 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 226 optimal weight: 5.9990 chunk 172 optimal weight: 0.3980 chunk 118 optimal weight: 0.0000 chunk 25 optimal weight: 0.8980 chunk 109 optimal weight: 0.8980 chunk 153 optimal weight: 6.9990 chunk 230 optimal weight: 0.9990 chunk 243 optimal weight: 2.9990 chunk 120 optimal weight: 0.8980 chunk 218 optimal weight: 9.9990 chunk 65 optimal weight: 0.9990 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6687 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 19860 Z= 0.132 Angle : 0.519 9.839 26850 Z= 0.240 Chirality : 0.041 0.229 3102 Planarity : 0.003 0.038 3492 Dihedral : 7.665 124.557 2778 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.49 % Allowed : 10.12 % Favored : 89.39 % 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: -0.15 (0.18), residues: 2484 helix: 0.05 (0.16), residues: 1194 sheet: 2.08 (0.36), residues: 198 loop : -0.57 (0.20), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 526 HIS 0.002 0.000 HIS F 252 PHE 0.032 0.001 PHE E 246 TYR 0.007 0.001 TYR C 545 ARG 0.006 0.000 ARG B 308 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 2082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 103 time to evaluate : 2.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 3 residues processed: 111 average time/residue: 0.4364 time to fit residues: 69.2396 Evaluate side-chains 98 residues out of total 2082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 95 time to evaluate : 2.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain E residue 291 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 202 optimal weight: 4.9990 chunk 138 optimal weight: 20.0000 chunk 3 optimal weight: 0.6980 chunk 181 optimal weight: 9.9990 chunk 100 optimal weight: 4.9990 chunk 207 optimal weight: 0.1980 chunk 168 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 124 optimal weight: 1.9990 chunk 218 optimal weight: 9.9990 chunk 61 optimal weight: 0.8980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 343 HIS ** D 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 343 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6739 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19860 Z= 0.192 Angle : 0.534 8.799 26850 Z= 0.249 Chirality : 0.041 0.159 3102 Planarity : 0.004 0.039 3492 Dihedral : 7.219 111.893 2778 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 0.68 % Allowed : 11.19 % Favored : 88.12 % 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 (0.18), residues: 2484 helix: 0.34 (0.16), residues: 1206 sheet: 2.09 (0.37), residues: 198 loop : -0.51 (0.20), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 526 HIS 0.004 0.001 HIS F 252 PHE 0.032 0.001 PHE E 246 TYR 0.007 0.001 TYR B 545 ARG 0.009 0.000 ARG B 308 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 2082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 99 time to evaluate : 2.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 9 residues processed: 111 average time/residue: 0.4083 time to fit residues: 65.0968 Evaluate side-chains 105 residues out of total 2082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 96 time to evaluate : 2.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain B residue 303 MET Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain C residue 255 CYS Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 467 VAL Chi-restraints excluded: chain D residue 467 VAL Chi-restraints excluded: chain E residue 467 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 81 optimal weight: 0.7980 chunk 219 optimal weight: 7.9990 chunk 48 optimal weight: 6.9990 chunk 143 optimal weight: 4.9990 chunk 60 optimal weight: 0.2980 chunk 243 optimal weight: 0.5980 chunk 202 optimal weight: 0.0970 chunk 112 optimal weight: 8.9990 chunk 20 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 chunk 128 optimal weight: 4.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6692 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 19860 Z= 0.130 Angle : 0.509 7.960 26850 Z= 0.234 Chirality : 0.040 0.133 3102 Planarity : 0.003 0.035 3492 Dihedral : 6.861 103.685 2778 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 0.39 % Allowed : 11.83 % Favored : 87.78 % 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: 0.35 (0.18), residues: 2484 helix: 0.61 (0.16), residues: 1200 sheet: 2.23 (0.37), residues: 198 loop : -0.49 (0.20), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 526 HIS 0.002 0.001 HIS B 427 PHE 0.026 0.001 PHE E 246 TYR 0.008 0.001 TYR C 545 ARG 0.007 0.000 ARG D 243 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 2082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 102 time to evaluate : 2.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 110 average time/residue: 0.4223 time to fit residues: 66.3833 Evaluate side-chains 100 residues out of total 2082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 97 time to evaluate : 2.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain C residue 467 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 235 optimal weight: 0.9990 chunk 27 optimal weight: 0.0170 chunk 138 optimal weight: 0.0670 chunk 178 optimal weight: 1.9990 chunk 137 optimal weight: 7.9990 chunk 205 optimal weight: 0.7980 chunk 136 optimal weight: 4.9990 chunk 242 optimal weight: 7.9990 chunk 152 optimal weight: 7.9990 chunk 148 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6699 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 19860 Z= 0.134 Angle : 0.510 10.283 26850 Z= 0.232 Chirality : 0.040 0.132 3102 Planarity : 0.003 0.034 3492 Dihedral : 6.541 93.727 2778 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.49 % Allowed : 12.22 % Favored : 87.29 % 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: 0.71 (0.18), residues: 2484 helix: 0.99 (0.16), residues: 1194 sheet: 2.32 (0.36), residues: 198 loop : -0.40 (0.20), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 526 HIS 0.002 0.001 HIS E 458 PHE 0.023 0.001 PHE E 246 TYR 0.007 0.001 TYR C 545 ARG 0.004 0.000 ARG D 243 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 2082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 102 time to evaluate : 2.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 9 residues processed: 112 average time/residue: 0.4153 time to fit residues: 66.9068 Evaluate side-chains 106 residues out of total 2082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 97 time to evaluate : 2.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain C residue 467 VAL Chi-restraints excluded: chain D residue 467 VAL Chi-restraints excluded: chain E residue 362 THR Chi-restraints excluded: chain E residue 467 VAL Chi-restraints excluded: chain F residue 362 THR Chi-restraints excluded: chain F residue 380 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 150 optimal weight: 5.9990 chunk 96 optimal weight: 20.0000 chunk 145 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 154 optimal weight: 8.9990 chunk 165 optimal weight: 1.9990 chunk 120 optimal weight: 7.9990 chunk 22 optimal weight: 0.9990 chunk 190 optimal weight: 5.9990 chunk 220 optimal weight: 7.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 ASN B 187 ASN C 187 ASN D 187 ASN D 343 HIS F 343 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6792 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 19860 Z= 0.257 Angle : 0.568 10.490 26850 Z= 0.267 Chirality : 0.042 0.138 3102 Planarity : 0.004 0.034 3492 Dihedral : 6.301 81.769 2778 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 0.78 % Allowed : 12.61 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.18), residues: 2484 helix: 0.92 (0.16), residues: 1200 sheet: 2.11 (0.35), residues: 198 loop : -0.46 (0.20), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 526 HIS 0.005 0.001 HIS E 458 PHE 0.022 0.001 PHE E 246 TYR 0.009 0.001 TYR A 465 ARG 0.004 0.000 ARG F 469 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 2082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 95 time to evaluate : 2.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 13 residues processed: 110 average time/residue: 0.4030 time to fit residues: 63.8782 Evaluate side-chains 106 residues out of total 2082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 93 time to evaluate : 2.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain B residue 303 MET Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 467 VAL Chi-restraints excluded: chain D residue 343 HIS Chi-restraints excluded: chain D residue 467 VAL Chi-restraints excluded: chain E residue 362 THR Chi-restraints excluded: chain E residue 467 VAL Chi-restraints excluded: chain E residue 514 GLN Chi-restraints excluded: chain F residue 362 THR Chi-restraints excluded: chain F residue 380 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 232 optimal weight: 5.9990 chunk 212 optimal weight: 6.9990 chunk 226 optimal weight: 3.9990 chunk 136 optimal weight: 6.9990 chunk 98 optimal weight: 8.9990 chunk 177 optimal weight: 8.9990 chunk 69 optimal weight: 0.9980 chunk 204 optimal weight: 2.9990 chunk 214 optimal weight: 0.0970 chunk 225 optimal weight: 0.2980 chunk 148 optimal weight: 7.9990 overall best weight: 1.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6766 moved from start: 0.3421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 19860 Z= 0.183 Angle : 0.539 9.578 26850 Z= 0.250 Chirality : 0.041 0.166 3102 Planarity : 0.003 0.034 3492 Dihedral : 5.887 80.510 2778 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.64 % Allowed : 13.20 % Favored : 86.17 % 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: 0.74 (0.18), residues: 2484 helix: 1.06 (0.16), residues: 1194 sheet: 2.23 (0.35), residues: 198 loop : -0.42 (0.20), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 526 HIS 0.005 0.001 HIS D 343 PHE 0.022 0.001 PHE E 246 TYR 0.008 0.001 TYR F 545 ARG 0.004 0.000 ARG D 345 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 2082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 96 time to evaluate : 2.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 11 residues processed: 107 average time/residue: 0.4139 time to fit residues: 63.4112 Evaluate side-chains 103 residues out of total 2082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 92 time to evaluate : 2.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain C residue 467 VAL Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 467 VAL Chi-restraints excluded: chain E residue 362 THR Chi-restraints excluded: chain E residue 467 VAL Chi-restraints excluded: chain E residue 514 GLN Chi-restraints excluded: chain F residue 362 THR Chi-restraints excluded: chain F residue 380 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 239 optimal weight: 0.0370 chunk 146 optimal weight: 0.8980 chunk 113 optimal weight: 10.0000 chunk 166 optimal weight: 0.9990 chunk 251 optimal weight: 3.9990 chunk 231 optimal weight: 2.9990 chunk 199 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 154 optimal weight: 0.7980 chunk 122 optimal weight: 1.9990 chunk 158 optimal weight: 0.0050 overall best weight: 0.5472 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6720 moved from start: 0.3572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 19860 Z= 0.132 Angle : 0.526 11.482 26850 Z= 0.241 Chirality : 0.041 0.149 3102 Planarity : 0.003 0.034 3492 Dihedral : 5.353 75.380 2778 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.49 % Allowed : 13.29 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.06 (0.18), residues: 2484 helix: 1.38 (0.16), residues: 1188 sheet: 2.41 (0.36), residues: 198 loop : -0.33 (0.20), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 526 HIS 0.003 0.001 HIS D 343 PHE 0.020 0.001 PHE E 246 TYR 0.007 0.001 TYR C 545 ARG 0.007 0.000 ARG C 308 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 2082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 94 time to evaluate : 2.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 10 residues processed: 104 average time/residue: 0.4131 time to fit residues: 61.9228 Evaluate side-chains 102 residues out of total 2082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 92 time to evaluate : 2.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 467 VAL Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 467 VAL Chi-restraints excluded: chain E residue 362 THR Chi-restraints excluded: chain E residue 467 VAL Chi-restraints excluded: chain F residue 362 THR Chi-restraints excluded: chain F residue 380 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 3.9990 chunk 61 optimal weight: 0.5980 chunk 184 optimal weight: 0.9990 chunk 29 optimal weight: 7.9990 chunk 55 optimal weight: 7.9990 chunk 200 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 205 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 175 optimal weight: 9.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.099003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.064186 restraints weight = 48802.056| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 4.25 r_work: 0.2737 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.3669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 19860 Z= 0.137 Angle : 0.520 10.912 26850 Z= 0.237 Chirality : 0.041 0.147 3102 Planarity : 0.003 0.034 3492 Dihedral : 4.859 67.639 2778 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.59 % Allowed : 13.34 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.22 (0.18), residues: 2484 helix: 1.55 (0.16), residues: 1188 sheet: 2.49 (0.36), residues: 198 loop : -0.30 (0.20), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 526 HIS 0.002 0.001 HIS E 458 PHE 0.020 0.001 PHE E 246 TYR 0.007 0.001 TYR C 545 ARG 0.006 0.000 ARG F 308 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3144.89 seconds wall clock time: 59 minutes 3.72 seconds (3543.72 seconds total)