Starting phenix.real_space_refine (version: dev) on Wed Dec 14 07:12:30 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tdo_25837/12_2022/7tdo_25837_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tdo_25837/12_2022/7tdo_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_25837/12_2022/7tdo_25837.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tdo_25837/12_2022/7tdo_25837.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tdo_25837/12_2022/7tdo_25837_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tdo_25837/12_2022/7tdo_25837_updated.pdb" } resolution = 3.15 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= 0.012 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 Convert atoms to be neutral 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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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: 11.88, per 1000 atoms: 0.61 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: 8.04 Conformation dependent library (CDL) restraints added in 3.1 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: 2.03 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: 5.35 Time building geometry restraints manager: 8.67 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 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. 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: 0.320 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: 3.890 Check model and map are aligned: 0.340 Convert atoms to be neutral: 0.160 Process input model: 50.810 Find NCS groups from input model: 1.500 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6785 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 % 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 *********************** 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 : 2.472 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: 0.3887 time to fit residues: 97.6683 Evaluate side-chains 109 residues out of total 2082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 2.449 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.3353 ------------------------------------------------------------------------------- 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: 2.9990 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: 1.6442 ------------------------------------------------------------------------------- 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: 0.6841 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 19860 Z= 0.207 Angle : 0.609 15.305 26850 Z= 0.290 Chirality : 0.042 0.153 3102 Planarity : 0.004 0.046 3492 Dihedral : 9.909 146.738 2778 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer Outliers : 0.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.17), residues: 2484 helix: -0.67 (0.15), residues: 1200 sheet: 1.74 (0.36), residues: 198 loop : -0.69 (0.20), residues: 1086 *********************** 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 121 residues out of total 2082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 118 time to evaluate : 2.583 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: 3 outliers final: 3 residues processed: 118 average time/residue: 0.3923 time to fit residues: 68.4913 Evaluate side-chains 112 residues out of total 2082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 109 time to evaluate : 2.498 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1908 time to fit residues: 4.4097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 127 optimal weight: 0.4980 chunk 71 optimal weight: 3.9990 chunk 190 optimal weight: 1.9990 chunk 155 optimal weight: 6.9990 chunk 63 optimal weight: 10.0000 chunk 229 optimal weight: 1.9990 chunk 247 optimal weight: 0.7980 chunk 204 optimal weight: 1.9990 chunk 227 optimal weight: 0.9990 chunk 78 optimal weight: 0.3980 chunk 183 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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: 0.6834 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.053 19860 Z= 0.156 Angle : 0.566 14.509 26850 Z= 0.259 Chirality : 0.041 0.144 3102 Planarity : 0.004 0.042 3492 Dihedral : 8.383 134.000 2778 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer Outliers : 0.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.17), residues: 2484 helix: -0.27 (0.15), residues: 1200 sheet: 1.91 (0.36), residues: 198 loop : -0.59 (0.20), residues: 1086 *********************** 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: 3 poor density : 108 time to evaluate : 2.498 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: 3 outliers final: 2 residues processed: 109 average time/residue: 0.4028 time to fit residues: 64.2528 Evaluate side-chains 102 residues out of total 2082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 100 time to evaluate : 2.442 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1805 time to fit residues: 4.0303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0370 chunk 118 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 109 optimal weight: 0.8980 chunk 153 optimal weight: 5.9990 chunk 230 optimal weight: 0.9990 chunk 243 optimal weight: 1.9990 chunk 120 optimal weight: 0.9980 chunk 218 optimal weight: 9.9990 chunk 65 optimal weight: 2.9990 overall best weight: 0.7860 ------------------------------------------------------------------------------- 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: 0.6833 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 19860 Z= 0.141 Angle : 0.536 10.842 26850 Z= 0.244 Chirality : 0.041 0.188 3102 Planarity : 0.004 0.042 3492 Dihedral : 7.648 126.242 2778 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer Outliers : 0.20 % 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: -0.13 (0.18), residues: 2484 helix: 0.04 (0.16), residues: 1194 sheet: 2.08 (0.37), residues: 198 loop : -0.52 (0.20), residues: 1092 *********************** 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 108 residues out of total 2082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 104 time to evaluate : 2.470 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: 4 outliers final: 1 residues processed: 107 average time/residue: 0.3905 time to fit residues: 61.5004 Evaluate side-chains 98 residues out of total 2082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 97 time to evaluate : 2.598 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1805 time to fit residues: 3.7994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 202 optimal weight: 0.2980 chunk 138 optimal weight: 7.9990 chunk 3 optimal weight: 0.0040 chunk 181 optimal weight: 10.0000 chunk 100 optimal weight: 1.9990 chunk 207 optimal weight: 0.0070 chunk 168 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 124 optimal weight: 3.9990 chunk 218 optimal weight: 0.9980 chunk 61 optimal weight: 0.3980 overall best weight: 0.3410 ------------------------------------------------------------------------------- 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: 0.6808 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 19860 Z= 0.124 Angle : 0.516 9.341 26850 Z= 0.233 Chirality : 0.040 0.132 3102 Planarity : 0.003 0.035 3492 Dihedral : 7.130 113.825 2778 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer Outliers : 0.20 % 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: 0.30 (0.18), residues: 2484 helix: 0.47 (0.16), residues: 1182 sheet: 2.54 (0.37), residues: 192 loop : -0.43 (0.20), residues: 1110 *********************** 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: 4 poor density : 109 time to evaluate : 2.684 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: 4 outliers final: 1 residues processed: 113 average time/residue: 0.4025 time to fit residues: 65.7807 Evaluate side-chains 100 residues out of total 2082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 99 time to evaluate : 2.265 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1952 time to fit residues: 3.3448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 81 optimal weight: 2.9990 chunk 219 optimal weight: 5.9990 chunk 48 optimal weight: 9.9990 chunk 143 optimal weight: 5.9990 chunk 60 optimal weight: 0.0870 chunk 243 optimal weight: 0.9990 chunk 202 optimal weight: 0.0770 chunk 112 optimal weight: 3.9990 chunk 20 optimal weight: 7.9990 chunk 80 optimal weight: 4.9990 chunk 128 optimal weight: 3.9990 overall best weight: 1.6322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 187 ASN C 343 HIS D 343 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6876 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 19860 Z= 0.185 Angle : 0.533 9.721 26850 Z= 0.244 Chirality : 0.041 0.151 3102 Planarity : 0.003 0.034 3492 Dihedral : 6.810 102.014 2778 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer Outliers : 0.68 % 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: 0.45 (0.18), residues: 2484 helix: 0.66 (0.16), residues: 1206 sheet: 2.45 (0.36), residues: 192 loop : -0.42 (0.20), residues: 1086 *********************** 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 114 residues out of total 2082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 100 time to evaluate : 2.809 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: 14 outliers final: 7 residues processed: 112 average time/residue: 0.4112 time to fit residues: 67.2527 Evaluate side-chains 102 residues out of total 2082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 95 time to evaluate : 2.482 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1683 time to fit residues: 5.5988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 235 optimal weight: 0.5980 chunk 27 optimal weight: 7.9990 chunk 138 optimal weight: 2.9990 chunk 178 optimal weight: 10.0000 chunk 137 optimal weight: 7.9990 chunk 205 optimal weight: 3.9990 chunk 136 optimal weight: 7.9990 chunk 242 optimal weight: 10.0000 chunk 152 optimal weight: 7.9990 chunk 148 optimal weight: 4.9990 chunk 112 optimal weight: 6.9990 overall best weight: 3.9188 ------------------------------------------------------------------------------- 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 B 343 HIS C 343 HIS D 187 ASN D 343 HIS E 187 ASN F 343 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6990 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.053 19860 Z= 0.349 Angle : 0.625 9.619 26850 Z= 0.299 Chirality : 0.044 0.144 3102 Planarity : 0.004 0.037 3492 Dihedral : 6.770 89.526 2778 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer Outliers : 0.49 % 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: 0.25 (0.18), residues: 2484 helix: 0.55 (0.16), residues: 1200 sheet: 1.90 (0.35), residues: 198 loop : -0.52 (0.20), residues: 1086 *********************** 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 107 residues out of total 2082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 97 time to evaluate : 2.326 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: 2 residues processed: 107 average time/residue: 0.4321 time to fit residues: 66.5398 Evaluate side-chains 95 residues out of total 2082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 93 time to evaluate : 2.517 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1774 time to fit residues: 4.0628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 150 optimal weight: 1.9990 chunk 96 optimal weight: 10.0000 chunk 145 optimal weight: 4.9990 chunk 73 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 154 optimal weight: 7.9990 chunk 165 optimal weight: 0.9990 chunk 120 optimal weight: 6.9990 chunk 22 optimal weight: 2.9990 chunk 190 optimal weight: 5.9990 chunk 220 optimal weight: 20.0000 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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: 0.6956 moved from start: 0.3378 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= 0.213 Angle : 0.558 9.669 26850 Z= 0.260 Chirality : 0.042 0.156 3102 Planarity : 0.003 0.039 3492 Dihedral : 6.421 81.012 2778 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer Outliers : 0.20 % 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: 0.48 (0.18), residues: 2484 helix: 0.77 (0.16), residues: 1194 sheet: 2.03 (0.35), residues: 198 loop : -0.43 (0.20), residues: 1092 *********************** 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 96 residues out of total 2082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 92 time to evaluate : 2.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 96 average time/residue: 0.4258 time to fit residues: 58.9910 Evaluate side-chains 91 residues out of total 2082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 89 time to evaluate : 2.383 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1650 time to fit residues: 3.7601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 232 optimal weight: 0.8980 chunk 212 optimal weight: 4.9990 chunk 226 optimal weight: 4.9990 chunk 136 optimal weight: 5.9990 chunk 98 optimal weight: 7.9990 chunk 177 optimal weight: 9.9990 chunk 69 optimal weight: 0.7980 chunk 204 optimal weight: 0.7980 chunk 214 optimal weight: 0.0470 chunk 225 optimal weight: 4.9990 chunk 148 optimal weight: 0.9980 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6904 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.039 19860 Z= 0.141 Angle : 0.540 11.103 26850 Z= 0.248 Chirality : 0.041 0.158 3102 Planarity : 0.004 0.047 3492 Dihedral : 5.776 80.951 2778 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer Outliers : 0.20 % 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: 0.80 (0.18), residues: 2484 helix: 1.09 (0.15), residues: 1200 sheet: 2.26 (0.35), residues: 198 loop : -0.38 (0.21), residues: 1086 *********************** 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 102 residues out of total 2082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 98 time to evaluate : 2.511 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: 4 outliers final: 1 residues processed: 102 average time/residue: 0.4211 time to fit residues: 62.6167 Evaluate side-chains 95 residues out of total 2082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 94 time to evaluate : 2.529 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1710 time to fit residues: 3.6612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 239 optimal weight: 0.7980 chunk 146 optimal weight: 7.9990 chunk 113 optimal weight: 0.7980 chunk 166 optimal weight: 1.9990 chunk 251 optimal weight: 0.6980 chunk 231 optimal weight: 4.9990 chunk 199 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 154 optimal weight: 0.9980 chunk 122 optimal weight: 0.5980 chunk 158 optimal weight: 0.0770 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6895 moved from start: 0.3644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 19860 Z= 0.133 Angle : 0.532 10.846 26850 Z= 0.243 Chirality : 0.041 0.151 3102 Planarity : 0.003 0.037 3492 Dihedral : 5.272 76.284 2778 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer Outliers : 0.00 % 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: 1.05 (0.18), residues: 2484 helix: 1.26 (0.15), residues: 1218 sheet: 2.37 (0.35), residues: 198 loop : -0.23 (0.21), residues: 1068 ********************** 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 95 residues out of total 2082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 2.544 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: 95 average time/residue: 0.4655 time to fit residues: 63.2496 Evaluate side-chains 92 residues out of total 2082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 2.504 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 184 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 55 optimal weight: 7.9990 chunk 200 optimal weight: 10.0000 chunk 83 optimal weight: 6.9990 chunk 205 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 175 optimal weight: 5.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 187 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.096753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.061214 restraints weight = 48305.473| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 4.23 r_work: 0.2675 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.3737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.028 19860 Z= 0.249 Angle : 0.571 10.569 26850 Z= 0.267 Chirality : 0.043 0.148 3102 Planarity : 0.004 0.035 3492 Dihedral : 5.022 71.338 2778 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer Outliers : 0.20 % 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: 0.97 (0.18), residues: 2484 helix: 1.25 (0.16), residues: 1200 sheet: 2.23 (0.35), residues: 198 loop : -0.28 (0.21), residues: 1086 =============================================================================== Job complete usr+sys time: 3128.04 seconds wall clock time: 57 minutes 46.15 seconds (3466.15 seconds total)