Starting phenix.real_space_refine on Sat Mar 16 11:18:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7apk_11857/03_2024/7apk_11857.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7apk_11857/03_2024/7apk_11857.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7apk_11857/03_2024/7apk_11857.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7apk_11857/03_2024/7apk_11857.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7apk_11857/03_2024/7apk_11857.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7apk_11857/03_2024/7apk_11857.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 352 5.16 5 C 46063 2.51 5 N 12747 2.21 5 O 13535 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 145": "NH1" <-> "NH2" Residue "A ARG 165": "NH1" <-> "NH2" Residue "B ARG 268": "NH1" <-> "NH2" Residue "B ARG 396": "NH1" <-> "NH2" Residue "B ARG 520": "NH1" <-> "NH2" Residue "B ARG 555": "NH1" <-> "NH2" Residue "E ARG 660": "NH1" <-> "NH2" Residue "E ARG 663": "NH1" <-> "NH2" Residue "F ARG 115": "NH1" <-> "NH2" Residue "F ARG 221": "NH1" <-> "NH2" Residue "F ARG 258": "NH1" <-> "NH2" Residue "F ARG 335": "NH1" <-> "NH2" Residue "F PHE 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 145": "NH1" <-> "NH2" Residue "I ARG 165": "NH1" <-> "NH2" Residue "J ARG 268": "NH1" <-> "NH2" Residue "J ARG 396": "NH1" <-> "NH2" Residue "J ARG 520": "NH1" <-> "NH2" Residue "J ARG 555": "NH1" <-> "NH2" Residue "M ARG 64": "NH1" <-> "NH2" Residue "M ARG 113": "NH1" <-> "NH2" Residue "M ARG 663": "NH1" <-> "NH2" Residue "N ARG 115": "NH1" <-> "NH2" Residue "N ARG 221": "NH1" <-> "NH2" Residue "N ARG 258": "NH1" <-> "NH2" Residue "N ARG 335": "NH1" <-> "NH2" Residue "O ARG 52": "NH1" <-> "NH2" Residue "O ARG 116": "NH1" <-> "NH2" Residue "O ARG 132": "NH1" <-> "NH2" Residue "a ARG 145": "NH1" <-> "NH2" Residue "a ARG 165": "NH1" <-> "NH2" Residue "b ARG 268": "NH1" <-> "NH2" Residue "b ARG 396": "NH1" <-> "NH2" Residue "b ARG 520": "NH1" <-> "NH2" Residue "b ARG 555": "NH1" <-> "NH2" Residue "e ARG 660": "NH1" <-> "NH2" Residue "e ARG 663": "NH1" <-> "NH2" Residue "f ARG 115": "NH1" <-> "NH2" Residue "f ARG 221": "NH1" <-> "NH2" Residue "f ARG 258": "NH1" <-> "NH2" Residue "f ARG 335": "NH1" <-> "NH2" Residue "i ARG 145": "NH1" <-> "NH2" Residue "i ARG 165": "NH1" <-> "NH2" Residue "j ARG 268": "NH1" <-> "NH2" Residue "j ARG 396": "NH1" <-> "NH2" Residue "j ARG 520": "NH1" <-> "NH2" Residue "j ARG 555": "NH1" <-> "NH2" Residue "m ARG 64": "NH1" <-> "NH2" Residue "m ARG 113": "NH1" <-> "NH2" Residue "m ARG 663": "NH1" <-> "NH2" Residue "n ARG 115": "NH1" <-> "NH2" Residue "n ARG 221": "NH1" <-> "NH2" Residue "n ARG 258": "NH1" <-> "NH2" Residue "n ARG 335": "NH1" <-> "NH2" Residue "n PHE 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ARG 52": "NH1" <-> "NH2" Residue "o ARG 116": "NH1" <-> "NH2" Residue "o ARG 132": "NH1" <-> "NH2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 72697 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 2165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2165 Classifications: {'peptide': 266} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 8, 'TRANS': 257} Chain breaks: 8 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 4700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 706, 4700 Classifications: {'peptide': 706} Incomplete info: {'truncation_to_alanine': 293} Link IDs: {'PTRANS': 22, 'TRANS': 683} Chain breaks: 30 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 1102 Unresolved non-hydrogen angles: 1404 Unresolved non-hydrogen dihedrals: 923 Unresolved non-hydrogen chiralities: 100 Planarities with less than four sites: {'GLN:plan1': 20, 'ARG:plan': 16, 'TYR:plan': 14, 'ASN:plan1': 6, 'TRP:plan': 3, 'HIS:plan': 13, 'PHE:plan': 14, 'GLU:plan': 30, 'ASP:plan': 13} Unresolved non-hydrogen planarities: 611 Chain: "C" Number of atoms: 2349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2349 Classifications: {'peptide': 304} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 12, 'TRANS': 291} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "E" Number of atoms: 3687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 3687 Classifications: {'peptide': 523} Incomplete info: {'truncation_to_alanine': 149} Link IDs: {'PTRANS': 24, 'TRANS': 498} Chain breaks: 8 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 566 Unresolved non-hydrogen angles: 706 Unresolved non-hydrogen dihedrals: 468 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'GLN:plan1': 13, 'ASP:plan': 11, 'TYR:plan': 7, 'ASN:plan1': 4, 'TRP:plan': 1, 'HIS:plan': 5, 'PHE:plan': 1, 'GLU:plan': 18, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 323 Chain: "F" Number of atoms: 2604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2604 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 19, 'TRANS': 317} Chain: "G" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 760 Classifications: {'peptide': 153} Incomplete info: {'truncation_to_alanine': 140} Link IDs: {'TRANS': 152} Chain breaks: 2 Unresolved non-hydrogen bonds: 528 Unresolved non-hydrogen angles: 661 Unresolved non-hydrogen dihedrals: 440 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 7, 'TYR:plan': 6, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 3, 'GLU:plan': 20, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 299 Chain: "H" Number of atoms: 1398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1398 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 4, 'TRANS': 165} Chain: "I" Number of atoms: 2228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2228 Classifications: {'peptide': 275} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 8, 'TRANS': 266} Chain breaks: 9 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 4, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 28 Chain: "J" Number of atoms: 4702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 707, 4702 Classifications: {'peptide': 707} Incomplete info: {'truncation_to_alanine': 294} Link IDs: {'PTRANS': 22, 'TRANS': 684} Chain breaks: 30 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 1108 Unresolved non-hydrogen angles: 1411 Unresolved non-hydrogen dihedrals: 928 Unresolved non-hydrogen chiralities: 100 Planarities with less than four sites: {'GLN:plan1': 20, 'ASP:plan': 13, 'TYR:plan': 14, 'ASN:plan1': 6, 'TRP:plan': 3, 'HIS:plan': 13, 'PHE:plan': 14, 'GLU:plan': 30, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 616 Chain: "K" Number of atoms: 2349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2349 Classifications: {'peptide': 304} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 12, 'TRANS': 291} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "M" Number of atoms: 4216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 549, 4216 Classifications: {'peptide': 549} Incomplete info: {'truncation_to_alanine': 72} Link IDs: {'PTRANS': 27, 'TRANS': 521} Chain breaks: 9 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 249 Unresolved non-hydrogen angles: 309 Unresolved non-hydrogen dihedrals: 200 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 7, 'TYR:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 10, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 132 Chain: "N" Number of atoms: 2604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2604 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 19, 'TRANS': 317} Chain: "O" Number of atoms: 1084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1084 Classifications: {'peptide': 155} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 1, 'TRANS': 153} Chain breaks: 1 Unresolved non-hydrogen bonds: 212 Unresolved non-hydrogen angles: 268 Unresolved non-hydrogen dihedrals: 175 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 4, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 116 Chain: "P" Number of atoms: 1398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1398 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 4, 'TRANS': 165} Chain: "X" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 185 Classifications: {'peptide': 37} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'TRANS': 36} Chain breaks: 1 Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'UNK:plan-1': 37} Unresolved non-hydrogen planarities: 37 Chain: "a" Number of atoms: 2165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2165 Classifications: {'peptide': 266} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 8, 'TRANS': 257} Chain breaks: 8 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 23 Chain: "b" Number of atoms: 4700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 706, 4700 Classifications: {'peptide': 706} Incomplete info: {'truncation_to_alanine': 293} Link IDs: {'PTRANS': 22, 'TRANS': 683} Chain breaks: 30 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 1102 Unresolved non-hydrogen angles: 1404 Unresolved non-hydrogen dihedrals: 923 Unresolved non-hydrogen chiralities: 100 Planarities with less than four sites: {'GLN:plan1': 20, 'ARG:plan': 16, 'TYR:plan': 14, 'ASN:plan1': 6, 'TRP:plan': 3, 'HIS:plan': 13, 'PHE:plan': 14, 'GLU:plan': 30, 'ASP:plan': 13} Unresolved non-hydrogen planarities: 611 Chain: "c" Number of atoms: 2349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2349 Classifications: {'peptide': 304} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 12, 'TRANS': 291} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "e" Number of atoms: 3598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 3598 Classifications: {'peptide': 512} Incomplete info: {'truncation_to_alanine': 148} Link IDs: {'PTRANS': 22, 'TRANS': 489} Chain breaks: 9 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 562 Unresolved non-hydrogen angles: 702 Unresolved non-hydrogen dihedrals: 464 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'GLN:plan1': 13, 'ASP:plan': 11, 'TYR:plan': 7, 'ASN:plan1': 4, 'TRP:plan': 1, 'HIS:plan': 5, 'PHE:plan': 1, 'GLU:plan': 18, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 323 Chain: "f" Number of atoms: 2537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2537 Classifications: {'peptide': 329} Link IDs: {'PTRANS': 18, 'TRANS': 310} Chain breaks: 1 Chain: "g" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 760 Classifications: {'peptide': 153} Incomplete info: {'truncation_to_alanine': 140} Link IDs: {'TRANS': 152} Chain breaks: 2 Unresolved non-hydrogen bonds: 528 Unresolved non-hydrogen angles: 661 Unresolved non-hydrogen dihedrals: 440 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 7, 'TYR:plan': 6, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 3, 'GLU:plan': 20, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 299 Chain: "h" Number of atoms: 1398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1398 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 4, 'TRANS': 165} Chain: "i" Number of atoms: 2229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2229 Classifications: {'peptide': 275} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 8, 'TRANS': 266} Chain breaks: 9 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 4, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 28 Chain: "j" Number of atoms: 4696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 707, 4696 Classifications: {'peptide': 707} Incomplete info: {'truncation_to_alanine': 295} Link IDs: {'PTRANS': 22, 'TRANS': 684} Chain breaks: 30 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 1115 Unresolved non-hydrogen angles: 1420 Unresolved non-hydrogen dihedrals: 935 Unresolved non-hydrogen chiralities: 100 Planarities with less than four sites: {'GLN:plan1': 20, 'ASP:plan': 13, 'TYR:plan': 14, 'ASN:plan1': 6, 'TRP:plan': 3, 'HIS:plan': 13, 'PHE:plan': 15, 'GLU:plan': 30, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 622 Chain: "k" Number of atoms: 2349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2349 Classifications: {'peptide': 304} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 12, 'TRANS': 291} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "m" Number of atoms: 4216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 549, 4216 Classifications: {'peptide': 549} Incomplete info: {'truncation_to_alanine': 72} Link IDs: {'PTRANS': 27, 'TRANS': 521} Chain breaks: 9 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 249 Unresolved non-hydrogen angles: 309 Unresolved non-hydrogen dihedrals: 200 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 7, 'TYR:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 10, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 132 Chain: "n" Number of atoms: 2604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2604 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 19, 'TRANS': 317} Chain: "o" Number of atoms: 1084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1084 Classifications: {'peptide': 155} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 1, 'TRANS': 153} Chain breaks: 1 Unresolved non-hydrogen bonds: 212 Unresolved non-hydrogen angles: 268 Unresolved non-hydrogen dihedrals: 175 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 4, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 116 Chain: "p" Number of atoms: 1398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1398 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 4, 'TRANS': 165} Chain: "x" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 185 Classifications: {'peptide': 37} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'TRANS': 36} Chain breaks: 1 Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'UNK:plan-1': 37} Unresolved non-hydrogen planarities: 37 Time building chain proxies: 28.34, per 1000 atoms: 0.39 Number of scatterers: 72697 At special positions: 0 Unit cell: (343.04, 190.28, 335, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 352 16.00 O 13535 8.00 N 12747 7.00 C 46063 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: 21.92 Conformation dependent library (CDL) restraints added in 10.2 seconds 18858 Ramachandran restraints generated. 9429 Oldfield, 0 Emsley, 9429 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 19078 Finding SS restraints... Secondary structure from input PDB file: 374 helices and 72 sheets defined 57.7% alpha, 13.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.08 Creating SS restraints... Processing helix chain 'A' and resid 10 through 22 Processing helix chain 'A' and resid 30 through 37 Processing helix chain 'A' and resid 45 through 65 Processing helix chain 'A' and resid 72 through 84 Processing helix chain 'A' and resid 92 through 104 Processing helix chain 'A' and resid 106 through 120 Processing helix chain 'A' and resid 134 through 147 Processing helix chain 'A' and resid 152 through 167 Processing helix chain 'A' and resid 231 through 247 Processing helix chain 'A' and resid 254 through 275 removed outlier: 4.005A pdb=" N LYS A 275 " --> pdb=" O PHE A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 314 Processing helix chain 'A' and resid 314 through 334 removed outlier: 3.878A pdb=" N ARG A 318 " --> pdb=" O ASP A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 366 Processing helix chain 'A' and resid 370 through 392 Processing helix chain 'B' and resid 168 through 180 removed outlier: 4.143A pdb=" N TYR B 172 " --> pdb=" O GLU B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 204 Processing helix chain 'B' and resid 206 through 221 Processing helix chain 'B' and resid 224 through 237 removed outlier: 3.959A pdb=" N PHE B 228 " --> pdb=" O HIS B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 255 removed outlier: 4.185A pdb=" N CYS B 245 " --> pdb=" O PRO B 241 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR B 255 " --> pdb=" O LYS B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 274 Processing helix chain 'B' and resid 281 through 288 Processing helix chain 'B' and resid 296 through 307 Processing helix chain 'B' and resid 344 through 353 removed outlier: 3.615A pdb=" N LEU B 353 " --> pdb=" O LEU B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 376 through 391 removed outlier: 3.608A pdb=" N ALA B 380 " --> pdb=" O HIS B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 398 removed outlier: 3.602A pdb=" N TYR B 395 " --> pdb=" O ILE B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 439 Processing helix chain 'B' and resid 445 through 463 removed outlier: 3.928A pdb=" N PHE B 449 " --> pdb=" O ASP B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 497 removed outlier: 4.695A pdb=" N LEU B 492 " --> pdb=" O ASP B 488 " (cutoff:3.500A) Proline residue: B 493 - end of helix Processing helix chain 'B' and resid 503 through 513 removed outlier: 3.656A pdb=" N GLU B 507 " --> pdb=" O CYS B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 526 Processing helix chain 'B' and resid 535 through 554 removed outlier: 3.531A pdb=" N VAL B 539 " --> pdb=" O HIS B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 575 removed outlier: 3.531A pdb=" N GLN B 567 " --> pdb=" O PRO B 563 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N SER B 574 " --> pdb=" O LYS B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 575 through 590 removed outlier: 3.699A pdb=" N LEU B 579 " --> pdb=" O ASN B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 593 through 601 removed outlier: 3.566A pdb=" N VAL B 597 " --> pdb=" O LEU B 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 604 No H-bonds generated for 'chain 'B' and resid 602 through 604' Processing helix chain 'B' and resid 606 through 620 removed outlier: 4.360A pdb=" N ASP B 610 " --> pdb=" O SER B 606 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL B 611 " --> pdb=" O LEU B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 653 Processing helix chain 'B' and resid 657 through 670 Processing helix chain 'B' and resid 674 through 687 Processing helix chain 'B' and resid 697 through 701 Processing helix chain 'B' and resid 707 through 714 Processing helix chain 'B' and resid 724 through 733 Processing helix chain 'B' and resid 741 through 749 removed outlier: 3.655A pdb=" N GLN B 749 " --> pdb=" O LEU B 745 " (cutoff:3.500A) Processing helix chain 'B' and resid 753 through 757 removed outlier: 4.003A pdb=" N GLU B 757 " --> pdb=" O ILE B 754 " (cutoff:3.500A) Processing helix chain 'B' and resid 764 through 786 removed outlier: 3.661A pdb=" N SER B 786 " --> pdb=" O GLY B 782 " (cutoff:3.500A) Processing helix chain 'B' and resid 856 through 867 Processing helix chain 'B' and resid 873 through 884 Proline residue: B 878 - end of helix Processing helix chain 'B' and resid 889 through 893 removed outlier: 3.631A pdb=" N ALA B 893 " --> pdb=" O TYR B 890 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 928 through 959 Processing helix chain 'B' and resid 972 through 988 Proline residue: B 984 - end of helix Processing helix chain 'B' and resid 991 through 1005 removed outlier: 4.050A pdb=" N TYR B 995 " --> pdb=" O ILE B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1015 through 1021 removed outlier: 3.651A pdb=" N PHE B1021 " --> pdb=" O TYR B1017 " (cutoff:3.500A) Processing helix chain 'B' and resid 1025 through 1030 removed outlier: 4.182A pdb=" N SER B1030 " --> pdb=" O TYR B1026 " (cutoff:3.500A) Processing helix chain 'B' and resid 1035 through 1054 Processing helix chain 'B' and resid 1088 through 1113 Processing helix chain 'B' and resid 1118 through 1131 Processing helix chain 'B' and resid 1138 through 1154 Processing helix chain 'B' and resid 1161 through 1175 removed outlier: 3.694A pdb=" N SER B1175 " --> pdb=" O GLY B1171 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 42 Processing helix chain 'E' and resid 42 through 47 Processing helix chain 'E' and resid 56 through 74 Processing helix chain 'E' and resid 82 through 137 Processing helix chain 'E' and resid 190 through 247 Proline residue: E 231 - end of helix Proline residue: E 242 - end of helix Processing helix chain 'E' and resid 253 through 262 Processing helix chain 'E' and resid 265 through 282 Processing helix chain 'E' and resid 293 through 299 removed outlier: 3.612A pdb=" N ALA E 299 " --> pdb=" O ASP E 295 " (cutoff:3.500A) Processing helix chain 'E' and resid 334 through 341 Processing helix chain 'E' and resid 415 through 424 removed outlier: 3.622A pdb=" N GLN E 419 " --> pdb=" O ASN E 415 " (cutoff:3.500A) Processing helix chain 'E' and resid 431 through 438 Processing helix chain 'E' and resid 441 through 449 removed outlier: 3.960A pdb=" N GLN E 445 " --> pdb=" O TYR E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 464 through 497 removed outlier: 4.661A pdb=" N SER E 470 " --> pdb=" O SER E 466 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N HIS E 471 " --> pdb=" O LEU E 467 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLU E 473 " --> pdb=" O ALA E 469 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLN E 484 " --> pdb=" O LYS E 480 " (cutoff:3.500A) Processing helix chain 'E' and resid 506 through 511 removed outlier: 4.351A pdb=" N TYR E 509 " --> pdb=" O ASP E 506 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE E 511 " --> pdb=" O GLN E 508 " (cutoff:3.500A) Processing helix chain 'E' and resid 526 through 532 Processing helix chain 'E' and resid 536 through 543 removed outlier: 3.754A pdb=" N VAL E 540 " --> pdb=" O THR E 536 " (cutoff:3.500A) Processing helix chain 'E' and resid 595 through 607 removed outlier: 4.055A pdb=" N ARG E 599 " --> pdb=" O ASP E 595 " (cutoff:3.500A) Processing helix chain 'E' and resid 608 through 612 removed outlier: 3.502A pdb=" N GLU E 611 " --> pdb=" O CYS E 608 " (cutoff:3.500A) Processing helix chain 'E' and resid 620 through 639 Processing helix chain 'F' and resid 12 through 24 Processing helix chain 'F' and resid 53 through 57 Processing helix chain 'F' and resid 62 through 66 removed outlier: 3.696A pdb=" N LYS F 66 " --> pdb=" O GLU F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 106 removed outlier: 4.084A pdb=" N LEU F 106 " --> pdb=" O TRP F 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 102 through 106' Processing helix chain 'G' and resid 22 through 39 Processing helix chain 'G' and resid 45 through 128 removed outlier: 3.541A pdb=" N HIS G 128 " --> pdb=" O LYS G 124 " (cutoff:3.500A) Processing helix chain 'G' and resid 134 through 181 removed outlier: 3.880A pdb=" N LEU G 162 " --> pdb=" O ASP G 158 " (cutoff:3.500A) Processing helix chain 'H' and resid 273 through 285 Processing helix chain 'H' and resid 296 through 310 Processing helix chain 'H' and resid 322 through 335 Processing helix chain 'H' and resid 367 through 376 Processing helix chain 'H' and resid 393 through 408 removed outlier: 3.629A pdb=" N ALA H 397 " --> pdb=" O ASP H 393 " (cutoff:3.500A) Processing helix chain 'I' and resid 11 through 22 Processing helix chain 'I' and resid 30 through 37 Processing helix chain 'I' and resid 45 through 65 Processing helix chain 'I' and resid 71 through 84 Processing helix chain 'I' and resid 92 through 104 Processing helix chain 'I' and resid 106 through 119 Processing helix chain 'I' and resid 134 through 147 Processing helix chain 'I' and resid 152 through 167 Processing helix chain 'I' and resid 231 through 247 removed outlier: 3.612A pdb=" N TYR I 235 " --> pdb=" O ASP I 231 " (cutoff:3.500A) Processing helix chain 'I' and resid 248 through 251 removed outlier: 3.537A pdb=" N CYS I 251 " --> pdb=" O PRO I 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 248 through 251' Processing helix chain 'I' and resid 254 through 275 removed outlier: 4.166A pdb=" N LYS I 275 " --> pdb=" O PHE I 271 " (cutoff:3.500A) Processing helix chain 'I' and resid 315 through 333 Processing helix chain 'I' and resid 346 through 366 Processing helix chain 'I' and resid 370 through 392 removed outlier: 3.695A pdb=" N TRP I 391 " --> pdb=" O ASN I 387 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS I 392 " --> pdb=" O TRP I 388 " (cutoff:3.500A) Processing helix chain 'J' and resid 168 through 180 removed outlier: 3.579A pdb=" N TYR J 172 " --> pdb=" O GLU J 168 " (cutoff:3.500A) Processing helix chain 'J' and resid 189 through 204 Processing helix chain 'J' and resid 206 through 221 Processing helix chain 'J' and resid 225 through 237 Processing helix chain 'J' and resid 241 through 255 removed outlier: 4.411A pdb=" N CYS J 245 " --> pdb=" O PRO J 241 " (cutoff:3.500A) Processing helix chain 'J' and resid 264 through 276 removed outlier: 3.977A pdb=" N PHE J 276 " --> pdb=" O VAL J 272 " (cutoff:3.500A) Processing helix chain 'J' and resid 280 through 288 removed outlier: 3.931A pdb=" N LEU J 284 " --> pdb=" O ASP J 280 " (cutoff:3.500A) Processing helix chain 'J' and resid 296 through 307 Processing helix chain 'J' and resid 344 through 353 removed outlier: 3.637A pdb=" N LEU J 353 " --> pdb=" O LEU J 349 " (cutoff:3.500A) Processing helix chain 'J' and resid 359 through 366 Processing helix chain 'J' and resid 376 through 391 removed outlier: 3.607A pdb=" N ALA J 380 " --> pdb=" O HIS J 376 " (cutoff:3.500A) Processing helix chain 'J' and resid 391 through 398 removed outlier: 3.606A pdb=" N TYR J 395 " --> pdb=" O ILE J 391 " (cutoff:3.500A) Processing helix chain 'J' and resid 425 through 439 Processing helix chain 'J' and resid 445 through 463 removed outlier: 3.930A pdb=" N PHE J 449 " --> pdb=" O ASP J 445 " (cutoff:3.500A) Processing helix chain 'J' and resid 477 through 497 removed outlier: 4.695A pdb=" N LEU J 492 " --> pdb=" O ASP J 488 " (cutoff:3.500A) Proline residue: J 493 - end of helix Processing helix chain 'J' and resid 503 through 513 removed outlier: 3.656A pdb=" N GLU J 507 " --> pdb=" O CYS J 503 " (cutoff:3.500A) Processing helix chain 'J' and resid 518 through 526 Processing helix chain 'J' and resid 535 through 554 removed outlier: 3.530A pdb=" N VAL J 539 " --> pdb=" O HIS J 535 " (cutoff:3.500A) Processing helix chain 'J' and resid 563 through 575 removed outlier: 3.531A pdb=" N GLN J 567 " --> pdb=" O PRO J 563 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N SER J 574 " --> pdb=" O LYS J 570 " (cutoff:3.500A) Processing helix chain 'J' and resid 575 through 590 removed outlier: 3.700A pdb=" N LEU J 579 " --> pdb=" O ASN J 575 " (cutoff:3.500A) Processing helix chain 'J' and resid 593 through 601 removed outlier: 3.566A pdb=" N VAL J 597 " --> pdb=" O LEU J 593 " (cutoff:3.500A) Processing helix chain 'J' and resid 602 through 604 No H-bonds generated for 'chain 'J' and resid 602 through 604' Processing helix chain 'J' and resid 606 through 620 removed outlier: 4.362A pdb=" N ASP J 610 " --> pdb=" O SER J 606 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL J 611 " --> pdb=" O LEU J 607 " (cutoff:3.500A) Processing helix chain 'J' and resid 637 through 653 Processing helix chain 'J' and resid 657 through 670 Processing helix chain 'J' and resid 674 through 687 Processing helix chain 'J' and resid 697 through 701 Processing helix chain 'J' and resid 707 through 714 Processing helix chain 'J' and resid 724 through 733 Processing helix chain 'J' and resid 741 through 749 removed outlier: 3.658A pdb=" N GLN J 749 " --> pdb=" O LEU J 745 " (cutoff:3.500A) Processing helix chain 'J' and resid 753 through 757 removed outlier: 4.003A pdb=" N GLU J 757 " --> pdb=" O ILE J 754 " (cutoff:3.500A) Processing helix chain 'J' and resid 764 through 786 removed outlier: 3.661A pdb=" N SER J 786 " --> pdb=" O GLY J 782 " (cutoff:3.500A) Processing helix chain 'J' and resid 856 through 867 Processing helix chain 'J' and resid 873 through 884 Proline residue: J 878 - end of helix Processing helix chain 'J' and resid 889 through 893 removed outlier: 3.634A pdb=" N ALA J 893 " --> pdb=" O TYR J 890 " (cutoff:3.500A) Processing helix chain 'J' and resid 897 through 908 Processing helix chain 'J' and resid 928 through 959 Processing helix chain 'J' and resid 972 through 988 Proline residue: J 984 - end of helix Processing helix chain 'J' and resid 991 through 1005 removed outlier: 4.051A pdb=" N TYR J 995 " --> pdb=" O ILE J 991 " (cutoff:3.500A) Processing helix chain 'J' and resid 1015 through 1021 removed outlier: 3.652A pdb=" N PHE J1021 " --> pdb=" O TYR J1017 " (cutoff:3.500A) Processing helix chain 'J' and resid 1025 through 1030 removed outlier: 4.183A pdb=" N SER J1030 " --> pdb=" O TYR J1026 " (cutoff:3.500A) Processing helix chain 'J' and resid 1035 through 1054 Processing helix chain 'J' and resid 1088 through 1113 Processing helix chain 'J' and resid 1118 through 1131 Processing helix chain 'J' and resid 1138 through 1154 Processing helix chain 'J' and resid 1161 through 1175 removed outlier: 3.692A pdb=" N SER J1175 " --> pdb=" O GLY J1171 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 42 Processing helix chain 'M' and resid 48 through 73 Processing helix chain 'M' and resid 81 through 148 removed outlier: 3.852A pdb=" N ALA M 119 " --> pdb=" O GLN M 115 " (cutoff:3.500A) Processing helix chain 'M' and resid 161 through 169 Processing helix chain 'M' and resid 170 through 175 Processing helix chain 'M' and resid 176 through 179 Processing helix chain 'M' and resid 183 through 240 Proline residue: M 231 - end of helix Processing helix chain 'M' and resid 244 through 248 Processing helix chain 'M' and resid 260 through 264 removed outlier: 3.597A pdb=" N HIS M 263 " --> pdb=" O THR M 260 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU M 264 " --> pdb=" O ALA M 261 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 260 through 264' Processing helix chain 'M' and resid 265 through 282 removed outlier: 3.554A pdb=" N CYS M 282 " --> pdb=" O TYR M 278 " (cutoff:3.500A) Processing helix chain 'M' and resid 293 through 299 removed outlier: 3.846A pdb=" N ALA M 299 " --> pdb=" O ASP M 295 " (cutoff:3.500A) Processing helix chain 'M' and resid 335 through 342 Processing helix chain 'M' and resid 415 through 425 removed outlier: 3.864A pdb=" N GLN M 419 " --> pdb=" O ASN M 415 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL M 425 " --> pdb=" O GLN M 421 " (cutoff:3.500A) Processing helix chain 'M' and resid 431 through 438 Processing helix chain 'M' and resid 441 through 449 removed outlier: 3.916A pdb=" N GLN M 445 " --> pdb=" O TYR M 441 " (cutoff:3.500A) Processing helix chain 'M' and resid 471 through 497 Processing helix chain 'M' and resid 506 through 511 removed outlier: 4.353A pdb=" N TYR M 509 " --> pdb=" O ASP M 506 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE M 511 " --> pdb=" O GLN M 508 " (cutoff:3.500A) Processing helix chain 'M' and resid 526 through 532 Processing helix chain 'M' and resid 536 through 543 removed outlier: 3.752A pdb=" N VAL M 540 " --> pdb=" O THR M 536 " (cutoff:3.500A) Processing helix chain 'M' and resid 595 through 607 removed outlier: 4.055A pdb=" N ARG M 599 " --> pdb=" O ASP M 595 " (cutoff:3.500A) Processing helix chain 'M' and resid 608 through 612 Processing helix chain 'M' and resid 620 through 639 Processing helix chain 'N' and resid 12 through 24 Processing helix chain 'N' and resid 53 through 57 Processing helix chain 'N' and resid 62 through 66 removed outlier: 3.695A pdb=" N LYS N 66 " --> pdb=" O GLU N 63 " (cutoff:3.500A) Processing helix chain 'N' and resid 102 through 106 removed outlier: 4.079A pdb=" N LEU N 106 " --> pdb=" O TRP N 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 102 through 106' Processing helix chain 'O' and resid 22 through 39 Processing helix chain 'O' and resid 47 through 127 removed outlier: 3.904A pdb=" N LEU O 68 " --> pdb=" O MET O 64 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU O 69 " --> pdb=" O GLY O 65 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LYS O 86 " --> pdb=" O GLU O 82 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU O 87 " --> pdb=" O LYS O 83 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLU O 97 " --> pdb=" O ALA O 93 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL O 125 " --> pdb=" O ALA O 121 " (cutoff:3.500A) Processing helix chain 'O' and resid 132 through 181 Processing helix chain 'P' and resid 273 through 285 Processing helix chain 'P' and resid 296 through 310 Processing helix chain 'P' and resid 322 through 335 Processing helix chain 'P' and resid 367 through 376 Processing helix chain 'P' and resid 393 through 408 removed outlier: 3.629A pdb=" N ALA P 397 " --> pdb=" O ASP P 393 " (cutoff:3.500A) Processing helix chain 'X' and resid 2 through 20 removed outlier: 3.553A pdb=" N UNK X 20 " --> pdb=" O UNK X 16 " (cutoff:3.500A) Processing helix chain 'X' and resid 51 through 66 Processing helix chain 'a' and resid 11 through 22 Processing helix chain 'a' and resid 30 through 37 Processing helix chain 'a' and resid 45 through 65 Processing helix chain 'a' and resid 72 through 84 Processing helix chain 'a' and resid 92 through 104 Processing helix chain 'a' and resid 106 through 120 Processing helix chain 'a' and resid 134 through 147 Processing helix chain 'a' and resid 152 through 167 Processing helix chain 'a' and resid 231 through 247 Processing helix chain 'a' and resid 254 through 275 removed outlier: 4.005A pdb=" N LYS a 275 " --> pdb=" O PHE a 271 " (cutoff:3.500A) Processing helix chain 'a' and resid 309 through 314 Processing helix chain 'a' and resid 314 through 334 removed outlier: 3.878A pdb=" N ARG a 318 " --> pdb=" O ASP a 314 " (cutoff:3.500A) Processing helix chain 'a' and resid 346 through 366 Processing helix chain 'a' and resid 370 through 392 Processing helix chain 'b' and resid 168 through 180 removed outlier: 4.144A pdb=" N TYR b 172 " --> pdb=" O GLU b 168 " (cutoff:3.500A) Processing helix chain 'b' and resid 189 through 204 Processing helix chain 'b' and resid 206 through 221 Processing helix chain 'b' and resid 224 through 237 removed outlier: 3.958A pdb=" N PHE b 228 " --> pdb=" O HIS b 224 " (cutoff:3.500A) Processing helix chain 'b' and resid 241 through 255 removed outlier: 4.185A pdb=" N CYS b 245 " --> pdb=" O PRO b 241 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR b 255 " --> pdb=" O LYS b 251 " (cutoff:3.500A) Processing helix chain 'b' and resid 264 through 274 Processing helix chain 'b' and resid 281 through 288 Processing helix chain 'b' and resid 296 through 307 Processing helix chain 'b' and resid 344 through 353 removed outlier: 3.616A pdb=" N LEU b 353 " --> pdb=" O LEU b 349 " (cutoff:3.500A) Processing helix chain 'b' and resid 359 through 366 Processing helix chain 'b' and resid 376 through 391 removed outlier: 3.607A pdb=" N ALA b 380 " --> pdb=" O HIS b 376 " (cutoff:3.500A) Processing helix chain 'b' and resid 391 through 398 removed outlier: 3.602A pdb=" N TYR b 395 " --> pdb=" O ILE b 391 " (cutoff:3.500A) Processing helix chain 'b' and resid 425 through 439 Processing helix chain 'b' and resid 445 through 463 removed outlier: 3.930A pdb=" N PHE b 449 " --> pdb=" O ASP b 445 " (cutoff:3.500A) Processing helix chain 'b' and resid 477 through 497 removed outlier: 4.696A pdb=" N LEU b 492 " --> pdb=" O ASP b 488 " (cutoff:3.500A) Proline residue: b 493 - end of helix Processing helix chain 'b' and resid 503 through 513 removed outlier: 3.656A pdb=" N GLU b 507 " --> pdb=" O CYS b 503 " (cutoff:3.500A) Processing helix chain 'b' and resid 518 through 526 Processing helix chain 'b' and resid 535 through 554 removed outlier: 3.530A pdb=" N VAL b 539 " --> pdb=" O HIS b 535 " (cutoff:3.500A) Processing helix chain 'b' and resid 563 through 575 removed outlier: 3.531A pdb=" N GLN b 567 " --> pdb=" O PRO b 563 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N SER b 574 " --> pdb=" O LYS b 570 " (cutoff:3.500A) Processing helix chain 'b' and resid 575 through 590 removed outlier: 3.699A pdb=" N LEU b 579 " --> pdb=" O ASN b 575 " (cutoff:3.500A) Processing helix chain 'b' and resid 593 through 601 removed outlier: 3.566A pdb=" N VAL b 597 " --> pdb=" O LEU b 593 " (cutoff:3.500A) Processing helix chain 'b' and resid 602 through 604 No H-bonds generated for 'chain 'b' and resid 602 through 604' Processing helix chain 'b' and resid 606 through 620 removed outlier: 4.359A pdb=" N ASP b 610 " --> pdb=" O SER b 606 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL b 611 " --> pdb=" O LEU b 607 " (cutoff:3.500A) Processing helix chain 'b' and resid 637 through 653 Processing helix chain 'b' and resid 657 through 670 Processing helix chain 'b' and resid 674 through 687 Processing helix chain 'b' and resid 697 through 701 Processing helix chain 'b' and resid 707 through 714 Processing helix chain 'b' and resid 724 through 733 Processing helix chain 'b' and resid 741 through 749 removed outlier: 3.658A pdb=" N GLN b 749 " --> pdb=" O LEU b 745 " (cutoff:3.500A) Processing helix chain 'b' and resid 753 through 757 removed outlier: 4.004A pdb=" N GLU b 757 " --> pdb=" O ILE b 754 " (cutoff:3.500A) Processing helix chain 'b' and resid 764 through 786 removed outlier: 3.662A pdb=" N SER b 786 " --> pdb=" O GLY b 782 " (cutoff:3.500A) Processing helix chain 'b' and resid 856 through 867 removed outlier: 3.501A pdb=" N LEU b 867 " --> pdb=" O ALA b 863 " (cutoff:3.500A) Processing helix chain 'b' and resid 873 through 884 Proline residue: b 878 - end of helix Processing helix chain 'b' and resid 889 through 893 removed outlier: 3.635A pdb=" N ALA b 893 " --> pdb=" O TYR b 890 " (cutoff:3.500A) Processing helix chain 'b' and resid 897 through 908 Processing helix chain 'b' and resid 928 through 959 Processing helix chain 'b' and resid 972 through 988 Proline residue: b 984 - end of helix Processing helix chain 'b' and resid 991 through 1005 removed outlier: 4.049A pdb=" N TYR b 995 " --> pdb=" O ILE b 991 " (cutoff:3.500A) Processing helix chain 'b' and resid 1015 through 1021 removed outlier: 3.652A pdb=" N PHE b1021 " --> pdb=" O TYR b1017 " (cutoff:3.500A) Processing helix chain 'b' and resid 1025 through 1030 removed outlier: 4.183A pdb=" N SER b1030 " --> pdb=" O TYR b1026 " (cutoff:3.500A) Processing helix chain 'b' and resid 1035 through 1054 Processing helix chain 'b' and resid 1088 through 1113 Processing helix chain 'b' and resid 1118 through 1131 Processing helix chain 'b' and resid 1138 through 1154 Processing helix chain 'b' and resid 1161 through 1175 removed outlier: 3.690A pdb=" N SER b1175 " --> pdb=" O GLY b1171 " (cutoff:3.500A) Processing helix chain 'c' and resid 28 through 42 Processing helix chain 'e' and resid 42 through 47 Processing helix chain 'e' and resid 56 through 74 Processing helix chain 'e' and resid 82 through 137 Processing helix chain 'e' and resid 190 through 247 Proline residue: e 231 - end of helix Proline residue: e 242 - end of helix Processing helix chain 'e' and resid 253 through 262 Processing helix chain 'e' and resid 265 through 282 Processing helix chain 'e' and resid 293 through 299 removed outlier: 3.617A pdb=" N ALA e 299 " --> pdb=" O ASP e 295 " (cutoff:3.500A) Processing helix chain 'e' and resid 334 through 341 Processing helix chain 'e' and resid 415 through 424 removed outlier: 3.623A pdb=" N GLN e 419 " --> pdb=" O ASN e 415 " (cutoff:3.500A) Processing helix chain 'e' and resid 431 through 438 Processing helix chain 'e' and resid 441 through 449 removed outlier: 3.959A pdb=" N GLN e 445 " --> pdb=" O TYR e 441 " (cutoff:3.500A) Processing helix chain 'e' and resid 464 through 497 removed outlier: 4.663A pdb=" N SER e 470 " --> pdb=" O SER e 466 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N HIS e 471 " --> pdb=" O LEU e 467 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU e 473 " --> pdb=" O ALA e 469 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLN e 484 " --> pdb=" O LYS e 480 " (cutoff:3.500A) Processing helix chain 'e' and resid 506 through 511 removed outlier: 4.354A pdb=" N TYR e 509 " --> pdb=" O ASP e 506 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE e 511 " --> pdb=" O GLN e 508 " (cutoff:3.500A) Processing helix chain 'e' and resid 526 through 532 Processing helix chain 'e' and resid 536 through 543 removed outlier: 3.756A pdb=" N VAL e 540 " --> pdb=" O THR e 536 " (cutoff:3.500A) Processing helix chain 'e' and resid 595 through 607 removed outlier: 4.056A pdb=" N ARG e 599 " --> pdb=" O ASP e 595 " (cutoff:3.500A) Processing helix chain 'e' and resid 608 through 612 removed outlier: 3.500A pdb=" N GLU e 611 " --> pdb=" O CYS e 608 " (cutoff:3.500A) Processing helix chain 'e' and resid 620 through 639 Processing helix chain 'f' and resid 12 through 24 Processing helix chain 'f' and resid 53 through 57 Processing helix chain 'f' and resid 62 through 66 removed outlier: 3.697A pdb=" N LYS f 66 " --> pdb=" O GLU f 63 " (cutoff:3.500A) Processing helix chain 'f' and resid 102 through 106 removed outlier: 4.082A pdb=" N LEU f 106 " --> pdb=" O TRP f 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 102 through 106' Processing helix chain 'g' and resid 22 through 39 Processing helix chain 'g' and resid 45 through 128 removed outlier: 3.540A pdb=" N HIS g 128 " --> pdb=" O LYS g 124 " (cutoff:3.500A) Processing helix chain 'g' and resid 134 through 181 removed outlier: 3.878A pdb=" N LEU g 162 " --> pdb=" O ASP g 158 " (cutoff:3.500A) Processing helix chain 'h' and resid 273 through 285 Processing helix chain 'h' and resid 296 through 310 Processing helix chain 'h' and resid 322 through 335 Processing helix chain 'h' and resid 367 through 376 Processing helix chain 'h' and resid 393 through 408 removed outlier: 3.627A pdb=" N ALA h 397 " --> pdb=" O ASP h 393 " (cutoff:3.500A) Processing helix chain 'i' and resid 11 through 22 Processing helix chain 'i' and resid 30 through 37 Processing helix chain 'i' and resid 45 through 65 Processing helix chain 'i' and resid 71 through 84 Processing helix chain 'i' and resid 92 through 104 Processing helix chain 'i' and resid 106 through 119 Processing helix chain 'i' and resid 134 through 147 Processing helix chain 'i' and resid 152 through 167 Processing helix chain 'i' and resid 231 through 247 removed outlier: 3.611A pdb=" N TYR i 235 " --> pdb=" O ASP i 231 " (cutoff:3.500A) Processing helix chain 'i' and resid 248 through 251 removed outlier: 3.539A pdb=" N CYS i 251 " --> pdb=" O PRO i 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 248 through 251' Processing helix chain 'i' and resid 254 through 275 removed outlier: 4.169A pdb=" N LYS i 275 " --> pdb=" O PHE i 271 " (cutoff:3.500A) Processing helix chain 'i' and resid 315 through 333 Processing helix chain 'i' and resid 346 through 366 Processing helix chain 'i' and resid 370 through 392 removed outlier: 3.698A pdb=" N TRP i 391 " --> pdb=" O ASN i 387 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS i 392 " --> pdb=" O TRP i 388 " (cutoff:3.500A) Processing helix chain 'j' and resid 168 through 180 removed outlier: 3.580A pdb=" N TYR j 172 " --> pdb=" O GLU j 168 " (cutoff:3.500A) Processing helix chain 'j' and resid 189 through 204 Processing helix chain 'j' and resid 206 through 221 Processing helix chain 'j' and resid 225 through 237 Processing helix chain 'j' and resid 241 through 255 removed outlier: 4.411A pdb=" N CYS j 245 " --> pdb=" O PRO j 241 " (cutoff:3.500A) Processing helix chain 'j' and resid 264 through 276 removed outlier: 3.978A pdb=" N PHE j 276 " --> pdb=" O VAL j 272 " (cutoff:3.500A) Processing helix chain 'j' and resid 280 through 288 removed outlier: 3.931A pdb=" N LEU j 284 " --> pdb=" O ASP j 280 " (cutoff:3.500A) Processing helix chain 'j' and resid 296 through 307 Processing helix chain 'j' and resid 344 through 353 removed outlier: 3.640A pdb=" N LEU j 353 " --> pdb=" O LEU j 349 " (cutoff:3.500A) Processing helix chain 'j' and resid 359 through 366 Processing helix chain 'j' and resid 376 through 391 removed outlier: 3.609A pdb=" N ALA j 380 " --> pdb=" O HIS j 376 " (cutoff:3.500A) Processing helix chain 'j' and resid 391 through 398 removed outlier: 3.601A pdb=" N TYR j 395 " --> pdb=" O ILE j 391 " (cutoff:3.500A) Processing helix chain 'j' and resid 425 through 439 Processing helix chain 'j' and resid 445 through 463 removed outlier: 3.928A pdb=" N PHE j 449 " --> pdb=" O ASP j 445 " (cutoff:3.500A) Processing helix chain 'j' and resid 477 through 497 removed outlier: 4.695A pdb=" N LEU j 492 " --> pdb=" O ASP j 488 " (cutoff:3.500A) Proline residue: j 493 - end of helix Processing helix chain 'j' and resid 503 through 513 removed outlier: 3.657A pdb=" N GLU j 507 " --> pdb=" O CYS j 503 " (cutoff:3.500A) Processing helix chain 'j' and resid 518 through 526 Processing helix chain 'j' and resid 535 through 554 removed outlier: 3.528A pdb=" N VAL j 539 " --> pdb=" O HIS j 535 " (cutoff:3.500A) Processing helix chain 'j' and resid 563 through 575 removed outlier: 3.531A pdb=" N GLN j 567 " --> pdb=" O PRO j 563 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N SER j 574 " --> pdb=" O LYS j 570 " (cutoff:3.500A) Processing helix chain 'j' and resid 575 through 590 removed outlier: 3.700A pdb=" N LEU j 579 " --> pdb=" O ASN j 575 " (cutoff:3.500A) Processing helix chain 'j' and resid 593 through 601 removed outlier: 3.565A pdb=" N VAL j 597 " --> pdb=" O LEU j 593 " (cutoff:3.500A) Processing helix chain 'j' and resid 602 through 604 No H-bonds generated for 'chain 'j' and resid 602 through 604' Processing helix chain 'j' and resid 606 through 620 removed outlier: 4.358A pdb=" N ASP j 610 " --> pdb=" O SER j 606 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL j 611 " --> pdb=" O LEU j 607 " (cutoff:3.500A) Processing helix chain 'j' and resid 637 through 653 Processing helix chain 'j' and resid 657 through 670 Processing helix chain 'j' and resid 674 through 687 Processing helix chain 'j' and resid 697 through 701 Processing helix chain 'j' and resid 707 through 714 Processing helix chain 'j' and resid 724 through 733 Processing helix chain 'j' and resid 741 through 749 removed outlier: 3.656A pdb=" N GLN j 749 " --> pdb=" O LEU j 745 " (cutoff:3.500A) Processing helix chain 'j' and resid 753 through 757 removed outlier: 4.002A pdb=" N GLU j 757 " --> pdb=" O ILE j 754 " (cutoff:3.500A) Processing helix chain 'j' and resid 764 through 786 removed outlier: 3.659A pdb=" N SER j 786 " --> pdb=" O GLY j 782 " (cutoff:3.500A) Processing helix chain 'j' and resid 856 through 867 Processing helix chain 'j' and resid 873 through 884 Proline residue: j 878 - end of helix Processing helix chain 'j' and resid 889 through 893 removed outlier: 3.635A pdb=" N ALA j 893 " --> pdb=" O TYR j 890 " (cutoff:3.500A) Processing helix chain 'j' and resid 897 through 908 Processing helix chain 'j' and resid 928 through 959 Processing helix chain 'j' and resid 972 through 988 Proline residue: j 984 - end of helix Processing helix chain 'j' and resid 991 through 1005 removed outlier: 4.059A pdb=" N TYR j 995 " --> pdb=" O ILE j 991 " (cutoff:3.500A) Processing helix chain 'j' and resid 1015 through 1021 removed outlier: 3.652A pdb=" N PHE j1021 " --> pdb=" O TYR j1017 " (cutoff:3.500A) Processing helix chain 'j' and resid 1025 through 1030 removed outlier: 4.181A pdb=" N SER j1030 " --> pdb=" O TYR j1026 " (cutoff:3.500A) Processing helix chain 'j' and resid 1035 through 1054 Processing helix chain 'j' and resid 1088 through 1113 Processing helix chain 'j' and resid 1118 through 1131 Processing helix chain 'j' and resid 1138 through 1154 Processing helix chain 'j' and resid 1161 through 1175 removed outlier: 3.694A pdb=" N SER j1175 " --> pdb=" O GLY j1171 " (cutoff:3.500A) Processing helix chain 'k' and resid 28 through 42 Processing helix chain 'm' and resid 48 through 73 Processing helix chain 'm' and resid 81 through 148 removed outlier: 3.851A pdb=" N ALA m 119 " --> pdb=" O GLN m 115 " (cutoff:3.500A) Processing helix chain 'm' and resid 161 through 169 Processing helix chain 'm' and resid 170 through 175 Processing helix chain 'm' and resid 176 through 179 Processing helix chain 'm' and resid 183 through 240 Proline residue: m 231 - end of helix Processing helix chain 'm' and resid 244 through 248 Processing helix chain 'm' and resid 260 through 264 removed outlier: 3.596A pdb=" N HIS m 263 " --> pdb=" O THR m 260 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU m 264 " --> pdb=" O ALA m 261 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 260 through 264' Processing helix chain 'm' and resid 265 through 282 removed outlier: 3.555A pdb=" N CYS m 282 " --> pdb=" O TYR m 278 " (cutoff:3.500A) Processing helix chain 'm' and resid 293 through 299 removed outlier: 3.847A pdb=" N ALA m 299 " --> pdb=" O ASP m 295 " (cutoff:3.500A) Processing helix chain 'm' and resid 335 through 342 Processing helix chain 'm' and resid 415 through 425 removed outlier: 3.864A pdb=" N GLN m 419 " --> pdb=" O ASN m 415 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL m 425 " --> pdb=" O GLN m 421 " (cutoff:3.500A) Processing helix chain 'm' and resid 431 through 438 Processing helix chain 'm' and resid 441 through 449 removed outlier: 3.914A pdb=" N GLN m 445 " --> pdb=" O TYR m 441 " (cutoff:3.500A) Processing helix chain 'm' and resid 471 through 497 Processing helix chain 'm' and resid 506 through 511 removed outlier: 4.351A pdb=" N TYR m 509 " --> pdb=" O ASP m 506 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE m 511 " --> pdb=" O GLN m 508 " (cutoff:3.500A) Processing helix chain 'm' and resid 526 through 532 Processing helix chain 'm' and resid 536 through 543 removed outlier: 3.756A pdb=" N VAL m 540 " --> pdb=" O THR m 536 " (cutoff:3.500A) Processing helix chain 'm' and resid 595 through 607 removed outlier: 4.057A pdb=" N ARG m 599 " --> pdb=" O ASP m 595 " (cutoff:3.500A) Processing helix chain 'm' and resid 608 through 612 Processing helix chain 'm' and resid 620 through 639 Processing helix chain 'n' and resid 12 through 24 Processing helix chain 'n' and resid 53 through 57 Processing helix chain 'n' and resid 62 through 66 removed outlier: 3.694A pdb=" N LYS n 66 " --> pdb=" O GLU n 63 " (cutoff:3.500A) Processing helix chain 'n' and resid 102 through 106 removed outlier: 4.082A pdb=" N LEU n 106 " --> pdb=" O TRP n 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 102 through 106' Processing helix chain 'o' and resid 22 through 39 Processing helix chain 'o' and resid 47 through 127 removed outlier: 3.900A pdb=" N LEU o 68 " --> pdb=" O MET o 64 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU o 69 " --> pdb=" O GLY o 65 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LYS o 86 " --> pdb=" O GLU o 82 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU o 87 " --> pdb=" O LYS o 83 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLU o 97 " --> pdb=" O ALA o 93 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL o 125 " --> pdb=" O ALA o 121 " (cutoff:3.500A) Processing helix chain 'o' and resid 132 through 181 Processing helix chain 'p' and resid 273 through 285 Processing helix chain 'p' and resid 296 through 310 Processing helix chain 'p' and resid 322 through 335 Processing helix chain 'p' and resid 367 through 376 Processing helix chain 'p' and resid 393 through 408 removed outlier: 3.627A pdb=" N ALA p 397 " --> pdb=" O ASP p 393 " (cutoff:3.500A) Processing helix chain 'x' and resid 2 through 20 removed outlier: 3.553A pdb=" N UNK x 20 " --> pdb=" O UNK x 16 " (cutoff:3.500A) Processing helix chain 'x' and resid 51 through 66 Processing sheet with id=AA1, first strand: chain 'C' and resid 49 through 50 Processing sheet with id=AA2, first strand: chain 'C' and resid 58 through 64 removed outlier: 4.130A pdb=" N SER C 64 " --> pdb=" O ARG C 69 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ARG C 69 " --> pdb=" O SER C 64 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N LEU C 83 " --> pdb=" O LYS C 91 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N LYS C 91 " --> pdb=" O LEU C 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 102 through 107 removed outlier: 6.878A pdb=" N ALA C 118 " --> pdb=" O ASP C 103 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N LEU C 105 " --> pdb=" O VAL C 116 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N VAL C 116 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N TRP C 107 " --> pdb=" O LEU C 114 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N LEU C 114 " --> pdb=" O TRP C 107 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N PHE C 115 " --> pdb=" O TRP C 127 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER C 119 " --> pdb=" O THR C 123 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N THR C 123 " --> pdb=" O SER C 119 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N ASP C 128 " --> pdb=" O CYS C 134 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N CYS C 134 " --> pdb=" O ASP C 128 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 146 through 149 removed outlier: 3.770A pdb=" N ASN C 146 " --> pdb=" O GLY C 159 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N VAL C 165 " --> pdb=" O GLU C 178 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLU C 178 " --> pdb=" O VAL C 165 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N PHE C 167 " --> pdb=" O LYS C 176 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 188 through 190 removed outlier: 6.563A pdb=" N SER C 210 " --> pdb=" O PRO C 216 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 227 through 232 removed outlier: 3.585A pdb=" N CYS C 229 " --> pdb=" O GLY C 242 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS C 231 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA C 240 " --> pdb=" O LYS C 231 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL C 248 " --> pdb=" O PHE C 262 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ASP C 252 " --> pdb=" O CYS C 258 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N CYS C 258 " --> pdb=" O ASP C 252 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 269 through 274 removed outlier: 3.563A pdb=" N THR C 271 " --> pdb=" O ALA C 284 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA C 284 " --> pdb=" O THR C 271 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N SER C 285 " --> pdb=" O PHE C 289 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N PHE C 289 " --> pdb=" O SER C 285 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ILE C 290 " --> pdb=" O GLU C 303 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N GLU C 303 " --> pdb=" O ILE C 290 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ILE C 292 " --> pdb=" O LEU C 301 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 286 through 291 removed outlier: 4.197A pdb=" N SER E 358 " --> pdb=" O CYS E 354 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 518 through 525 removed outlier: 5.897A pdb=" N LEU E 519 " --> pdb=" O GLU E 557 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N GLU E 557 " --> pdb=" O LEU E 519 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS E 521 " --> pdb=" O LEU E 555 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N TYR E 551 " --> pdb=" O ILE E 525 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LYS E 562 " --> pdb=" O ASN E 585 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 672 through 674 Processing sheet with id=AB2, first strand: chain 'F' and resid 30 through 32 removed outlier: 3.893A pdb=" N VAL F 70 " --> pdb=" O ILE F 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 81 through 84 removed outlier: 3.687A pdb=" N SER F 81 " --> pdb=" O ALA F 92 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 129 through 135 removed outlier: 3.529A pdb=" N ALA F 144 " --> pdb=" O ALA F 131 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL F 135 " --> pdb=" O SER F 140 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N SER F 140 " --> pdb=" O VAL F 135 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ARG F 162 " --> pdb=" O THR F 152 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N ASP F 154 " --> pdb=" O PHE F 160 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N PHE F 160 " --> pdb=" O ASP F 154 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 171 through 174 removed outlier: 7.071A pdb=" N GLY F 186 " --> pdb=" O HIS F 172 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N LEU F 174 " --> pdb=" O LEU F 184 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LEU F 184 " --> pdb=" O LEU F 174 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLY F 187 " --> pdb=" O ALA F 191 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ALA F 191 " --> pdb=" O GLY F 187 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLN F 204 " --> pdb=" O LEU F 194 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 223 through 225 removed outlier: 7.020A pdb=" N GLY F 236 " --> pdb=" O GLY F 224 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N LEU F 241 " --> pdb=" O PHE F 255 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR F 253 " --> pdb=" O LEU F 243 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N HIS F 245 " --> pdb=" O PRO F 251 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 261 through 266 removed outlier: 5.038A pdb=" N GLY F 275 " --> pdb=" O CYS F 279 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N CYS F 279 " --> pdb=" O GLY F 275 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N GLN F 284 " --> pdb=" O LEU F 289 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N LEU F 289 " --> pdb=" O GLN F 284 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 300 through 305 removed outlier: 6.689A pdb=" N ALA F 320 " --> pdb=" O LEU F 301 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N LEU F 303 " --> pdb=" O THR F 318 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N THR F 318 " --> pdb=" O LEU F 303 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N GLY F 321 " --> pdb=" O ARG F 325 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N ARG F 325 " --> pdb=" O GLY F 321 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE F 337 " --> pdb=" O VAL F 328 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 314 through 317 removed outlier: 6.432A pdb=" N VAL H 290 " --> pdb=" O LEU H 341 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ALA H 343 " --> pdb=" O VAL H 290 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N ILE H 292 " --> pdb=" O ALA H 343 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N GLN H 289 " --> pdb=" O VAL H 356 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ILE H 358 " --> pdb=" O GLN H 289 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL H 291 " --> pdb=" O ILE H 358 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ASN H 357 " --> pdb=" O LEU H 386 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N ILE H 388 " --> pdb=" O ASN H 357 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ALA H 359 " --> pdb=" O ILE H 388 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N PHE H 390 " --> pdb=" O ALA H 359 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N ASN H 361 " --> pdb=" O PHE H 390 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N GLN H 263 " --> pdb=" O ALA H 387 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N THR H 389 " --> pdb=" O GLN H 263 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TYR H 265 " --> pdb=" O THR H 389 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N VAL H 391 " --> pdb=" O TYR H 265 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N VAL H 267 " --> pdb=" O VAL H 391 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N SER H 412 " --> pdb=" O GLN H 264 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'K' and resid 49 through 50 Processing sheet with id=AC2, first strand: chain 'K' and resid 58 through 64 removed outlier: 4.127A pdb=" N SER K 64 " --> pdb=" O ARG K 69 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ARG K 69 " --> pdb=" O SER K 64 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N LEU K 83 " --> pdb=" O LYS K 91 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N LYS K 91 " --> pdb=" O LEU K 83 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 102 through 107 removed outlier: 6.877A pdb=" N ALA K 118 " --> pdb=" O ASP K 103 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N LEU K 105 " --> pdb=" O VAL K 116 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N VAL K 116 " --> pdb=" O LEU K 105 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N TRP K 107 " --> pdb=" O LEU K 114 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N LEU K 114 " --> pdb=" O TRP K 107 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N PHE K 115 " --> pdb=" O TRP K 127 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N SER K 119 " --> pdb=" O THR K 123 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N THR K 123 " --> pdb=" O SER K 119 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N ASP K 128 " --> pdb=" O CYS K 134 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N CYS K 134 " --> pdb=" O ASP K 128 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 146 through 149 removed outlier: 3.770A pdb=" N ASN K 146 " --> pdb=" O GLY K 159 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N VAL K 165 " --> pdb=" O GLU K 178 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N GLU K 178 " --> pdb=" O VAL K 165 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N PHE K 167 " --> pdb=" O LYS K 176 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'K' and resid 188 through 190 removed outlier: 6.565A pdb=" N SER K 210 " --> pdb=" O PRO K 216 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'K' and resid 227 through 232 removed outlier: 3.585A pdb=" N CYS K 229 " --> pdb=" O GLY K 242 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS K 231 " --> pdb=" O ALA K 240 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA K 240 " --> pdb=" O LYS K 231 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL K 248 " --> pdb=" O PHE K 262 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ASP K 252 " --> pdb=" O CYS K 258 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N CYS K 258 " --> pdb=" O ASP K 252 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 269 through 274 removed outlier: 3.564A pdb=" N THR K 271 " --> pdb=" O ALA K 284 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA K 284 " --> pdb=" O THR K 271 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N SER K 285 " --> pdb=" O PHE K 289 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N PHE K 289 " --> pdb=" O SER K 285 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ILE K 290 " --> pdb=" O GLU K 303 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLU K 303 " --> pdb=" O ILE K 290 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE K 292 " --> pdb=" O LEU K 301 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'M' and resid 286 through 291 Processing sheet with id=AC9, first strand: chain 'M' and resid 518 through 525 removed outlier: 5.894A pdb=" N LEU M 519 " --> pdb=" O GLU M 557 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N GLU M 557 " --> pdb=" O LEU M 519 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS M 521 " --> pdb=" O LEU M 555 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N TYR M 551 " --> pdb=" O ILE M 525 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LYS M 562 " --> pdb=" O ASN M 585 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'M' and resid 672 through 674 Processing sheet with id=AD2, first strand: chain 'N' and resid 30 through 32 removed outlier: 3.891A pdb=" N VAL N 70 " --> pdb=" O ILE N 50 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'N' and resid 81 through 84 removed outlier: 3.687A pdb=" N SER N 81 " --> pdb=" O ALA N 92 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'N' and resid 129 through 135 removed outlier: 3.530A pdb=" N ALA N 144 " --> pdb=" O ALA N 131 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL N 135 " --> pdb=" O SER N 140 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N SER N 140 " --> pdb=" O VAL N 135 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ARG N 162 " --> pdb=" O THR N 152 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N ASP N 154 " --> pdb=" O PHE N 160 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N PHE N 160 " --> pdb=" O ASP N 154 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'N' and resid 171 through 174 removed outlier: 7.071A pdb=" N GLY N 186 " --> pdb=" O HIS N 172 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N LEU N 174 " --> pdb=" O LEU N 184 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LEU N 184 " --> pdb=" O LEU N 174 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLY N 187 " --> pdb=" O ALA N 191 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ALA N 191 " --> pdb=" O GLY N 187 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLN N 204 " --> pdb=" O LEU N 194 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'N' and resid 223 through 225 removed outlier: 7.018A pdb=" N GLY N 236 " --> pdb=" O GLY N 224 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N LEU N 241 " --> pdb=" O ILE N 254 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ILE N 254 " --> pdb=" O LEU N 241 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU N 243 " --> pdb=" O THR N 252 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N THR N 250 " --> pdb=" O HIS N 245 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'N' and resid 261 through 266 removed outlier: 5.038A pdb=" N GLY N 275 " --> pdb=" O CYS N 279 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N CYS N 279 " --> pdb=" O GLY N 275 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N GLN N 284 " --> pdb=" O LEU N 289 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N LEU N 289 " --> pdb=" O GLN N 284 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'N' and resid 300 through 305 removed outlier: 6.690A pdb=" N ALA N 320 " --> pdb=" O LEU N 301 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N LEU N 303 " --> pdb=" O THR N 318 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N THR N 318 " --> pdb=" O LEU N 303 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N GLY N 321 " --> pdb=" O ARG N 325 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N ARG N 325 " --> pdb=" O GLY N 321 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N PHE N 337 " --> pdb=" O VAL N 328 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'P' and resid 314 through 317 removed outlier: 6.429A pdb=" N VAL P 290 " --> pdb=" O LEU P 341 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ALA P 343 " --> pdb=" O VAL P 290 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N ILE P 292 " --> pdb=" O ALA P 343 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N GLN P 289 " --> pdb=" O VAL P 356 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE P 358 " --> pdb=" O GLN P 289 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL P 291 " --> pdb=" O ILE P 358 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ASN P 357 " --> pdb=" O LEU P 386 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N ILE P 388 " --> pdb=" O ASN P 357 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ALA P 359 " --> pdb=" O ILE P 388 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N PHE P 390 " --> pdb=" O ALA P 359 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N ASN P 361 " --> pdb=" O PHE P 390 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N GLN P 263 " --> pdb=" O ALA P 387 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N THR P 389 " --> pdb=" O GLN P 263 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TYR P 265 " --> pdb=" O THR P 389 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N VAL P 391 " --> pdb=" O TYR P 265 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N VAL P 267 " --> pdb=" O VAL P 391 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N SER P 412 " --> pdb=" O GLN P 264 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'c' and resid 49 through 50 Processing sheet with id=AE2, first strand: chain 'c' and resid 58 through 64 removed outlier: 4.130A pdb=" N SER c 64 " --> pdb=" O ARG c 69 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ARG c 69 " --> pdb=" O SER c 64 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N LEU c 83 " --> pdb=" O LYS c 91 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N LYS c 91 " --> pdb=" O LEU c 83 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'c' and resid 102 through 107 removed outlier: 6.878A pdb=" N ALA c 118 " --> pdb=" O ASP c 103 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N LEU c 105 " --> pdb=" O VAL c 116 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N VAL c 116 " --> pdb=" O LEU c 105 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N TRP c 107 " --> pdb=" O LEU c 114 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N LEU c 114 " --> pdb=" O TRP c 107 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N PHE c 115 " --> pdb=" O TRP c 127 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER c 119 " --> pdb=" O THR c 123 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N THR c 123 " --> pdb=" O SER c 119 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N ASP c 128 " --> pdb=" O CYS c 134 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N CYS c 134 " --> pdb=" O ASP c 128 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'c' and resid 146 through 149 removed outlier: 3.770A pdb=" N ASN c 146 " --> pdb=" O GLY c 159 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N VAL c 165 " --> pdb=" O GLU c 178 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N GLU c 178 " --> pdb=" O VAL c 165 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N PHE c 167 " --> pdb=" O LYS c 176 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'c' and resid 188 through 190 removed outlier: 6.563A pdb=" N SER c 210 " --> pdb=" O PRO c 216 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'c' and resid 227 through 232 removed outlier: 3.585A pdb=" N CYS c 229 " --> pdb=" O GLY c 242 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS c 231 " --> pdb=" O ALA c 240 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA c 240 " --> pdb=" O LYS c 231 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL c 248 " --> pdb=" O PHE c 262 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ASP c 252 " --> pdb=" O CYS c 258 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N CYS c 258 " --> pdb=" O ASP c 252 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'c' and resid 269 through 274 removed outlier: 3.562A pdb=" N THR c 271 " --> pdb=" O ALA c 284 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA c 284 " --> pdb=" O THR c 271 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N SER c 285 " --> pdb=" O PHE c 289 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N PHE c 289 " --> pdb=" O SER c 285 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ILE c 290 " --> pdb=" O GLU c 303 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLU c 303 " --> pdb=" O ILE c 290 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE c 292 " --> pdb=" O LEU c 301 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'e' and resid 286 through 291 Processing sheet with id=AE9, first strand: chain 'e' and resid 518 through 525 removed outlier: 5.895A pdb=" N LEU e 519 " --> pdb=" O GLU e 557 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N GLU e 557 " --> pdb=" O LEU e 519 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS e 521 " --> pdb=" O LEU e 555 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N TYR e 551 " --> pdb=" O ILE e 525 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LYS e 562 " --> pdb=" O ASN e 585 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'e' and resid 672 through 674 Processing sheet with id=AF2, first strand: chain 'f' and resid 30 through 32 removed outlier: 3.894A pdb=" N VAL f 70 " --> pdb=" O ILE f 50 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'f' and resid 81 through 84 removed outlier: 3.691A pdb=" N SER f 81 " --> pdb=" O ALA f 92 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'f' and resid 129 through 135 removed outlier: 3.528A pdb=" N ALA f 144 " --> pdb=" O ALA f 131 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL f 135 " --> pdb=" O SER f 140 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N SER f 140 " --> pdb=" O VAL f 135 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ARG f 162 " --> pdb=" O THR f 152 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N ASP f 154 " --> pdb=" O PHE f 160 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N PHE f 160 " --> pdb=" O ASP f 154 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'f' and resid 171 through 174 removed outlier: 7.071A pdb=" N GLY f 186 " --> pdb=" O HIS f 172 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N LEU f 174 " --> pdb=" O LEU f 184 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LEU f 184 " --> pdb=" O LEU f 174 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLY f 187 " --> pdb=" O ALA f 191 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ALA f 191 " --> pdb=" O GLY f 187 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLN f 204 " --> pdb=" O LEU f 194 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'f' and resid 223 through 225 removed outlier: 7.021A pdb=" N GLY f 236 " --> pdb=" O GLY f 224 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N LEU f 241 " --> pdb=" O PHE f 255 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR f 253 " --> pdb=" O LEU f 243 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N HIS f 245 " --> pdb=" O PRO f 251 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'f' and resid 261 through 266 removed outlier: 5.037A pdb=" N GLY f 275 " --> pdb=" O CYS f 279 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N CYS f 279 " --> pdb=" O GLY f 275 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N GLN f 284 " --> pdb=" O LEU f 289 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N LEU f 289 " --> pdb=" O GLN f 284 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'f' and resid 300 through 305 removed outlier: 6.690A pdb=" N ALA f 320 " --> pdb=" O LEU f 301 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N LEU f 303 " --> pdb=" O THR f 318 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N THR f 318 " --> pdb=" O LEU f 303 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N GLY f 321 " --> pdb=" O ARG f 325 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ARG f 325 " --> pdb=" O GLY f 321 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N PHE f 337 " --> pdb=" O VAL f 328 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'h' and resid 314 through 317 removed outlier: 6.432A pdb=" N VAL h 290 " --> pdb=" O LEU h 341 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ALA h 343 " --> pdb=" O VAL h 290 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N ILE h 292 " --> pdb=" O ALA h 343 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N GLN h 289 " --> pdb=" O VAL h 356 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE h 358 " --> pdb=" O GLN h 289 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL h 291 " --> pdb=" O ILE h 358 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ASN h 357 " --> pdb=" O LEU h 386 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N ILE h 388 " --> pdb=" O ASN h 357 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ALA h 359 " --> pdb=" O ILE h 388 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N PHE h 390 " --> pdb=" O ALA h 359 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N ASN h 361 " --> pdb=" O PHE h 390 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N GLN h 263 " --> pdb=" O ALA h 387 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N THR h 389 " --> pdb=" O GLN h 263 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N TYR h 265 " --> pdb=" O THR h 389 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N VAL h 391 " --> pdb=" O TYR h 265 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N VAL h 267 " --> pdb=" O VAL h 391 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N SER h 412 " --> pdb=" O GLN h 264 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'k' and resid 49 through 50 Processing sheet with id=AG2, first strand: chain 'k' and resid 58 through 64 removed outlier: 4.127A pdb=" N SER k 64 " --> pdb=" O ARG k 69 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ARG k 69 " --> pdb=" O SER k 64 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N LEU k 83 " --> pdb=" O LYS k 91 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N LYS k 91 " --> pdb=" O LEU k 83 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'k' and resid 102 through 107 removed outlier: 6.878A pdb=" N ALA k 118 " --> pdb=" O ASP k 103 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N LEU k 105 " --> pdb=" O VAL k 116 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N VAL k 116 " --> pdb=" O LEU k 105 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N TRP k 107 " --> pdb=" O LEU k 114 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N LEU k 114 " --> pdb=" O TRP k 107 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N PHE k 115 " --> pdb=" O TRP k 127 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER k 119 " --> pdb=" O THR k 123 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N THR k 123 " --> pdb=" O SER k 119 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N ASP k 128 " --> pdb=" O CYS k 134 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N CYS k 134 " --> pdb=" O ASP k 128 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'k' and resid 146 through 149 removed outlier: 3.769A pdb=" N ASN k 146 " --> pdb=" O GLY k 159 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N VAL k 165 " --> pdb=" O GLU k 178 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N GLU k 178 " --> pdb=" O VAL k 165 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N PHE k 167 " --> pdb=" O LYS k 176 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'k' and resid 188 through 190 removed outlier: 6.565A pdb=" N SER k 210 " --> pdb=" O PRO k 216 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'k' and resid 227 through 232 removed outlier: 3.586A pdb=" N CYS k 229 " --> pdb=" O GLY k 242 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS k 231 " --> pdb=" O ALA k 240 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA k 240 " --> pdb=" O LYS k 231 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL k 248 " --> pdb=" O PHE k 262 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ASP k 252 " --> pdb=" O CYS k 258 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N CYS k 258 " --> pdb=" O ASP k 252 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'k' and resid 269 through 274 removed outlier: 3.562A pdb=" N THR k 271 " --> pdb=" O ALA k 284 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA k 284 " --> pdb=" O THR k 271 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N SER k 285 " --> pdb=" O PHE k 289 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N PHE k 289 " --> pdb=" O SER k 285 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ILE k 290 " --> pdb=" O GLU k 303 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N GLU k 303 " --> pdb=" O ILE k 290 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ILE k 292 " --> pdb=" O LEU k 301 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'm' and resid 286 through 291 Processing sheet with id=AG9, first strand: chain 'm' and resid 518 through 525 removed outlier: 5.896A pdb=" N LEU m 519 " --> pdb=" O GLU m 557 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N GLU m 557 " --> pdb=" O LEU m 519 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS m 521 " --> pdb=" O LEU m 555 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N TYR m 551 " --> pdb=" O ILE m 525 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LYS m 562 " --> pdb=" O ASN m 585 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'm' and resid 672 through 674 Processing sheet with id=AH2, first strand: chain 'n' and resid 30 through 32 removed outlier: 3.894A pdb=" N VAL n 70 " --> pdb=" O ILE n 50 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'n' and resid 81 through 84 removed outlier: 3.689A pdb=" N SER n 81 " --> pdb=" O ALA n 92 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'n' and resid 129 through 135 removed outlier: 3.529A pdb=" N ALA n 144 " --> pdb=" O ALA n 131 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL n 135 " --> pdb=" O SER n 140 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N SER n 140 " --> pdb=" O VAL n 135 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ARG n 162 " --> pdb=" O THR n 152 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ASP n 154 " --> pdb=" O PHE n 160 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N PHE n 160 " --> pdb=" O ASP n 154 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'n' and resid 171 through 174 removed outlier: 7.069A pdb=" N GLY n 186 " --> pdb=" O HIS n 172 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N LEU n 174 " --> pdb=" O LEU n 184 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEU n 184 " --> pdb=" O LEU n 174 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLY n 187 " --> pdb=" O ALA n 191 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ALA n 191 " --> pdb=" O GLY n 187 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLN n 204 " --> pdb=" O LEU n 194 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'n' and resid 223 through 225 removed outlier: 7.019A pdb=" N GLY n 236 " --> pdb=" O GLY n 224 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N LEU n 241 " --> pdb=" O ILE n 254 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ILE n 254 " --> pdb=" O LEU n 241 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LEU n 243 " --> pdb=" O THR n 252 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR n 250 " --> pdb=" O HIS n 245 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'n' and resid 261 through 266 removed outlier: 5.038A pdb=" N GLY n 275 " --> pdb=" O CYS n 279 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N CYS n 279 " --> pdb=" O GLY n 275 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N GLN n 284 " --> pdb=" O LEU n 289 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N LEU n 289 " --> pdb=" O GLN n 284 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'n' and resid 300 through 305 removed outlier: 6.690A pdb=" N ALA n 320 " --> pdb=" O LEU n 301 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N LEU n 303 " --> pdb=" O THR n 318 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N THR n 318 " --> pdb=" O LEU n 303 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N GLY n 321 " --> pdb=" O ARG n 325 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N ARG n 325 " --> pdb=" O GLY n 321 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE n 337 " --> pdb=" O VAL n 328 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'p' and resid 314 through 317 removed outlier: 6.429A pdb=" N VAL p 290 " --> pdb=" O LEU p 341 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ALA p 343 " --> pdb=" O VAL p 290 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N ILE p 292 " --> pdb=" O ALA p 343 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N GLN p 289 " --> pdb=" O VAL p 356 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ILE p 358 " --> pdb=" O GLN p 289 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL p 291 " --> pdb=" O ILE p 358 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ASN p 357 " --> pdb=" O LEU p 386 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N ILE p 388 " --> pdb=" O ASN p 357 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ALA p 359 " --> pdb=" O ILE p 388 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N PHE p 390 " --> pdb=" O ALA p 359 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N ASN p 361 " --> pdb=" O PHE p 390 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N GLN p 263 " --> pdb=" O ALA p 387 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N THR p 389 " --> pdb=" O GLN p 263 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N TYR p 265 " --> pdb=" O THR p 389 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N VAL p 391 " --> pdb=" O TYR p 265 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N VAL p 267 " --> pdb=" O VAL p 391 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N SER p 412 " --> pdb=" O GLN p 264 " (cutoff:3.500A) 4705 hydrogen bonds defined for protein. 13887 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: 33.95 Time building geometry restraints manager: 23.99 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: 23433 1.34 - 1.46: 15492 1.46 - 1.58: 34457 1.58 - 1.70: 0 1.70 - 1.83: 503 Bond restraints: 73885 Sorted by residual: bond pdb=" C PRO e 670 " pdb=" N PHE e 671 " ideal model delta sigma weight residual 1.333 1.395 -0.062 1.51e-02 4.39e+03 1.68e+01 bond pdb=" C PRO E 670 " pdb=" N PHE E 671 " ideal model delta sigma weight residual 1.333 1.394 -0.061 1.51e-02 4.39e+03 1.62e+01 bond pdb=" C LYS M 214 " pdb=" N ILE M 215 " ideal model delta sigma weight residual 1.335 1.378 -0.043 1.26e-02 6.30e+03 1.17e+01 bond pdb=" C LEU j 497 " pdb=" N MET j 498 " ideal model delta sigma weight residual 1.328 1.290 0.038 1.13e-02 7.83e+03 1.13e+01 bond pdb=" C LYS m 214 " pdb=" N ILE m 215 " ideal model delta sigma weight residual 1.335 1.377 -0.042 1.26e-02 6.30e+03 1.11e+01 ... (remaining 73880 not shown) Histogram of bond angle deviations from ideal: 99.10 - 106.19: 1636 106.19 - 113.28: 40905 113.28 - 120.37: 28033 120.37 - 127.46: 29002 127.46 - 134.56: 694 Bond angle restraints: 100270 Sorted by residual: angle pdb=" C GLY e 407 " pdb=" N ASP e 408 " pdb=" CA ASP e 408 " ideal model delta sigma weight residual 121.54 131.16 -9.62 1.91e+00 2.74e-01 2.54e+01 angle pdb=" C GLY E 407 " pdb=" N ASP E 408 " pdb=" CA ASP E 408 " ideal model delta sigma weight residual 121.54 131.01 -9.47 1.91e+00 2.74e-01 2.46e+01 angle pdb=" C LEU f 246 " pdb=" N ARG f 247 " pdb=" CA ARG f 247 " ideal model delta sigma weight residual 121.54 130.58 -9.04 1.91e+00 2.74e-01 2.24e+01 angle pdb=" C LEU N 246 " pdb=" N ARG N 247 " pdb=" CA ARG N 247 " ideal model delta sigma weight residual 121.54 130.47 -8.93 1.91e+00 2.74e-01 2.19e+01 angle pdb=" C LEU n 246 " pdb=" N ARG n 247 " pdb=" CA ARG n 247 " ideal model delta sigma weight residual 121.54 130.45 -8.91 1.91e+00 2.74e-01 2.17e+01 ... (remaining 100265 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.31: 42868 15.31 - 30.63: 1124 30.63 - 45.94: 229 45.94 - 61.25: 4 61.25 - 76.57: 34 Dihedral angle restraints: 44259 sinusoidal: 15165 harmonic: 29094 Sorted by residual: dihedral pdb=" CA LYS j 562 " pdb=" C LYS j 562 " pdb=" N PRO j 563 " pdb=" CA PRO j 563 " ideal model delta harmonic sigma weight residual 180.00 134.80 45.20 0 5.00e+00 4.00e-02 8.17e+01 dihedral pdb=" CA LYS b 562 " pdb=" C LYS b 562 " pdb=" N PRO b 563 " pdb=" CA PRO b 563 " ideal model delta harmonic sigma weight residual 180.00 134.85 45.15 0 5.00e+00 4.00e-02 8.15e+01 dihedral pdb=" CA LYS B 562 " pdb=" C LYS B 562 " pdb=" N PRO B 563 " pdb=" CA PRO B 563 " ideal model delta harmonic sigma weight residual 180.00 134.89 45.11 0 5.00e+00 4.00e-02 8.14e+01 ... (remaining 44256 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 10526 0.074 - 0.149: 1097 0.149 - 0.223: 109 0.223 - 0.298: 12 0.298 - 0.372: 4 Chirality restraints: 11748 Sorted by residual: chirality pdb=" CA LYS J 562 " pdb=" N LYS J 562 " pdb=" C LYS J 562 " pdb=" CB LYS J 562 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.47e+00 chirality pdb=" CA LYS B 562 " pdb=" N LYS B 562 " pdb=" C LYS B 562 " pdb=" CB LYS B 562 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.30e+00 chirality pdb=" CA LYS b 562 " pdb=" N LYS b 562 " pdb=" C LYS b 562 " pdb=" CB LYS b 562 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.26e+00 ... (remaining 11745 not shown) Planarity restraints: 12916 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP k 63 " -0.028 2.00e-02 2.50e+03 2.52e-02 1.59e+01 pdb=" CG TRP k 63 " 0.067 2.00e-02 2.50e+03 pdb=" CD1 TRP k 63 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 TRP k 63 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP k 63 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP k 63 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP k 63 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP k 63 " -0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP k 63 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP k 63 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 63 " -0.027 2.00e-02 2.50e+03 2.50e-02 1.56e+01 pdb=" CG TRP C 63 " 0.067 2.00e-02 2.50e+03 pdb=" CD1 TRP C 63 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 TRP C 63 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 63 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP C 63 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP C 63 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 63 " -0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 63 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP C 63 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP K 63 " -0.026 2.00e-02 2.50e+03 2.50e-02 1.56e+01 pdb=" CG TRP K 63 " 0.067 2.00e-02 2.50e+03 pdb=" CD1 TRP K 63 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 TRP K 63 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP K 63 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP K 63 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP K 63 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP K 63 " -0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP K 63 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP K 63 " 0.002 2.00e-02 2.50e+03 ... (remaining 12913 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 16484 2.78 - 3.31: 64865 3.31 - 3.84: 116567 3.84 - 4.37: 129838 4.37 - 4.90: 225520 Nonbonded interactions: 553274 Sorted by model distance: nonbonded pdb=" OG SER N 33 " pdb=" O CYS N 35 " model vdw 2.256 2.440 nonbonded pdb=" OG SER F 33 " pdb=" O CYS F 35 " model vdw 2.258 2.440 nonbonded pdb=" OG SER n 33 " pdb=" O CYS n 35 " model vdw 2.258 2.440 nonbonded pdb=" OG SER f 33 " pdb=" O CYS f 35 " model vdw 2.259 2.440 nonbonded pdb=" OE2 GLU n 202 " pdb=" OG1 THR n 205 " model vdw 2.318 2.440 ... (remaining 553269 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 'I' and (resid 10 through 64 or (resid 65 and (name N or name CA or name \ C or name O or name CB )) or resid 71 through 120 or resid 133 through 278 or re \ sid 296 through 392)) selection = chain 'a' selection = (chain 'i' and (resid 10 through 37 or (resid 38 through 47 and (name N or name \ CA or name C or name O or name CB )) or resid 48 through 64 or (resid 65 and (na \ me N or name CA or name C or name O or name CB )) or resid 71 through 120 or res \ id 133 through 278 or resid 296 through 392)) } ncs_group { reference = (chain 'B' and (resid 165 or (resid 166 through 168 and (name N or name CA or na \ me C or name O or name CB )) or resid 169 through 249 or (resid 250 and (name N \ or name CA or name C or name O or name CB )) or resid 251 through 252 or (resid \ 253 through 255 and (name N or name CA or name C or name O or name CB )) or resi \ d 263 through 1175)) selection = (chain 'J' and (resid 165 through 249 or (resid 250 and (name N or name CA or na \ me C or name O or name CB )) or resid 251 through 252 or (resid 253 through 255 \ and (name N or name CA or name C or name O or name CB )) or resid 263 through 11 \ 75)) selection = (chain 'b' and (resid 165 or (resid 166 through 168 and (name N or name CA or na \ me C or name O or name CB )) or resid 169 through 249 or (resid 250 and (name N \ or name CA or name C or name O or name CB )) or resid 251 through 252 or (resid \ 253 through 255 and (name N or name CA or name C or name O or name CB )) or resi \ d 263 through 1175)) selection = (chain 'j' and (resid 165 through 299 or (resid 300 through 307 and (name N or n \ ame CA or name C or name O or name CB )) or resid 343 through 1175)) } ncs_group { reference = chain 'C' selection = chain 'K' selection = chain 'c' selection = chain 'k' } ncs_group { reference = (chain 'E' and (resid 44 or resid 55 through 73 or resid 81 through 240 or resid \ 243 through 247 or resid 253 or resid 258 through 299 or resid 334 through 453 \ or resid 466 or resid 471 through 642 or resid 659 through 675 or resid 678 thro \ ugh 683)) selection = (chain 'M' and ((resid 51 and (name N or name CA or name C or name O or name CB \ )) or (resid 55 through 73 and (name N or name CA or name C or name O or name CB \ )) or (resid 81 through 111 and (name N or name CA or name C or name O or name \ CB )) or resid 112 or (resid 113 through 137 and (name N or name CA or name C or \ name O or name CB )) or (resid 189 through 247 and (name N or name CA or name C \ or name O or name CB )) or (resid 257 and (name N or name CA or name C or name \ O or name CB )) or resid 258 through 425 or resid 430 through 453 or resid 470 t \ hrough 675 or resid 678 through 683)) selection = (chain 'e' and (resid 44 or resid 55 through 73 or resid 81 through 240 or resid \ 243 through 247 or resid 253 or resid 258 through 299 or resid 334 through 453 \ or resid 466 or resid 471 through 683)) selection = (chain 'm' and ((resid 51 and (name N or name CA or name C or name O or name CB \ )) or (resid 55 through 73 and (name N or name CA or name C or name O or name CB \ )) or (resid 81 through 111 and (name N or name CA or name C or name O or name \ CB )) or resid 112 or (resid 113 through 137 and (name N or name CA or name C or \ name O or name CB )) or (resid 189 through 247 and (name N or name CA or name C \ or name O or name CB )) or (resid 257 and (name N or name CA or name C or name \ O or name CB )) or resid 258 through 425 or resid 430 through 453 or resid 470 t \ hrough 675 or resid 678 through 683)) } ncs_group { reference = (chain 'F' and (resid 5 through 119 or resid 128 through 341)) selection = (chain 'N' and (resid 5 through 119 or resid 128 through 341)) selection = chain 'f' selection = (chain 'n' and (resid 5 through 119 or resid 128 through 341)) } ncs_group { reference = (chain 'G' and (resid 21 through 39 or resid 46 through 181)) selection = (chain 'O' and ((resid 21 through 64 and (name N or name CA or name C or name O \ or name CB )) or resid 65 or (resid 66 through 93 and (name N or name CA or name \ C or name O or name CB )) or (resid 94 through 129 and (name N or name CA or na \ me C or name O or name CB )) or (resid 134 through 142 and (name N or name CA or \ name C or name O or name CB )) or resid 143 through 181)) selection = (chain 'g' and (resid 21 through 39 or resid 46 through 181)) selection = (chain 'o' and ((resid 21 through 64 and (name N or name CA or name C or name O \ or name CB )) or resid 65 or (resid 66 through 93 and (name N or name CA or name \ C or name O or name CB )) or (resid 94 through 129 and (name N or name CA or na \ me C or name O or name CB )) or (resid 134 through 142 and (name N or name CA or \ name C or name O or name CB )) or resid 143 through 181)) } ncs_group { reference = chain 'H' selection = chain 'P' selection = chain 'h' selection = chain 'p' } ncs_group { reference = chain 'X' selection = chain 'x' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.47 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: 3.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.090 Extract box with map and model: 20.220 Check model and map are aligned: 0.870 Set scattering table: 0.510 Process input model: 152.450 Find NCS groups from input model: 4.590 Set up NCS constraints: 0.470 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: 0.020 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: 185.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2218 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 0.062 73885 Z= 0.290 Angle : 0.808 14.990 100270 Z= 0.458 Chirality : 0.048 0.372 11748 Planarity : 0.006 0.090 12916 Dihedral : 8.498 76.565 25181 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.67 % Favored : 95.19 % Rotamer: Outliers : 0.10 % Allowed : 1.43 % Favored : 98.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.30 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.73 (0.07), residues: 9429 helix: -1.43 (0.05), residues: 5192 sheet: -0.36 (0.15), residues: 1214 loop : -2.89 (0.09), residues: 3023 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.003 TRP k 63 HIS 0.023 0.002 HIS B 573 PHE 0.033 0.002 PHE i 245 TYR 0.033 0.002 TYR A 325 ARG 0.006 0.001 ARG I 318 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18858 Ramachandran restraints generated. 9429 Oldfield, 0 Emsley, 9429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18858 Ramachandran restraints generated. 9429 Oldfield, 0 Emsley, 9429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1053 residues out of total 8871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 1046 time to evaluate : 6.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LEU cc_start: 0.4168 (mt) cc_final: 0.3790 (tp) REVERT: E 390 SER cc_start: 0.7164 (m) cc_final: 0.6822 (p) REVERT: E 493 PHE cc_start: 0.3409 (m-10) cc_final: 0.2896 (m-80) REVERT: E 568 VAL cc_start: 0.5180 (t) cc_final: 0.3480 (m) REVERT: E 580 PHE cc_start: 0.5209 (m-10) cc_final: 0.4235 (m-80) REVERT: F 48 ILE cc_start: 0.3645 (mt) cc_final: 0.3395 (mt) REVERT: H 355 ARG cc_start: 0.1285 (tpm170) cc_final: 0.0271 (ttm-80) REVERT: H 364 MET cc_start: -0.0425 (tpt) cc_final: -0.1170 (tpp) REVERT: H 410 ASN cc_start: 0.2529 (p0) cc_final: 0.2122 (m-40) REVERT: H 423 TYR cc_start: 0.1378 (p90) cc_final: 0.0982 (p90) REVERT: I 139 MET cc_start: 0.3293 (mtm) cc_final: 0.2611 (mmt) REVERT: I 377 MET cc_start: 0.0592 (mtp) cc_final: -0.0217 (tpp) REVERT: J 385 LYS cc_start: 0.1380 (mttt) cc_final: 0.0924 (ttpt) REVERT: M 66 MET cc_start: -0.0990 (ptp) cc_final: -0.1261 (mtm) REVERT: M 632 LEU cc_start: 0.4688 (mt) cc_final: 0.4212 (mp) REVERT: N 155 LEU cc_start: 0.2310 (mt) cc_final: 0.2043 (tp) REVERT: O 73 MET cc_start: 0.2708 (tmm) cc_final: 0.1325 (ppp) REVERT: P 321 MET cc_start: -0.0820 (mtp) cc_final: -0.1738 (ttt) REVERT: b 238 MET cc_start: 0.1058 (mtm) cc_final: 0.0330 (mmt) REVERT: b 460 MET cc_start: 0.0663 (mmm) cc_final: -0.0271 (ptm) REVERT: e 340 MET cc_start: 0.0522 (tpp) cc_final: 0.0068 (ptt) REVERT: i 114 THR cc_start: 0.6224 (p) cc_final: 0.5909 (p) REVERT: i 272 LYS cc_start: 0.6795 (mttt) cc_final: 0.6414 (tptt) REVERT: j 551 TYR cc_start: 0.5364 (t80) cc_final: 0.5145 (t80) REVERT: m 166 TYR cc_start: 0.4084 (t80) cc_final: 0.3410 (t80) outliers start: 7 outliers final: 3 residues processed: 1051 average time/residue: 0.6911 time to fit residues: 1224.4168 Evaluate side-chains 541 residues out of total 8871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 538 time to evaluate : 6.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 523 VAL Chi-restraints excluded: chain E residue 524 THR Chi-restraints excluded: chain E residue 525 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 982 random chunks: chunk 829 optimal weight: 30.0000 chunk 744 optimal weight: 1.9990 chunk 413 optimal weight: 4.9990 chunk 254 optimal weight: 30.0000 chunk 502 optimal weight: 20.0000 chunk 397 optimal weight: 9.9990 chunk 769 optimal weight: 0.9980 chunk 297 optimal weight: 30.0000 chunk 468 optimal weight: 8.9990 chunk 572 optimal weight: 50.0000 chunk 891 optimal weight: 2.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 ASN ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 320 HIS A 367 ASN B 204 ASN B 489 GLN B 560 ASN ** B 573 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 588 GLN B 608 ASN B 667 GLN C 94 ASN C 98 HIS C 276 HIS ** C 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 274 GLN E 418 ASN ** E 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 451 HIS E 564 GLN ** E 675 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 88 HIS F 151 HIS F 211 HIS F 261 GLN F 281 ASN F 306 ASN H 264 GLN ** H 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 204 ASN J 287 HIS J 489 GLN ** J 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 573 HIS J 588 GLN J 608 ASN J 667 GLN K 221 ASN ** K 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 361 HIS M 451 HIS M 490 HIS N 130 ASN N 149 GLN N 172 HIS N 261 GLN N 331 ASN P 404 GLN ** a 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 320 HIS b 204 ASN b 489 GLN ** b 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 573 HIS b 588 GLN b 608 ASN b 667 GLN c 93 ASN c 98 HIS c 173 HIS ** c 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 274 GLN e 369 ASN ** e 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 508 GLN e 624 ASN ** f 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 218 HIS f 261 GLN f 263 HIS ** f 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 284 GLN h 404 GLN i 53 GLN i 242 GLN i 387 ASN j 204 ASN j 224 HIS j 287 HIS j 363 ASN j 489 GLN j 560 ASN ** j 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 667 GLN ** k 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 102 ASN m 106 HIS ** m 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 675 HIS n 149 GLN n 172 HIS n 261 GLN n 263 HIS n 292 GLN o 74 ASN p 404 GLN Total number of N/Q/H flips: 79 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3449 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.121 73885 Z= 0.393 Angle : 0.766 22.559 100270 Z= 0.393 Chirality : 0.045 0.297 11748 Planarity : 0.006 0.108 12916 Dihedral : 5.300 41.200 10383 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.06 % Favored : 94.81 % Rotamer: Outliers : 1.68 % Allowed : 5.74 % Favored : 92.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.15 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.08), residues: 9429 helix: 0.52 (0.06), residues: 5182 sheet: -0.32 (0.15), residues: 1240 loop : -2.43 (0.10), residues: 3007 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.079 0.003 TRP N 100 HIS 0.019 0.002 HIS E 471 PHE 0.033 0.002 PHE E 662 TYR 0.039 0.002 TYR f 170 ARG 0.018 0.001 ARG F 177 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18858 Ramachandran restraints generated. 9429 Oldfield, 0 Emsley, 9429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18858 Ramachandran restraints generated. 9429 Oldfield, 0 Emsley, 9429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 635 residues out of total 8871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 522 time to evaluate : 8.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LEU cc_start: 0.4200 (mt) cc_final: 0.3817 (tp) REVERT: E 555 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8219 (mp) REVERT: E 669 LYS cc_start: 0.8500 (OUTLIER) cc_final: 0.8135 (mttm) REVERT: F 273 SER cc_start: 0.8981 (OUTLIER) cc_final: 0.8766 (p) REVERT: H 321 MET cc_start: -0.0480 (mtp) cc_final: -0.1109 (mtt) REVERT: H 355 ARG cc_start: 0.1088 (tpm170) cc_final: -0.0335 (ttm-80) REVERT: H 364 MET cc_start: -0.0537 (tpt) cc_final: -0.1114 (tpp) REVERT: I 377 MET cc_start: 0.2247 (mtp) cc_final: -0.0037 (tpp) REVERT: J 236 MET cc_start: 0.0940 (tpp) cc_final: 0.0575 (tpt) REVERT: J 590 TYR cc_start: 0.1251 (m-10) cc_final: 0.0595 (m-80) REVERT: M 66 MET cc_start: -0.1245 (ptp) cc_final: -0.1658 (mtm) REVERT: M 442 LEU cc_start: 0.5893 (OUTLIER) cc_final: 0.5468 (pp) REVERT: M 629 LEU cc_start: 0.7115 (pp) cc_final: 0.6417 (tp) REVERT: M 668 MET cc_start: 0.5667 (tpp) cc_final: 0.5383 (tpp) REVERT: N 11 LEU cc_start: 0.6544 (mt) cc_final: 0.6311 (mt) REVERT: O 73 MET cc_start: 0.2479 (tmm) cc_final: 0.1919 (ppp) REVERT: P 321 MET cc_start: 0.0159 (mtp) cc_final: -0.0683 (ttm) REVERT: a 377 MET cc_start: 0.0515 (mmp) cc_final: -0.2202 (ttm) REVERT: b 238 MET cc_start: 0.0538 (mtm) cc_final: -0.0773 (mmt) REVERT: b 460 MET cc_start: 0.0467 (mmm) cc_final: -0.0450 (ptm) REVERT: c 173 HIS cc_start: 0.0585 (OUTLIER) cc_final: 0.0202 (m-70) REVERT: e 340 MET cc_start: 0.0832 (tpp) cc_final: 0.0107 (ptt) REVERT: f 177 ARG cc_start: 0.1266 (OUTLIER) cc_final: 0.0882 (ptm160) REVERT: i 272 LYS cc_start: 0.7570 (mttt) cc_final: 0.6254 (tptt) REVERT: j 388 HIS cc_start: 0.5220 (OUTLIER) cc_final: 0.4179 (t70) REVERT: j 660 LEU cc_start: 0.5200 (OUTLIER) cc_final: 0.4867 (tm) REVERT: k 66 ASP cc_start: 0.2235 (m-30) cc_final: 0.1999 (m-30) REVERT: n 153 MET cc_start: 0.1031 (tpp) cc_final: -0.0745 (tmm) REVERT: n 195 TRP cc_start: 0.1129 (m100) cc_final: 0.0196 (m100) outliers start: 113 outliers final: 46 residues processed: 617 average time/residue: 0.6764 time to fit residues: 716.8640 Evaluate side-chains 427 residues out of total 8871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 373 time to evaluate : 6.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain E residue 367 LEU Chi-restraints excluded: chain E residue 375 VAL Chi-restraints excluded: chain E residue 401 LEU Chi-restraints excluded: chain E residue 420 TYR Chi-restraints excluded: chain E residue 522 TRP Chi-restraints excluded: chain E residue 523 VAL Chi-restraints excluded: chain E residue 524 THR Chi-restraints excluded: chain E residue 540 VAL Chi-restraints excluded: chain E residue 555 LEU Chi-restraints excluded: chain E residue 669 LYS Chi-restraints excluded: chain E residue 681 SER Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 231 ASP Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain F residue 273 SER Chi-restraints excluded: chain J residue 490 VAL Chi-restraints excluded: chain M residue 258 TYR Chi-restraints excluded: chain M residue 368 MET Chi-restraints excluded: chain M residue 374 THR Chi-restraints excluded: chain M residue 379 VAL Chi-restraints excluded: chain M residue 434 VAL Chi-restraints excluded: chain M residue 442 LEU Chi-restraints excluded: chain M residue 547 ASP Chi-restraints excluded: chain M residue 570 ASN Chi-restraints excluded: chain N residue 71 THR Chi-restraints excluded: chain O residue 55 SER Chi-restraints excluded: chain a residue 307 LEU Chi-restraints excluded: chain a residue 316 ASN Chi-restraints excluded: chain b residue 225 ASP Chi-restraints excluded: chain b residue 229 ILE Chi-restraints excluded: chain b residue 360 HIS Chi-restraints excluded: chain c residue 173 HIS Chi-restraints excluded: chain e residue 380 THR Chi-restraints excluded: chain f residue 177 ARG Chi-restraints excluded: chain f residue 209 TYR Chi-restraints excluded: chain h residue 351 MET Chi-restraints excluded: chain i residue 92 THR Chi-restraints excluded: chain j residue 244 LEU Chi-restraints excluded: chain j residue 375 SER Chi-restraints excluded: chain j residue 378 LEU Chi-restraints excluded: chain j residue 388 HIS Chi-restraints excluded: chain j residue 490 VAL Chi-restraints excluded: chain j residue 597 VAL Chi-restraints excluded: chain j residue 636 SER Chi-restraints excluded: chain j residue 645 PHE Chi-restraints excluded: chain j residue 660 LEU Chi-restraints excluded: chain k residue 76 ASP Chi-restraints excluded: chain m residue 130 LEU Chi-restraints excluded: chain m residue 161 SER Chi-restraints excluded: chain o residue 73 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 982 random chunks: chunk 495 optimal weight: 30.0000 chunk 276 optimal weight: 7.9990 chunk 742 optimal weight: 7.9990 chunk 607 optimal weight: 5.9990 chunk 245 optimal weight: 0.0570 chunk 893 optimal weight: 4.9990 chunk 965 optimal weight: 9.9990 chunk 795 optimal weight: 7.9990 chunk 885 optimal weight: 9.9990 chunk 304 optimal weight: 4.9990 chunk 716 optimal weight: 9.9990 overall best weight: 4.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 GLN B 224 HIS ** B 573 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 144 ASN ** C 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 288 HIS ** C 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 274 GLN E 451 HIS E 492 GLN ** E 675 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 149 GLN F 172 HIS ** F 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 141 ASN ** I 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 367 ASN J 444 HIS J 489 GLN J 588 GLN ** K 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 624 ASN ** M 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 245 HIS P 401 ASN P 404 GLN ** a 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 380 HIS b 224 HIS b 489 GLN ** b 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 535 HIS b 560 ASN ** c 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 451 HIS ** e 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 597 ASN e 627 GLN e 642 HIS f 151 HIS f 218 HIS ** f 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 306 ASN i 53 GLN i 65 ASN j 246 HIS ** j 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 667 GLN k 186 ASN ** k 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 149 GLN n 211 HIS n 322 ASN o 96 HIS Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3763 moved from start: 0.5482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.132 73885 Z= 0.438 Angle : 0.781 17.329 100270 Z= 0.400 Chirality : 0.046 0.270 11748 Planarity : 0.006 0.078 12916 Dihedral : 5.406 39.924 10381 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.31 % Favored : 94.56 % Rotamer: Outliers : 2.30 % Allowed : 7.34 % Favored : 90.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.86 % Twisted General : 0.08 % 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: -0.09 (0.08), residues: 9429 helix: 1.29 (0.07), residues: 5171 sheet: -0.63 (0.14), residues: 1426 loop : -2.30 (0.11), residues: 2832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.003 TRP J 509 HIS 0.046 0.002 HIS c 173 PHE 0.035 0.003 PHE E 364 TYR 0.058 0.003 TYR E 405 ARG 0.025 0.001 ARG j 520 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18858 Ramachandran restraints generated. 9429 Oldfield, 0 Emsley, 9429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18858 Ramachandran restraints generated. 9429 Oldfield, 0 Emsley, 9429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 572 residues out of total 8871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 417 time to evaluate : 6.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LEU cc_start: 0.3601 (mt) cc_final: 0.3231 (tp) REVERT: A 55 PHE cc_start: -0.0054 (OUTLIER) cc_final: -0.0285 (m-10) REVERT: A 348 GLU cc_start: 0.4184 (mt-10) cc_final: 0.3941 (tm-30) REVERT: B 236 MET cc_start: 0.1170 (tpt) cc_final: 0.0277 (tpp) REVERT: B 365 MET cc_start: 0.4926 (ptp) cc_final: 0.2641 (mmm) REVERT: B 498 MET cc_start: 0.1194 (ttm) cc_final: 0.0112 (tpt) REVERT: H 321 MET cc_start: -0.1021 (mtp) cc_final: -0.1502 (mtt) REVERT: H 355 ARG cc_start: 0.1104 (tpm170) cc_final: -0.0789 (ttt90) REVERT: H 410 ASN cc_start: 0.2116 (OUTLIER) cc_final: 0.1855 (m-40) REVERT: I 107 ASP cc_start: 0.3877 (OUTLIER) cc_final: 0.3526 (p0) REVERT: I 253 GLU cc_start: 0.3053 (tm-30) cc_final: 0.2737 (tt0) REVERT: J 236 MET cc_start: 0.0498 (tpp) cc_final: -0.0114 (tpp) REVERT: J 365 MET cc_start: 0.1880 (mtt) cc_final: -0.2092 (mmm) REVERT: J 434 MET cc_start: 0.1448 (mmm) cc_final: 0.1183 (mmm) REVERT: J 504 MET cc_start: 0.2250 (mtm) cc_final: 0.1733 (mmm) REVERT: J 521 TYR cc_start: 0.0745 (OUTLIER) cc_final: 0.0081 (t80) REVERT: K 235 MET cc_start: 0.2724 (mtm) cc_final: 0.2457 (mtp) REVERT: N 11 LEU cc_start: 0.7798 (mt) cc_final: 0.7584 (mt) REVERT: O 53 MET cc_start: -0.0505 (mtt) cc_final: -0.1770 (ptm) REVERT: O 64 MET cc_start: 0.1081 (mmp) cc_final: 0.0725 (mmp) REVERT: P 321 MET cc_start: 0.0746 (mtp) cc_final: -0.0357 (ttm) REVERT: a 377 MET cc_start: 0.0234 (mmp) cc_final: -0.2574 (ttm) REVERT: b 238 MET cc_start: 0.0918 (mtm) cc_final: -0.0511 (mmt) REVERT: b 397 ARG cc_start: 0.2194 (OUTLIER) cc_final: 0.1798 (ptm-80) REVERT: b 434 MET cc_start: 0.0998 (mtt) cc_final: 0.0080 (mtp) REVERT: b 460 MET cc_start: 0.0224 (mmm) cc_final: -0.0783 (ptm) REVERT: b 498 MET cc_start: 0.3353 (ttt) cc_final: 0.2877 (ttt) REVERT: c 127 TRP cc_start: 0.1605 (m100) cc_final: 0.1294 (m100) REVERT: e 340 MET cc_start: 0.0637 (tpp) cc_final: 0.0052 (ptt) REVERT: j 388 HIS cc_start: 0.4178 (OUTLIER) cc_final: 0.3512 (t70) REVERT: j 660 LEU cc_start: 0.5711 (OUTLIER) cc_final: 0.5110 (tm) REVERT: m 531 MET cc_start: 0.0289 (ptp) cc_final: -0.0625 (tpt) REVERT: n 153 MET cc_start: 0.0291 (tpp) cc_final: -0.0086 (tpp) REVERT: n 195 TRP cc_start: 0.0621 (m100) cc_final: 0.0230 (m100) REVERT: o 114 LYS cc_start: 0.8459 (OUTLIER) cc_final: 0.8179 (ttpp) outliers start: 155 outliers final: 65 residues processed: 545 average time/residue: 0.6463 time to fit residues: 619.9555 Evaluate side-chains 400 residues out of total 8871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 327 time to evaluate : 6.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 PHE Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 308 MET Chi-restraints excluded: chain B residue 511 MET Chi-restraints excluded: chain B residue 607 LEU Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain E residue 401 LEU Chi-restraints excluded: chain E residue 420 TYR Chi-restraints excluded: chain E residue 450 LEU Chi-restraints excluded: chain E residue 523 VAL Chi-restraints excluded: chain E residue 524 THR Chi-restraints excluded: chain E residue 584 LEU Chi-restraints excluded: chain E residue 669 LYS Chi-restraints excluded: chain E residue 677 GLN Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 83 VAL Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain F residue 231 ASP Chi-restraints excluded: chain F residue 235 CYS Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain F residue 304 SER Chi-restraints excluded: chain H residue 410 ASN Chi-restraints excluded: chain I residue 107 ASP Chi-restraints excluded: chain I residue 277 ASP Chi-restraints excluded: chain J residue 490 VAL Chi-restraints excluded: chain J residue 521 TYR Chi-restraints excluded: chain J residue 557 THR Chi-restraints excluded: chain J residue 617 ILE Chi-restraints excluded: chain K residue 158 VAL Chi-restraints excluded: chain M residue 258 TYR Chi-restraints excluded: chain M residue 368 MET Chi-restraints excluded: chain M residue 516 VAL Chi-restraints excluded: chain M residue 539 ILE Chi-restraints excluded: chain M residue 556 ILE Chi-restraints excluded: chain M residue 585 ASN Chi-restraints excluded: chain N residue 16 VAL Chi-restraints excluded: chain a residue 307 LEU Chi-restraints excluded: chain a residue 316 ASN Chi-restraints excluded: chain b residue 225 ASP Chi-restraints excluded: chain b residue 229 ILE Chi-restraints excluded: chain b residue 245 CYS Chi-restraints excluded: chain b residue 397 ARG Chi-restraints excluded: chain e residue 520 VAL Chi-restraints excluded: chain f residue 139 ASN Chi-restraints excluded: chain f residue 209 TYR Chi-restraints excluded: chain h residue 351 MET Chi-restraints excluded: chain i residue 92 THR Chi-restraints excluded: chain i residue 107 ASP Chi-restraints excluded: chain i residue 344 VAL Chi-restraints excluded: chain j residue 206 ASP Chi-restraints excluded: chain j residue 375 SER Chi-restraints excluded: chain j residue 378 LEU Chi-restraints excluded: chain j residue 388 HIS Chi-restraints excluded: chain j residue 597 VAL Chi-restraints excluded: chain j residue 645 PHE Chi-restraints excluded: chain j residue 660 LEU Chi-restraints excluded: chain j residue 661 LEU Chi-restraints excluded: chain k residue 76 ASP Chi-restraints excluded: chain k residue 256 LEU Chi-restraints excluded: chain m residue 130 LEU Chi-restraints excluded: chain m residue 161 SER Chi-restraints excluded: chain m residue 164 GLU Chi-restraints excluded: chain m residue 369 ASN Chi-restraints excluded: chain n residue 105 MET Chi-restraints excluded: chain o residue 57 LEU Chi-restraints excluded: chain o residue 73 MET Chi-restraints excluded: chain o residue 114 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 982 random chunks: chunk 882 optimal weight: 0.0070 chunk 671 optimal weight: 10.0000 chunk 463 optimal weight: 7.9990 chunk 98 optimal weight: 30.0000 chunk 426 optimal weight: 10.0000 chunk 599 optimal weight: 20.0000 chunk 896 optimal weight: 6.9990 chunk 949 optimal weight: 0.9980 chunk 468 optimal weight: 1.9990 chunk 849 optimal weight: 4.9990 chunk 255 optimal weight: 7.9990 overall best weight: 3.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 489 GLN ** B 573 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 451 HIS E 492 GLN E 581 GLN E 597 ASN E 620 GLN ** E 675 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 30 GLN ** H 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 489 GLN K 221 ASN K 276 HIS ** K 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 624 ASN ** M 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 75 HIS ** N 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 160 GLN ** a 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 489 GLN ** b 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 588 GLN ** c 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 624 ASN ** f 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 218 HIS ** f 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 292 GLN j 441 HIS j 489 GLN j 529 ASN ** m 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 149 GLN n 281 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3763 moved from start: 0.5921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 73885 Z= 0.275 Angle : 0.611 17.770 100270 Z= 0.311 Chirality : 0.041 0.228 11748 Planarity : 0.004 0.078 12916 Dihedral : 4.936 37.797 10381 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.85 % Favored : 95.04 % Rotamer: Outliers : 2.14 % Allowed : 8.34 % Favored : 89.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.86 % Twisted General : 0.06 % 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: 0.68 (0.09), residues: 9429 helix: 2.05 (0.07), residues: 5178 sheet: -0.56 (0.13), residues: 1448 loop : -2.14 (0.11), residues: 2803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP K 315 HIS 0.012 0.001 HIS c 173 PHE 0.044 0.002 PHE M 511 TYR 0.022 0.002 TYR a 343 ARG 0.010 0.001 ARG f 247 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18858 Ramachandran restraints generated. 9429 Oldfield, 0 Emsley, 9429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18858 Ramachandran restraints generated. 9429 Oldfield, 0 Emsley, 9429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 8871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 356 time to evaluate : 6.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LEU cc_start: 0.3684 (mt) cc_final: 0.3255 (tp) REVERT: A 55 PHE cc_start: -0.0047 (OUTLIER) cc_final: -0.0253 (m-10) REVERT: A 348 GLU cc_start: 0.4411 (mt-10) cc_final: 0.3933 (tm-30) REVERT: B 365 MET cc_start: 0.5233 (ptp) cc_final: 0.2797 (tpp) REVERT: B 498 MET cc_start: 0.1491 (ttm) cc_final: 0.1071 (ttm) REVERT: E 601 MET cc_start: 0.7973 (mtt) cc_final: 0.7308 (mtt) REVERT: H 321 MET cc_start: -0.1009 (mtp) cc_final: -0.1457 (mtt) REVERT: H 355 ARG cc_start: 0.1535 (tpm170) cc_final: 0.0302 (ttm170) REVERT: I 253 GLU cc_start: 0.2740 (tm-30) cc_final: 0.2473 (tt0) REVERT: J 236 MET cc_start: 0.0352 (tpp) cc_final: -0.0249 (tpp) REVERT: J 504 MET cc_start: 0.3077 (mtm) cc_final: 0.1598 (mmp) REVERT: J 521 TYR cc_start: 0.1157 (OUTLIER) cc_final: 0.0437 (t80) REVERT: M 66 MET cc_start: 0.0948 (mmt) cc_final: 0.0232 (mtm) REVERT: M 268 LEU cc_start: 0.7521 (OUTLIER) cc_final: 0.7311 (mm) REVERT: M 408 ASP cc_start: 0.6239 (OUTLIER) cc_final: 0.5847 (m-30) REVERT: M 539 ILE cc_start: 0.6845 (mm) cc_final: 0.6587 (mm) REVERT: M 622 LEU cc_start: 0.7644 (tp) cc_final: 0.7407 (tt) REVERT: M 626 LEU cc_start: 0.7233 (mt) cc_final: 0.6906 (mt) REVERT: M 629 LEU cc_start: 0.7527 (pp) cc_final: 0.7115 (tp) REVERT: P 321 MET cc_start: 0.0662 (mtp) cc_final: -0.0477 (ttm) REVERT: a 139 MET cc_start: 0.1243 (mmp) cc_final: 0.0848 (mmp) REVERT: a 377 MET cc_start: 0.0612 (mmp) cc_final: -0.2087 (ttm) REVERT: b 238 MET cc_start: 0.1126 (mtm) cc_final: -0.0175 (mmt) REVERT: b 365 MET cc_start: 0.0174 (tmm) cc_final: -0.0558 (tmm) REVERT: b 384 CYS cc_start: 0.2388 (OUTLIER) cc_final: 0.0938 (m) REVERT: b 434 MET cc_start: 0.1230 (mtt) cc_final: 0.0385 (mtp) REVERT: b 460 MET cc_start: 0.0524 (mmm) cc_final: -0.0623 (ptm) REVERT: c 127 TRP cc_start: 0.1832 (m100) cc_final: 0.1527 (m100) REVERT: e 340 MET cc_start: 0.1097 (tpp) cc_final: 0.0200 (ptt) REVERT: f 178 GLU cc_start: 0.4173 (OUTLIER) cc_final: 0.3830 (mt-10) REVERT: j 388 HIS cc_start: 0.4254 (OUTLIER) cc_final: 0.3724 (t70) REVERT: k 196 MET cc_start: 0.3344 (OUTLIER) cc_final: 0.2300 (mtt) REVERT: m 340 MET cc_start: -0.0780 (ppp) cc_final: -0.1348 (tmm) REVERT: n 153 MET cc_start: 0.1396 (tpp) cc_final: 0.1154 (tpp) REVERT: n 195 TRP cc_start: 0.0650 (m100) cc_final: 0.0111 (m100) outliers start: 144 outliers final: 75 residues processed: 479 average time/residue: 0.6209 time to fit residues: 535.9343 Evaluate side-chains 401 residues out of total 8871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 318 time to evaluate : 6.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 PHE Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 308 MET Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 511 MET Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 607 LEU Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 226 ASN Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain E residue 372 ILE Chi-restraints excluded: chain E residue 378 LYS Chi-restraints excluded: chain E residue 384 GLU Chi-restraints excluded: chain E residue 401 LEU Chi-restraints excluded: chain E residue 408 ASP Chi-restraints excluded: chain E residue 420 TYR Chi-restraints excluded: chain E residue 451 HIS Chi-restraints excluded: chain E residue 538 ASP Chi-restraints excluded: chain E residue 540 VAL Chi-restraints excluded: chain E residue 629 LEU Chi-restraints excluded: chain E residue 655 GLU Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 83 VAL Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 231 ASP Chi-restraints excluded: chain F residue 235 CYS Chi-restraints excluded: chain F residue 304 SER Chi-restraints excluded: chain J residue 490 VAL Chi-restraints excluded: chain J residue 521 TYR Chi-restraints excluded: chain J residue 557 THR Chi-restraints excluded: chain K residue 158 VAL Chi-restraints excluded: chain K residue 160 ASN Chi-restraints excluded: chain M residue 258 TYR Chi-restraints excluded: chain M residue 268 LEU Chi-restraints excluded: chain M residue 368 MET Chi-restraints excluded: chain M residue 408 ASP Chi-restraints excluded: chain M residue 547 ASP Chi-restraints excluded: chain M residue 568 VAL Chi-restraints excluded: chain M residue 585 ASN Chi-restraints excluded: chain N residue 69 VAL Chi-restraints excluded: chain P residue 418 ILE Chi-restraints excluded: chain a residue 148 SER Chi-restraints excluded: chain a residue 276 LEU Chi-restraints excluded: chain a residue 307 LEU Chi-restraints excluded: chain a residue 316 ASN Chi-restraints excluded: chain b residue 192 ILE Chi-restraints excluded: chain b residue 225 ASP Chi-restraints excluded: chain b residue 245 CYS Chi-restraints excluded: chain b residue 360 HIS Chi-restraints excluded: chain b residue 384 CYS Chi-restraints excluded: chain b residue 437 TYR Chi-restraints excluded: chain b residue 616 ILE Chi-restraints excluded: chain c residue 301 LEU Chi-restraints excluded: chain e residue 375 VAL Chi-restraints excluded: chain e residue 380 THR Chi-restraints excluded: chain e residue 557 GLU Chi-restraints excluded: chain f residue 178 GLU Chi-restraints excluded: chain f residue 209 TYR Chi-restraints excluded: chain i residue 59 LEU Chi-restraints excluded: chain i residue 92 THR Chi-restraints excluded: chain i residue 107 ASP Chi-restraints excluded: chain i residue 344 VAL Chi-restraints excluded: chain i residue 362 GLN Chi-restraints excluded: chain j residue 165 LEU Chi-restraints excluded: chain j residue 375 SER Chi-restraints excluded: chain j residue 388 HIS Chi-restraints excluded: chain j residue 490 VAL Chi-restraints excluded: chain j residue 508 LEU Chi-restraints excluded: chain j residue 597 VAL Chi-restraints excluded: chain j residue 645 PHE Chi-restraints excluded: chain k residue 76 ASP Chi-restraints excluded: chain k residue 158 VAL Chi-restraints excluded: chain k residue 171 LYS Chi-restraints excluded: chain k residue 196 MET Chi-restraints excluded: chain k residue 199 LEU Chi-restraints excluded: chain m residue 66 MET Chi-restraints excluded: chain m residue 130 LEU Chi-restraints excluded: chain m residue 161 SER Chi-restraints excluded: chain m residue 164 GLU Chi-restraints excluded: chain m residue 369 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 982 random chunks: chunk 790 optimal weight: 2.9990 chunk 538 optimal weight: 6.9990 chunk 13 optimal weight: 0.5980 chunk 706 optimal weight: 9.9990 chunk 391 optimal weight: 4.9990 chunk 809 optimal weight: 0.7980 chunk 656 optimal weight: 7.9990 chunk 1 optimal weight: 8.9990 chunk 484 optimal weight: 30.0000 chunk 851 optimal weight: 0.0370 chunk 239 optimal weight: 10.0000 overall best weight: 1.8862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 367 ASN B 489 GLN ** B 573 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 675 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 219 ASN ** H 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 53 GLN I 152 ASN ** I 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 489 GLN K 221 ASN ** K 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 508 GLN ** M 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 677 GLN ** N 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 401 ASN P 404 GLN ** a 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 275 GLN b 489 GLN ** b 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 581 GLN e 606 ASN e 624 ASN ** f 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 218 HIS ** f 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 284 GLN j 529 ASN ** m 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 597 ASN n 149 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3752 moved from start: 0.6134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 73885 Z= 0.200 Angle : 0.560 14.070 100270 Z= 0.283 Chirality : 0.039 0.236 11748 Planarity : 0.004 0.062 12916 Dihedral : 4.671 36.448 10379 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.88 % Favored : 94.99 % Rotamer: Outliers : 1.71 % Allowed : 9.02 % Favored : 89.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.57 % Twisted General : 0.05 % 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: 1.17 (0.09), residues: 9429 helix: 2.52 (0.07), residues: 5196 sheet: -0.44 (0.14), residues: 1439 loop : -2.07 (0.11), residues: 2794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP c 63 HIS 0.023 0.001 HIS E 451 PHE 0.021 0.001 PHE M 511 TYR 0.023 0.001 TYR a 343 ARG 0.007 0.000 ARG f 177 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18858 Ramachandran restraints generated. 9429 Oldfield, 0 Emsley, 9429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18858 Ramachandran restraints generated. 9429 Oldfield, 0 Emsley, 9429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 8871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 338 time to evaluate : 6.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LEU cc_start: 0.3680 (mt) cc_final: 0.3251 (tp) REVERT: A 348 GLU cc_start: 0.4540 (mt-10) cc_final: 0.3997 (tm-30) REVERT: B 236 MET cc_start: 0.0868 (tpt) cc_final: 0.0652 (tpp) REVERT: B 498 MET cc_start: 0.1601 (ttm) cc_final: 0.1182 (ttm) REVERT: E 601 MET cc_start: 0.7861 (mtt) cc_final: 0.7514 (mtt) REVERT: F 266 PHE cc_start: 0.8377 (OUTLIER) cc_final: 0.7936 (t80) REVERT: H 321 MET cc_start: -0.0987 (mtp) cc_final: -0.1450 (mtt) REVERT: H 355 ARG cc_start: 0.1427 (tpm170) cc_final: 0.0292 (ttm170) REVERT: I 107 ASP cc_start: 0.3624 (OUTLIER) cc_final: 0.3410 (p0) REVERT: I 253 GLU cc_start: 0.3307 (tm-30) cc_final: 0.2790 (tt0) REVERT: J 193 LEU cc_start: 0.2434 (OUTLIER) cc_final: 0.2197 (tt) REVERT: J 236 MET cc_start: 0.0367 (tpp) cc_final: -0.0241 (tpp) REVERT: J 365 MET cc_start: 0.1811 (mtt) cc_final: -0.1694 (mmm) REVERT: J 434 MET cc_start: 0.1351 (mmm) cc_final: 0.1107 (mmm) REVERT: J 504 MET cc_start: 0.3076 (mtm) cc_final: 0.1690 (mmp) REVERT: J 521 TYR cc_start: 0.1474 (OUTLIER) cc_final: 0.0604 (t80) REVERT: M 66 MET cc_start: 0.0709 (mmt) cc_final: -0.0208 (mtm) REVERT: M 626 LEU cc_start: 0.7079 (mt) cc_final: 0.6750 (mt) REVERT: M 629 LEU cc_start: 0.7834 (pp) cc_final: 0.7067 (tp) REVERT: P 321 MET cc_start: 0.0813 (mtp) cc_final: -0.0546 (ttm) REVERT: a 139 MET cc_start: 0.1311 (mmp) cc_final: 0.0971 (mmp) REVERT: a 377 MET cc_start: 0.0525 (mmp) cc_final: -0.2225 (ttm) REVERT: b 236 MET cc_start: 0.2517 (tpp) cc_final: 0.2163 (tpt) REVERT: b 238 MET cc_start: 0.1170 (mtm) cc_final: -0.0128 (mmt) REVERT: b 365 MET cc_start: 0.0277 (tmm) cc_final: -0.0462 (tmm) REVERT: b 384 CYS cc_start: 0.2375 (OUTLIER) cc_final: 0.0948 (m) REVERT: b 434 MET cc_start: 0.0989 (mtt) cc_final: 0.0711 (mtt) REVERT: b 460 MET cc_start: 0.0152 (mmm) cc_final: -0.0840 (ptm) REVERT: b 498 MET cc_start: 0.3435 (ttt) cc_final: 0.2986 (ttt) REVERT: c 127 TRP cc_start: 0.1907 (m100) cc_final: 0.1584 (m100) REVERT: e 340 MET cc_start: 0.1065 (tpp) cc_final: 0.0169 (ptt) REVERT: f 178 GLU cc_start: 0.4160 (OUTLIER) cc_final: 0.3832 (mt-10) REVERT: j 491 LEU cc_start: 0.4717 (OUTLIER) cc_final: 0.4281 (mt) REVERT: j 660 LEU cc_start: 0.5759 (OUTLIER) cc_final: 0.5550 (tm) REVERT: k 196 MET cc_start: 0.2993 (OUTLIER) cc_final: 0.2168 (mtt) REVERT: k 235 MET cc_start: 0.2089 (ptt) cc_final: 0.1500 (mtm) REVERT: m 340 MET cc_start: -0.0813 (ppp) cc_final: -0.1358 (tmm) REVERT: n 195 TRP cc_start: 0.0888 (m100) cc_final: 0.0392 (m100) outliers start: 115 outliers final: 69 residues processed: 439 average time/residue: 0.6306 time to fit residues: 496.9729 Evaluate side-chains 392 residues out of total 8871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 314 time to evaluate : 6.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 607 LEU Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 226 ASN Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 378 LYS Chi-restraints excluded: chain E residue 401 LEU Chi-restraints excluded: chain E residue 420 TYR Chi-restraints excluded: chain E residue 538 ASP Chi-restraints excluded: chain E residue 584 LEU Chi-restraints excluded: chain E residue 629 LEU Chi-restraints excluded: chain E residue 655 GLU Chi-restraints excluded: chain E residue 681 SER Chi-restraints excluded: chain F residue 13 GLN Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 83 VAL Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 231 ASP Chi-restraints excluded: chain F residue 266 PHE Chi-restraints excluded: chain F residue 304 SER Chi-restraints excluded: chain I residue 107 ASP Chi-restraints excluded: chain J residue 193 LEU Chi-restraints excluded: chain J residue 490 VAL Chi-restraints excluded: chain J residue 521 TYR Chi-restraints excluded: chain J residue 557 THR Chi-restraints excluded: chain J residue 559 GLU Chi-restraints excluded: chain K residue 158 VAL Chi-restraints excluded: chain M residue 258 TYR Chi-restraints excluded: chain M residue 368 MET Chi-restraints excluded: chain M residue 369 ASN Chi-restraints excluded: chain M residue 408 ASP Chi-restraints excluded: chain M residue 547 ASP Chi-restraints excluded: chain M residue 585 ASN Chi-restraints excluded: chain N residue 32 VAL Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain N residue 89 LEU Chi-restraints excluded: chain P residue 418 ILE Chi-restraints excluded: chain a residue 148 SER Chi-restraints excluded: chain a residue 276 LEU Chi-restraints excluded: chain a residue 307 LEU Chi-restraints excluded: chain a residue 316 ASN Chi-restraints excluded: chain b residue 225 ASP Chi-restraints excluded: chain b residue 245 CYS Chi-restraints excluded: chain b residue 384 CYS Chi-restraints excluded: chain b residue 437 TYR Chi-restraints excluded: chain b residue 616 ILE Chi-restraints excluded: chain c residue 200 THR Chi-restraints excluded: chain c residue 301 LEU Chi-restraints excluded: chain e residue 375 VAL Chi-restraints excluded: chain e residue 380 THR Chi-restraints excluded: chain e residue 520 VAL Chi-restraints excluded: chain e residue 557 GLU Chi-restraints excluded: chain f residue 178 GLU Chi-restraints excluded: chain f residue 209 TYR Chi-restraints excluded: chain i residue 92 THR Chi-restraints excluded: chain i residue 107 ASP Chi-restraints excluded: chain i residue 305 GLU Chi-restraints excluded: chain i residue 344 VAL Chi-restraints excluded: chain j residue 165 LEU Chi-restraints excluded: chain j residue 375 SER Chi-restraints excluded: chain j residue 438 LEU Chi-restraints excluded: chain j residue 490 VAL Chi-restraints excluded: chain j residue 491 LEU Chi-restraints excluded: chain j residue 597 VAL Chi-restraints excluded: chain j residue 645 PHE Chi-restraints excluded: chain j residue 660 LEU Chi-restraints excluded: chain k residue 76 ASP Chi-restraints excluded: chain k residue 158 VAL Chi-restraints excluded: chain k residue 196 MET Chi-restraints excluded: chain k residue 199 LEU Chi-restraints excluded: chain m residue 161 SER Chi-restraints excluded: chain m residue 164 GLU Chi-restraints excluded: chain o residue 73 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 982 random chunks: chunk 319 optimal weight: 50.0000 chunk 854 optimal weight: 8.9990 chunk 187 optimal weight: 0.9980 chunk 557 optimal weight: 6.9990 chunk 234 optimal weight: 30.0000 chunk 950 optimal weight: 0.7980 chunk 788 optimal weight: 0.9990 chunk 439 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 chunk 314 optimal weight: 30.0000 chunk 498 optimal weight: 20.0000 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 489 GLN ** B 573 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 675 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 489 GLN K 221 ASN ** K 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 570 ASN M 627 GLN M 674 ASN ** N 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 152 ASN ** a 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 489 GLN ** c 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 624 ASN ** f 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 667 GLN ** k 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 117 HIS m 369 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3717 moved from start: 0.6234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 73885 Z= 0.145 Angle : 0.529 13.632 100270 Z= 0.265 Chirality : 0.038 0.241 11748 Planarity : 0.003 0.066 12916 Dihedral : 4.424 35.047 10379 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.44 % Favored : 95.46 % Rotamer: Outliers : 1.44 % Allowed : 9.47 % Favored : 89.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.29 % Twisted General : 0.04 % 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: 1.64 (0.09), residues: 9429 helix: 2.97 (0.07), residues: 5198 sheet: -0.30 (0.14), residues: 1419 loop : -1.96 (0.11), residues: 2812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP K 315 HIS 0.011 0.001 HIS j 573 PHE 0.033 0.001 PHE M 511 TYR 0.020 0.001 TYR a 343 ARG 0.006 0.000 ARG M 628 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18858 Ramachandran restraints generated. 9429 Oldfield, 0 Emsley, 9429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18858 Ramachandran restraints generated. 9429 Oldfield, 0 Emsley, 9429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 8871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 337 time to evaluate : 6.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LEU cc_start: 0.3819 (mt) cc_final: 0.3359 (tp) REVERT: B 498 MET cc_start: 0.1192 (ttm) cc_final: 0.0132 (tpt) REVERT: E 601 MET cc_start: 0.7932 (mtt) cc_final: 0.7602 (mtt) REVERT: F 266 PHE cc_start: 0.8250 (OUTLIER) cc_final: 0.7871 (t80) REVERT: H 321 MET cc_start: -0.1005 (mtp) cc_final: -0.1419 (mtt) REVERT: H 355 ARG cc_start: 0.1383 (tpm170) cc_final: 0.0248 (ttm170) REVERT: H 423 TYR cc_start: 0.1414 (p90) cc_final: 0.0852 (p90) REVERT: I 253 GLU cc_start: 0.3009 (tm-30) cc_final: 0.2486 (tt0) REVERT: J 193 LEU cc_start: 0.2362 (OUTLIER) cc_final: 0.2143 (tt) REVERT: J 236 MET cc_start: 0.0354 (tpp) cc_final: -0.0266 (tpp) REVERT: J 365 MET cc_start: 0.1744 (mtt) cc_final: -0.1392 (mmm) REVERT: J 504 MET cc_start: 0.2700 (mtm) cc_final: 0.1347 (mmp) REVERT: J 521 TYR cc_start: 0.1734 (OUTLIER) cc_final: 0.0682 (t80) REVERT: M 66 MET cc_start: 0.0666 (mmt) cc_final: -0.0408 (mtm) REVERT: M 622 LEU cc_start: 0.7634 (tp) cc_final: 0.7432 (tt) REVERT: M 626 LEU cc_start: 0.6810 (mt) cc_final: 0.6558 (mt) REVERT: M 629 LEU cc_start: 0.7393 (pp) cc_final: 0.7162 (tp) REVERT: N 25 MET cc_start: 0.4011 (tmm) cc_final: 0.2679 (tmm) REVERT: O 73 MET cc_start: 0.3300 (tmm) cc_final: 0.2689 (ppp) REVERT: P 321 MET cc_start: 0.0796 (mtp) cc_final: -0.0572 (ttm) REVERT: a 139 MET cc_start: 0.1296 (mmp) cc_final: 0.0945 (mmp) REVERT: a 363 LEU cc_start: 0.1538 (OUTLIER) cc_final: 0.1247 (tt) REVERT: a 377 MET cc_start: 0.0558 (mmp) cc_final: -0.2087 (ttm) REVERT: b 236 MET cc_start: 0.2515 (tpp) cc_final: 0.2207 (tpt) REVERT: b 238 MET cc_start: 0.0773 (mtm) cc_final: -0.0479 (mmt) REVERT: b 365 MET cc_start: 0.0291 (tmm) cc_final: -0.0509 (tmm) REVERT: b 434 MET cc_start: 0.0997 (mtt) cc_final: 0.0698 (mtt) REVERT: b 460 MET cc_start: 0.0176 (mmm) cc_final: -0.0817 (ptm) REVERT: b 498 MET cc_start: 0.3497 (ttt) cc_final: 0.3065 (ttt) REVERT: c 127 TRP cc_start: 0.1214 (m100) cc_final: 0.0991 (m100) REVERT: e 340 MET cc_start: 0.1138 (tpp) cc_final: 0.0235 (ptt) REVERT: f 178 GLU cc_start: 0.4440 (OUTLIER) cc_final: 0.4128 (mt-10) REVERT: j 491 LEU cc_start: 0.4766 (tp) cc_final: 0.4353 (mt) REVERT: k 196 MET cc_start: 0.2767 (OUTLIER) cc_final: 0.2130 (mtt) REVERT: k 235 MET cc_start: 0.1505 (ptt) cc_final: 0.0909 (mtm) REVERT: m 340 MET cc_start: -0.0228 (ppp) cc_final: -0.1037 (tmm) REVERT: n 153 MET cc_start: 0.0927 (tpp) cc_final: -0.0867 (tmm) REVERT: n 195 TRP cc_start: 0.0774 (m100) cc_final: 0.0267 (m100) outliers start: 97 outliers final: 53 residues processed: 421 average time/residue: 0.6221 time to fit residues: 471.4702 Evaluate side-chains 373 residues out of total 8871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 314 time to evaluate : 6.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 372 TYR Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 607 LEU Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain C residue 149 TRP Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 408 ASP Chi-restraints excluded: chain E residue 420 TYR Chi-restraints excluded: chain E residue 504 THR Chi-restraints excluded: chain E residue 538 ASP Chi-restraints excluded: chain E residue 629 LEU Chi-restraints excluded: chain F residue 13 GLN Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 231 ASP Chi-restraints excluded: chain F residue 235 CYS Chi-restraints excluded: chain F residue 266 PHE Chi-restraints excluded: chain J residue 193 LEU Chi-restraints excluded: chain J residue 490 VAL Chi-restraints excluded: chain J residue 521 TYR Chi-restraints excluded: chain J residue 557 THR Chi-restraints excluded: chain J residue 646 CYS Chi-restraints excluded: chain K residue 158 VAL Chi-restraints excluded: chain K residue 160 ASN Chi-restraints excluded: chain M residue 258 TYR Chi-restraints excluded: chain M residue 369 ASN Chi-restraints excluded: chain M residue 408 ASP Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain P residue 418 ILE Chi-restraints excluded: chain a residue 148 SER Chi-restraints excluded: chain a residue 276 LEU Chi-restraints excluded: chain a residue 307 LEU Chi-restraints excluded: chain a residue 363 LEU Chi-restraints excluded: chain b residue 225 ASP Chi-restraints excluded: chain b residue 360 HIS Chi-restraints excluded: chain b residue 384 CYS Chi-restraints excluded: chain b residue 437 TYR Chi-restraints excluded: chain c residue 149 TRP Chi-restraints excluded: chain c residue 301 LEU Chi-restraints excluded: chain e residue 375 VAL Chi-restraints excluded: chain e residue 555 LEU Chi-restraints excluded: chain e residue 557 GLU Chi-restraints excluded: chain f residue 178 GLU Chi-restraints excluded: chain i residue 107 ASP Chi-restraints excluded: chain i residue 362 GLN Chi-restraints excluded: chain j residue 165 LEU Chi-restraints excluded: chain j residue 490 VAL Chi-restraints excluded: chain j residue 645 PHE Chi-restraints excluded: chain j residue 661 LEU Chi-restraints excluded: chain k residue 158 VAL Chi-restraints excluded: chain k residue 196 MET Chi-restraints excluded: chain k residue 199 LEU Chi-restraints excluded: chain m residue 161 SER Chi-restraints excluded: chain m residue 164 GLU Chi-restraints excluded: chain o residue 73 MET Chi-restraints excluded: chain o residue 117 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 982 random chunks: chunk 916 optimal weight: 30.0000 chunk 107 optimal weight: 8.9990 chunk 541 optimal weight: 40.0000 chunk 693 optimal weight: 7.9990 chunk 537 optimal weight: 30.0000 chunk 799 optimal weight: 0.9980 chunk 530 optimal weight: 8.9990 chunk 946 optimal weight: 7.9990 chunk 592 optimal weight: 10.0000 chunk 577 optimal weight: 20.0000 chunk 436 optimal weight: 10.0000 overall best weight: 6.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 489 GLN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 573 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 667 GLN C 146 ASN C 173 HIS ** C 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 675 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 211 HIS ** H 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 242 GLN J 363 ASN ** J 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 195 ASN K 221 ASN ** K 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 624 ASN ** N 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 331 ASN O 117 GLN P 404 GLN ** a 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 363 ASN b 489 GLN ** b 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 619 HIS e 624 ASN f 47 GLN ** f 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 218 HIS ** f 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 204 ASN j 501 ASN ** j 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 667 GLN ** k 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 186 GLN ** m 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3959 moved from start: 0.7469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.165 73885 Z= 0.570 Angle : 0.854 19.309 100270 Z= 0.436 Chirality : 0.048 0.273 11748 Planarity : 0.006 0.072 12916 Dihedral : 5.568 39.035 10379 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 15.63 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.32 % Favored : 93.54 % Rotamer: Outliers : 2.15 % Allowed : 9.85 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.57 % Twisted General : 0.08 % 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 (0.09), residues: 9429 helix: 1.90 (0.07), residues: 5171 sheet: -0.67 (0.14), residues: 1397 loop : -2.32 (0.11), residues: 2861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP C 190 HIS 0.013 0.002 HIS m 139 PHE 0.039 0.003 PHE F 341 TYR 0.042 0.003 TYR B 603 ARG 0.011 0.001 ARG j 209 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18858 Ramachandran restraints generated. 9429 Oldfield, 0 Emsley, 9429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18858 Ramachandran restraints generated. 9429 Oldfield, 0 Emsley, 9429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 8871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 333 time to evaluate : 6.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ARG cc_start: 0.2171 (mtt180) cc_final: 0.0498 (mmt180) REVERT: A 51 LEU cc_start: 0.3396 (mt) cc_final: 0.2744 (tp) REVERT: A 348 GLU cc_start: 0.4656 (mt-10) cc_final: 0.4151 (tm-30) REVERT: B 498 MET cc_start: 0.0761 (ttm) cc_final: 0.0318 (ttm) REVERT: E 384 GLU cc_start: 0.6395 (OUTLIER) cc_final: 0.5873 (tt0) REVERT: E 601 MET cc_start: 0.7878 (mtt) cc_final: 0.7340 (mtt) REVERT: H 355 ARG cc_start: 0.1176 (tpm170) cc_final: 0.0009 (ttm170) REVERT: H 423 TYR cc_start: 0.1306 (p90) cc_final: 0.1092 (p90) REVERT: J 236 MET cc_start: 0.0475 (tpp) cc_final: -0.0142 (tpp) REVERT: J 504 MET cc_start: 0.3200 (mtm) cc_final: 0.1802 (mmt) REVERT: M 66 MET cc_start: 0.1308 (mmt) cc_final: 0.0058 (mtm) REVERT: M 507 CYS cc_start: 0.3359 (m) cc_final: 0.2812 (t) REVERT: N 60 GLU cc_start: 0.1602 (tp30) cc_final: 0.0785 (mt-10) REVERT: P 321 MET cc_start: 0.0614 (mtp) cc_final: -0.0581 (ttm) REVERT: a 139 MET cc_start: 0.1306 (mmp) cc_final: 0.1004 (mmp) REVERT: a 363 LEU cc_start: 0.1531 (OUTLIER) cc_final: 0.1114 (tt) REVERT: b 238 MET cc_start: 0.0399 (mtm) cc_final: 0.0050 (mmm) REVERT: b 365 MET cc_start: 0.0812 (tmm) cc_final: -0.0123 (tmm) REVERT: b 460 MET cc_start: 0.0820 (mmm) cc_final: -0.0521 (ptm) REVERT: e 340 MET cc_start: 0.1130 (tpp) cc_final: 0.0053 (ptt) REVERT: f 178 GLU cc_start: 0.4576 (OUTLIER) cc_final: 0.4259 (mt-10) REVERT: j 233 GLU cc_start: 0.6697 (OUTLIER) cc_final: 0.5198 (pp20) REVERT: m 340 MET cc_start: -0.0875 (ppp) cc_final: -0.1645 (tmm) REVERT: n 195 TRP cc_start: 0.0713 (m100) cc_final: 0.0243 (m100) outliers start: 145 outliers final: 100 residues processed: 455 average time/residue: 0.6336 time to fit residues: 513.3139 Evaluate side-chains 399 residues out of total 8871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 295 time to evaluate : 7.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 149 TRP Chi-restraints excluded: chain C residue 226 ASN Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 368 MET Chi-restraints excluded: chain E residue 372 ILE Chi-restraints excluded: chain E residue 378 LYS Chi-restraints excluded: chain E residue 384 GLU Chi-restraints excluded: chain E residue 401 LEU Chi-restraints excluded: chain E residue 420 TYR Chi-restraints excluded: chain E residue 464 ASP Chi-restraints excluded: chain E residue 485 SER Chi-restraints excluded: chain E residue 504 THR Chi-restraints excluded: chain E residue 538 ASP Chi-restraints excluded: chain E residue 540 VAL Chi-restraints excluded: chain E residue 596 ASP Chi-restraints excluded: chain E residue 629 LEU Chi-restraints excluded: chain E residue 655 GLU Chi-restraints excluded: chain E residue 659 LEU Chi-restraints excluded: chain E residue 681 SER Chi-restraints excluded: chain F residue 13 GLN Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 83 VAL Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 182 GLU Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain F residue 231 ASP Chi-restraints excluded: chain F residue 235 CYS Chi-restraints excluded: chain F residue 266 PHE Chi-restraints excluded: chain H residue 420 ILE Chi-restraints excluded: chain J residue 490 VAL Chi-restraints excluded: chain J residue 521 TYR Chi-restraints excluded: chain J residue 559 GLU Chi-restraints excluded: chain J residue 617 ILE Chi-restraints excluded: chain J residue 646 CYS Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain K residue 158 VAL Chi-restraints excluded: chain K residue 160 ASN Chi-restraints excluded: chain M residue 258 TYR Chi-restraints excluded: chain M residue 516 VAL Chi-restraints excluded: chain M residue 585 ASN Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 16 VAL Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain N residue 69 VAL Chi-restraints excluded: chain N residue 105 MET Chi-restraints excluded: chain P residue 418 ILE Chi-restraints excluded: chain a residue 148 SER Chi-restraints excluded: chain a residue 276 LEU Chi-restraints excluded: chain a residue 307 LEU Chi-restraints excluded: chain a residue 316 ASN Chi-restraints excluded: chain a residue 363 LEU Chi-restraints excluded: chain b residue 192 ILE Chi-restraints excluded: chain b residue 225 ASP Chi-restraints excluded: chain b residue 245 CYS Chi-restraints excluded: chain b residue 616 ILE Chi-restraints excluded: chain c residue 200 THR Chi-restraints excluded: chain c residue 301 LEU Chi-restraints excluded: chain e residue 375 VAL Chi-restraints excluded: chain e residue 380 THR Chi-restraints excluded: chain e residue 503 VAL Chi-restraints excluded: chain e residue 520 VAL Chi-restraints excluded: chain e residue 555 LEU Chi-restraints excluded: chain e residue 557 GLU Chi-restraints excluded: chain f residue 178 GLU Chi-restraints excluded: chain f residue 209 TYR Chi-restraints excluded: chain f residue 269 ASP Chi-restraints excluded: chain i residue 107 ASP Chi-restraints excluded: chain i residue 305 GLU Chi-restraints excluded: chain i residue 344 VAL Chi-restraints excluded: chain j residue 165 LEU Chi-restraints excluded: chain j residue 233 GLU Chi-restraints excluded: chain j residue 269 VAL Chi-restraints excluded: chain j residue 282 ASP Chi-restraints excluded: chain j residue 375 SER Chi-restraints excluded: chain j residue 438 LEU Chi-restraints excluded: chain j residue 490 VAL Chi-restraints excluded: chain j residue 504 MET Chi-restraints excluded: chain j residue 597 VAL Chi-restraints excluded: chain j residue 645 PHE Chi-restraints excluded: chain k residue 76 ASP Chi-restraints excluded: chain k residue 124 ILE Chi-restraints excluded: chain k residue 171 LYS Chi-restraints excluded: chain k residue 196 MET Chi-restraints excluded: chain k residue 199 LEU Chi-restraints excluded: chain k residue 226 ASN Chi-restraints excluded: chain m residue 126 TYR Chi-restraints excluded: chain m residue 130 LEU Chi-restraints excluded: chain m residue 161 SER Chi-restraints excluded: chain m residue 164 GLU Chi-restraints excluded: chain m residue 383 MET Chi-restraints excluded: chain m residue 444 VAL Chi-restraints excluded: chain o residue 73 MET Chi-restraints excluded: chain o residue 84 ILE Chi-restraints excluded: chain o residue 117 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 982 random chunks: chunk 585 optimal weight: 0.0470 chunk 377 optimal weight: 8.9990 chunk 565 optimal weight: 7.9990 chunk 285 optimal weight: 0.8980 chunk 185 optimal weight: 0.9990 chunk 183 optimal weight: 0.9990 chunk 601 optimal weight: 8.9990 chunk 644 optimal weight: 7.9990 chunk 467 optimal weight: 0.8980 chunk 88 optimal weight: 7.9990 chunk 743 optimal weight: 0.9990 overall best weight: 0.7682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 441 HIS ** B 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 573 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 667 GLN ** C 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 675 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 489 GLN K 221 ASN ** M 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 88 HIS ** N 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 404 GLN ** a 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 489 GLN ** c 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 624 ASN ** f 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 218 HIS f 263 HIS ** f 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 181 GLN o 80 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3798 moved from start: 0.7325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.072 73885 Z= 0.158 Angle : 0.568 13.636 100270 Z= 0.287 Chirality : 0.039 0.233 11748 Planarity : 0.004 0.073 12916 Dihedral : 4.719 35.198 10379 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.48 % Favored : 95.42 % Rotamer: Outliers : 1.28 % Allowed : 11.05 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.29 % Twisted General : 0.03 % 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: 1.36 (0.09), residues: 9429 helix: 2.73 (0.07), residues: 5198 sheet: -0.53 (0.14), residues: 1437 loop : -2.01 (0.11), residues: 2794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP n 244 HIS 0.010 0.001 HIS k 276 PHE 0.022 0.001 PHE M 511 TYR 0.052 0.001 TYR E 258 ARG 0.009 0.000 ARG m 206 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18858 Ramachandran restraints generated. 9429 Oldfield, 0 Emsley, 9429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18858 Ramachandran restraints generated. 9429 Oldfield, 0 Emsley, 9429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 8871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 323 time to evaluate : 6.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ARG cc_start: 0.1865 (mtt180) cc_final: 0.0349 (mmt180) REVERT: A 51 LEU cc_start: 0.3667 (mt) cc_final: 0.3002 (tp) REVERT: A 348 GLU cc_start: 0.4663 (mt-10) cc_final: 0.3943 (tm-30) REVERT: B 498 MET cc_start: 0.1255 (ttm) cc_final: 0.0843 (ttm) REVERT: B 607 LEU cc_start: 0.0933 (OUTLIER) cc_final: 0.0715 (tm) REVERT: E 601 MET cc_start: 0.7849 (mtt) cc_final: 0.7517 (mtt) REVERT: H 355 ARG cc_start: 0.1606 (tpm170) cc_final: 0.0343 (ttm170) REVERT: H 423 TYR cc_start: 0.1461 (p90) cc_final: 0.1193 (p90) REVERT: J 236 MET cc_start: 0.0352 (tpp) cc_final: -0.0253 (tpp) REVERT: J 365 MET cc_start: 0.1775 (mtt) cc_final: -0.1828 (mmm) REVERT: J 434 MET cc_start: 0.1738 (mmm) cc_final: 0.1384 (mmm) REVERT: J 504 MET cc_start: 0.2649 (mtm) cc_final: 0.1474 (mmp) REVERT: J 521 TYR cc_start: 0.1501 (OUTLIER) cc_final: 0.0501 (t80) REVERT: M 66 MET cc_start: 0.0933 (mmt) cc_final: -0.0282 (mtm) REVERT: M 507 CYS cc_start: 0.3069 (m) cc_final: 0.2647 (t) REVERT: M 629 LEU cc_start: 0.7148 (pp) cc_final: 0.6852 (tp) REVERT: N 25 MET cc_start: 0.4466 (tmm) cc_final: 0.2995 (tmm) REVERT: N 37 LYS cc_start: 0.4937 (mmtt) cc_final: 0.4498 (mtpt) REVERT: O 73 MET cc_start: 0.3504 (tmm) cc_final: 0.2462 (ppp) REVERT: P 321 MET cc_start: 0.0685 (mtp) cc_final: -0.0607 (ttm) REVERT: a 139 MET cc_start: 0.1135 (mmp) cc_final: 0.0793 (mmp) REVERT: a 363 LEU cc_start: 0.1499 (OUTLIER) cc_final: 0.1194 (tt) REVERT: a 377 MET cc_start: 0.0081 (mmp) cc_final: -0.2664 (ttm) REVERT: b 236 MET cc_start: 0.2227 (tpp) cc_final: 0.1918 (tpt) REVERT: b 238 MET cc_start: 0.0284 (mtm) cc_final: -0.0033 (mmm) REVERT: b 365 MET cc_start: 0.0564 (tmm) cc_final: -0.0346 (tmm) REVERT: b 460 MET cc_start: 0.0508 (mmm) cc_final: -0.0637 (ptm) REVERT: k 196 MET cc_start: 0.3204 (OUTLIER) cc_final: 0.2326 (mtt) REVERT: k 235 MET cc_start: 0.2205 (ptt) cc_final: 0.1643 (mtm) REVERT: m 340 MET cc_start: -0.0760 (ppp) cc_final: -0.1308 (tmm) REVERT: m 531 MET cc_start: 0.0033 (ppp) cc_final: -0.1349 (tpt) REVERT: n 153 MET cc_start: 0.2396 (tpp) cc_final: 0.0829 (tmm) REVERT: n 195 TRP cc_start: 0.0741 (m100) cc_final: 0.0202 (m100) outliers start: 86 outliers final: 60 residues processed: 396 average time/residue: 0.6172 time to fit residues: 439.5128 Evaluate side-chains 368 residues out of total 8871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 304 time to evaluate : 6.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 607 LEU Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 149 TRP Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 378 LYS Chi-restraints excluded: chain E residue 420 TYR Chi-restraints excluded: chain E residue 504 THR Chi-restraints excluded: chain E residue 538 ASP Chi-restraints excluded: chain E residue 629 LEU Chi-restraints excluded: chain E residue 657 MET Chi-restraints excluded: chain E residue 659 LEU Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain F residue 231 ASP Chi-restraints excluded: chain F residue 235 CYS Chi-restraints excluded: chain F residue 266 PHE Chi-restraints excluded: chain J residue 490 VAL Chi-restraints excluded: chain J residue 521 TYR Chi-restraints excluded: chain J residue 557 THR Chi-restraints excluded: chain J residue 559 GLU Chi-restraints excluded: chain J residue 646 CYS Chi-restraints excluded: chain K residue 158 VAL Chi-restraints excluded: chain K residue 160 ASN Chi-restraints excluded: chain M residue 258 TYR Chi-restraints excluded: chain M residue 585 ASN Chi-restraints excluded: chain N residue 32 VAL Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain a residue 148 SER Chi-restraints excluded: chain a residue 276 LEU Chi-restraints excluded: chain a residue 307 LEU Chi-restraints excluded: chain a residue 316 ASN Chi-restraints excluded: chain a residue 363 LEU Chi-restraints excluded: chain b residue 225 ASP Chi-restraints excluded: chain c residue 200 THR Chi-restraints excluded: chain c residue 301 LEU Chi-restraints excluded: chain e residue 375 VAL Chi-restraints excluded: chain e residue 503 VAL Chi-restraints excluded: chain e residue 520 VAL Chi-restraints excluded: chain e residue 557 GLU Chi-restraints excluded: chain i residue 261 LEU Chi-restraints excluded: chain i residue 305 GLU Chi-restraints excluded: chain j residue 165 LEU Chi-restraints excluded: chain j residue 490 VAL Chi-restraints excluded: chain j residue 645 PHE Chi-restraints excluded: chain j residue 661 LEU Chi-restraints excluded: chain k residue 196 MET Chi-restraints excluded: chain k residue 199 LEU Chi-restraints excluded: chain m residue 130 LEU Chi-restraints excluded: chain m residue 161 SER Chi-restraints excluded: chain m residue 164 GLU Chi-restraints excluded: chain m residue 444 VAL Chi-restraints excluded: chain n residue 16 VAL Chi-restraints excluded: chain n residue 281 ASN Chi-restraints excluded: chain n residue 330 THR Chi-restraints excluded: chain o residue 73 MET Chi-restraints excluded: chain o residue 80 ASN Chi-restraints excluded: chain p residue 352 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 982 random chunks: chunk 860 optimal weight: 10.0000 chunk 906 optimal weight: 6.9990 chunk 827 optimal weight: 50.0000 chunk 882 optimal weight: 30.0000 chunk 530 optimal weight: 10.0000 chunk 384 optimal weight: 6.9990 chunk 692 optimal weight: 20.0000 chunk 270 optimal weight: 30.0000 chunk 797 optimal weight: 0.8980 chunk 834 optimal weight: 8.9990 chunk 878 optimal weight: 30.0000 overall best weight: 6.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 GLN B 224 HIS ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 573 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 667 GLN ** C 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 675 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 489 GLN ** J 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 221 ASN ** M 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 287 HIS b 489 GLN ** b 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 288 HIS ** c 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 624 ASN e 625 GLN ** f 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 218 HIS ** f 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 181 GLN ** j 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 667 GLN ** k 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3988 moved from start: 0.8115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.171 73885 Z= 0.564 Angle : 0.837 16.355 100270 Z= 0.428 Chirality : 0.048 0.315 11748 Planarity : 0.006 0.077 12916 Dihedral : 5.568 38.623 10379 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 16.04 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.76 % Favored : 93.11 % Rotamer: Outliers : 1.65 % Allowed : 11.25 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.57 % Twisted General : 0.06 % 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: 0.37 (0.09), residues: 9429 helix: 1.87 (0.07), residues: 5170 sheet: -0.85 (0.14), residues: 1401 loop : -2.32 (0.11), residues: 2858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.003 TRP K 315 HIS 0.014 0.002 HIS k 98 PHE 0.033 0.003 PHE F 341 TYR 0.038 0.003 TYR B 603 ARG 0.014 0.001 ARG F 177 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18858 Ramachandran restraints generated. 9429 Oldfield, 0 Emsley, 9429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18858 Ramachandran restraints generated. 9429 Oldfield, 0 Emsley, 9429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 8871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 310 time to evaluate : 6.927 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 ARG cc_start: 0.1739 (mtt180) cc_final: 0.0389 (mmt180) REVERT: A 348 GLU cc_start: 0.4874 (mt-10) cc_final: 0.4206 (tm-30) REVERT: B 498 MET cc_start: 0.0656 (ttm) cc_final: 0.0220 (ttm) REVERT: B 594 ILE cc_start: 0.1582 (pt) cc_final: 0.1212 (pt) REVERT: B 607 LEU cc_start: 0.1270 (OUTLIER) cc_final: 0.1019 (tm) REVERT: E 601 MET cc_start: 0.7851 (mtt) cc_final: 0.7356 (mtt) REVERT: H 355 ARG cc_start: 0.1288 (tpm170) cc_final: -0.1085 (mmt90) REVERT: H 423 TYR cc_start: 0.1209 (p90) cc_final: 0.0595 (p90) REVERT: J 236 MET cc_start: 0.0487 (tpp) cc_final: -0.0156 (tpp) REVERT: J 504 MET cc_start: 0.3060 (mtm) cc_final: 0.1742 (mmm) REVERT: J 521 TYR cc_start: 0.2444 (OUTLIER) cc_final: 0.1183 (t80) REVERT: M 66 MET cc_start: 0.1348 (mmt) cc_final: -0.0075 (mtm) REVERT: M 507 CYS cc_start: 0.4078 (m) cc_final: 0.3350 (t) REVERT: N 37 LYS cc_start: 0.5298 (mmtt) cc_final: 0.4775 (mtpt) REVERT: N 60 GLU cc_start: 0.1582 (tp30) cc_final: 0.0738 (mt-10) REVERT: O 73 MET cc_start: 0.3461 (tmm) cc_final: 0.2639 (ppp) REVERT: P 321 MET cc_start: 0.0525 (mtp) cc_final: -0.0672 (ttm) REVERT: a 139 MET cc_start: 0.1393 (mmp) cc_final: 0.1107 (mmt) REVERT: a 363 LEU cc_start: 0.1417 (OUTLIER) cc_final: 0.1038 (tt) REVERT: a 377 MET cc_start: 0.0095 (mmp) cc_final: -0.2580 (ttm) REVERT: b 236 MET cc_start: 0.2278 (tpp) cc_final: 0.1809 (tpt) REVERT: b 238 MET cc_start: 0.0114 (mtm) cc_final: -0.0132 (mmm) REVERT: b 365 MET cc_start: 0.0924 (tmm) cc_final: -0.0047 (tmm) REVERT: c 267 TRP cc_start: 0.0684 (m100) cc_final: 0.0327 (m100) REVERT: e 509 TYR cc_start: 0.4662 (OUTLIER) cc_final: 0.2426 (p90) REVERT: i 261 LEU cc_start: 0.7935 (OUTLIER) cc_final: 0.7652 (mm) REVERT: j 233 GLU cc_start: 0.6436 (OUTLIER) cc_final: 0.4933 (pp20) REVERT: j 504 MET cc_start: 0.3095 (OUTLIER) cc_final: 0.2644 (mmp) REVERT: k 265 LEU cc_start: -0.0301 (OUTLIER) cc_final: -0.0709 (mm) REVERT: m 340 MET cc_start: -0.0590 (ppp) cc_final: -0.1301 (tmm) REVERT: m 531 MET cc_start: 0.0500 (ppp) cc_final: -0.1202 (tpt) REVERT: n 195 TRP cc_start: 0.0697 (m100) cc_final: 0.0315 (m100) REVERT: p 413 GLU cc_start: 0.4407 (tt0) cc_final: 0.4150 (tt0) outliers start: 111 outliers final: 80 residues processed: 406 average time/residue: 0.6328 time to fit residues: 461.7730 Evaluate side-chains 381 residues out of total 8871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 293 time to evaluate : 6.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 607 LEU Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 149 TRP Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain E residue 258 TYR Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 368 MET Chi-restraints excluded: chain E residue 372 ILE Chi-restraints excluded: chain E residue 378 LYS Chi-restraints excluded: chain E residue 401 LEU Chi-restraints excluded: chain E residue 408 ASP Chi-restraints excluded: chain E residue 420 TYR Chi-restraints excluded: chain E residue 433 TYR Chi-restraints excluded: chain E residue 485 SER Chi-restraints excluded: chain E residue 504 THR Chi-restraints excluded: chain E residue 538 ASP Chi-restraints excluded: chain E residue 540 VAL Chi-restraints excluded: chain E residue 629 LEU Chi-restraints excluded: chain E residue 655 GLU Chi-restraints excluded: chain E residue 659 LEU Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 83 VAL Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain F residue 231 ASP Chi-restraints excluded: chain F residue 235 CYS Chi-restraints excluded: chain F residue 266 PHE Chi-restraints excluded: chain J residue 217 VAL Chi-restraints excluded: chain J residue 490 VAL Chi-restraints excluded: chain J residue 521 TYR Chi-restraints excluded: chain J residue 557 THR Chi-restraints excluded: chain J residue 559 GLU Chi-restraints excluded: chain J residue 646 CYS Chi-restraints excluded: chain K residue 158 VAL Chi-restraints excluded: chain K residue 160 ASN Chi-restraints excluded: chain M residue 258 TYR Chi-restraints excluded: chain M residue 516 VAL Chi-restraints excluded: chain M residue 585 ASN Chi-restraints excluded: chain N residue 32 VAL Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain N residue 69 VAL Chi-restraints excluded: chain N residue 203 VAL Chi-restraints excluded: chain P residue 418 ILE Chi-restraints excluded: chain a residue 148 SER Chi-restraints excluded: chain a residue 276 LEU Chi-restraints excluded: chain a residue 307 LEU Chi-restraints excluded: chain a residue 316 ASN Chi-restraints excluded: chain a residue 363 LEU Chi-restraints excluded: chain b residue 225 ASP Chi-restraints excluded: chain b residue 245 CYS Chi-restraints excluded: chain b residue 616 ILE Chi-restraints excluded: chain c residue 200 THR Chi-restraints excluded: chain c residue 301 LEU Chi-restraints excluded: chain e residue 380 THR Chi-restraints excluded: chain e residue 503 VAL Chi-restraints excluded: chain e residue 509 TYR Chi-restraints excluded: chain e residue 520 VAL Chi-restraints excluded: chain e residue 557 GLU Chi-restraints excluded: chain f residue 209 TYR Chi-restraints excluded: chain i residue 261 LEU Chi-restraints excluded: chain j residue 165 LEU Chi-restraints excluded: chain j residue 233 GLU Chi-restraints excluded: chain j residue 375 SER Chi-restraints excluded: chain j residue 378 LEU Chi-restraints excluded: chain j residue 438 LEU Chi-restraints excluded: chain j residue 490 VAL Chi-restraints excluded: chain j residue 504 MET Chi-restraints excluded: chain j residue 597 VAL Chi-restraints excluded: chain j residue 605 THR Chi-restraints excluded: chain j residue 645 PHE Chi-restraints excluded: chain k residue 196 MET Chi-restraints excluded: chain k residue 199 LEU Chi-restraints excluded: chain k residue 206 ILE Chi-restraints excluded: chain k residue 265 LEU Chi-restraints excluded: chain m residue 126 TYR Chi-restraints excluded: chain m residue 130 LEU Chi-restraints excluded: chain m residue 161 SER Chi-restraints excluded: chain m residue 164 GLU Chi-restraints excluded: chain m residue 383 MET Chi-restraints excluded: chain m residue 430 LEU Chi-restraints excluded: chain m residue 444 VAL Chi-restraints excluded: chain n residue 16 VAL Chi-restraints excluded: chain n residue 330 THR Chi-restraints excluded: chain o residue 117 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 982 random chunks: chunk 579 optimal weight: 8.9990 chunk 932 optimal weight: 6.9990 chunk 569 optimal weight: 4.9990 chunk 442 optimal weight: 7.9990 chunk 648 optimal weight: 5.9990 chunk 978 optimal weight: 2.9990 chunk 900 optimal weight: 6.9990 chunk 779 optimal weight: 0.9990 chunk 80 optimal weight: 5.9990 chunk 601 optimal weight: 20.0000 chunk 477 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 HIS ** B 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 573 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 675 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 367 ASN J 489 GLN ** J 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 221 ASN ** M 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 606 ASN ** N 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 441 HIS ** b 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 276 HIS c 288 HIS ** c 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 624 ASN e 625 GLN f 47 GLN ** f 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 218 HIS ** f 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 98 HIS p 263 GLN ** p 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3918 moved from start: 0.8214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 73885 Z= 0.322 Angle : 0.656 13.763 100270 Z= 0.333 Chirality : 0.042 0.230 11748 Planarity : 0.004 0.069 12916 Dihedral : 5.129 36.706 10379 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.80 % Favored : 94.08 % Rotamer: Outliers : 1.32 % Allowed : 11.74 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.29 % Twisted General : 0.05 % 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: 0.78 (0.09), residues: 9429 helix: 2.26 (0.07), residues: 5208 sheet: -0.77 (0.14), residues: 1385 loop : -2.23 (0.11), residues: 2836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP K 315 HIS 0.019 0.001 HIS p 318 PHE 0.034 0.002 PHE p 279 TYR 0.022 0.002 TYR B 603 ARG 0.008 0.001 ARG m 206 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18858 Ramachandran restraints generated. 9429 Oldfield, 0 Emsley, 9429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18858 Ramachandran restraints generated. 9429 Oldfield, 0 Emsley, 9429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 8871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 306 time to evaluate : 6.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ARG cc_start: 0.1426 (mtt180) cc_final: 0.0103 (mmt180) REVERT: A 51 LEU cc_start: 0.3032 (mt) cc_final: 0.2247 (tp) REVERT: A 348 GLU cc_start: 0.4992 (mt-10) cc_final: 0.4264 (tm-30) REVERT: B 238 MET cc_start: 0.2878 (OUTLIER) cc_final: 0.0646 (mmt) REVERT: B 498 MET cc_start: 0.1234 (ttm) cc_final: 0.0823 (ttm) REVERT: B 594 ILE cc_start: 0.1660 (pt) cc_final: 0.1240 (pt) REVERT: B 607 LEU cc_start: 0.1343 (OUTLIER) cc_final: 0.1044 (tm) REVERT: E 601 MET cc_start: 0.7887 (mtt) cc_final: 0.7539 (mtt) REVERT: H 355 ARG cc_start: 0.1358 (tpm170) cc_final: -0.1014 (mmt90) REVERT: H 423 TYR cc_start: 0.1209 (p90) cc_final: 0.0677 (p90) REVERT: J 236 MET cc_start: 0.0377 (tpp) cc_final: -0.0242 (tpp) REVERT: J 365 MET cc_start: 0.2121 (mtt) cc_final: -0.1354 (mmm) REVERT: J 504 MET cc_start: 0.2726 (mtm) cc_final: 0.1558 (mmp) REVERT: J 521 TYR cc_start: 0.1921 (OUTLIER) cc_final: 0.0744 (t80) REVERT: M 66 MET cc_start: 0.1242 (mmt) cc_final: -0.0105 (mtm) REVERT: M 507 CYS cc_start: 0.4268 (m) cc_final: 0.3657 (t) REVERT: N 37 LYS cc_start: 0.5153 (mmtt) cc_final: 0.4694 (mtpt) REVERT: N 60 GLU cc_start: 0.1263 (tp30) cc_final: 0.0588 (mt-10) REVERT: O 73 MET cc_start: 0.3508 (tmm) cc_final: 0.2659 (ppp) REVERT: P 321 MET cc_start: 0.0132 (mtp) cc_final: -0.1106 (ttm) REVERT: a 363 LEU cc_start: 0.1391 (OUTLIER) cc_final: 0.1013 (tt) REVERT: a 377 MET cc_start: 0.0280 (mmp) cc_final: -0.2542 (ttm) REVERT: b 238 MET cc_start: -0.0013 (mtm) cc_final: -0.0950 (mmt) REVERT: b 365 MET cc_start: 0.0907 (tmm) cc_final: -0.0075 (tmm) REVERT: b 498 MET cc_start: 0.3869 (ttt) cc_final: 0.3504 (ptm) REVERT: e 509 TYR cc_start: 0.4581 (OUTLIER) cc_final: 0.2392 (p90) REVERT: i 261 LEU cc_start: 0.7773 (OUTLIER) cc_final: 0.7496 (mm) REVERT: j 504 MET cc_start: 0.3050 (mmm) cc_final: 0.2728 (mmp) REVERT: k 196 MET cc_start: 0.3251 (OUTLIER) cc_final: 0.2597 (mtt) REVERT: k 265 LEU cc_start: -0.0808 (OUTLIER) cc_final: -0.1239 (mm) REVERT: m 340 MET cc_start: -0.0545 (ppp) cc_final: -0.1073 (tmm) REVERT: m 531 MET cc_start: 0.0685 (ppp) cc_final: -0.0966 (tpt) REVERT: n 153 MET cc_start: 0.2117 (tpp) cc_final: 0.0281 (tmm) REVERT: n 195 TRP cc_start: 0.0616 (m100) cc_final: 0.0215 (m100) REVERT: p 413 GLU cc_start: 0.4435 (tt0) cc_final: 0.4164 (tt0) outliers start: 89 outliers final: 67 residues processed: 385 average time/residue: 0.6604 time to fit residues: 460.0033 Evaluate side-chains 374 residues out of total 8871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 299 time to evaluate : 6.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 607 LEU Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 149 TRP Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain E residue 258 TYR Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 368 MET Chi-restraints excluded: chain E residue 372 ILE Chi-restraints excluded: chain E residue 378 LYS Chi-restraints excluded: chain E residue 401 LEU Chi-restraints excluded: chain E residue 408 ASP Chi-restraints excluded: chain E residue 420 TYR Chi-restraints excluded: chain E residue 504 THR Chi-restraints excluded: chain E residue 538 ASP Chi-restraints excluded: chain E residue 629 LEU Chi-restraints excluded: chain E residue 659 LEU Chi-restraints excluded: chain E residue 681 SER Chi-restraints excluded: chain F residue 13 GLN Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 83 VAL Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 182 GLU Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain F residue 231 ASP Chi-restraints excluded: chain F residue 235 CYS Chi-restraints excluded: chain F residue 266 PHE Chi-restraints excluded: chain J residue 490 VAL Chi-restraints excluded: chain J residue 521 TYR Chi-restraints excluded: chain J residue 557 THR Chi-restraints excluded: chain J residue 559 GLU Chi-restraints excluded: chain J residue 646 CYS Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain K residue 158 VAL Chi-restraints excluded: chain K residue 160 ASN Chi-restraints excluded: chain M residue 258 TYR Chi-restraints excluded: chain M residue 585 ASN Chi-restraints excluded: chain N residue 16 VAL Chi-restraints excluded: chain N residue 32 VAL Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain a residue 148 SER Chi-restraints excluded: chain a residue 276 LEU Chi-restraints excluded: chain a residue 307 LEU Chi-restraints excluded: chain a residue 316 ASN Chi-restraints excluded: chain a residue 363 LEU Chi-restraints excluded: chain b residue 225 ASP Chi-restraints excluded: chain b residue 616 ILE Chi-restraints excluded: chain c residue 200 THR Chi-restraints excluded: chain c residue 301 LEU Chi-restraints excluded: chain e residue 380 THR Chi-restraints excluded: chain e residue 503 VAL Chi-restraints excluded: chain e residue 509 TYR Chi-restraints excluded: chain e residue 557 GLU Chi-restraints excluded: chain i residue 261 LEU Chi-restraints excluded: chain j residue 165 LEU Chi-restraints excluded: chain j residue 229 ILE Chi-restraints excluded: chain j residue 375 SER Chi-restraints excluded: chain j residue 490 VAL Chi-restraints excluded: chain j residue 645 PHE Chi-restraints excluded: chain k residue 196 MET Chi-restraints excluded: chain k residue 199 LEU Chi-restraints excluded: chain k residue 265 LEU Chi-restraints excluded: chain m residue 126 TYR Chi-restraints excluded: chain m residue 130 LEU Chi-restraints excluded: chain m residue 161 SER Chi-restraints excluded: chain m residue 164 GLU Chi-restraints excluded: chain m residue 430 LEU Chi-restraints excluded: chain m residue 444 VAL Chi-restraints excluded: chain n residue 16 VAL Chi-restraints excluded: chain n residue 330 THR Chi-restraints excluded: chain o residue 117 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 982 random chunks: chunk 618 optimal weight: 50.0000 chunk 829 optimal weight: 50.0000 chunk 238 optimal weight: 0.4980 chunk 718 optimal weight: 7.9990 chunk 115 optimal weight: 0.6980 chunk 216 optimal weight: 7.9990 chunk 780 optimal weight: 6.9990 chunk 326 optimal weight: 5.9990 chunk 801 optimal weight: 0.9980 chunk 98 optimal weight: 8.9990 chunk 143 optimal weight: 0.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 573 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 675 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 489 GLN K 221 ASN ** M 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 489 GLN ** b 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 288 HIS ** c 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 218 HIS ** f 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5026 r_free = 0.5026 target = 0.193554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4906 r_free = 0.4906 target = 0.185903 restraints weight = 281219.181| |-----------------------------------------------------------------------------| r_work (start): 0.4906 rms_B_bonded: 2.27 r_work: 0.4786 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.4771 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.4771 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4765 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4765 r_free = 0.4765 target_work(ls_wunit_k1) = 0.178 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4765 r_free = 0.4765 target_work(ls_wunit_k1) = 0.177 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.4765 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4303 moved from start: 0.8239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 73885 Z= 0.200 Angle : 0.592 16.034 100270 Z= 0.298 Chirality : 0.040 0.233 11748 Planarity : 0.004 0.058 12916 Dihedral : 4.796 35.621 10379 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.88 % Favored : 94.01 % Rotamer: Outliers : 1.07 % Allowed : 11.98 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.29 % Twisted General : 0.05 % 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: 1.23 (0.09), residues: 9429 helix: 2.65 (0.07), residues: 5197 sheet: -0.64 (0.14), residues: 1400 loop : -2.06 (0.11), residues: 2832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP K 315 HIS 0.009 0.001 HIS e 527 PHE 0.016 0.001 PHE a 167 TYR 0.018 0.001 TYR a 343 ARG 0.009 0.000 ARG m 206 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13600.08 seconds wall clock time: 242 minutes 2.99 seconds (14522.99 seconds total)