Starting phenix.real_space_refine on Wed Mar 20 01:30:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8err_28559/03_2024/8err_28559.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8err_28559/03_2024/8err_28559.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8err_28559/03_2024/8err_28559.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8err_28559/03_2024/8err_28559.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8err_28559/03_2024/8err_28559.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8err_28559/03_2024/8err_28559.pdb" } resolution = 3.1 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= -0.001 sd= 0.079 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 122 5.16 5 C 16395 2.51 5 N 4465 2.21 5 O 4798 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 398": "OD1" <-> "OD2" Residue "A ASP 405": "OD1" <-> "OD2" Residue "A TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 578": "OD1" <-> "OD2" Residue "A PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 619": "OE1" <-> "OE2" Residue "A TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 918": "OE1" <-> "OE2" Residue "A PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 981": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 820": "OD1" <-> "OD2" Residue "B TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 981": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1111": "OE1" <-> "OE2" Residue "C PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 224": "OE1" <-> "OE2" Residue "C PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 927": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 25780 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 7537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1018, 7537 Classifications: {'peptide': 1018} Incomplete info: {'truncation_to_alanine': 174} Link IDs: {'PTRANS': 55, 'TRANS': 962} Chain breaks: 8 Unresolved non-hydrogen bonds: 460 Unresolved non-hydrogen angles: 580 Unresolved non-hydrogen dihedrals: 354 Unresolved non-hydrogen chiralities: 46 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 3, 'ASN:plan1': 15, 'ASP:plan': 21, 'PHE:plan': 4, 'GLU:plan': 14, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 246 Chain: "B" Number of atoms: 6965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1009, 6965 Classifications: {'peptide': 1009} Incomplete info: {'truncation_to_alanine': 328} Link IDs: {'PTRANS': 55, 'TRANS': 953} Chain breaks: 9 Unresolved non-hydrogen bonds: 977 Unresolved non-hydrogen angles: 1253 Unresolved non-hydrogen dihedrals: 750 Unresolved non-hydrogen chiralities: 120 Planarities with less than four sites: {'GLN:plan1': 13, 'ASP:plan': 27, 'TYR:plan': 5, 'ASN:plan1': 33, 'HIS:plan': 4, 'PHE:plan': 13, 'GLU:plan': 23, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 512 Chain: "C" Number of atoms: 7164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1037, 7164 Classifications: {'peptide': 1037} Incomplete info: {'truncation_to_alanine': 308} Link IDs: {'PTRANS': 57, 'TRANS': 979} Chain breaks: 9 Unresolved non-hydrogen bonds: 1020 Unresolved non-hydrogen angles: 1308 Unresolved non-hydrogen dihedrals: 828 Unresolved non-hydrogen chiralities: 97 Planarities with less than four sites: {'GLN:plan1': 13, 'ARG:plan': 11, 'TYR:plan': 14, 'ASN:plan1': 25, 'TRP:plan': 2, 'HIS:plan': 3, 'PHE:plan': 17, 'GLU:plan': 20, 'ASP:plan': 30} Unresolved non-hydrogen planarities: 585 Chain: "H" Number of atoms: 591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 591 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 97} Link IDs: {'PTRANS': 6, 'TRANS': 110} Unresolved non-hydrogen bonds: 337 Unresolved non-hydrogen angles: 443 Unresolved non-hydrogen dihedrals: 278 Unresolved non-hydrogen chiralities: 46 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 6, 'ASN:plan1': 2, 'TRP:plan': 3, 'ASP:plan': 7, 'PHE:plan': 3, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 163 Chain: "L" Number of atoms: 547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 547 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 83} Link IDs: {'PTRANS': 5, 'TRANS': 103} Unresolved non-hydrogen bonds: 265 Unresolved non-hydrogen angles: 344 Unresolved non-hydrogen dihedrals: 222 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 2, 'TYR:plan': 7, 'ASN:plan1': 5, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 142 Chain: "E" Number of atoms: 591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 591 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 97} Link IDs: {'PTRANS': 6, 'TRANS': 110} Unresolved non-hydrogen bonds: 337 Unresolved non-hydrogen angles: 443 Unresolved non-hydrogen dihedrals: 278 Unresolved non-hydrogen chiralities: 46 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 6, 'ASN:plan1': 2, 'TRP:plan': 3, 'ASP:plan': 7, 'PHE:plan': 3, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 163 Chain: "F" Number of atoms: 547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 547 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 83} Link IDs: {'PTRANS': 5, 'TRANS': 103} Unresolved non-hydrogen bonds: 265 Unresolved non-hydrogen angles: 344 Unresolved non-hydrogen dihedrals: 222 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 2, 'TYR:plan': 7, 'ASN:plan1': 5, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 142 Chain: "I" Number of atoms: 591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 591 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 97} Link IDs: {'PTRANS': 6, 'TRANS': 110} Unresolved non-hydrogen bonds: 337 Unresolved non-hydrogen angles: 443 Unresolved non-hydrogen dihedrals: 278 Unresolved non-hydrogen chiralities: 46 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 6, 'ASN:plan1': 2, 'TRP:plan': 3, 'ASP:plan': 7, 'PHE:plan': 3, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 163 Chain: "J" Number of atoms: 547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 547 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 83} Link IDs: {'PTRANS': 5, 'TRANS': 103} Unresolved non-hydrogen bonds: 265 Unresolved non-hydrogen angles: 344 Unresolved non-hydrogen dihedrals: 222 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 2, 'TYR:plan': 7, 'ASN:plan1': 5, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 142 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 224 Unusual residues: {'NAG': 16} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 16 Chain: "B" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Chain: "C" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 238 Unusual residues: {'NAG': 17} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 17 Time building chain proxies: 12.02, per 1000 atoms: 0.47 Number of scatterers: 25780 At special positions: 0 Unit cell: (171, 131, 209, 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 122 16.00 O 4798 8.00 N 4465 7.00 C 16395 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=49, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.06 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.02 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 707 " - pdb=" SG CYS C 883 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.06 Simple disulfide: pdb=" SG CYS A 883 " - pdb=" SG CYS B 707 " distance=2.08 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.02 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.23 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.15 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.22 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.20 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.06 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.06 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B 883 " - pdb=" SG CYS C 707 " distance=2.06 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.05 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.20 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.14 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.02 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.07 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.01 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.10 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.13 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 97 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 91 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 97 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 91 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 97 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 91 " distance=2.03 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 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 234 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A 331 " " NAG A1307 " - " ASN A 343 " " NAG A1308 " - " ASN A 603 " " NAG A1309 " - " ASN A 616 " " NAG A1310 " - " ASN A 657 " " NAG A1311 " - " ASN A 709 " " NAG A1312 " - " ASN A 717 " " NAG A1313 " - " ASN A 801 " " NAG A1314 " - " ASN A1074 " " NAG A1315 " - " ASN A1098 " " NAG A1316 " - " ASN A1134 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 165 " " NAG B1304 " - " ASN B 234 " " NAG B1305 " - " ASN B 282 " " NAG B1306 " - " ASN B 331 " " NAG B1307 " - " ASN B 343 " " NAG B1308 " - " ASN B 603 " " NAG B1309 " - " ASN B 616 " " NAG B1310 " - " ASN B 657 " " NAG B1311 " - " ASN B 709 " " NAG B1312 " - " ASN B 717 " " NAG B1313 " - " ASN B1074 " " NAG B1314 " - " ASN B1098 " " NAG B1315 " - " ASN B1134 " " NAG C1301 " - " ASN C 17 " " NAG C1302 " - " ASN C 61 " " NAG C1303 " - " ASN C 122 " " NAG C1304 " - " ASN C 165 " " NAG C1305 " - " ASN C 234 " " NAG C1306 " - " ASN C 282 " " NAG C1307 " - " ASN C 331 " " NAG C1308 " - " ASN C 343 " " NAG C1309 " - " ASN C 603 " " NAG C1310 " - " ASN C 616 " " NAG C1311 " - " ASN C 657 " " NAG C1312 " - " ASN C 709 " " NAG C1313 " - " ASN C 717 " " NAG C1314 " - " ASN C 801 " " NAG C1315 " - " ASN C1074 " " NAG C1316 " - " ASN C1098 " " NAG C1317 " - " ASN C1134 " " NAG D 1 " - " ASN B 801 " Time building additional restraints: 10.51 Conformation dependent library (CDL) restraints added in 4.8 seconds 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7000 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 65 sheets defined 21.1% alpha, 36.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.48 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.819A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 371 removed outlier: 3.864A pdb=" N TYR A 369 " --> pdb=" O SER A 366 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASN A 370 " --> pdb=" O VAL A 367 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU A 371 " --> pdb=" O LEU A 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 366 through 371' Processing helix chain 'A' and resid 386 through 389 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.622A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.694A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.632A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 751 Processing helix chain 'A' and resid 752 through 756 Processing helix chain 'A' and resid 757 through 783 removed outlier: 4.295A pdb=" N THR A 761 " --> pdb=" O GLY A 757 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 823 Processing helix chain 'A' and resid 851 through 855 Processing helix chain 'A' and resid 866 through 884 removed outlier: 3.665A pdb=" N GLN A 872 " --> pdb=" O GLU A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 removed outlier: 4.224A pdb=" N GLY A 891 " --> pdb=" O PHE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.582A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 933 Processing helix chain 'A' and resid 934 through 938 Processing helix chain 'A' and resid 945 through 964 removed outlier: 3.995A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU A 962 " --> pdb=" O ALA A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 965 through 968 Processing helix chain 'A' and resid 978 through 983 removed outlier: 3.648A pdb=" N SER A 982 " --> pdb=" O ASN A 978 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG A 983 " --> pdb=" O ASP A 979 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 978 through 983' Processing helix chain 'A' and resid 985 through 1032 removed outlier: 3.634A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE A 993 " --> pdb=" O ALA A 989 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1145 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.764A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 370 removed outlier: 3.991A pdb=" N ASN B 370 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.382A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 737 through 742 Processing helix chain 'B' and resid 746 through 751 Processing helix chain 'B' and resid 757 through 783 removed outlier: 3.850A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 818 through 823 Processing helix chain 'B' and resid 851 through 855 removed outlier: 3.559A pdb=" N PHE B 855 " --> pdb=" O CYS B 851 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 851 through 855' Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.515A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 940 removed outlier: 3.737A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 941 through 944 Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.043A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 977 through 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.808A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1145 removed outlier: 3.510A pdb=" N GLU B1144 " --> pdb=" O LEU B1141 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.776A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 370 removed outlier: 3.969A pdb=" N ASN C 370 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.714A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 619 through 624 Processing helix chain 'C' and resid 625 through 629 Processing helix chain 'C' and resid 630 through 635 removed outlier: 3.727A pdb=" N VAL C 635 " --> pdb=" O PRO C 631 " (cutoff:3.500A) Processing helix chain 'C' and resid 748 through 756 removed outlier: 4.000A pdb=" N LEU C 753 " --> pdb=" O SER C 750 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N LEU C 754 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.649A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLN C 779 " --> pdb=" O ASP C 775 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 821 Processing helix chain 'C' and resid 822 through 824 No H-bonds generated for 'chain 'C' and resid 822 through 824' Processing helix chain 'C' and resid 850 through 855 Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.977A pdb=" N GLN C 872 " --> pdb=" O GLU C 868 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.563A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 940 removed outlier: 3.810A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 941 through 946 removed outlier: 4.203A pdb=" N LEU C 945 " --> pdb=" O PRO C 942 " (cutoff:3.500A) Processing helix chain 'C' and resid 948 through 965 Processing helix chain 'C' and resid 977 through 982 removed outlier: 3.547A pdb=" N SER C 982 " --> pdb=" O ASN C 978 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.525A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1145 Processing helix chain 'L' and resid 27 through 31 removed outlier: 4.118A pdb=" N VAL L 30 " --> pdb=" O SER L 27 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 86 removed outlier: 4.114A pdb=" N GLU L 86 " --> pdb=" O ALA L 83 " (cutoff:3.500A) Processing helix chain 'F' and resid 27 through 31 removed outlier: 4.072A pdb=" N VAL F 30 " --> pdb=" O SER F 27 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 86 removed outlier: 3.794A pdb=" N GLU F 86 " --> pdb=" O ALA F 83 " (cutoff:3.500A) Processing helix chain 'J' and resid 82 through 86 removed outlier: 3.776A pdb=" N GLU J 86 " --> pdb=" O ALA J 83 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 30 removed outlier: 8.312A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU A 224 " --> pdb=" O SER A 205 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.701A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.832A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.322A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 9.245A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 8.593A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N CYS A 136 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 10.171A pdb=" N SER A 162 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 10.237A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 13.376A pdb=" N PHE A 238 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 13.284A pdb=" N PHE A 135 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 12.999A pdb=" N THR A 240 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 11.056A pdb=" N ASN A 137 " --> pdb=" O THR A 240 " (cutoff:3.500A) removed outlier: 11.143A pdb=" N LEU A 242 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N LEU A 244 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 9.245A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 8.593A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N CYS A 136 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 10.171A pdb=" N SER A 162 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 10.237A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 4.535A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.242A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.598A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.665A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.157A pdb=" N ALA A 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N LYS C 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N ASN A 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.947A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.947A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.552A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 789 Processing sheet with id=AB9, first strand: chain 'A' and resid 796 through 797 Processing sheet with id=AC1, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.837A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.369A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU B 224 " --> pdb=" O SER B 205 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 42 through 43 removed outlier: 3.872A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 48 through 55 removed outlier: 7.704A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 83 through 85 removed outlier: 6.767A pdb=" N VAL B 126 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N TYR B 170 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ILE B 128 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N PHE B 168 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N VAL B 130 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N CYS B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N GLU B 132 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N CYS B 136 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N TYR B 160 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ASP B 138 " --> pdb=" O ARG B 158 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N ARG B 158 " --> pdb=" O ASP B 138 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 314 Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 358 removed outlier: 7.806A pdb=" N ASN B 394 " --> pdb=" O ALA B 522 " (cutoff:3.500A) removed outlier: 9.707A pdb=" N ALA B 522 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.571A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD2, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.648A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.507A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.507A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.474A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 787 through 789 Processing sheet with id=AD7, first strand: chain 'B' and resid 796 through 797 Processing sheet with id=AD8, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.973A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 27 through 28 removed outlier: 6.082A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 48 through 55 removed outlier: 7.523A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.646A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL C 126 " --> pdb=" O TYR C 170 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N TYR C 170 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ILE C 128 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N PHE C 168 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N VAL C 130 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N CYS C 166 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N GLU C 132 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N SER C 162 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N CYS C 136 " --> pdb=" O TYR C 160 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N TYR C 160 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N ASP C 138 " --> pdb=" O ARG C 158 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N ARG C 158 " --> pdb=" O ASP C 138 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 84 through 85 removed outlier: 13.227A pdb=" N PHE C 238 " --> pdb=" O PHE C 133 " (cutoff:3.500A) removed outlier: 13.082A pdb=" N PHE C 135 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 12.889A pdb=" N THR C 240 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 10.839A pdb=" N ASN C 137 " --> pdb=" O THR C 240 " (cutoff:3.500A) removed outlier: 11.381A pdb=" N LEU C 242 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N LEU C 244 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL C 126 " --> pdb=" O TYR C 170 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N TYR C 170 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ILE C 128 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N PHE C 168 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N VAL C 130 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N CYS C 166 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N GLU C 132 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N SER C 162 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N CYS C 136 " --> pdb=" O TYR C 160 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N TYR C 160 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N ASP C 138 " --> pdb=" O ARG C 158 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N ARG C 158 " --> pdb=" O ASP C 138 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 311 through 314 Processing sheet with id=AE5, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.790A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE7, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE8, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.288A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.705A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER C 691 " --> pdb=" O GLN C 675 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.601A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.601A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF3, first strand: chain 'C' and resid 796 through 797 Processing sheet with id=AF4, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.900A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AF6, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.744A pdb=" N VAL H 36 " --> pdb=" O LEU H 52 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N LEU H 52 " --> pdb=" O VAL H 36 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N TRP H 38 " --> pdb=" O LEU H 50 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AF8, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.528A pdb=" N VAL L 11 " --> pdb=" O THR L 108 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N TRP L 38 " --> pdb=" O MET L 50 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.528A pdb=" N VAL L 11 " --> pdb=" O THR L 108 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=AG2, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AG3, first strand: chain 'E' and resid 11 through 12 removed outlier: 6.733A pdb=" N VAL E 36 " --> pdb=" O LEU E 52 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N LEU E 52 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N TRP E 38 " --> pdb=" O LEU E 50 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.558A pdb=" N VAL F 11 " --> pdb=" O THR F 108 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N GLN F 40 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N LEU F 49 " --> pdb=" O GLN F 40 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.558A pdb=" N VAL F 11 " --> pdb=" O THR F 108 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'F' and resid 19 through 24 Processing sheet with id=AG7, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AG8, first strand: chain 'I' and resid 11 through 12 removed outlier: 6.659A pdb=" N VAL I 36 " --> pdb=" O LEU I 52 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N LEU I 52 " --> pdb=" O VAL I 36 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N TRP I 38 " --> pdb=" O LEU I 50 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'J' and resid 10 through 13 removed outlier: 3.671A pdb=" N GLY J 13 " --> pdb=" O THR J 108 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N GLN J 40 " --> pdb=" O LEU J 49 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N LEU J 49 " --> pdb=" O GLN J 40 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'J' and resid 10 through 13 removed outlier: 3.671A pdb=" N GLY J 13 " --> pdb=" O THR J 108 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'J' and resid 19 through 24 1245 hydrogen bonds defined for protein. 3219 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: 12.69 Time building geometry restraints manager: 11.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 4302 1.31 - 1.44: 6825 1.44 - 1.58: 15036 1.58 - 1.72: 2 1.72 - 1.86: 145 Bond restraints: 26310 Sorted by residual: bond pdb=" C ASN A 616 " pdb=" O ASN A 616 " ideal model delta sigma weight residual 1.236 1.169 0.067 1.21e-02 6.83e+03 3.06e+01 bond pdb=" CB LEU A1141 " pdb=" CG LEU A1141 " ideal model delta sigma weight residual 1.530 1.629 -0.099 2.00e-02 2.50e+03 2.47e+01 bond pdb=" N PRO C 728 " pdb=" CD PRO C 728 " ideal model delta sigma weight residual 1.473 1.539 -0.066 1.40e-02 5.10e+03 2.21e+01 bond pdb=" C ASN A 657 " pdb=" O ASN A 657 " ideal model delta sigma weight residual 1.232 1.172 0.060 1.32e-02 5.74e+03 2.06e+01 bond pdb=" C ASN B 616 " pdb=" O ASN B 616 " ideal model delta sigma weight residual 1.234 1.189 0.045 1.00e-02 1.00e+04 2.05e+01 ... (remaining 26305 not shown) Histogram of bond angle deviations from ideal: 95.34 - 103.07: 413 103.07 - 110.81: 9494 110.81 - 118.55: 10911 118.55 - 126.28: 15056 126.28 - 134.02: 215 Bond angle restraints: 36089 Sorted by residual: angle pdb=" C LEU B 861 " pdb=" N PRO B 862 " pdb=" CA PRO B 862 " ideal model delta sigma weight residual 119.66 126.31 -6.65 7.20e-01 1.93e+00 8.53e+01 angle pdb=" C LEU A 861 " pdb=" N PRO A 862 " pdb=" CA PRO A 862 " ideal model delta sigma weight residual 119.66 126.03 -6.37 7.20e-01 1.93e+00 7.82e+01 angle pdb=" C GLN I 41 " pdb=" N PRO I 42 " pdb=" CA PRO I 42 " ideal model delta sigma weight residual 119.66 125.58 -5.92 7.20e-01 1.93e+00 6.77e+01 angle pdb=" C GLN H 41 " pdb=" N PRO H 42 " pdb=" CA PRO H 42 " ideal model delta sigma weight residual 119.66 125.49 -5.83 7.20e-01 1.93e+00 6.55e+01 angle pdb=" N ASN A 801 " pdb=" CA ASN A 801 " pdb=" C ASN A 801 " ideal model delta sigma weight residual 108.76 95.34 13.42 1.69e+00 3.50e-01 6.31e+01 ... (remaining 36084 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 15636 17.83 - 35.67: 435 35.67 - 53.50: 101 53.50 - 71.33: 40 71.33 - 89.16: 18 Dihedral angle restraints: 16230 sinusoidal: 5406 harmonic: 10824 Sorted by residual: dihedral pdb=" CB CYS C 15 " pdb=" SG CYS C 15 " pdb=" SG CYS C 136 " pdb=" CB CYS C 136 " ideal model delta sinusoidal sigma weight residual 93.00 -177.84 -89.16 1 1.00e+01 1.00e-02 9.46e+01 dihedral pdb=" N ASN A 801 " pdb=" C ASN A 801 " pdb=" CA ASN A 801 " pdb=" CB ASN A 801 " ideal model delta harmonic sigma weight residual 122.80 100.86 21.94 0 2.50e+00 1.60e-01 7.70e+01 dihedral pdb=" CB CYS C 336 " pdb=" SG CYS C 336 " pdb=" SG CYS C 361 " pdb=" CB CYS C 361 " ideal model delta sinusoidal sigma weight residual -86.00 -43.57 -42.43 1 1.00e+01 1.00e-02 2.51e+01 ... (remaining 16227 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.129: 3999 0.129 - 0.257: 339 0.257 - 0.386: 57 0.386 - 0.514: 0 0.514 - 0.643: 1 Chirality restraints: 4396 Sorted by residual: chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.50 0.10 2.00e-02 2.50e+03 2.47e+01 chirality pdb=" CA ASN A 801 " pdb=" N ASN A 801 " pdb=" C ASN A 801 " pdb=" CB ASN A 801 " both_signs ideal model delta sigma weight residual False 2.51 3.15 -0.64 2.00e-01 2.50e+01 1.03e+01 chirality pdb=" C1 NAG C1315 " pdb=" ND2 ASN C1074 " pdb=" C2 NAG C1315 " pdb=" O5 NAG C1315 " both_signs ideal model delta sigma weight residual False -2.40 -2.78 0.38 2.00e-01 2.50e+01 3.57e+00 ... (remaining 4393 not shown) Planarity restraints: 4801 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 122 " -0.232 2.00e-02 2.50e+03 3.04e-01 1.16e+03 pdb=" CG ASN C 122 " 0.106 2.00e-02 2.50e+03 pdb=" OD1 ASN C 122 " -0.022 2.00e-02 2.50e+03 pdb=" ND2 ASN C 122 " 0.514 2.00e-02 2.50e+03 pdb=" C1 NAG C1303 " -0.366 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1312 " 0.104 2.00e-02 2.50e+03 8.58e-02 9.21e+01 pdb=" C7 NAG C1312 " -0.029 2.00e-02 2.50e+03 pdb=" C8 NAG C1312 " 0.079 2.00e-02 2.50e+03 pdb=" N2 NAG C1312 " -0.136 2.00e-02 2.50e+03 pdb=" O7 NAG C1312 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C1098 " -0.052 2.00e-02 2.50e+03 5.16e-02 3.33e+01 pdb=" CG ASN C1098 " 0.030 2.00e-02 2.50e+03 pdb=" OD1 ASN C1098 " 0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN C1098 " 0.076 2.00e-02 2.50e+03 pdb=" C1 NAG C1316 " -0.063 2.00e-02 2.50e+03 ... (remaining 4798 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 8756 2.86 - 3.37: 21070 3.37 - 3.88: 39543 3.88 - 4.39: 44240 4.39 - 4.90: 76265 Nonbonded interactions: 189874 Sorted by model distance: nonbonded pdb=" OD1 ASP A 389 " pdb=" NZ LYS A 528 " model vdw 2.346 2.520 nonbonded pdb=" N SER A 112 " pdb=" O PHE A 133 " model vdw 2.428 2.520 nonbonded pdb=" O GLU A 619 " pdb=" CG GLU A 619 " model vdw 2.447 3.440 nonbonded pdb=" OD1 ASN B 165 " pdb=" O5 NAG B1303 " model vdw 2.453 3.040 nonbonded pdb=" O THR C 739 " pdb=" O ILE C 742 " model vdw 2.470 3.040 ... (remaining 189869 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 26 through 28 or (resid 29 through 31 and (name N or name \ CA or name C or name O or name CB )) or resid 32 or (resid 33 and (name N or nam \ e CA or name C or name O or name CB )) or resid 34 through 35 or (resid 36 and ( \ name N or name CA or name C or name O or name CB )) or resid 37 through 39 or (r \ esid 40 through 41 and (name N or name CA or name C or name O or name CB )) or r \ esid 42 through 44 or (resid 45 through 46 and (name N or name CA or name C or n \ ame O or name CB )) or resid 47 through 50 or (resid 51 and (name N or name CA o \ r name C or name O or name CB )) or resid 52 through 59 or (resid 60 and (name N \ or name CA or name C or name O or name CB )) or resid 61 or (resid 62 and (name \ N or name CA or name C or name O or name CB )) or resid 63 through 65 or (resid \ 66 through 68 and (name N or name CA or name C or name O or name CB )) or (resi \ d 78 through 81 and (name N or name CA or name C or name O or name CB )) or resi \ d 82 or (resid 83 and (name N or name CA or name C or name O or name CB )) or re \ sid 84 through 86 or (resid 87 through 88 and (name N or name CA or name C or na \ me O or name CB )) or resid 89 through 94 or (resid 95 through 100 and (name N o \ r name CA or name C or name O or name CB )) or resid 101 or (resid 102 and (name \ N or name CA or name C or name O or name CB )) or resid 103 through 116 or (res \ id 117 through 120 and (name N or name CA or name C or name O or name CB )) or r \ esid 121 through 127 or (resid 128 through 130 and (name N or name CA or name C \ or name O or name CB )) or resid 131 through 132 or (resid 133 through 138 and ( \ name N or name CA or name C or name O or name CB )) or resid 139 or (resid 140 t \ hrough 164 and (name N or name CA or name C or name O or name CB )) or resid 165 \ through 187 or (resid 188 through 191 and (name N or name CA or name C or name \ O or name CB )) or resid 192 through 195 or (resid 196 through 198 and (name N o \ r name CA or name C or name O or name CB )) or resid 199 through 202 or (resid 2 \ 03 and (name N or name CA or name C or name O or name CB )) or resid 204 through \ 206 or (resid 207 through 208 and (name N or name CA or name C or name O or nam \ e CB )) or resid 209 through 210 or resid 216 through 217 or (resid 218 and (nam \ e N or name CA or name C or name O or name CB )) or resid 219 through 228 or (re \ sid 229 and (name N or name CA or name C or name O or name CB )) or resid 230 or \ (resid 231 and (name N or name CA or name C or name O or name CB )) or resid 23 \ 2 or (resid 233 and (name N or name CA or name C or name O or name CB )) or resi \ d 234 or (resid 235 through 243 and (name N or name CA or name C or name O or na \ me CB )) or resid 263 through 266 or (resid 267 and (name N or name CA or name C \ or name O or name CB )) or resid 268 through 270 or (resid 271 and (name N or n \ ame CA or name C or name O or name CB )) or resid 272 through 279 or (resid 280 \ through 281 and (name N or name CA or name C or name O or name CB )) or resid 28 \ 2 through 288 or (resid 289 and (name N or name CA or name C or name O or name C \ B )) or resid 290 through 293 or (resid 294 and (name N or name CA or name C or \ name O or name CB )) or resid 295 through 307 or (resid 308 through 309 and (nam \ e N or name CA or name C or name O or name CB )) or resid 310 through 313 or (re \ sid 314 and (name N or name CA or name C or name O or name CB )) or resid 315 th \ rough 316 or (resid 317 and (name N or name CA or name C or name O or name CB )) \ or resid 318 through 319 or (resid 320 through 321 and (name N or name CA or na \ me C or name O or name CB )) or resid 322 or (resid 323 through 327 and (name N \ or name CA or name C or name O or name CB )) or resid 328 through 331 or (resid \ 332 through 335 and (name N or name CA or name C or name O or name CB )) or resi \ d 336 through 339 or (resid 340 through 342 and (name N or name CA or name C or \ name O or name CB )) or resid 343 through 344 or (resid 345 through 360 and (nam \ e N or name CA or name C or name O or name CB )) or resid 361 or (resid 362 thro \ ugh 364 and (name N or name CA or name C or name O or name CB )) or resid 365 th \ rough 366 or (resid 367 through 372 and (name N or name CA or name C or name O o \ r name CB )) or resid 373 or (resid 374 through 378 and (name N or name CA or na \ me C or name O or name CB )) or resid 379 or (resid 380 and (name N or name CA o \ r name C or name O or name CB )) or resid 381 or (resid 382 through 383 and (nam \ e N or name CA or name C or name O or name CB )) or resid 384 or (resid 385 thro \ ugh 390 and (name N or name CA or name C or name O or name CB )) or resid 391 or \ (resid 392 through 403 and (name N or name CA or name C or name O or name CB )) \ or resid 404 or (resid 405 through 411 and (name N or name CA or name C or name \ O or name CB )) or resid 412 through 413 or (resid 414 through 415 and (name N \ or name CA or name C or name O or name CB )) or resid 416 or (resid 417 through \ 425 and (name N or name CA or name C or name O or name CB )) or resid 426 throug \ h 428 or (resid 429 through 430 and (name N or name CA or name C or name O or na \ me CB )) or resid 431 through 432 or (resid 433 through 446 and (name N or name \ CA or name C or name O or name CB )) or resid 447 or (resid 448 through 462 and \ (name N or name CA or name C or name O or name CB )) or resid 463 or (resid 464 \ through 475 and (name N or name CA or name C or name O or name CB )) or resid 47 \ 6 through 488 or (resid 489 through 490 and (name N or name CA or name C or name \ O or name CB )) or resid 491 or (resid 492 through 498 and (name N or name CA o \ r name C or name O or name CB )) or resid 499 or (resid 500 through 501 and (nam \ e N or name CA or name C or name O or name CB )) or resid 502 or (resid 503 and \ (name N or name CA or name C or name O or name CB )) or resid 504 or (resid 505 \ through 506 and (name N or name CA or name C or name O or name CB )) or resid 50 \ 7 or (resid 508 through 516 and (name N or name CA or name C or name O or name C \ B )) or (resid 524 and (name N or name CA or name C or name O or name CB )) or r \ esid 525 through 527 or (resid 528 through 537 and (name N or name CA or name C \ or name O or name CB )) or resid 538 or (resid 539 through 542 and (name N or na \ me CA or name C or name O or name CB )) or resid 543 or (resid 544 and (name N o \ r name CA or name C or name O or name CB )) or resid 545 through 546 or (resid 5 \ 47 and (name N or name CA or name C or name O or name CB )) or resid 548 or (res \ id 549 and (name N or name CA or name C or name O or name CB )) or resid 550 or \ (resid 551 through 556 and (name N or name CA or name C or name O or name CB )) \ or resid 557 through 559 or (resid 560 and (name N or name CA or name C or name \ O or name CB )) or resid 561 or (resid 562 and (name N or name CA or name C or n \ ame O or name CB )) or resid 563 through 572 or (resid 573 through 576 and (name \ N or name CA or name C or name O or name CB )) or resid 577 or (resid 578 and ( \ name N or name CA or name C or name O or name CB )) or resid 579 or (resid 580 t \ hrough 584 and (name N or name CA or name C or name O or name CB )) or resid 585 \ through 586 or (resid 587 through 588 and (name N or name CA or name C or name \ O or name CB )) or resid 589 through 591 or (resid 592 and (name N or name CA or \ name C or name O or name CB )) or resid 593 through 601 or (resid 602 and (name \ N or name CA or name C or name O or name CB )) or resid 603 or (resid 604 throu \ gh 606 and (name N or name CA or name C or name O or name CB )) or resid 607 thr \ ough 614 or (resid 615 and (name N or name CA or name C or name O or name CB )) \ or resid 616 through 617 or (resid 618 through 620 and (name N or name CA or nam \ e C or name O or name CB )) or resid 621 through 644 or (resid 645 through 647 a \ nd (name N or name CA or name C or name O or name CB )) or resid 648 through 660 \ or (resid 661 and (name N or name CA or name C or name O or name CB )) or resid \ 662 through 676 or resid 690 through 701 or (resid 702 and (name N or name CA o \ r name C or name O or name CB )) or resid 703 through 707 or (resid 708 and (nam \ e N or name CA or name C or name O or name CB )) or resid 709 through 734 or (re \ sid 735 through 737 and (name N or name CA or name C or name O or name CB )) or \ resid 738 or (resid 739 through 740 and (name N or name CA or name C or name O o \ r name CB )) or resid 741 through 754 or (resid 755 and (name N or name CA or na \ me C or name O or name CB )) or resid 756 through 779 or (resid 780 and (name N \ or name CA or name C or name O or name CB )) or resid 781 through 784 or (resid \ 785 through 786 and (name N or name CA or name C or name O or name CB )) or resi \ d 787 through 789 or (resid 790 and (name N or name CA or name C or name O or na \ me CB )) or resid 791 through 813 or (resid 814 and (name N or name CA or name C \ or name O or name CB )) or resid 815 through 858 or (resid 859 and (name N or n \ ame CA or name C or name O or name CB )) or resid 860 through 865 or (resid 866 \ through 868 and (name N or name CA or name C or name O or name CB )) or resid 86 \ 9 through 920 or (resid 921 and (name N or name CA or name C or name O or name C \ B )) or resid 922 through 935 or (resid 936 through 937 and (name N or name CA o \ r name C or name O or name CB )) or resid 938 through 966 or (resid 967 through \ 968 and (name N or name CA or name C or name O or name CB )) or resid 969 throug \ h 990 or (resid 991 and (name N or name CA or name C or name O or name CB )) or \ resid 992 through 994 or (resid 995 and (name N or name CA or name C or name O o \ r name CB )) or resid 996 through 1009 or (resid 1010 and (name N or name CA or \ name C or name O or name CB )) or resid 1011 through 1036 or (resid 1037 through \ 1038 and (name N or name CA or name C or name O or name CB )) or resid 1039 thr \ ough 1040 or (resid 1041 and (name N or name CA or name C or name O or name CB ) \ ) or resid 1042 through 1071 or (resid 1072 through 1073 and (name N or name CA \ or name C or name O or name CB )) or resid 1074 through 1127 or (resid 1128 and \ (name N or name CA or name C or name O or name CB )) or resid 1129 through 1145 \ or resid 1301 through 1315)) selection = (chain 'B' and (resid 26 through 50 or (resid 51 and (name N or name CA or name \ C or name O or name CB )) or resid 52 through 104 or (resid 105 and (name N or n \ ame CA or name C or name O or name CB )) or resid 106 through 172 or (resid 173 \ and (name N or name CA or name C or name O or name CB )) or resid 174 through 28 \ 5 or (resid 286 through 289 and (name N or name CA or name C or name O or name C \ B )) or resid 290 through 297 or (resid 298 and (name N or name CA or name C or \ name O or name CB )) or resid 299 through 307 or (resid 308 through 309 and (nam \ e N or name CA or name C or name O or name CB )) or resid 310 through 333 or (re \ sid 334 through 335 and (name N or name CA or name C or name O or name CB )) or \ resid 336 through 341 or (resid 342 and (name N or name CA or name C or name O o \ r name CB )) or resid 343 through 346 or (resid 347 through 360 and (name N or n \ ame CA or name C or name O or name CB )) or resid 361 through 379 or (resid 380 \ and (name N or name CA or name C or name O or name CB )) or resid 381 through 39 \ 1 or (resid 392 through 403 and (name N or name CA or name C or name O or name C \ B )) or (resid 404 through 411 and (name N or name CA or name C or name O or nam \ e CB )) or resid 412 through 413 or (resid 414 through 415 and (name N or name C \ A or name C or name O or name CB )) or (resid 416 through 425 and (name N or nam \ e CA or name C or name O or name CB )) or resid 426 through 428 or (resid 429 th \ rough 430 and (name N or name CA or name C or name O or name CB )) or resid 431 \ through 435 or (resid 436 through 446 and (name N or name CA or name C or name O \ or name CB )) or (resid 447 through 462 and (name N or name CA or name C or nam \ e O or name CB )) or resid 463 or (resid 464 through 475 and (name N or name CA \ or name C or name O or name CB )) or resid 476 through 488 or (resid 489 through \ 490 and (name N or name CA or name C or name O or name CB )) or resid 491 or (r \ esid 492 through 498 and (name N or name CA or name C or name O or name CB )) or \ resid 499 through 500 or (resid 501 and (name N or name CA or name C or name O \ or name CB )) or resid 502 through 507 or (resid 508 through 516 and (name N or \ name CA or name C or name O or name CB )) or resid 524 through 535 or (resid 536 \ through 537 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 38 through 559 or (resid 560 and (name N or name CA or name C or name O or name \ CB )) or resid 561 or (resid 562 and (name N or name CA or name C or name O or n \ ame CB )) or resid 563 through 591 or (resid 592 and (name N or name CA or name \ C or name O or name CB )) or resid 593 through 598 or (resid 599 and (name N or \ name CA or name C or name O or name CB )) or resid 600 through 601 or (resid 602 \ and (name N or name CA or name C or name O or name CB )) or resid 603 or (resid \ 604 through 606 and (name N or name CA or name C or name O or name CB )) or res \ id 607 through 618 or (resid 619 through 620 and (name N or name CA or name C or \ name O or name CB )) or resid 621 through 645 or (resid 646 through 647 and (na \ me N or name CA or name C or name O or name CB )) or resid 648 through 674 or (r \ esid 675 through 676 and (name N or name CA or name C or name O or name CB )) or \ resid 690 through 701 or (resid 702 and (name N or name CA or name C or name O \ or name CB )) or resid 703 or (resid 704 and (name N or name CA or name C or nam \ e O or name CB )) or resid 705 through 709 or (resid 710 through 711 and (name N \ or name CA or name C or name O or name CB )) or resid 712 through 736 or (resid \ 737 and (name N or name CA or name C or name O or name CB )) or resid 738 throu \ gh 739 or (resid 740 and (name N or name CA or name C or name O or name CB )) or \ resid 741 through 744 or (resid 745 through 748 and (name N or name CA or name \ C or name O or name CB )) or resid 749 through 750 or (resid 751 and (name N or \ name CA or name C or name O or name CB )) or resid 752 through 754 or (resid 755 \ and (name N or name CA or name C or name O or name CB )) or resid 756 through 7 \ 57 or (resid 758 and (name N or name CA or name C or name O or name CB )) or res \ id 759 through 785 or (resid 786 and (name N or name CA or name C or name O or n \ ame CB )) or resid 787 through 789 or (resid 790 and (name N or name CA or name \ C or name O or name CB )) or resid 791 through 813 or (resid 814 and (name N or \ name CA or name C or name O or name CB )) or resid 815 through 858 or (resid 859 \ and (name N or name CA or name C or name O or name CB )) or resid 860 through 8 \ 65 or (resid 866 through 868 and (name N or name CA or name C or name O or name \ CB )) or resid 869 through 935 or (resid 936 through 937 and (name N or name CA \ or name C or name O or name CB )) or resid 938 through 973 or (resid 974 and (na \ me N or name CA or name C or name O or name CB )) or resid 975 through 979 or (r \ esid 980 and (name N or name CA or name C or name O or name CB )) or resid 981 t \ hrough 982 or (resid 983 through 986 and (name N or name CA or name C or name O \ or name CB )) or resid 987 through 993 or (resid 994 through 995 and (name N or \ name CA or name C or name O or name CB )) or resid 996 through 1004 or (resid 10 \ 05 and (name N or name CA or name C or name O or name CB )) or resid 1006 throug \ h 1037 or (resid 1038 and (name N or name CA or name C or name O or name CB )) o \ r resid 1039 through 1072 or (resid 1073 and (name N or name CA or name C or nam \ e O or name CB )) or resid 1074 through 1083 or (resid 1084 and (name N or name \ CA or name C or name O or name CB )) or resid 1085 through 1110 or (resid 1111 a \ nd (name N or name CA or name C or name O or name CB )) or resid 1112 through 11 \ 44 or (resid 1145 and (name N or name CA or name C or name O or name CB )) or re \ sid 1301 through 1315)) selection = (chain 'C' and (resid 26 through 29 or (resid 30 through 31 and (name N or name \ CA or name C or name O or name CB )) or resid 32 or (resid 33 and (name N or nam \ e CA or name C or name O or name CB )) or resid 34 through 35 or (resid 36 and ( \ name N or name CA or name C or name O or name CB )) or resid 37 through 39 or (r \ esid 40 through 41 and (name N or name CA or name C or name O or name CB )) or r \ esid 42 through 45 or (resid 46 and (name N or name CA or name C or name O or na \ me CB )) or resid 47 through 61 or (resid 62 and (name N or name CA or name C or \ name O or name CB )) or resid 63 through 65 or (resid 66 through 68 and (name N \ or name CA or name C or name O or name CB )) or (resid 78 through 81 and (name \ N or name CA or name C or name O or name CB )) or resid 82 or (resid 83 and (nam \ e N or name CA or name C or name O or name CB )) or resid 84 through 86 or (resi \ d 87 through 88 and (name N or name CA or name C or name O or name CB )) or resi \ d 89 through 93 or (resid 94 through 100 and (name N or name CA or name C or nam \ e O or name CB )) or resid 101 or (resid 102 and (name N or name CA or name C or \ name O or name CB )) or resid 103 through 104 or (resid 105 and (name N or name \ CA or name C or name O or name CB )) or resid 106 through 109 or (resid 110 thr \ ough 120 and (name N or name CA or name C or name O or name CB )) or resid 121 t \ hrough 124 or (resid 125 through 130 and (name N or name CA or name C or name O \ or name CB )) or resid 131 or (resid 132 through 138 and (name N or name CA or n \ ame C or name O or name CB )) or resid 139 or (resid 140 through 164 and (name N \ or name CA or name C or name O or name CB )) or resid 165 through 166 or (resid \ 167 and (name N or name CA or name C or name O or name CB )) or resid 168 or (r \ esid 169 and (name N or name CA or name C or name O or name CB )) or resid 170 t \ hrough 186 or (resid 187 through 191 and (name N or name CA or name C or name O \ or name CB )) or resid 192 through 195 or (resid 196 through 198 and (name N or \ name CA or name C or name O or name CB )) or resid 199 through 202 or (resid 203 \ and (name N or name CA or name C or name O or name CB )) or resid 204 through 2 \ 06 or (resid 207 through 208 and (name N or name CA or name C or name O or name \ CB )) or resid 209 through 210 or resid 216 through 227 or (resid 228 through 22 \ 9 and (name N or name CA or name C or name O or name CB )) or resid 230 or (resi \ d 231 and (name N or name CA or name C or name O or name CB )) or resid 232 or ( \ resid 233 and (name N or name CA or name C or name O or name CB )) or resid 234 \ or (resid 235 through 243 and (name N or name CA or name C or name O or name CB \ )) or resid 263 through 266 or (resid 267 and (name N or name CA or name C or na \ me O or name CB )) or resid 268 through 270 or (resid 271 and (name N or name CA \ or name C or name O or name CB )) or resid 272 through 279 or (resid 280 throug \ h 281 and (name N or name CA or name C or name O or name CB )) or resid 282 thro \ ugh 285 or (resid 286 through 289 and (name N or name CA or name C or name O or \ name CB )) or resid 290 through 297 or (resid 298 and (name N or name CA or name \ C or name O or name CB )) or resid 299 through 308 or (resid 309 and (name N or \ name CA or name C or name O or name CB )) or resid 310 through 313 or (resid 31 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 315 through \ 325 or (resid 326 through 327 and (name N or name CA or name C or name O or name \ CB )) or resid 328 through 534 or (resid 535 through 537 and (name N or name CA \ or name C or name O or name CB )) or resid 538 through 540 or (resid 541 throug \ h 542 and (name N or name CA or name C or name O or name CB )) or resid 543 thro \ ugh 550 or (resid 551 through 556 and (name N or name CA or name C or name O or \ name CB )) or resid 557 through 581 or (resid 582 through 584 and (name N or nam \ e CA or name C or name O or name CB )) or resid 585 through 586 or (resid 587 th \ rough 588 and (name N or name CA or name C or name O or name CB )) or resid 589 \ through 598 or (resid 599 and (name N or name CA or name C or name O or name CB \ )) or resid 600 through 614 or (resid 615 and (name N or name CA or name C or na \ me O or name CB )) or resid 616 through 617 or (resid 618 through 620 and (name \ N or name CA or name C or name O or name CB )) or resid 621 or resid 641 through \ 644 or (resid 645 through 647 and (name N or name CA or name C or name O or nam \ e CB )) or resid 648 through 658 or (resid 659 and (name N or name CA or name C \ or name O or name CB )) or resid 660 through 676 or (resid 690 through 691 and ( \ name N or name CA or name C or name O or name CB )) or resid 692 through 709 or \ (resid 710 through 711 and (name N or name CA or name C or name O or name CB )) \ or resid 712 through 734 or (resid 735 through 737 and (name N or name CA or nam \ e C or name O or name CB )) or resid 738 or (resid 739 through 740 and (name N o \ r name CA or name C or name O or name CB )) or resid 741 through 744 or (resid 7 \ 45 through 748 and (name N or name CA or name C or name O or name CB )) or resid \ 749 or (resid 750 through 751 and (name N or name CA or name C or name O or nam \ e CB )) or resid 752 through 779 or (resid 780 and (name N or name CA or name C \ or name O or name CB )) or resid 781 through 784 or (resid 785 through 786 and ( \ name N or name CA or name C or name O or name CB )) or resid 787 through 826 or \ resid 850 through 966 or (resid 967 through 968 and (name N or name CA or name C \ or name O or name CB )) or resid 969 through 972 or (resid 973 through 974 and \ (name N or name CA or name C or name O or name CB )) or resid 975 through 979 or \ (resid 980 and (name N or name CA or name C or name O or name CB )) or resid 98 \ 1 through 982 or (resid 983 through 986 and (name N or name CA or name C or name \ O or name CB )) or resid 987 through 989 or (resid 990 through 991 and (name N \ or name CA or name C or name O or name CB )) or resid 992 through 993 or (resid \ 994 through 995 and (name N or name CA or name C or name O or name CB )) or resi \ d 996 through 1004 or (resid 1005 and (name N or name CA or name C or name O or \ name CB )) or resid 1006 through 1009 or (resid 1010 and (name N or name CA or n \ ame C or name O or name CB )) or resid 1011 through 1036 or (resid 1037 through \ 1038 and (name N or name CA or name C or name O or name CB )) or resid 1039 thro \ ugh 1071 or (resid 1072 through 1073 and (name N or name CA or name C or name O \ or name CB )) or resid 1074 through 1083 or (resid 1084 and (name N or name CA o \ r name C or name O or name CB )) or resid 1085 through 1124 or (resid 1125 and ( \ name N or name CA or name C or name O or name CB )) or resid 1126 through 1135 o \ r (resid 1136 and (name N or name CA or name C or name O or name CB )) or resid \ 1137 through 1145 or resid 1301 through 1315)) } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'F' selection = chain 'J' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 39.390 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 73.210 Find NCS groups from input model: 2.120 Set up NCS constraints: 0.210 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: 0.010 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 124.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.099 26310 Z= 0.690 Angle : 1.341 13.422 36089 Z= 0.914 Chirality : 0.080 0.643 4396 Planarity : 0.005 0.086 4752 Dihedral : 9.906 88.141 9083 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.00 % Favored : 96.68 % Rotamer: Outliers : 0.88 % Allowed : 1.45 % Favored : 97.67 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.13), residues: 3672 helix: -0.69 (0.19), residues: 653 sheet: 1.23 (0.16), residues: 970 loop : 0.04 (0.13), residues: 2049 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.004 TRP B 886 HIS 0.005 0.001 HIS A1083 PHE 0.016 0.003 PHE C 140 TYR 0.035 0.004 TYR C 796 ARG 0.003 0.000 ARG C 34 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 340 time to evaluate : 2.843 Fit side-chains revert: symmetry clash REVERT: A 367 VAL cc_start: 0.8649 (t) cc_final: 0.8395 (m) REVERT: A 444 LYS cc_start: 0.6759 (mttt) cc_final: 0.5956 (mmtt) REVERT: B 403 ARG cc_start: 0.6115 (mtm180) cc_final: 0.5090 (mtt180) REVERT: C 697 MET cc_start: 0.8219 (ptm) cc_final: 0.7973 (ptm) REVERT: C 763 LEU cc_start: 0.8482 (tt) cc_final: 0.8033 (mp) REVERT: C 1019 ARG cc_start: 0.8143 (tpt170) cc_final: 0.7862 (ttp-110) outliers start: 17 outliers final: 4 residues processed: 352 average time/residue: 0.3757 time to fit residues: 205.1746 Evaluate side-chains 191 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 187 time to evaluate : 2.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 1098 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 309 optimal weight: 8.9990 chunk 278 optimal weight: 0.5980 chunk 154 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 chunk 187 optimal weight: 0.5980 chunk 148 optimal weight: 2.9990 chunk 287 optimal weight: 0.8980 chunk 111 optimal weight: 6.9990 chunk 174 optimal weight: 0.5980 chunk 214 optimal weight: 2.9990 chunk 333 optimal weight: 50.0000 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 439 ASN A 536 ASN A 540 ASN A 613 GLN A 935 GLN B 613 GLN B 992 GLN B1023 ASN C 935 GLN C1101 HIS C1125 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 26310 Z= 0.225 Angle : 0.597 12.937 36089 Z= 0.314 Chirality : 0.049 0.516 4396 Planarity : 0.005 0.044 4752 Dihedral : 5.239 56.967 4962 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.15 % Favored : 97.82 % Rotamer: Outliers : 1.66 % Allowed : 5.59 % Favored : 92.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.14), residues: 3672 helix: 0.75 (0.21), residues: 651 sheet: 1.42 (0.16), residues: 991 loop : -0.05 (0.13), residues: 2030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 436 HIS 0.008 0.001 HIS C1058 PHE 0.021 0.002 PHE B 58 TYR 0.023 0.001 TYR B 265 ARG 0.003 0.001 ARG A1014 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 190 time to evaluate : 2.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 776 LYS cc_start: 0.8522 (ttpt) cc_final: 0.8212 (ttpp) REVERT: B 403 ARG cc_start: 0.6137 (mtm180) cc_final: 0.5337 (mtt180) REVERT: B 821 LEU cc_start: 0.8203 (tm) cc_final: 0.7897 (tp) REVERT: B 1139 ASP cc_start: 0.7409 (t0) cc_final: 0.6997 (t0) REVERT: C 646 ARG cc_start: 0.7170 (mtm180) cc_final: 0.6908 (mtm180) REVERT: C 1019 ARG cc_start: 0.8140 (tpt170) cc_final: 0.7782 (ttm170) outliers start: 32 outliers final: 20 residues processed: 209 average time/residue: 0.3521 time to fit residues: 120.9364 Evaluate side-chains 181 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 161 time to evaluate : 2.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1098 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 185 optimal weight: 0.0470 chunk 103 optimal weight: 7.9990 chunk 277 optimal weight: 1.9990 chunk 226 optimal weight: 7.9990 chunk 91 optimal weight: 0.9980 chunk 333 optimal weight: 7.9990 chunk 360 optimal weight: 10.0000 chunk 297 optimal weight: 0.6980 chunk 331 optimal weight: 40.0000 chunk 113 optimal weight: 0.9980 chunk 267 optimal weight: 0.8980 overall best weight: 0.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 ASN A1002 GLN B 613 GLN B 762 GLN B 804 GLN B 965 GLN C1005 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 26310 Z= 0.205 Angle : 0.527 7.304 36089 Z= 0.278 Chirality : 0.047 0.458 4396 Planarity : 0.004 0.040 4752 Dihedral : 4.804 55.258 4962 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.56 % Favored : 97.41 % Rotamer: Outliers : 1.81 % Allowed : 7.30 % Favored : 90.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.14), residues: 3672 helix: 1.12 (0.21), residues: 640 sheet: 1.39 (0.16), residues: 1002 loop : -0.15 (0.13), residues: 2030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 436 HIS 0.006 0.001 HIS C1058 PHE 0.020 0.002 PHE B 58 TYR 0.022 0.001 TYR B 453 ARG 0.004 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 175 time to evaluate : 2.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 776 LYS cc_start: 0.8549 (ttpt) cc_final: 0.8249 (ttpp) REVERT: B 403 ARG cc_start: 0.6107 (mtm180) cc_final: 0.5313 (mtt-85) REVERT: B 821 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.7960 (tp) REVERT: C 1019 ARG cc_start: 0.8162 (tpt170) cc_final: 0.7954 (ttp-170) outliers start: 35 outliers final: 22 residues processed: 203 average time/residue: 0.3606 time to fit residues: 121.8888 Evaluate side-chains 181 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 158 time to evaluate : 2.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 707 CYS Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 764 LYS Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1098 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 329 optimal weight: 5.9990 chunk 251 optimal weight: 9.9990 chunk 173 optimal weight: 0.0370 chunk 36 optimal weight: 2.9990 chunk 159 optimal weight: 2.9990 chunk 224 optimal weight: 2.9990 chunk 335 optimal weight: 0.9980 chunk 354 optimal weight: 9.9990 chunk 175 optimal weight: 0.5980 chunk 317 optimal weight: 7.9990 chunk 95 optimal weight: 0.6980 overall best weight: 1.0660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1005 GLN C 762 GLN C1005 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 26310 Z= 0.272 Angle : 0.552 7.469 36089 Z= 0.290 Chirality : 0.049 0.433 4396 Planarity : 0.005 0.042 4752 Dihedral : 4.810 53.467 4960 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.45 % Favored : 97.52 % Rotamer: Outliers : 2.33 % Allowed : 8.33 % Favored : 89.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.14), residues: 3672 helix: 0.90 (0.21), residues: 652 sheet: 1.28 (0.16), residues: 1006 loop : -0.29 (0.13), residues: 2014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 436 HIS 0.008 0.002 HIS C1058 PHE 0.019 0.002 PHE A 168 TYR 0.025 0.001 TYR B 453 ARG 0.003 0.000 ARG B1107 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 164 time to evaluate : 2.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 776 LYS cc_start: 0.8577 (ttpt) cc_final: 0.8340 (ttpp) REVERT: B 403 ARG cc_start: 0.6260 (mtm180) cc_final: 0.5410 (mtt-85) REVERT: B 821 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.8050 (tp) REVERT: B 886 TRP cc_start: 0.7831 (p90) cc_final: 0.6582 (p-90) outliers start: 45 outliers final: 33 residues processed: 198 average time/residue: 0.3373 time to fit residues: 110.7771 Evaluate side-chains 180 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 146 time to evaluate : 2.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 707 CYS Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 764 LYS Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1098 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 295 optimal weight: 0.9990 chunk 201 optimal weight: 5.9990 chunk 5 optimal weight: 0.0470 chunk 264 optimal weight: 0.6980 chunk 146 optimal weight: 5.9990 chunk 302 optimal weight: 0.5980 chunk 245 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 181 optimal weight: 0.3980 chunk 318 optimal weight: 3.9990 chunk 89 optimal weight: 0.5980 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1005 GLN C 907 ASN C 913 GLN C1005 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.074 26310 Z= 0.152 Angle : 0.491 13.906 36089 Z= 0.256 Chirality : 0.046 0.389 4396 Planarity : 0.004 0.043 4752 Dihedral : 4.536 51.095 4960 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.48 % Favored : 97.49 % Rotamer: Outliers : 1.97 % Allowed : 8.90 % Favored : 89.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.68 (0.14), residues: 3672 helix: 1.20 (0.21), residues: 647 sheet: 1.34 (0.16), residues: 998 loop : -0.22 (0.14), residues: 2027 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 436 HIS 0.003 0.001 HIS C1058 PHE 0.012 0.001 PHE B 106 TYR 0.023 0.001 TYR B 453 ARG 0.004 0.000 ARG C1019 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 164 time to evaluate : 2.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 776 LYS cc_start: 0.8544 (ttpt) cc_final: 0.8301 (ttpp) REVERT: B 403 ARG cc_start: 0.6268 (mtm180) cc_final: 0.5391 (mtt180) REVERT: B 821 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.8051 (tp) outliers start: 38 outliers final: 26 residues processed: 191 average time/residue: 0.3330 time to fit residues: 106.6971 Evaluate side-chains 175 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 148 time to evaluate : 2.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 707 CYS Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 764 LYS Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1098 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 119 optimal weight: 9.9990 chunk 319 optimal weight: 10.0000 chunk 70 optimal weight: 2.9990 chunk 208 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 355 optimal weight: 2.9990 chunk 294 optimal weight: 0.0870 chunk 164 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 117 optimal weight: 2.9990 chunk 186 optimal weight: 1.9990 overall best weight: 1.5964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1002 GLN B 901 GLN C 613 GLN C1005 GLN C1135 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 26310 Z= 0.388 Angle : 0.620 10.777 36089 Z= 0.323 Chirality : 0.051 0.428 4396 Planarity : 0.005 0.068 4752 Dihedral : 5.089 52.937 4960 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.10 % Favored : 96.87 % Rotamer: Outliers : 2.64 % Allowed : 9.73 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.30 (0.14), residues: 3672 helix: 0.65 (0.21), residues: 659 sheet: 1.10 (0.16), residues: 1025 loop : -0.42 (0.14), residues: 1988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 886 HIS 0.010 0.002 HIS B1058 PHE 0.021 0.002 PHE A 275 TYR 0.025 0.002 TYR B 453 ARG 0.008 0.001 ARG A1039 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 160 time to evaluate : 2.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 776 LYS cc_start: 0.8617 (ttpt) cc_final: 0.8392 (ttmm) REVERT: B 403 ARG cc_start: 0.6196 (mtm180) cc_final: 0.5417 (mtt180) REVERT: B 821 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8147 (tp) REVERT: C 763 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.7935 (mt) outliers start: 51 outliers final: 34 residues processed: 195 average time/residue: 0.3433 time to fit residues: 111.9951 Evaluate side-chains 183 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 147 time to evaluate : 2.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 707 CYS Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 764 LYS Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1098 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 342 optimal weight: 40.0000 chunk 40 optimal weight: 0.0570 chunk 202 optimal weight: 1.9990 chunk 259 optimal weight: 0.7980 chunk 200 optimal weight: 0.6980 chunk 298 optimal weight: 0.3980 chunk 198 optimal weight: 0.6980 chunk 353 optimal weight: 6.9990 chunk 221 optimal weight: 2.9990 chunk 215 optimal weight: 0.8980 chunk 163 optimal weight: 0.6980 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 GLN A1002 GLN B 901 GLN B1005 GLN C 613 GLN C 644 GLN ** C 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 26310 Z= 0.164 Angle : 0.491 7.159 36089 Z= 0.255 Chirality : 0.046 0.369 4396 Planarity : 0.004 0.050 4752 Dihedral : 4.638 50.931 4960 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.86 % Allowed : 10.51 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.56 (0.14), residues: 3672 helix: 1.10 (0.21), residues: 653 sheet: 1.22 (0.16), residues: 1014 loop : -0.30 (0.14), residues: 2005 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 436 HIS 0.003 0.001 HIS C1058 PHE 0.018 0.001 PHE C 58 TYR 0.024 0.001 TYR B 453 ARG 0.003 0.000 ARG C1019 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 156 time to evaluate : 2.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 981 PHE cc_start: 0.7762 (OUTLIER) cc_final: 0.7507 (t80) REVERT: B 403 ARG cc_start: 0.6211 (mtm180) cc_final: 0.5423 (mtt180) REVERT: B 821 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.8137 (tp) REVERT: B 886 TRP cc_start: 0.7821 (p90) cc_final: 0.6489 (p-90) REVERT: C 763 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7815 (mt) outliers start: 36 outliers final: 27 residues processed: 177 average time/residue: 0.3556 time to fit residues: 104.6418 Evaluate side-chains 176 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 146 time to evaluate : 2.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 981 PHE Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 707 CYS Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 764 LYS Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1098 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 218 optimal weight: 0.1980 chunk 141 optimal weight: 0.9980 chunk 211 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 chunk 69 optimal weight: 0.9990 chunk 68 optimal weight: 0.3980 chunk 224 optimal weight: 0.8980 chunk 240 optimal weight: 7.9990 chunk 174 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 278 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 644 GLN B 965 GLN C 613 GLN ** C 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 26310 Z= 0.181 Angle : 0.495 8.440 36089 Z= 0.256 Chirality : 0.046 0.372 4396 Planarity : 0.004 0.050 4752 Dihedral : 4.524 52.194 4960 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.17 % Allowed : 10.61 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.64 (0.14), residues: 3672 helix: 1.22 (0.21), residues: 656 sheet: 1.31 (0.16), residues: 989 loop : -0.28 (0.14), residues: 2027 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.004 0.001 HIS C1058 PHE 0.018 0.001 PHE B 65 TYR 0.023 0.001 TYR B 453 ARG 0.003 0.000 ARG A1039 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 147 time to evaluate : 3.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 403 ARG cc_start: 0.6123 (mtm180) cc_final: 0.5406 (mtt180) REVERT: B 821 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.8100 (tp) REVERT: B 886 TRP cc_start: 0.7780 (p90) cc_final: 0.6434 (p-90) REVERT: C 763 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7818 (mt) outliers start: 42 outliers final: 35 residues processed: 174 average time/residue: 0.3581 time to fit residues: 104.4136 Evaluate side-chains 181 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 144 time to evaluate : 2.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 707 CYS Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 690 GLN Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 764 LYS Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1098 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 321 optimal weight: 5.9990 chunk 338 optimal weight: 40.0000 chunk 309 optimal weight: 0.0970 chunk 329 optimal weight: 8.9990 chunk 198 optimal weight: 1.9990 chunk 143 optimal weight: 7.9990 chunk 258 optimal weight: 0.7980 chunk 101 optimal weight: 9.9990 chunk 297 optimal weight: 0.0980 chunk 311 optimal weight: 8.9990 chunk 328 optimal weight: 10.0000 overall best weight: 1.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN B 901 GLN B 965 GLN C 613 GLN ** C 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.3567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 26310 Z= 0.427 Angle : 0.631 9.616 36089 Z= 0.327 Chirality : 0.052 0.409 4396 Planarity : 0.005 0.082 4752 Dihedral : 5.070 53.165 4960 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.12 % Allowed : 10.92 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.25 (0.14), residues: 3672 helix: 0.66 (0.21), residues: 661 sheet: 1.13 (0.16), residues: 992 loop : -0.47 (0.14), residues: 2019 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 886 HIS 0.010 0.002 HIS B1058 PHE 0.022 0.002 PHE B1121 TYR 0.026 0.002 TYR A 265 ARG 0.007 0.001 ARG A1039 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 154 time to evaluate : 2.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 403 ARG cc_start: 0.6296 (mtm180) cc_final: 0.5558 (mtt180) REVERT: B 821 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8208 (tp) REVERT: C 763 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.7957 (mt) outliers start: 41 outliers final: 34 residues processed: 181 average time/residue: 0.3245 time to fit residues: 98.0991 Evaluate side-chains 183 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 147 time to evaluate : 2.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 707 CYS Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 764 LYS Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1098 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 216 optimal weight: 0.8980 chunk 348 optimal weight: 40.0000 chunk 212 optimal weight: 0.3980 chunk 165 optimal weight: 1.9990 chunk 242 optimal weight: 0.5980 chunk 365 optimal weight: 7.9990 chunk 336 optimal weight: 0.8980 chunk 291 optimal weight: 0.5980 chunk 30 optimal weight: 0.0980 chunk 224 optimal weight: 0.5980 chunk 178 optimal weight: 0.7980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN C 613 GLN ** C 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.3626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 26310 Z= 0.158 Angle : 0.487 8.912 36089 Z= 0.252 Chirality : 0.046 0.360 4396 Planarity : 0.004 0.053 4752 Dihedral : 4.575 51.495 4960 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.76 % Allowed : 11.44 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.57 (0.14), residues: 3672 helix: 1.19 (0.21), residues: 652 sheet: 1.27 (0.16), residues: 990 loop : -0.32 (0.14), residues: 2030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 436 HIS 0.002 0.001 HIS A 66 PHE 0.016 0.001 PHE A 168 TYR 0.023 0.001 TYR B 453 ARG 0.003 0.000 ARG C1019 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 146 time to evaluate : 2.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 403 ARG cc_start: 0.6307 (mtm180) cc_final: 0.5594 (mtt180) REVERT: B 457 ARG cc_start: 0.6095 (tpt170) cc_final: 0.5757 (ttt-90) REVERT: B 821 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8141 (tp) REVERT: B 886 TRP cc_start: 0.7842 (p90) cc_final: 0.6466 (p-90) REVERT: C 763 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7792 (mt) outliers start: 34 outliers final: 29 residues processed: 170 average time/residue: 0.3179 time to fit residues: 90.8737 Evaluate side-chains 174 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 143 time to evaluate : 2.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 707 CYS Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 764 LYS Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1098 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 231 optimal weight: 30.0000 chunk 310 optimal weight: 0.0980 chunk 89 optimal weight: 1.9990 chunk 268 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 291 optimal weight: 0.6980 chunk 122 optimal weight: 0.0870 chunk 299 optimal weight: 0.1980 chunk 36 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 overall best weight: 0.3358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN C 30 ASN C 613 GLN ** C 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.200367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.190248 restraints weight = 28667.857| |-----------------------------------------------------------------------------| r_work (start): 0.4176 rms_B_bonded: 0.56 r_work: 0.4039 rms_B_bonded: 0.75 restraints_weight: 0.5000 r_work: 0.3985 rms_B_bonded: 1.42 restraints_weight: 0.2500 r_work: 0.3921 rms_B_bonded: 2.45 restraints_weight: 0.1250 r_work (final): 0.3921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.3707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 26310 Z= 0.135 Angle : 0.469 11.386 36089 Z= 0.241 Chirality : 0.045 0.358 4396 Planarity : 0.004 0.051 4752 Dihedral : 4.292 52.692 4960 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.78 % Favored : 97.19 % Rotamer: Outliers : 1.50 % Allowed : 11.70 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.14), residues: 3672 helix: 1.57 (0.21), residues: 641 sheet: 1.35 (0.16), residues: 1002 loop : -0.25 (0.14), residues: 2029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.004 0.001 HIS C 207 PHE 0.018 0.001 PHE C 140 TYR 0.023 0.001 TYR B 453 ARG 0.005 0.000 ARG A 357 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5179.96 seconds wall clock time: 94 minutes 46.78 seconds (5686.78 seconds total)