Starting phenix.real_space_refine on Tue Feb 20 17:13:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yvn_34133/02_2024/7yvn_34133.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yvn_34133/02_2024/7yvn_34133.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yvn_34133/02_2024/7yvn_34133.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yvn_34133/02_2024/7yvn_34133.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yvn_34133/02_2024/7yvn_34133.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yvn_34133/02_2024/7yvn_34133.pdb" } resolution = 3.4 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= 0.033 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 129 5.16 5 C 18210 2.51 5 N 4695 2.21 5 O 5469 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ARG 34": "NH1" <-> "NH2" Residue "C PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 44": "NH1" <-> "NH2" Residue "C ARG 102": "NH1" <-> "NH2" Residue "C ASP 138": "OD1" <-> "OD2" Residue "C ARG 190": "NH1" <-> "NH2" Residue "C ASP 228": "OD1" <-> "OD2" Residue "C ARG 237": "NH1" <-> "NH2" Residue "C ASP 253": "OD1" <-> "OD2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 273": "NH1" <-> "NH2" Residue "C GLU 281": "OE1" <-> "OE2" Residue "C ARG 328": "NH1" <-> "NH2" Residue "C ARG 346": "NH1" <-> "NH2" Residue "C ARG 355": "NH1" <-> "NH2" Residue "C ARG 357": "NH1" <-> "NH2" Residue "C PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 454": "NH1" <-> "NH2" Residue "C ARG 457": "NH1" <-> "NH2" Residue "C ARG 498": "NH1" <-> "NH2" Residue "C ARG 567": "NH1" <-> "NH2" Residue "C ARG 577": "NH1" <-> "NH2" Residue "C GLU 583": "OE1" <-> "OE2" Residue "C GLU 654": "OE1" <-> "OE2" Residue "C GLU 702": "OE1" <-> "OE2" Residue "C ARG 765": "NH1" <-> "NH2" Residue "C ARG 815": "NH1" <-> "NH2" Residue "C GLU 868": "OE1" <-> "OE2" Residue "C ARG 905": "NH1" <-> "NH2" Residue "C ARG 983": "NH1" <-> "NH2" Residue "C ASP 994": "OD1" <-> "OD2" Residue "C ARG 995": "NH1" <-> "NH2" Residue "C ARG 1000": "NH1" <-> "NH2" Residue "C ARG 1014": "NH1" <-> "NH2" Residue "C ARG 1019": "NH1" <-> "NH2" Residue "C ARG 1039": "NH1" <-> "NH2" Residue "C ASP 1041": "OD1" <-> "OD2" Residue "C ARG 1091": "NH1" <-> "NH2" Residue "C GLU 1092": "OE1" <-> "OE2" Residue "C ASP 1118": "OD1" <-> "OD2" Residue "C ASP 1146": "OD1" <-> "OD2" Residue "B ARG 34": "NH1" <-> "NH2" Residue "B PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 44": "NH1" <-> "NH2" Residue "B ARG 102": "NH1" <-> "NH2" Residue "B ARG 190": "NH1" <-> "NH2" Residue "B ASP 228": "OD1" <-> "OD2" Residue "B ARG 237": "NH1" <-> "NH2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 273": "NH1" <-> "NH2" Residue "B GLU 324": "OE1" <-> "OE2" Residue "B PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 346": "NH1" <-> "NH2" Residue "B ARG 355": "NH1" <-> "NH2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 389": "OD1" <-> "OD2" Residue "B ARG 454": "NH1" <-> "NH2" Residue "B PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 457": "NH1" <-> "NH2" Residue "B GLU 471": "OE1" <-> "OE2" Residue "B ARG 498": "NH1" <-> "NH2" Residue "B PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 567": "NH1" <-> "NH2" Residue "B ARG 577": "NH1" <-> "NH2" Residue "B ASP 578": "OD1" <-> "OD2" Residue "B GLU 583": "OE1" <-> "OE2" Residue "B GLU 654": "OE1" <-> "OE2" Residue "B GLU 702": "OE1" <-> "OE2" Residue "B ARG 765": "NH1" <-> "NH2" Residue "B GLU 780": "OE1" <-> "OE2" Residue "B ARG 815": "NH1" <-> "NH2" Residue "B GLU 868": "OE1" <-> "OE2" Residue "B ARG 905": "NH1" <-> "NH2" Residue "B PHE 906": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 950": "OD1" <-> "OD2" Residue "B ASP 979": "OD1" <-> "OD2" Residue "B ARG 983": "NH1" <-> "NH2" Residue "B GLU 990": "OE1" <-> "OE2" Residue "B ASP 994": "OD1" <-> "OD2" Residue "B ARG 995": "NH1" <-> "NH2" Residue "B ARG 1000": "NH1" <-> "NH2" Residue "B ARG 1014": "NH1" <-> "NH2" Residue "B GLU 1017": "OE1" <-> "OE2" Residue "B ARG 1019": "NH1" <-> "NH2" Residue "B ARG 1039": "NH1" <-> "NH2" Residue "B ASP 1041": "OD1" <-> "OD2" Residue "B ARG 1091": "NH1" <-> "NH2" Residue "B ASP 1139": "OD1" <-> "OD2" Residue "B ASP 1146": "OD1" <-> "OD2" Residue "A ARG 34": "NH1" <-> "NH2" Residue "A PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 44": "NH1" <-> "NH2" Residue "A ASP 88": "OD1" <-> "OD2" Residue "A ARG 102": "NH1" <-> "NH2" Residue "A GLU 169": "OE1" <-> "OE2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A ASP 228": "OD1" <-> "OD2" Residue "A ARG 237": "NH1" <-> "NH2" Residue "A ASP 253": "OD1" <-> "OD2" Residue "A ARG 273": "NH1" <-> "NH2" Residue "A ASP 294": "OD1" <-> "OD2" Residue "A GLU 324": "OE1" <-> "OE2" Residue "A ARG 346": "NH1" <-> "NH2" Residue "A ARG 355": "NH1" <-> "NH2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 454": "NH1" <-> "NH2" Residue "A ARG 457": "NH1" <-> "NH2" Residue "A GLU 471": "OE1" <-> "OE2" Residue "A ARG 498": "NH1" <-> "NH2" Residue "A PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 567": "NH1" <-> "NH2" Residue "A ARG 577": "NH1" <-> "NH2" Residue "A GLU 583": "OE1" <-> "OE2" Residue "A GLU 654": "OE1" <-> "OE2" Residue "A GLU 702": "OE1" <-> "OE2" Residue "A ARG 765": "NH1" <-> "NH2" Residue "A ARG 815": "NH1" <-> "NH2" Residue "A ARG 905": "NH1" <-> "NH2" Residue "A ASP 950": "OD1" <-> "OD2" Residue "A ASP 979": "OD1" <-> "OD2" Residue "A ARG 983": "NH1" <-> "NH2" Residue "A GLU 990": "OE1" <-> "OE2" Residue "A ARG 995": "NH1" <-> "NH2" Residue "A ARG 1000": "NH1" <-> "NH2" Residue "A ARG 1014": "NH1" <-> "NH2" Residue "A GLU 1017": "OE1" <-> "OE2" Residue "A ARG 1019": "NH1" <-> "NH2" Residue "A ARG 1039": "NH1" <-> "NH2" Residue "A ASP 1041": "OD1" <-> "OD2" Residue "A ARG 1091": "NH1" <-> "NH2" Residue "A GLU 1092": "OE1" <-> "OE2" Residue "A ASP 1118": "OD1" <-> "OD2" Residue "A ASP 1146": "OD1" <-> "OD2" Residue "H GLU 1": "OE1" <-> "OE2" Residue "H ARG 18": "NH1" <-> "NH2" Residue "H ARG 24": "NH1" <-> "NH2" Residue "H ARG 45": "NH1" <-> "NH2" Residue "H ARG 54": "NH1" <-> "NH2" Residue "H ARG 61": "NH1" <-> "NH2" Residue "H GLU 107": "OE1" <-> "OE2" Residue "I ARG 19": "NH1" <-> "NH2" Residue "I ARG 38": "NH1" <-> "NH2" Residue "I PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 61": "OD1" <-> "OD2" Residue "I ARG 66": "NH1" <-> "NH2" Residue "I ARG 86": "NH1" <-> "NH2" Residue "I ARG 97": "NH1" <-> "NH2" Residue "K ARG 18": "NH1" <-> "NH2" Residue "K ARG 24": "NH1" <-> "NH2" Residue "K ARG 45": "NH1" <-> "NH2" Residue "K ARG 54": "NH1" <-> "NH2" Residue "K ARG 61": "NH1" <-> "NH2" Residue "K GLU 81": "OE1" <-> "OE2" Residue "L GLU 1": "OE1" <-> "OE2" Residue "L ARG 19": "NH1" <-> "NH2" Residue "L GLU 26": "OE1" <-> "OE2" Residue "L ARG 38": "NH1" <-> "NH2" Residue "L ASP 61": "OD1" <-> "OD2" Residue "L ARG 66": "NH1" <-> "NH2" Residue "L ARG 86": "NH1" <-> "NH2" Residue "L ARG 97": "NH1" <-> "NH2" Residue "L ASP 106": "OD1" <-> "OD2" Residue "N ARG 18": "NH1" <-> "NH2" Residue "N ARG 24": "NH1" <-> "NH2" Residue "N ARG 45": "NH1" <-> "NH2" Residue "N ARG 54": "NH1" <-> "NH2" Residue "N ARG 61": "NH1" <-> "NH2" Residue "N GLU 70": "OE1" <-> "OE2" Residue "O ARG 19": "NH1" <-> "NH2" Residue "O ARG 38": "NH1" <-> "NH2" Residue "O ASP 61": "OD1" <-> "OD2" Residue "O ARG 66": "NH1" <-> "NH2" Residue "O ARG 86": "NH1" <-> "NH2" Residue "O GLU 88": "OE1" <-> "OE2" Residue "O ARG 97": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 28503 Number of models: 1 Model: "" Number of chains: 12 Chain: "C" Number of atoms: 7649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 7649 Classifications: {'peptide': 1024} Incomplete info: {'truncation_to_alanine': 100} Link IDs: {'PTRANS': 56, 'TRANS': 967} Chain breaks: 7 Unresolved non-hydrogen bonds: 364 Unresolved non-hydrogen angles: 450 Unresolved non-hydrogen dihedrals: 296 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 9, 'TYR:plan': 4, 'ASN:plan1': 9, 'ASP:plan': 13, 'PHE:plan': 3, 'GLU:plan': 11, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 237 Chain: "B" Number of atoms: 7643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 7643 Classifications: {'peptide': 1024} Incomplete info: {'truncation_to_alanine': 101} Link IDs: {'PTRANS': 56, 'TRANS': 967} Chain breaks: 7 Unresolved non-hydrogen bonds: 370 Unresolved non-hydrogen angles: 457 Unresolved non-hydrogen dihedrals: 301 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 9, 'TYR:plan': 4, 'ASN:plan1': 9, 'ASP:plan': 13, 'PHE:plan': 3, 'GLU:plan': 11, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 242 Chain: "A" Number of atoms: 7634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 7634 Classifications: {'peptide': 1024} Incomplete info: {'truncation_to_alanine': 103} Link IDs: {'PTRANS': 56, 'TRANS': 967} Chain breaks: 7 Unresolved non-hydrogen bonds: 380 Unresolved non-hydrogen angles: 470 Unresolved non-hydrogen dihedrals: 310 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 9, 'TYR:plan': 4, 'ASN:plan1': 9, 'ASP:plan': 13, 'PHE:plan': 4, 'GLU:plan': 11, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 248 Chain: "H" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 821 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 101} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "I" Number of atoms: 870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 870 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 115} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "K" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 821 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 101} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "L" Number of atoms: 870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 870 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 115} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "N" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 821 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 101} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "O" Number of atoms: 870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 870 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 115} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "C" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "B" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 15.09, per 1000 atoms: 0.53 Number of scatterers: 28503 At special positions: 0 Unit cell: (145.14, 149.24, 225.5, 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 129 16.00 O 5469 8.00 N 4695 7.00 C 18210 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 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=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.05 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.05 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.04 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=2.05 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=2.04 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.05 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=2.01 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 95 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 95 " distance=2.04 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.04 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 95 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.27 Conformation dependent library (CDL) restraints added in 5.4 seconds 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6972 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 52 sheets defined 21.3% alpha, 28.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.73 Creating SS restraints... Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 344 Processing helix chain 'C' and resid 383 through 390 Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.876A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 569 through 571 No H-bonds generated for 'chain 'C' and resid 569 through 571' Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.686A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.532A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.634A pdb=" N GLY C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.682A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.967A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 976 through 983 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.097A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 removed outlier: 3.934A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 344 Processing helix chain 'B' and resid 383 through 390 Processing helix chain 'B' and resid 403 through 410 removed outlier: 4.852A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 569 through 571 No H-bonds generated for 'chain 'B' and resid 569 through 571' Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.585A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.626A pdb=" N GLY B 885 " --> pdb=" O THR B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.867A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.956A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 976 through 983 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.078A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 removed outlier: 3.845A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 344 Processing helix chain 'A' and resid 383 through 390 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.888A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 569 through 571 No H-bonds generated for 'chain 'A' and resid 569 through 571' Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.650A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.647A pdb=" N GLY A 885 " --> pdb=" O THR A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.782A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 919 through 941 removed outlier: 4.015A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 976 through 983 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.139A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1145 removed outlier: 3.791A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 83 removed outlier: 4.134A pdb=" N SER H 83 " --> pdb=" O SER H 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 72 through 75 Processing helix chain 'I' and resid 86 through 90 removed outlier: 4.050A pdb=" N THR I 90 " --> pdb=" O ALA I 87 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 83 removed outlier: 4.060A pdb=" N SER K 83 " --> pdb=" O SER K 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 72 through 75 Processing helix chain 'L' and resid 86 through 90 removed outlier: 3.982A pdb=" N THR L 90 " --> pdb=" O ALA L 87 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 83 removed outlier: 4.026A pdb=" N SER N 83 " --> pdb=" O SER N 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 72 through 75 Processing helix chain 'O' and resid 86 through 90 removed outlier: 3.952A pdb=" N THR O 90 " --> pdb=" O ALA O 87 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 28 through 31 removed outlier: 8.814A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 42 through 43 removed outlier: 3.611A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 47 through 55 removed outlier: 7.471A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.169A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.320A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 324 through 325 removed outlier: 6.933A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.843A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N PHE C 565 " --> pdb=" O PHE A 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.949A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY C 431 " --> pdb=" O TYR C 380 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR C 380 " --> pdb=" O GLY C 431 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL C 433 " --> pdb=" O LYS C 378 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.125A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.649A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 702 through 703 Processing sheet with id=AB2, first strand: chain 'C' and resid 711 through 728 removed outlier: 7.100A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE C1052 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 711 through 728 removed outlier: 7.100A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.465A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 788 through 789 removed outlier: 6.150A pdb=" N ILE C 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.455A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 29 through 31 removed outlier: 3.568A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.855A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR B 95 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 42 through 43 removed outlier: 6.210A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.550A pdb=" N VAL B 47 " --> pdb=" O TYR B 279 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.877A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.144A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.646A pdb=" N VAL B 433 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 361 through 362 removed outlier: 3.852A pdb=" N CYS B 525 " --> pdb=" O CYS B 361 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC6, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.940A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 711 through 728 removed outlier: 7.133A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY B1059 " --> pdb=" O ALA B1056 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 711 through 728 removed outlier: 7.133A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.441A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 788 through 789 removed outlier: 6.221A pdb=" N ILE B 788 " --> pdb=" O ASN A 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.440A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 29 through 31 removed outlier: 3.527A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.583A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR A 95 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.609A pdb=" N VAL A 47 " --> pdb=" O TYR A 279 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.830A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE A 106 " --> pdb=" O LEU A 117 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER A 172 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 311 through 319 removed outlier: 7.157A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N CYS A 649 " --> pdb=" O TYR A 612 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.854A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL A 433 " --> pdb=" O LYS A 378 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA A 376 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AD9, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.988A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.482A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE A 664 " --> pdb=" O ALA A 672 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'A' and resid 711 through 728 removed outlier: 7.091A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'A' and resid 711 through 728 removed outlier: 7.091A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.565A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.505A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 5 through 7 removed outlier: 3.815A pdb=" N GLU H 70 " --> pdb=" O SER H 67 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.772A pdb=" N LEU H 11 " --> pdb=" O GLU H 107 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL H 85 " --> pdb=" O GLN H 38 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 3 through 7 removed outlier: 4.075A pdb=" N GLN I 3 " --> pdb=" O SER I 25 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N SER I 25 " --> pdb=" O GLN I 3 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL I 5 " --> pdb=" O ALA I 23 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 10 through 12 removed outlier: 5.808A pdb=" N GLY I 10 " --> pdb=" O THR I 115 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N THR I 112 " --> pdb=" O TYR I 93 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 5 through 7 removed outlier: 3.782A pdb=" N GLU K 70 " --> pdb=" O SER K 67 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'K' and resid 10 through 13 removed outlier: 6.408A pdb=" N LEU K 11 " --> pdb=" O GLU K 107 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL K 85 " --> pdb=" O GLN K 38 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 3 through 7 removed outlier: 4.029A pdb=" N GLN L 3 " --> pdb=" O SER L 25 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER L 25 " --> pdb=" O GLN L 3 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 11 through 12 removed outlier: 3.593A pdb=" N VAL L 12 " --> pdb=" O THR L 115 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N MET L 34 " --> pdb=" O VAL L 50 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N VAL L 50 " --> pdb=" O MET L 34 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N TRP L 36 " --> pdb=" O VAL L 48 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'N' and resid 5 through 7 removed outlier: 3.587A pdb=" N PHE N 71 " --> pdb=" O CYS N 23 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU N 70 " --> pdb=" O SER N 67 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'N' and resid 10 through 13 removed outlier: 6.334A pdb=" N LEU N 11 " --> pdb=" O GLU N 107 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'O' and resid 3 through 7 Processing sheet with id=AF7, first strand: chain 'O' and resid 10 through 12 removed outlier: 6.450A pdb=" N GLY O 10 " --> pdb=" O THR O 115 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ARG O 38 " --> pdb=" O TRP O 47 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N TRP O 47 " --> pdb=" O ARG O 38 " (cutoff:3.500A) 1145 hydrogen bonds defined for protein. 3075 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: 15.01 Time building geometry restraints manager: 12.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 9150 1.35 - 1.49: 8156 1.49 - 1.62: 11688 1.62 - 1.76: 14 1.76 - 1.90: 151 Bond restraints: 29159 Sorted by residual: bond pdb=" C PHE B 329 " pdb=" N PRO B 330 " ideal model delta sigma weight residual 1.334 1.416 -0.082 2.34e-02 1.83e+03 1.22e+01 bond pdb=" CB CYS B 749 " pdb=" SG CYS B 749 " ideal model delta sigma weight residual 1.808 1.711 0.097 3.30e-02 9.18e+02 8.64e+00 bond pdb=" C PHE A 329 " pdb=" N PRO A 330 " ideal model delta sigma weight residual 1.334 1.401 -0.067 2.34e-02 1.83e+03 8.15e+00 bond pdb=" CB CYS B 743 " pdb=" SG CYS B 743 " ideal model delta sigma weight residual 1.808 1.716 0.092 3.30e-02 9.18e+02 7.79e+00 bond pdb=" CB CYS B 649 " pdb=" SG CYS B 649 " ideal model delta sigma weight residual 1.808 1.718 0.090 3.30e-02 9.18e+02 7.50e+00 ... (remaining 29154 not shown) Histogram of bond angle deviations from ideal: 97.95 - 105.39: 633 105.39 - 112.83: 15564 112.83 - 120.27: 11047 120.27 - 127.71: 12343 127.71 - 135.15: 241 Bond angle restraints: 39828 Sorted by residual: angle pdb=" CA CYS A 432 " pdb=" CB CYS A 432 " pdb=" SG CYS A 432 " ideal model delta sigma weight residual 114.40 130.35 -15.95 2.30e+00 1.89e-01 4.81e+01 angle pdb=" CA CYS C 432 " pdb=" CB CYS C 432 " pdb=" SG CYS C 432 " ideal model delta sigma weight residual 114.40 130.27 -15.87 2.30e+00 1.89e-01 4.76e+01 angle pdb=" N GLY C 526 " pdb=" CA GLY C 526 " pdb=" C GLY C 526 " ideal model delta sigma weight residual 112.34 125.56 -13.22 2.04e+00 2.40e-01 4.20e+01 angle pdb=" CA CYS A 525 " pdb=" CB CYS A 525 " pdb=" SG CYS A 525 " ideal model delta sigma weight residual 114.40 128.20 -13.80 2.30e+00 1.89e-01 3.60e+01 angle pdb=" CA TYR H 49 " pdb=" CB TYR H 49 " pdb=" CG TYR H 49 " ideal model delta sigma weight residual 113.90 124.41 -10.51 1.80e+00 3.09e-01 3.41e+01 ... (remaining 39823 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 16121 17.53 - 35.06: 1219 35.06 - 52.59: 219 52.59 - 70.12: 73 70.12 - 87.65: 27 Dihedral angle restraints: 17659 sinusoidal: 6799 harmonic: 10860 Sorted by residual: dihedral pdb=" CA PRO N 95 " pdb=" C PRO N 95 " pdb=" N PRO N 96 " pdb=" CA PRO N 96 " ideal model delta harmonic sigma weight residual -180.00 -126.72 -53.28 0 5.00e+00 4.00e-02 1.14e+02 dihedral pdb=" CA PRO H 95 " pdb=" C PRO H 95 " pdb=" N PRO H 96 " pdb=" CA PRO H 96 " ideal model delta harmonic sigma weight residual -180.00 -130.73 -49.27 0 5.00e+00 4.00e-02 9.71e+01 dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual 93.00 5.62 87.38 1 1.00e+01 1.00e-02 9.16e+01 ... (remaining 17656 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 3904 0.077 - 0.154: 713 0.154 - 0.231: 46 0.231 - 0.308: 7 0.308 - 0.385: 6 Chirality restraints: 4676 Sorted by residual: chirality pdb=" CA CYS A 432 " pdb=" N CYS A 432 " pdb=" C CYS A 432 " pdb=" CB CYS A 432 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.71e+00 chirality pdb=" CA PRO A 330 " pdb=" N PRO A 330 " pdb=" C PRO A 330 " pdb=" CB PRO A 330 " both_signs ideal model delta sigma weight residual False 2.72 2.35 0.37 2.00e-01 2.50e+01 3.45e+00 chirality pdb=" CA CYS B 432 " pdb=" N CYS B 432 " pdb=" C CYS B 432 " pdb=" CB CYS B 432 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.35e+00 ... (remaining 4673 not shown) Planarity restraints: 5100 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP H 94 " -0.062 5.00e-02 4.00e+02 9.38e-02 1.41e+01 pdb=" N PRO H 95 " 0.162 5.00e-02 4.00e+02 pdb=" CA PRO H 95 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO H 95 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP K 94 " 0.062 5.00e-02 4.00e+02 9.29e-02 1.38e+01 pdb=" N PRO K 95 " -0.161 5.00e-02 4.00e+02 pdb=" CA PRO K 95 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO K 95 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO K 95 " 0.051 5.00e-02 4.00e+02 7.86e-02 9.88e+00 pdb=" N PRO K 96 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO K 96 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO K 96 " 0.043 5.00e-02 4.00e+02 ... (remaining 5097 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 2080 2.72 - 3.27: 28529 3.27 - 3.81: 43994 3.81 - 4.36: 51979 4.36 - 4.90: 91411 Nonbonded interactions: 217993 Sorted by model distance: nonbonded pdb=" O LEU B 455 " pdb=" OH TYR I 107 " model vdw 2.179 2.440 nonbonded pdb=" NH2 ARG C 454 " pdb=" O ASP C 467 " model vdw 2.192 2.520 nonbonded pdb=" OH TYR H 49 " pdb=" O VAL I 5 " model vdw 2.203 2.440 nonbonded pdb=" OG SER H 83 " pdb=" OE1 GLU H 107 " model vdw 2.205 2.440 nonbonded pdb=" NH1 ARG C 34 " pdb=" O GLY C 219 " model vdw 2.211 2.520 ... (remaining 217988 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 27 through 328 or (resid 329 and (name N or name CA or nam \ e C or name O or name CB )) or resid 330 through 532 or (resid 533 and (name N o \ r name CA or name C or name O or name CB )) or resid 534 through 1146 or resid 1 \ 301 through 1311)) selection = (chain 'C' and (resid 27 through 327 or (resid 328 through 329 and (name N or na \ me CA or name C or name O or name CB )) or resid 330 through 532 or (resid 533 a \ nd (name N or name CA or name C or name O or name CB )) or resid 534 through 114 \ 6 or resid 1301 through 1311)) } ncs_group { reference = chain 'H' selection = chain 'K' selection = chain 'N' } ncs_group { reference = chain 'I' selection = chain 'L' selection = chain 'O' } 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: 10.750 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: 30.420 Check model and map are aligned: 0.370 Set scattering table: 0.270 Process input model: 80.070 Find NCS groups from input model: 2.210 Set up NCS constraints: 0.230 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:3.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 127.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 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 : 0.007 0.097 29159 Z= 0.461 Angle : 0.986 15.951 39828 Z= 0.534 Chirality : 0.058 0.385 4676 Planarity : 0.005 0.094 5100 Dihedral : 13.109 87.648 10552 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.62 % Allowed : 5.28 % Favored : 94.10 % Rotamer: Outliers : 1.06 % Allowed : 7.27 % Favored : 91.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.39 (0.12), residues: 3693 helix: 0.20 (0.20), residues: 649 sheet: -1.20 (0.14), residues: 997 loop : -2.48 (0.12), residues: 2047 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP N 94 HIS 0.011 0.001 HIS B 505 PHE 0.029 0.003 PHE B 456 TYR 0.051 0.002 TYR H 49 ARG 0.012 0.001 ARG H 61 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 3237 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 306 time to evaluate : 3.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 200 TYR cc_start: 0.8625 (m-80) cc_final: 0.8376 (m-80) REVERT: C 241 LEU cc_start: 0.7744 (pp) cc_final: 0.6926 (mp) REVERT: C 776 LYS cc_start: 0.8763 (ttpp) cc_final: 0.8434 (ttpp) REVERT: C 950 ASP cc_start: 0.7986 (m-30) cc_final: 0.7784 (m-30) REVERT: B 258 TRP cc_start: 0.5537 (t-100) cc_final: 0.4423 (m-90) REVERT: B 497 PHE cc_start: 0.4025 (m-80) cc_final: 0.3477 (m-80) REVERT: I 78 LEU cc_start: 0.4378 (mm) cc_final: 0.3953 (mt) REVERT: K 38 GLN cc_start: 0.6756 (tt0) cc_final: 0.6454 (tt0) REVERT: L 85 LEU cc_start: 0.2907 (OUTLIER) cc_final: 0.1988 (tp) REVERT: N 37 GLN cc_start: 0.8258 (tt0) cc_final: 0.7988 (tm-30) REVERT: N 99 THR cc_start: 0.7704 (m) cc_final: 0.7487 (m) REVERT: O 3 GLN cc_start: 0.7408 (tp-100) cc_final: 0.7126 (pp30) REVERT: O 36 TRP cc_start: 0.4306 (m100) cc_final: 0.3656 (m100) REVERT: O 45 LEU cc_start: 0.7651 (tp) cc_final: 0.7424 (tp) REVERT: O 108 TRP cc_start: 0.6578 (m100) cc_final: 0.5882 (m100) outliers start: 31 outliers final: 6 residues processed: 333 average time/residue: 0.4941 time to fit residues: 256.5187 Evaluate side-chains 192 residues out of total 3237 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 185 time to evaluate : 3.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain L residue 85 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 311 optimal weight: 6.9990 chunk 279 optimal weight: 0.6980 chunk 155 optimal weight: 0.7980 chunk 95 optimal weight: 1.9990 chunk 188 optimal weight: 6.9990 chunk 149 optimal weight: 0.0770 chunk 289 optimal weight: 0.9990 chunk 111 optimal weight: 6.9990 chunk 175 optimal weight: 3.9990 chunk 215 optimal weight: 2.9990 chunk 335 optimal weight: 50.0000 overall best weight: 0.9142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 506 GLN C 540 ASN C 657 ASN C 762 GLN C1074 ASN ** C1134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 ASN B 360 ASN B 493 GLN B 505 HIS B 506 GLN B 657 ASN A 354 ASN A 417 ASN A 493 GLN A 506 GLN A 657 ASN A 762 GLN ** A 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 953 ASN A 955 ASN A1005 GLN A1074 ASN ** A1098 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1134 ASN ** H 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 92 ASN O 81 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 29159 Z= 0.217 Angle : 0.654 10.625 39828 Z= 0.339 Chirality : 0.046 0.250 4676 Planarity : 0.004 0.051 5100 Dihedral : 6.435 53.851 4758 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.47 % Favored : 95.42 % Rotamer: Outliers : 2.09 % Allowed : 11.25 % Favored : 86.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 1.54 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.13), residues: 3693 helix: 1.59 (0.21), residues: 659 sheet: -0.67 (0.15), residues: 978 loop : -1.81 (0.13), residues: 2056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP H 94 HIS 0.006 0.001 HIS B 505 PHE 0.025 0.002 PHE A 970 TYR 0.019 0.001 TYR H 49 ARG 0.006 0.001 ARG C 357 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 3237 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 212 time to evaluate : 3.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 241 LEU cc_start: 0.7885 (pp) cc_final: 0.7319 (mp) REVERT: B 237 ARG cc_start: 0.7550 (OUTLIER) cc_final: 0.6866 (ptm-80) REVERT: B 258 TRP cc_start: 0.5613 (t-100) cc_final: 0.4501 (m-90) REVERT: B 282 ASN cc_start: 0.9074 (OUTLIER) cc_final: 0.8829 (m110) REVERT: B 497 PHE cc_start: 0.4284 (m-80) cc_final: 0.3779 (m-80) REVERT: A 135 PHE cc_start: 0.7102 (OUTLIER) cc_final: 0.5919 (m-80) REVERT: A 351 TYR cc_start: 0.8071 (t80) cc_final: 0.7672 (t80) REVERT: A 578 ASP cc_start: 0.3239 (m-30) cc_final: 0.2917 (t0) REVERT: A 950 ASP cc_start: 0.8072 (m-30) cc_final: 0.7806 (m-30) REVERT: K 37 GLN cc_start: 0.7144 (tt0) cc_final: 0.6921 (pm20) REVERT: K 86 TYR cc_start: 0.5973 (m-80) cc_final: 0.5271 (m-10) REVERT: L 82 MET cc_start: 0.5861 (mtm) cc_final: 0.5468 (mpp) REVERT: N 37 GLN cc_start: 0.8433 (tt0) cc_final: 0.8064 (tm-30) REVERT: O 34 MET cc_start: 0.7031 (mmt) cc_final: 0.6804 (mmp) REVERT: O 45 LEU cc_start: 0.7595 (tp) cc_final: 0.7376 (tp) outliers start: 61 outliers final: 33 residues processed: 256 average time/residue: 0.3860 time to fit residues: 161.2490 Evaluate side-chains 216 residues out of total 3237 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 180 time to evaluate : 3.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 762 GLN Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 953 ASN Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 71 PHE Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 49 TYR Chi-restraints excluded: chain O residue 68 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 186 optimal weight: 6.9990 chunk 103 optimal weight: 0.0770 chunk 278 optimal weight: 0.9990 chunk 228 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 335 optimal weight: 30.0000 chunk 362 optimal weight: 20.0000 chunk 298 optimal weight: 1.9990 chunk 332 optimal weight: 40.0000 chunk 114 optimal weight: 9.9990 chunk 269 optimal weight: 0.9980 overall best weight: 1.4144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 417 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 801 ASN ** C1134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 ASN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN A 762 GLN ** A 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1098 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 29159 Z= 0.248 Angle : 0.631 14.578 39828 Z= 0.325 Chirality : 0.046 0.296 4676 Planarity : 0.004 0.050 5100 Dihedral : 5.820 54.122 4748 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.87 % Favored : 95.10 % Rotamer: Outliers : 2.50 % Allowed : 12.56 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 1.54 % 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: -0.87 (0.13), residues: 3693 helix: 1.98 (0.21), residues: 659 sheet: -0.40 (0.16), residues: 977 loop : -1.60 (0.13), residues: 2057 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP H 94 HIS 0.004 0.001 HIS A1088 PHE 0.029 0.002 PHE B 392 TYR 0.019 0.001 TYR I 79 ARG 0.005 0.000 ARG H 61 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 3237 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 188 time to evaluate : 3.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 200 TYR cc_start: 0.8430 (m-80) cc_final: 0.8219 (m-80) REVERT: B 237 ARG cc_start: 0.7456 (OUTLIER) cc_final: 0.6798 (ptm-80) REVERT: B 497 PHE cc_start: 0.4494 (m-80) cc_final: 0.3967 (m-80) REVERT: B 515 PHE cc_start: 0.7014 (OUTLIER) cc_final: 0.6165 (m-10) REVERT: A 118 LEU cc_start: 0.7224 (mp) cc_final: 0.6974 (tp) REVERT: A 135 PHE cc_start: 0.7064 (OUTLIER) cc_final: 0.5852 (m-80) REVERT: A 351 TYR cc_start: 0.8153 (t80) cc_final: 0.7786 (t80) REVERT: A 377 PHE cc_start: 0.7964 (t80) cc_final: 0.7757 (t80) REVERT: A 515 PHE cc_start: 0.7477 (m-80) cc_final: 0.7259 (m-10) REVERT: A 950 ASP cc_start: 0.7993 (m-30) cc_final: 0.7724 (m-30) REVERT: L 82 MET cc_start: 0.5743 (mtm) cc_final: 0.5394 (mpp) REVERT: L 85 LEU cc_start: 0.2919 (OUTLIER) cc_final: 0.1775 (tp) REVERT: N 37 GLN cc_start: 0.8513 (tt0) cc_final: 0.8231 (tm-30) REVERT: O 45 LEU cc_start: 0.7528 (tp) cc_final: 0.7295 (tp) REVERT: O 52 PHE cc_start: 0.7858 (m-80) cc_final: 0.7039 (m-80) outliers start: 73 outliers final: 38 residues processed: 245 average time/residue: 0.3840 time to fit residues: 155.4818 Evaluate side-chains 210 residues out of total 3237 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 168 time to evaluate : 3.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain K residue 4 MET Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 49 TYR Chi-restraints excluded: chain N residue 69 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 331 optimal weight: 8.9990 chunk 252 optimal weight: 1.9990 chunk 174 optimal weight: 0.8980 chunk 37 optimal weight: 7.9990 chunk 160 optimal weight: 3.9990 chunk 225 optimal weight: 4.9990 chunk 336 optimal weight: 8.9990 chunk 356 optimal weight: 30.0000 chunk 176 optimal weight: 0.6980 chunk 319 optimal weight: 8.9990 chunk 96 optimal weight: 0.3980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 417 ASN A 762 GLN ** A 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 953 ASN ** A1098 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 29159 Z= 0.259 Angle : 0.611 11.439 39828 Z= 0.315 Chirality : 0.045 0.210 4676 Planarity : 0.004 0.050 5100 Dihedral : 5.514 53.057 4747 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.06 % Favored : 94.91 % Rotamer: Outliers : 3.02 % Allowed : 13.96 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 1.03 % 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: -0.66 (0.14), residues: 3693 helix: 2.05 (0.21), residues: 667 sheet: -0.24 (0.16), residues: 959 loop : -1.43 (0.13), residues: 2067 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 104 HIS 0.004 0.001 HIS A1088 PHE 0.023 0.002 PHE C 238 TYR 0.031 0.001 TYR L 79 ARG 0.003 0.000 ARG B 905 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 3237 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 182 time to evaluate : 3.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 237 ARG cc_start: 0.7530 (OUTLIER) cc_final: 0.6894 (ptm-80) REVERT: B 365 TYR cc_start: 0.7575 (m-80) cc_final: 0.6859 (t80) REVERT: B 497 PHE cc_start: 0.4602 (m-80) cc_final: 0.4082 (m-80) REVERT: B 902 MET cc_start: 0.8762 (tpt) cc_final: 0.8532 (tpt) REVERT: A 135 PHE cc_start: 0.6830 (OUTLIER) cc_final: 0.5561 (m-80) REVERT: A 950 ASP cc_start: 0.8036 (m-30) cc_final: 0.7782 (m-30) REVERT: L 82 MET cc_start: 0.5854 (mtm) cc_final: 0.5447 (mpp) REVERT: L 85 LEU cc_start: 0.2524 (OUTLIER) cc_final: 0.1328 (tp) REVERT: N 37 GLN cc_start: 0.8536 (tt0) cc_final: 0.8294 (tm-30) REVERT: O 45 LEU cc_start: 0.7514 (tp) cc_final: 0.7295 (tp) outliers start: 88 outliers final: 57 residues processed: 252 average time/residue: 0.3800 time to fit residues: 159.4118 Evaluate side-chains 224 residues out of total 3237 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 164 time to evaluate : 3.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 978 ASN Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 953 ASN Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain I residue 51 MET Chi-restraints excluded: chain K residue 4 MET Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 4 MET Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 49 TYR Chi-restraints excluded: chain N residue 69 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 297 optimal weight: 0.7980 chunk 202 optimal weight: 4.9990 chunk 5 optimal weight: 9.9990 chunk 265 optimal weight: 0.6980 chunk 147 optimal weight: 30.0000 chunk 304 optimal weight: 2.9990 chunk 246 optimal weight: 9.9990 chunk 0 optimal weight: 8.9990 chunk 182 optimal weight: 0.3980 chunk 320 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 519 HIS ** C1134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1098 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 29159 Z= 0.256 Angle : 0.618 20.652 39828 Z= 0.319 Chirality : 0.045 0.248 4676 Planarity : 0.004 0.053 5100 Dihedral : 5.391 53.163 4747 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.44 % Favored : 94.53 % Rotamer: Outliers : 3.19 % Allowed : 15.06 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 1.03 % 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: 3693 helix: 2.11 (0.21), residues: 664 sheet: -0.20 (0.16), residues: 972 loop : -1.36 (0.13), residues: 2057 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 104 HIS 0.004 0.001 HIS A1088 PHE 0.024 0.001 PHE C 238 TYR 0.021 0.001 TYR I 79 ARG 0.006 0.000 ARG O 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 3237 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 174 time to evaluate : 3.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 237 ARG cc_start: 0.7600 (OUTLIER) cc_final: 0.6978 (ptm-80) REVERT: B 365 TYR cc_start: 0.7625 (m-80) cc_final: 0.6896 (t80) REVERT: B 497 PHE cc_start: 0.4696 (m-80) cc_final: 0.4193 (m-80) REVERT: B 902 MET cc_start: 0.8751 (tpt) cc_final: 0.8446 (tpt) REVERT: A 950 ASP cc_start: 0.8078 (m-30) cc_final: 0.7832 (m-30) REVERT: K 100 PHE cc_start: 0.5535 (OUTLIER) cc_final: 0.5016 (t80) REVERT: L 82 MET cc_start: 0.5812 (mtm) cc_final: 0.5425 (mpp) REVERT: L 85 LEU cc_start: 0.2592 (OUTLIER) cc_final: 0.1332 (tp) REVERT: N 37 GLN cc_start: 0.8521 (tt0) cc_final: 0.8269 (tm-30) REVERT: O 34 MET cc_start: 0.7335 (mmm) cc_final: 0.6417 (mmm) outliers start: 93 outliers final: 64 residues processed: 246 average time/residue: 0.3772 time to fit residues: 154.0796 Evaluate side-chains 232 residues out of total 3237 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 165 time to evaluate : 3.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 775 ASP Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 978 ASN Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1084 ASP Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain I residue 51 MET Chi-restraints excluded: chain K residue 4 MET Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 100 PHE Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 51 MET Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 49 TYR Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain O residue 68 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 120 optimal weight: 50.0000 chunk 321 optimal weight: 5.9990 chunk 70 optimal weight: 0.6980 chunk 209 optimal weight: 7.9990 chunk 88 optimal weight: 0.6980 chunk 357 optimal weight: 7.9990 chunk 296 optimal weight: 0.4980 chunk 165 optimal weight: 0.9990 chunk 29 optimal weight: 9.9990 chunk 118 optimal weight: 3.9990 chunk 187 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 953 ASN ** A1098 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 92 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 29159 Z= 0.173 Angle : 0.577 13.644 39828 Z= 0.297 Chirality : 0.044 0.282 4676 Planarity : 0.004 0.046 5100 Dihedral : 5.089 52.914 4747 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.77 % Favored : 95.21 % Rotamer: Outliers : 2.61 % Allowed : 16.09 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 1.03 % 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: -0.41 (0.14), residues: 3693 helix: 2.13 (0.21), residues: 674 sheet: -0.05 (0.16), residues: 964 loop : -1.24 (0.13), residues: 2055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 104 HIS 0.003 0.001 HIS C 69 PHE 0.026 0.001 PHE C 238 TYR 0.024 0.001 TYR I 79 ARG 0.007 0.000 ARG O 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 3237 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 183 time to evaluate : 3.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 237 ARG cc_start: 0.7525 (OUTLIER) cc_final: 0.6971 (ptm-80) REVERT: B 365 TYR cc_start: 0.7637 (m-80) cc_final: 0.6921 (t80) REVERT: B 497 PHE cc_start: 0.4809 (m-80) cc_final: 0.4302 (m-80) REVERT: A 950 ASP cc_start: 0.7994 (m-30) cc_final: 0.7755 (m-30) REVERT: K 100 PHE cc_start: 0.5330 (OUTLIER) cc_final: 0.4984 (t80) REVERT: L 82 MET cc_start: 0.5670 (mtm) cc_final: 0.5387 (mpp) REVERT: L 85 LEU cc_start: 0.2578 (OUTLIER) cc_final: 0.1300 (tp) REVERT: N 27 GLN cc_start: 0.6072 (mp-120) cc_final: 0.5831 (mp10) REVERT: N 37 GLN cc_start: 0.8521 (tt0) cc_final: 0.8177 (tm-30) REVERT: O 34 MET cc_start: 0.7212 (mmm) cc_final: 0.6583 (mmm) REVERT: O 45 LEU cc_start: 0.7514 (tp) cc_final: 0.6941 (mt) REVERT: O 51 MET cc_start: 0.4716 (ppp) cc_final: 0.4448 (ppp) outliers start: 76 outliers final: 50 residues processed: 240 average time/residue: 0.3864 time to fit residues: 154.1065 Evaluate side-chains 214 residues out of total 3237 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 161 time to evaluate : 3.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 775 ASP Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 749 CYS Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain K residue 4 MET Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 100 PHE Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 51 MET Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 73 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 344 optimal weight: 9.9990 chunk 40 optimal weight: 0.0170 chunk 203 optimal weight: 3.9990 chunk 260 optimal weight: 0.0570 chunk 202 optimal weight: 5.9990 chunk 300 optimal weight: 0.8980 chunk 199 optimal weight: 2.9990 chunk 355 optimal weight: 6.9990 chunk 222 optimal weight: 20.0000 chunk 216 optimal weight: 9.9990 chunk 164 optimal weight: 0.7980 overall best weight: 0.9538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 953 ASN ** A1098 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.3224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 29159 Z= 0.190 Angle : 0.575 10.762 39828 Z= 0.297 Chirality : 0.044 0.255 4676 Planarity : 0.004 0.045 5100 Dihedral : 4.949 53.130 4747 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.98 % Favored : 94.99 % Rotamer: Outliers : 2.71 % Allowed : 16.43 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.51 % 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: -0.33 (0.14), residues: 3693 helix: 2.23 (0.21), residues: 669 sheet: 0.02 (0.16), residues: 970 loop : -1.22 (0.13), residues: 2054 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP L 36 HIS 0.003 0.001 HIS C 69 PHE 0.023 0.001 PHE C 238 TYR 0.020 0.001 TYR I 79 ARG 0.008 0.000 ARG O 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 3237 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 174 time to evaluate : 3.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 237 ARG cc_start: 0.7609 (OUTLIER) cc_final: 0.7038 (ptm-80) REVERT: B 365 TYR cc_start: 0.7582 (m-80) cc_final: 0.6857 (t80) REVERT: B 497 PHE cc_start: 0.4851 (m-80) cc_final: 0.4335 (m-80) REVERT: B 773 GLU cc_start: 0.7805 (tt0) cc_final: 0.7545 (tt0) REVERT: A 743 CYS cc_start: 0.7873 (OUTLIER) cc_final: 0.7654 (p) REVERT: A 950 ASP cc_start: 0.8007 (m-30) cc_final: 0.7765 (m-30) REVERT: K 100 PHE cc_start: 0.5380 (OUTLIER) cc_final: 0.4986 (t80) REVERT: L 82 MET cc_start: 0.5725 (mtm) cc_final: 0.5431 (mpp) REVERT: L 85 LEU cc_start: 0.2662 (OUTLIER) cc_final: 0.1310 (tp) REVERT: N 27 GLN cc_start: 0.5987 (mp-120) cc_final: 0.5736 (mp10) REVERT: N 37 GLN cc_start: 0.8490 (tt0) cc_final: 0.8214 (tm-30) REVERT: O 19 ARG cc_start: 0.7304 (mmm160) cc_final: 0.6862 (tmm160) REVERT: O 34 MET cc_start: 0.7134 (mmm) cc_final: 0.6693 (mmm) REVERT: O 38 ARG cc_start: 0.4377 (ptt90) cc_final: 0.4022 (ptm-80) REVERT: O 45 LEU cc_start: 0.7491 (tp) cc_final: 0.6846 (mp) REVERT: O 51 MET cc_start: 0.4936 (ppp) cc_final: 0.4727 (ppp) outliers start: 79 outliers final: 60 residues processed: 238 average time/residue: 0.3616 time to fit residues: 143.4102 Evaluate side-chains 232 residues out of total 3237 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 168 time to evaluate : 3.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 978 ASN Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1084 ASP Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 749 CYS Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 953 ASN Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain K residue 4 MET Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 100 PHE Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 13 VAL Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 69 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 220 optimal weight: 2.9990 chunk 142 optimal weight: 6.9990 chunk 212 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 69 optimal weight: 0.2980 chunk 68 optimal weight: 3.9990 chunk 226 optimal weight: 0.9990 chunk 242 optimal weight: 20.0000 chunk 175 optimal weight: 5.9990 chunk 33 optimal weight: 9.9990 chunk 279 optimal weight: 2.9990 overall best weight: 2.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN A 30 ASN A 125 ASN A 751 ASN ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1098 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 29159 Z= 0.314 Angle : 0.630 14.136 39828 Z= 0.327 Chirality : 0.046 0.239 4676 Planarity : 0.004 0.047 5100 Dihedral : 5.279 54.189 4747 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.66 % Favored : 94.31 % Rotamer: Outliers : 2.92 % Allowed : 16.60 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: -0.47 (0.14), residues: 3693 helix: 2.06 (0.21), residues: 668 sheet: -0.09 (0.16), residues: 1010 loop : -1.29 (0.13), residues: 2015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP L 36 HIS 0.009 0.001 HIS A 954 PHE 0.025 0.002 PHE C 238 TYR 0.024 0.002 TYR I 79 ARG 0.007 0.001 ARG B 983 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 3237 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 173 time to evaluate : 3.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 238 PHE cc_start: 0.7663 (OUTLIER) cc_final: 0.7162 (p90) REVERT: B 237 ARG cc_start: 0.7731 (OUTLIER) cc_final: 0.7054 (ptt-90) REVERT: B 365 TYR cc_start: 0.7552 (m-80) cc_final: 0.6795 (t80) REVERT: B 497 PHE cc_start: 0.4941 (m-80) cc_final: 0.4378 (m-80) REVERT: A 368 LEU cc_start: 0.8837 (mm) cc_final: 0.8525 (tp) REVERT: A 950 ASP cc_start: 0.8025 (m-30) cc_final: 0.7762 (m-30) REVERT: K 100 PHE cc_start: 0.5692 (OUTLIER) cc_final: 0.5266 (t80) REVERT: L 82 MET cc_start: 0.5707 (mtm) cc_final: 0.5473 (mpp) REVERT: L 85 LEU cc_start: 0.2855 (OUTLIER) cc_final: 0.1341 (tp) REVERT: N 27 GLN cc_start: 0.6188 (mp-120) cc_final: 0.5905 (mp10) REVERT: N 37 GLN cc_start: 0.8438 (tt0) cc_final: 0.8165 (tm-30) REVERT: O 6 GLU cc_start: 0.6088 (mt-10) cc_final: 0.4053 (tp30) REVERT: O 19 ARG cc_start: 0.7311 (mmm160) cc_final: 0.6844 (tmm160) REVERT: O 34 MET cc_start: 0.7144 (mmm) cc_final: 0.6745 (mmm) REVERT: O 38 ARG cc_start: 0.4531 (ptt90) cc_final: 0.4181 (ptm-80) REVERT: O 45 LEU cc_start: 0.7625 (tp) cc_final: 0.6999 (mp) outliers start: 85 outliers final: 64 residues processed: 242 average time/residue: 0.4047 time to fit residues: 162.3297 Evaluate side-chains 232 residues out of total 3237 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 164 time to evaluate : 4.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 775 ASP Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 978 ASN Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 749 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 953 ASN Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain K residue 4 MET Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 100 PHE Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain N residue 13 VAL Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 73 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 323 optimal weight: 50.0000 chunk 340 optimal weight: 40.0000 chunk 310 optimal weight: 20.0000 chunk 331 optimal weight: 10.0000 chunk 199 optimal weight: 0.6980 chunk 144 optimal weight: 7.9990 chunk 260 optimal weight: 0.8980 chunk 101 optimal weight: 0.9980 chunk 299 optimal weight: 0.6980 chunk 313 optimal weight: 40.0000 chunk 330 optimal weight: 20.0000 overall best weight: 2.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 505 HIS ** C1134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 953 ASN ** A1098 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.3589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 29159 Z= 0.334 Angle : 0.623 12.270 39828 Z= 0.324 Chirality : 0.046 0.232 4676 Planarity : 0.004 0.044 5100 Dihedral : 5.325 55.659 4747 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.50 % Favored : 94.48 % Rotamer: Outliers : 2.71 % Allowed : 17.08 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.14), residues: 3693 helix: 2.07 (0.21), residues: 669 sheet: -0.01 (0.16), residues: 1034 loop : -1.31 (0.13), residues: 1990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP L 36 HIS 0.005 0.001 HIS C 505 PHE 0.024 0.002 PHE C 238 TYR 0.034 0.002 TYR I 79 ARG 0.006 0.000 ARG L 97 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 3237 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 169 time to evaluate : 3.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 238 PHE cc_start: 0.7681 (OUTLIER) cc_final: 0.7138 (p90) REVERT: B 237 ARG cc_start: 0.7728 (OUTLIER) cc_final: 0.7080 (ptm-80) REVERT: B 365 TYR cc_start: 0.7526 (m-80) cc_final: 0.6759 (t80) REVERT: B 497 PHE cc_start: 0.5058 (m-80) cc_final: 0.4466 (m-80) REVERT: B 598 ILE cc_start: 0.8959 (OUTLIER) cc_final: 0.8682 (mm) REVERT: B 902 MET cc_start: 0.8821 (tpt) cc_final: 0.8455 (tpt) REVERT: A 368 LEU cc_start: 0.8846 (mm) cc_final: 0.8523 (tp) REVERT: A 950 ASP cc_start: 0.8102 (m-30) cc_final: 0.7865 (m-30) REVERT: K 100 PHE cc_start: 0.5855 (OUTLIER) cc_final: 0.5358 (t80) REVERT: L 34 MET cc_start: 0.6340 (pmm) cc_final: 0.5275 (pmm) REVERT: L 82 MET cc_start: 0.5830 (mtm) cc_final: 0.5541 (mpp) REVERT: L 85 LEU cc_start: 0.3007 (OUTLIER) cc_final: 0.1460 (tp) REVERT: N 27 GLN cc_start: 0.6164 (mp-120) cc_final: 0.5887 (mp10) REVERT: N 37 GLN cc_start: 0.8428 (tt0) cc_final: 0.8194 (tm-30) REVERT: O 6 GLU cc_start: 0.5951 (mt-10) cc_final: 0.3961 (tp30) REVERT: O 19 ARG cc_start: 0.7403 (mmm160) cc_final: 0.6936 (tmm160) REVERT: O 38 ARG cc_start: 0.4579 (ptt90) cc_final: 0.4237 (ptm-80) REVERT: O 45 LEU cc_start: 0.7630 (tp) cc_final: 0.7018 (mp) outliers start: 79 outliers final: 68 residues processed: 234 average time/residue: 0.3677 time to fit residues: 143.8301 Evaluate side-chains 235 residues out of total 3237 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 162 time to evaluate : 3.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 978 ASN Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 749 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 953 ASN Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain K residue 4 MET Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 100 PHE Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain N residue 13 VAL Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain O residue 68 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 217 optimal weight: 0.7980 chunk 350 optimal weight: 5.9990 chunk 213 optimal weight: 3.9990 chunk 166 optimal weight: 0.5980 chunk 243 optimal weight: 30.0000 chunk 367 optimal weight: 50.0000 chunk 338 optimal weight: 40.0000 chunk 292 optimal weight: 0.8980 chunk 30 optimal weight: 9.9990 chunk 226 optimal weight: 4.9990 chunk 179 optimal weight: 1.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 953 ASN ** A1098 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.3730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 29159 Z= 0.262 Angle : 0.600 11.649 39828 Z= 0.310 Chirality : 0.045 0.222 4676 Planarity : 0.004 0.044 5100 Dihedral : 5.169 53.847 4747 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.39 % Favored : 94.58 % Rotamer: Outliers : 2.64 % Allowed : 17.29 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.14), residues: 3693 helix: 2.14 (0.21), residues: 667 sheet: -0.01 (0.16), residues: 1015 loop : -1.27 (0.13), residues: 2011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP L 36 HIS 0.004 0.001 HIS B 69 PHE 0.024 0.001 PHE C 238 TYR 0.027 0.001 TYR I 79 ARG 0.006 0.000 ARG O 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 3237 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 165 time to evaluate : 3.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 238 PHE cc_start: 0.7731 (OUTLIER) cc_final: 0.7150 (p90) REVERT: B 237 ARG cc_start: 0.7701 (OUTLIER) cc_final: 0.7074 (ptm-80) REVERT: B 365 TYR cc_start: 0.7528 (m-80) cc_final: 0.6747 (t80) REVERT: B 497 PHE cc_start: 0.5056 (m-80) cc_final: 0.4430 (m-80) REVERT: B 598 ILE cc_start: 0.8954 (OUTLIER) cc_final: 0.8668 (mm) REVERT: A 368 LEU cc_start: 0.8851 (mm) cc_final: 0.8535 (tp) REVERT: A 950 ASP cc_start: 0.8057 (m-30) cc_final: 0.7834 (m-30) REVERT: K 100 PHE cc_start: 0.5962 (OUTLIER) cc_final: 0.5437 (t80) REVERT: L 34 MET cc_start: 0.5772 (pmm) cc_final: 0.5339 (ppp) REVERT: L 82 MET cc_start: 0.5869 (mtm) cc_final: 0.5583 (mpp) REVERT: L 85 LEU cc_start: 0.3171 (OUTLIER) cc_final: 0.1503 (tp) REVERT: N 37 GLN cc_start: 0.8437 (tt0) cc_final: 0.8197 (tm-30) REVERT: O 6 GLU cc_start: 0.5819 (mt-10) cc_final: 0.3724 (tp30) REVERT: O 19 ARG cc_start: 0.7431 (mmm160) cc_final: 0.7018 (tmm160) REVERT: O 38 ARG cc_start: 0.4527 (ptt90) cc_final: 0.4201 (ptm-80) REVERT: O 45 LEU cc_start: 0.7672 (tp) cc_final: 0.7037 (mp) outliers start: 77 outliers final: 66 residues processed: 227 average time/residue: 0.3717 time to fit residues: 140.6416 Evaluate side-chains 232 residues out of total 3237 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 161 time to evaluate : 3.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 775 ASP Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 978 ASN Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 749 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 953 ASN Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain K residue 4 MET Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 100 PHE Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain N residue 13 VAL Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain O residue 51 MET Chi-restraints excluded: chain O residue 68 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 232 optimal weight: 0.5980 chunk 311 optimal weight: 30.0000 chunk 89 optimal weight: 0.9980 chunk 269 optimal weight: 4.9990 chunk 43 optimal weight: 20.0000 chunk 81 optimal weight: 0.0020 chunk 293 optimal weight: 0.9980 chunk 122 optimal weight: 0.7980 chunk 301 optimal weight: 0.9990 chunk 37 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 354 ASN C 544 ASN ** C1134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1098 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.155909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.100140 restraints weight = 69457.988| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 4.76 r_work: 0.3082 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.3858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 29159 Z= 0.163 Angle : 0.571 11.890 39828 Z= 0.294 Chirality : 0.044 0.212 4676 Planarity : 0.004 0.044 5100 Dihedral : 4.855 53.826 4747 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.71 % Favored : 95.26 % Rotamer: Outliers : 2.13 % Allowed : 17.87 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: -0.21 (0.14), residues: 3693 helix: 2.34 (0.21), residues: 667 sheet: 0.16 (0.16), residues: 988 loop : -1.19 (0.13), residues: 2038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 104 HIS 0.004 0.001 HIS B 69 PHE 0.022 0.001 PHE C 238 TYR 0.026 0.001 TYR I 79 ARG 0.006 0.000 ARG B 983 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6225.55 seconds wall clock time: 114 minutes 52.86 seconds (6892.86 seconds total)