Starting phenix.real_space_refine on Thu Mar 21 06:51:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ld1_23279/03_2024/7ld1_23279.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ld1_23279/03_2024/7ld1_23279.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/7ld1_23279/03_2024/7ld1_23279.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ld1_23279/03_2024/7ld1_23279.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ld1_23279/03_2024/7ld1_23279.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ld1_23279/03_2024/7ld1_23279.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= 0.000 sd= 0.044 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 115 5.16 5 C 18478 2.51 5 N 5018 2.21 5 O 5833 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 88": "OD1" <-> "OD2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 281": "OE1" <-> "OE2" Residue "A GLU 324": "OE1" <-> "OE2" Residue "A GLU 484": "OE1" <-> "OE2" Residue "A PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 578": "OD1" <-> "OD2" Residue "A TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 918": "OE1" <-> "OE2" Residue "A GLU 988": "OE1" <-> "OE2" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 228": "OD1" <-> "OD2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 281": "OE1" <-> "OE2" Residue "B GLU 324": "OE1" <-> "OE2" Residue "B GLU 484": "OE1" <-> "OE2" Residue "B PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 702": "OE1" <-> "OE2" Residue "B PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 867": "OD1" <-> "OD2" Residue "B PHE 898": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1111": "OE1" <-> "OE2" Residue "B PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 111": "OD1" <-> "OD2" Residue "C PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 191": "OE1" <-> "OE2" Residue "C PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 281": "OE1" <-> "OE2" Residue "C GLU 298": "OE1" <-> "OE2" Residue "C PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 355": "NH1" <-> "NH2" Residue "C TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 578": "OD1" <-> "OD2" Residue "C GLU 607": "OE1" <-> "OE2" Residue "C GLU 654": "OE1" <-> "OE2" Residue "C GLU 702": "OE1" <-> "OE2" Residue "C PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 868": "OE1" <-> "OE2" Residue "C PHE 898": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 100": "OD1" <-> "OD2" Residue "P TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 29444 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 7046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 973, 7046 Classifications: {'peptide': 973} Incomplete info: {'truncation_to_alanine': 150} Link IDs: {'PTRANS': 47, 'TRANS': 925} Chain breaks: 12 Unresolved non-hydrogen bonds: 576 Unresolved non-hydrogen angles: 742 Unresolved non-hydrogen dihedrals: 481 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'GLN:plan1': 9, 'TYR:plan': 13, 'ASN:plan1': 17, 'TRP:plan': 2, 'ASP:plan': 13, 'PHE:plan': 9, 'GLU:plan': 12, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 382 Chain: "B" Number of atoms: 7046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 973, 7046 Classifications: {'peptide': 973} Incomplete info: {'truncation_to_alanine': 150} Link IDs: {'PTRANS': 47, 'TRANS': 925} Chain breaks: 12 Unresolved non-hydrogen bonds: 576 Unresolved non-hydrogen angles: 742 Unresolved non-hydrogen dihedrals: 481 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'GLN:plan1': 9, 'TYR:plan': 13, 'ASN:plan1': 17, 'TRP:plan': 2, 'ASP:plan': 13, 'PHE:plan': 9, 'GLU:plan': 12, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 382 Chain: "C" Number of atoms: 7026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 949, 7026 Classifications: {'peptide': 949} Incomplete info: {'truncation_to_alanine': 107} Link IDs: {'PTRANS': 46, 'TRANS': 902} Chain breaks: 13 Unresolved non-hydrogen bonds: 405 Unresolved non-hydrogen angles: 518 Unresolved non-hydrogen dihedrals: 336 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 9, 'ASN:plan1': 12, 'TRP:plan': 1, 'ASP:plan': 10, 'PHE:plan': 5, 'GLU:plan': 12, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 264 Chain: "M" Number of atoms: 1248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1248 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 160} Link IDs: {'PTRANS': 12, 'TRANS': 219} Unresolved non-hydrogen bonds: 526 Unresolved non-hydrogen angles: 687 Unresolved non-hydrogen dihedrals: 438 Unresolved non-hydrogen chiralities: 61 Planarities with less than four sites: {'GLN:plan1': 10, 'ASP:plan': 6, 'TYR:plan': 9, 'ASN:plan1': 7, 'TRP:plan': 4, 'HIS:plan': 4, 'PHE:plan': 5, 'GLU:plan': 6, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 282 Chain: "N" Number of atoms: 1245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1245 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 139} Link IDs: {'PTRANS': 11, 'TRANS': 207} Chain breaks: 1 Unresolved non-hydrogen bonds: 485 Unresolved non-hydrogen angles: 620 Unresolved non-hydrogen dihedrals: 406 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 2, 'TYR:plan': 8, 'ASN:plan1': 5, 'TRP:plan': 2, 'ASP:plan': 7, 'PHE:plan': 7, 'GLU:plan': 12, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 290 Chain: "P" Number of atoms: 1235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1235 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 165} Link IDs: {'PTRANS': 12, 'TRANS': 219} Unresolved non-hydrogen bonds: 539 Unresolved non-hydrogen angles: 704 Unresolved non-hydrogen dihedrals: 447 Unresolved non-hydrogen chiralities: 62 Planarities with less than four sites: {'GLN:plan1': 10, 'ASP:plan': 9, 'TYR:plan': 9, 'ASN:plan1': 7, 'TRP:plan': 4, 'HIS:plan': 4, 'PHE:plan': 5, 'GLU:plan': 6, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 291 Chain: "O" Number of atoms: 1235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1235 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 143} Link IDs: {'PTRANS': 11, 'TRANS': 208} Unresolved non-hydrogen bonds: 501 Unresolved non-hydrogen angles: 640 Unresolved non-hydrogen dihedrals: 418 Unresolved non-hydrogen chiralities: 43 Planarities with less than four sites: {'GLN:plan1': 11, 'HIS:plan': 2, 'TYR:plan': 8, 'ASN:plan1': 5, 'TRP:plan': 2, 'ASP:plan': 7, 'PHE:plan': 7, 'GLU:plan': 12, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 299 Chain: "H" Number of atoms: 1235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1235 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 165} Link IDs: {'PTRANS': 12, 'TRANS': 219} Unresolved non-hydrogen bonds: 539 Unresolved non-hydrogen angles: 704 Unresolved non-hydrogen dihedrals: 447 Unresolved non-hydrogen chiralities: 62 Planarities with less than four sites: {'GLN:plan1': 10, 'ASP:plan': 9, 'TYR:plan': 9, 'ASN:plan1': 7, 'TRP:plan': 4, 'HIS:plan': 4, 'PHE:plan': 5, 'GLU:plan': 6, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 291 Chain: "L" Number of atoms: 1229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1229 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 143} Link IDs: {'PTRANS': 11, 'TRANS': 207} Chain breaks: 1 Unresolved non-hydrogen bonds: 501 Unresolved non-hydrogen angles: 640 Unresolved non-hydrogen dihedrals: 418 Unresolved non-hydrogen chiralities: 43 Planarities with less than four sites: {'GLN:plan1': 11, 'HIS:plan': 2, 'TYR:plan': 8, 'ASN:plan1': 5, 'TRP:plan': 2, 'ASP:plan': 7, 'PHE:plan': 7, 'GLU:plan': 12, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 299 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 16.28, per 1000 atoms: 0.55 Number of scatterers: 29444 At special positions: 0 Unit cell: (160.816, 168.222, 211.6, 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 115 16.00 O 5833 8.00 N 5018 7.00 C 18478 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=34, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.01 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.05 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.02 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.05 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.01 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.05 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.01 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.01 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.02 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.01 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 N 23 " - pdb=" SG CYS N 88 " distance=2.04 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " NAG-ASN " NAG A1201 " - " ASN A 709 " " NAG A1202 " - " ASN A1074 " " NAG A1203 " - " ASN A 61 " " NAG A1204 " - " ASN A 234 " " NAG A1205 " - " ASN A 603 " " NAG A1206 " - " ASN A 616 " " NAG A1207 " - " ASN A 657 " " NAG A1208 " - " ASN A 165 " " NAG B1201 " - " ASN B 616 " " NAG B1202 " - " ASN B 709 " " NAG B1203 " - " ASN B1074 " " NAG B1204 " - " ASN B 61 " " NAG B1205 " - " ASN B 122 " " NAG B1206 " - " ASN B 234 " " NAG B1207 " - " ASN B 603 " " NAG B1208 " - " ASN B 657 " " NAG B1209 " - " ASN B 165 " " NAG C1202 " - " ASN C 657 " " NAG C1203 " - " ASN C 122 " " NAG C1204 " - " ASN C 61 " " NAG C1205 " - " ASN C 616 " " NAG C1206 " - " ASN C 709 " " NAG C1207 " - " ASN C1074 " " NAG D 1 " - " ASN A1098 " " NAG E 1 " - " ASN A 282 " " NAG F 1 " - " ASN A 331 " " NAG G 1 " - " ASN A 343 " " NAG I 1 " - " ASN A 717 " " NAG J 1 " - " ASN A1134 " " NAG K 1 " - " ASN B1134 " " NAG Q 1 " - " ASN B 282 " " NAG R 1 " - " ASN B 331 " " NAG S 1 " - " ASN B 343 " " NAG T 1 " - " ASN B 717 " " NAG U 1 " - " ASN C 331 " " NAG W 1 " - " ASN C 343 " " NAG X 1 " - " ASN C 717 " Time building additional restraints: 12.68 Conformation dependent library (CDL) restraints added in 5.5 seconds 8306 Ramachandran restraints generated. 4153 Oldfield, 0 Emsley, 4153 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7934 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 66 sheets defined 21.4% alpha, 23.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.23 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 342 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.637A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.014A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 388 Processing helix chain 'A' and resid 404 through 408 Processing helix chain 'A' and resid 416 through 421 Processing helix chain 'A' and resid 426 through 430 removed outlier: 4.012A pdb=" N THR A 430 " --> pdb=" O ASP A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 441 Processing helix chain 'A' and resid 446 through 451 Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.730A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 756 removed outlier: 3.512A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N TYR A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.645A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 805 removed outlier: 4.617A pdb=" N GLN A 804 " --> pdb=" O ASN A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.685A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.590A pdb=" N GLY A 885 " --> pdb=" O THR A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 907 Processing helix chain 'A' and resid 908 through 910 No H-bonds generated for 'chain 'A' and resid 908 through 910' Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.593A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 968 removed outlier: 3.681A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N SER A 967 " --> pdb=" O VAL A 963 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER A 968 " --> pdb=" O LYS A 964 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.589A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.597A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 370 removed outlier: 3.741A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 388 Processing helix chain 'B' and resid 405 through 409 Processing helix chain 'B' and resid 416 through 421 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.658A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.798A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 805 removed outlier: 4.434A pdb=" N GLN B 804 " --> pdb=" O ASN B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.763A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.738A pdb=" N GLY B 885 " --> pdb=" O THR B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 907 Processing helix chain 'B' and resid 908 through 910 No H-bonds generated for 'chain 'B' and resid 908 through 910' Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 968 removed outlier: 3.745A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER B 967 " --> pdb=" O VAL B 963 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.667A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 364 through 370 Processing helix chain 'C' and resid 383 through 388 removed outlier: 4.585A pdb=" N ASN C 388 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 408 removed outlier: 4.268A pdb=" N ARG C 408 " --> pdb=" O GLY C 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 404 through 408' Processing helix chain 'C' and resid 446 through 450 Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 756 removed outlier: 3.776A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N TYR C 756 " --> pdb=" O LEU C 752 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.710A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 805 removed outlier: 4.528A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.744A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.801A pdb=" N GLY C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 891 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.798A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.800A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.183A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.770A pdb=" N LEU C 984 " --> pdb=" O ILE C 980 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.831A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'M' and resid 60 through 64 Processing helix chain 'M' and resid 72 through 76 Processing helix chain 'M' and resid 83 through 87 Processing helix chain 'M' and resid 187 through 191 Processing helix chain 'M' and resid 200 through 204 Processing helix chain 'N' and resid 140 through 144 removed outlier: 4.000A pdb=" N GLU N 143 " --> pdb=" O TYR N 140 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA N 144 " --> pdb=" O PRO N 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 140 through 144' Processing helix chain 'N' and resid 184 through 189 Processing helix chain 'P' and resid 26 through 31 Processing helix chain 'P' and resid 72 through 75 Processing helix chain 'P' and resid 100E through 100I removed outlier: 4.443A pdb=" N LEU P 100H" --> pdb=" O TYR P 100E" (cutoff:3.500A) Processing helix chain 'P' and resid 200 through 204 Processing helix chain 'O' and resid 49 through 52 Processing helix chain 'O' and resid 59 through 62 Processing helix chain 'O' and resid 121 through 131 removed outlier: 4.409A pdb=" N LEU O 125 " --> pdb=" O ASP O 122 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N GLY O 128 " --> pdb=" O LEU O 125 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N THR O 129 " --> pdb=" O LYS O 126 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N SER O 131 " --> pdb=" O GLY O 128 " (cutoff:3.500A) Processing helix chain 'O' and resid 149 through 153 Processing helix chain 'O' and resid 184 through 189 Processing helix chain 'H' and resid 60 through 65 removed outlier: 4.317A pdb=" N GLY H 65 " --> pdb=" O GLN H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 75 removed outlier: 4.223A pdb=" N SER H 74 " --> pdb=" O ARG H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 185 through 189 Processing helix chain 'L' and resid 59 through 62 Processing helix chain 'L' and resid 121 through 128 Processing helix chain 'L' and resid 150 through 153 Processing helix chain 'L' and resid 184 through 189 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.263A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 44 removed outlier: 4.024A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.925A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.942A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.699A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.868A pdb=" N THR A 376 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.080A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.006A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.865A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.865A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB4, first strand: chain 'A' and resid 788 through 790 Processing sheet with id=AB5, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 5.670A pdb=" N VAL A1122 " --> pdb=" O PHE A1089 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N PHE A1089 " --> pdb=" O VAL A1122 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N GLY A1124 " --> pdb=" O ALA A1087 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.128A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 50 through 55 removed outlier: 3.691A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AB9, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.315A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 325 through 327 removed outlier: 5.088A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 354 through 355 Processing sheet with id=AC3, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.840A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.942A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.382A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 702 through 704 removed outlier: 6.597A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.675A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AC8, first strand: chain 'B' and resid 1081 through 1082 Processing sheet with id=AC9, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD1, first strand: chain 'C' and resid 28 through 30 removed outlier: 7.534A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.783A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 83 through 85 Processing sheet with id=AD4, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.247A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 356 through 358 removed outlier: 3.615A pdb=" N TRP C 436 " --> pdb=" O ARG C 509 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AD7, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.128A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.512A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.567A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE1, first strand: chain 'C' and resid 1120 through 1123 Processing sheet with id=AE2, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AE3, first strand: chain 'M' and resid 9 through 12 removed outlier: 7.041A pdb=" N GLU M 10 " --> pdb=" O THR M 110 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'M' and resid 18 through 19 Processing sheet with id=AE5, first strand: chain 'M' and resid 50 through 51 Processing sheet with id=AE6, first strand: chain 'M' and resid 121 through 122 Processing sheet with id=AE7, first strand: chain 'M' and resid 137 through 138 removed outlier: 3.575A pdb=" N VAL M 181 " --> pdb=" O HIS M 164 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'N' and resid 5 through 6 Processing sheet with id=AE9, first strand: chain 'N' and resid 10 through 11 Processing sheet with id=AF1, first strand: chain 'N' and resid 53 through 54 removed outlier: 6.535A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N TYR N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N LEU N 33 " --> pdb=" O TYR N 49 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'N' and resid 134 through 139 removed outlier: 4.827A pdb=" N TYR N 173 " --> pdb=" O ASN N 138 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'N' and resid 145 through 146 Processing sheet with id=AF4, first strand: chain 'N' and resid 191 through 193 Processing sheet with id=AF5, first strand: chain 'P' and resid 5 through 7 removed outlier: 3.734A pdb=" N VAL P 5 " --> pdb=" O GLN P 23 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU P 80 " --> pdb=" O VAL P 20 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'P' and resid 10 through 12 Processing sheet with id=AF7, first strand: chain 'P' and resid 56 through 59 removed outlier: 6.756A pdb=" N TRP P 36 " --> pdb=" O MET P 48 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ILE P 50 " --> pdb=" O ILE P 34 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ILE P 34 " --> pdb=" O ILE P 50 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N TYR P 102 " --> pdb=" O ARG P 94 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'P' and resid 120 through 122 removed outlier: 3.847A pdb=" N SER P 120 " --> pdb=" O LYS P 143 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N LYS P 143 " --> pdb=" O LEU P 178 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N LEU P 178 " --> pdb=" O LYS P 143 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEU P 175 " --> pdb=" O GLN P 171 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'P' and resid 137 through 139 Processing sheet with id=AG1, first strand: chain 'P' and resid 194 through 195 Processing sheet with id=AG2, first strand: chain 'O' and resid 5 through 6 Processing sheet with id=AG3, first strand: chain 'O' and resid 46 through 48 removed outlier: 6.781A pdb=" N TRP O 35 " --> pdb=" O LEU O 47 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'O' and resid 134 through 136 removed outlier: 7.520A pdb=" N THR O 172 " --> pdb=" O GLN O 166 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N GLN O 166 " --> pdb=" O THR O 172 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N SER O 174 " --> pdb=" O THR O 164 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'O' and resid 144 through 147 removed outlier: 4.413A pdb=" N GLU O 195 " --> pdb=" O GLN O 147 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'H' and resid 19 through 23 Processing sheet with id=AG7, first strand: chain 'H' and resid 56 through 59 removed outlier: 6.407A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N ILE H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ILE H 34 " --> pdb=" O ILE H 50 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL H 37 " --> pdb=" O TYR H 91 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'H' and resid 120 through 123 Processing sheet with id=AG9, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AH1, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.505A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'L' and resid 132 through 135 Processing sheet with id=AH3, first strand: chain 'L' and resid 155 through 156 1182 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: 15.49 Time building geometry restraints manager: 13.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.27: 4992 1.27 - 1.41: 7286 1.41 - 1.55: 17392 1.55 - 1.69: 144 1.69 - 1.82: 148 Bond restraints: 29962 Sorted by residual: bond pdb=" CA PRO O 119 " pdb=" C PRO O 119 " ideal model delta sigma weight residual 1.514 1.542 -0.027 5.50e-03 3.31e+04 2.46e+01 bond pdb=" C LYS M 214 " pdb=" O LYS M 214 " ideal model delta sigma weight residual 1.231 1.136 0.095 2.00e-02 2.50e+03 2.23e+01 bond pdb=" C4 NAG T 2 " pdb=" O4 NAG T 2 " ideal model delta sigma weight residual 1.409 1.500 -0.091 2.00e-02 2.50e+03 2.08e+01 bond pdb=" C4 NAG R 2 " pdb=" O4 NAG R 2 " ideal model delta sigma weight residual 1.409 1.494 -0.085 2.00e-02 2.50e+03 1.79e+01 bond pdb=" C4 NAG K 2 " pdb=" O4 NAG K 2 " ideal model delta sigma weight residual 1.409 1.491 -0.082 2.00e-02 2.50e+03 1.68e+01 ... (remaining 29957 not shown) Histogram of bond angle deviations from ideal: 96.29 - 104.07: 404 104.07 - 111.85: 12401 111.85 - 119.62: 12471 119.62 - 127.40: 15594 127.40 - 135.18: 211 Bond angle restraints: 41081 Sorted by residual: angle pdb=" CA PHE B 559 " pdb=" CB PHE B 559 " pdb=" CG PHE B 559 " ideal model delta sigma weight residual 113.80 120.98 -7.18 1.00e+00 1.00e+00 5.16e+01 angle pdb=" N VAL A 289 " pdb=" CA VAL A 289 " pdb=" C VAL A 289 " ideal model delta sigma weight residual 111.90 117.33 -5.43 8.10e-01 1.52e+00 4.50e+01 angle pdb=" C SER B 45 " pdb=" N SER B 46 " pdb=" CA SER B 46 " ideal model delta sigma weight residual 120.90 129.92 -9.02 1.41e+00 5.03e-01 4.09e+01 angle pdb=" CA PHE A 643 " pdb=" CB PHE A 643 " pdb=" CG PHE A 643 " ideal model delta sigma weight residual 113.80 120.17 -6.37 1.00e+00 1.00e+00 4.06e+01 angle pdb=" C LEU M 100G" pdb=" N LEU M 100H" pdb=" CA LEU M 100H" ideal model delta sigma weight residual 120.23 130.54 -10.31 1.67e+00 3.59e-01 3.81e+01 ... (remaining 41076 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.09: 17594 21.09 - 42.18: 710 42.18 - 63.27: 151 63.27 - 84.36: 106 84.36 - 105.44: 57 Dihedral angle restraints: 18618 sinusoidal: 6368 harmonic: 12250 Sorted by residual: dihedral pdb=" C LYS B 300 " pdb=" N LYS B 300 " pdb=" CA LYS B 300 " pdb=" CB LYS B 300 " ideal model delta harmonic sigma weight residual -122.60 -137.63 15.03 0 2.50e+00 1.60e-01 3.61e+01 dihedral pdb=" CA PHE M 146 " pdb=" C PHE M 146 " pdb=" N PRO M 147 " pdb=" CA PRO M 147 " ideal model delta harmonic sigma weight residual 180.00 151.60 28.40 0 5.00e+00 4.00e-02 3.23e+01 dihedral pdb=" CA ASN P 56 " pdb=" C ASN P 56 " pdb=" N THR P 57 " pdb=" CA THR P 57 " ideal model delta harmonic sigma weight residual -180.00 -151.70 -28.30 0 5.00e+00 4.00e-02 3.20e+01 ... (remaining 18615 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.214: 4944 0.214 - 0.428: 177 0.428 - 0.643: 5 0.643 - 0.857: 1 0.857 - 1.071: 4 Chirality restraints: 5131 Sorted by residual: chirality pdb=" C1 BMA T 3 " pdb=" O4 NAG T 2 " pdb=" C2 BMA T 3 " pdb=" O5 BMA T 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.63 -0.77 2.00e-02 2.50e+03 1.49e+03 chirality pdb=" C1 BMA D 3 " pdb=" O4 NAG D 2 " pdb=" C2 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.09e+02 chirality pdb=" C1 NAG X 2 " pdb=" O4 NAG X 1 " pdb=" C2 NAG X 2 " pdb=" O5 NAG X 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 1.01e+02 ... (remaining 5128 not shown) Planarity restraints: 5419 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 904 " 0.261 2.00e-02 2.50e+03 1.44e-01 4.13e+02 pdb=" CG TYR A 904 " -0.065 2.00e-02 2.50e+03 pdb=" CD1 TYR A 904 " -0.116 2.00e-02 2.50e+03 pdb=" CD2 TYR A 904 " -0.135 2.00e-02 2.50e+03 pdb=" CE1 TYR A 904 " -0.094 2.00e-02 2.50e+03 pdb=" CE2 TYR A 904 " -0.073 2.00e-02 2.50e+03 pdb=" CZ TYR A 904 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR A 904 " 0.217 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 904 " 0.218 2.00e-02 2.50e+03 1.20e-01 2.88e+02 pdb=" CG TYR B 904 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 TYR B 904 " -0.099 2.00e-02 2.50e+03 pdb=" CD2 TYR B 904 " -0.112 2.00e-02 2.50e+03 pdb=" CE1 TYR B 904 " -0.079 2.00e-02 2.50e+03 pdb=" CE2 TYR B 904 " -0.058 2.00e-02 2.50e+03 pdb=" CZ TYR B 904 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 904 " 0.181 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 886 " -0.197 2.00e-02 2.50e+03 1.02e-01 2.62e+02 pdb=" CG TRP A 886 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 TRP A 886 " 0.080 2.00e-02 2.50e+03 pdb=" CD2 TRP A 886 " 0.074 2.00e-02 2.50e+03 pdb=" NE1 TRP A 886 " 0.074 2.00e-02 2.50e+03 pdb=" CE2 TRP A 886 " -0.016 2.00e-02 2.50e+03 pdb=" CE3 TRP A 886 " 0.125 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 886 " -0.138 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 886 " 0.068 2.00e-02 2.50e+03 pdb=" CH2 TRP A 886 " -0.094 2.00e-02 2.50e+03 ... (remaining 5416 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.99: 14962 2.99 - 3.47: 30271 3.47 - 3.95: 46781 3.95 - 4.42: 52279 4.42 - 4.90: 86446 Nonbonded interactions: 230739 Sorted by model distance: nonbonded pdb=" OE2 GLU C 819 " pdb=" OG SER C1055 " model vdw 2.514 2.440 nonbonded pdb=" OE2 GLU A 918 " pdb=" OG SER C1123 " model vdw 2.535 2.440 nonbonded pdb=" OH TYR A 756 " pdb=" OD1 ASP A 994 " model vdw 2.542 2.440 nonbonded pdb=" OG SER A1123 " pdb=" OE2 GLU B 918 " model vdw 2.543 2.440 nonbonded pdb=" O5 NAG D 1 " pdb=" O6 NAG D 1 " model vdw 2.546 2.432 ... (remaining 230734 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 466 or resid 491 through 1147 or resid 1201 thr \ ough 1207)) selection = (chain 'B' and (resid 27 through 466 or resid 491 through 1147 or resid 1201 thr \ ough 1207)) selection = (chain 'C' and (resid 27 through 352 or (resid 353 through 360 and (name N or na \ me CA or name C or name O or name CB )) or resid 361 or (resid 362 through 378 a \ nd (name N or name CA or name C or name O or name CB )) or resid 379 through 395 \ or (resid 396 through 403 and (name N or name CA or name C or name O or name CB \ )) or resid 404 or (resid 405 through 411 and (name N or name CA or name C or n \ ame O or name CB )) or resid 412 through 413 or (resid 414 through 415 and (name \ N or name CA or name C or name O or name CB )) or resid 416 through 436 or (res \ id 437 through 445 and (name N or name CA or name C or name O or name CB )) or r \ esid 446 through 499 or (resid 500 through 501 and (name N or name CA or name C \ or name O or name CB )) or resid 502 or (resid 503 and (name N or name CA or nam \ e C or name O or name CB )) or resid 504 or (resid 505 through 506 and (name N o \ r name CA or name C or name O or name CB )) or resid 507 through 508 or (resid 5 \ 09 through 524 and (name N or name CA or name C or name O or name CB )) or resid \ 525 through 1147 or resid 1201 through 1207)) } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } ncs_group { reference = chain 'E' selection = chain 'Q' } ncs_group { reference = chain 'H' selection = (chain 'M' and (resid 1 through 98 or (resid 99 through 100A and (name N or name \ CA or name C or name O or name CB )) or resid 100B through 100E or (resid 100F \ through 100G and (name N or name CA or name C or name O or name CB )) or resid 1 \ 00H through 214)) selection = chain 'P' } ncs_group { reference = chain 'L' selection = (chain 'N' and (resid 1 through 14 or (resid 15 and (name N or name CA or name C \ or name O or name CB )) or resid 16 through 76 or (resid 77 through 87 and (nam \ e N or name CA or name C or name O or name CB )) or resid 88 through 214)) selection = (chain 'O' and (resid 1 through 27E or resid 28 through 214)) } 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: 1.800 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: 8.630 Check model and map are aligned: 0.450 Set scattering table: 0.260 Process input model: 83.680 Find NCS groups from input model: 2.700 Set up NCS constraints: 0.370 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 100.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 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 : 0.013 0.095 29962 Z= 0.883 Angle : 1.930 11.075 41081 Z= 1.267 Chirality : 0.103 1.071 5131 Planarity : 0.013 0.147 5382 Dihedral : 15.986 105.444 10582 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 0.15 Ramachandran Plot: Outliers : 1.61 % Allowed : 9.22 % Favored : 89.16 % Rotamer: Outliers : 2.35 % Allowed : 4.15 % Favored : 93.50 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.12), residues: 4153 helix: -1.16 (0.16), residues: 726 sheet: -0.88 (0.21), residues: 537 loop : -1.78 (0.11), residues: 2890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.197 0.028 TRP A 886 HIS 0.017 0.005 HIS C1048 PHE 0.153 0.016 PHE B 43 TYR 0.261 0.023 TYR A 904 ARG 0.011 0.002 ARG B1039 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8306 Ramachandran restraints generated. 4153 Oldfield, 0 Emsley, 4153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8306 Ramachandran restraints generated. 4153 Oldfield, 0 Emsley, 4153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 3705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 150 time to evaluate : 3.414 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: A 338 PHE cc_start: 0.9014 (m-10) cc_final: 0.8730 (m-10) REVERT: A 697 MET cc_start: 0.8539 (ptm) cc_final: 0.8335 (ptm) REVERT: B 43 PHE cc_start: 0.6256 (t80) cc_final: 0.5760 (t80) REVERT: B 603 ASN cc_start: 0.8686 (OUTLIER) cc_final: 0.8475 (t0) REVERT: B 764 ASN cc_start: 0.8783 (OUTLIER) cc_final: 0.8460 (m110) REVERT: C 353 TRP cc_start: 0.6840 (OUTLIER) cc_final: 0.6618 (t60) REVERT: M 58 ILE cc_start: 0.9346 (OUTLIER) cc_final: 0.9126 (mt) REVERT: P 100 SER cc_start: 0.6280 (OUTLIER) cc_final: 0.5967 (p) REVERT: O 4 MET cc_start: -0.0872 (mmt) cc_final: -0.1406 (tpp) REVERT: O 31 ASN cc_start: 0.4655 (OUTLIER) cc_final: 0.4425 (p0) REVERT: O 36 TYR cc_start: 0.4681 (OUTLIER) cc_final: 0.3388 (t80) REVERT: O 92 TYR cc_start: 0.5546 (t80) cc_final: 0.3324 (t80) REVERT: L 2 ILE cc_start: 0.3907 (OUTLIER) cc_final: 0.3499 (tt) REVERT: L 27 GLN cc_start: 0.8038 (OUTLIER) cc_final: 0.7810 (pm20) outliers start: 56 outliers final: 10 residues processed: 200 average time/residue: 0.3931 time to fit residues: 131.5913 Evaluate side-chains 105 residues out of total 3705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 86 time to evaluate : 3.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 764 ASN Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain M residue 58 ILE Chi-restraints excluded: chain M residue 100 LEU Chi-restraints excluded: chain N residue 27 GLN Chi-restraints excluded: chain P residue 100 SER Chi-restraints excluded: chain O residue 31 ASN Chi-restraints excluded: chain O residue 36 TYR Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 27 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 355 optimal weight: 5.9990 chunk 319 optimal weight: 6.9990 chunk 177 optimal weight: 0.9980 chunk 109 optimal weight: 0.9990 chunk 215 optimal weight: 0.9990 chunk 170 optimal weight: 2.9990 chunk 329 optimal weight: 8.9990 chunk 127 optimal weight: 10.0000 chunk 200 optimal weight: 10.0000 chunk 245 optimal weight: 4.9990 chunk 382 optimal weight: 20.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1088 HIS B 606 ASN B 907 ASN B 919 ASN C 314 GLN C 317 ASN C 321 GLN C 919 ASN C 957 GLN ** P 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 29962 Z= 0.248 Angle : 0.746 13.699 41081 Z= 0.387 Chirality : 0.049 0.328 5131 Planarity : 0.005 0.055 5382 Dihedral : 11.546 73.276 5805 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.15 % Favored : 92.70 % Rotamer: Outliers : 1.47 % Allowed : 7.34 % Favored : 91.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.13), residues: 4153 helix: 0.66 (0.19), residues: 730 sheet: -1.25 (0.16), residues: 937 loop : -1.38 (0.12), residues: 2486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A1102 HIS 0.007 0.001 HIS A 207 PHE 0.027 0.002 PHE A1089 TYR 0.029 0.002 TYR C 505 ARG 0.006 0.001 ARG C1039 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8306 Ramachandran restraints generated. 4153 Oldfield, 0 Emsley, 4153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8306 Ramachandran restraints generated. 4153 Oldfield, 0 Emsley, 4153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 3705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 97 time to evaluate : 3.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 PHE cc_start: 0.9045 (m-10) cc_final: 0.8771 (m-10) REVERT: A 1029 MET cc_start: 0.8726 (tpp) cc_final: 0.8467 (tpp) REVERT: A 1031 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7077 (mp0) REVERT: B 287 ASP cc_start: 0.8249 (t0) cc_final: 0.7585 (m-30) REVERT: B 1050 MET cc_start: 0.8180 (ptt) cc_final: 0.7935 (ptp) REVERT: C 353 TRP cc_start: 0.6940 (OUTLIER) cc_final: 0.6736 (t60) REVERT: C 374 PHE cc_start: 0.8691 (m-10) cc_final: 0.8487 (m-10) REVERT: C 902 MET cc_start: 0.8823 (mmm) cc_final: 0.8572 (mmm) REVERT: M 58 ILE cc_start: 0.9383 (OUTLIER) cc_final: 0.9147 (mt) REVERT: N 27 GLN cc_start: 0.9035 (OUTLIER) cc_final: 0.8770 (pm20) REVERT: O 27 TYR cc_start: 0.7831 (t80) cc_final: 0.7017 (m-80) REVERT: O 36 TYR cc_start: 0.4420 (OUTLIER) cc_final: 0.3406 (t80) outliers start: 35 outliers final: 14 residues processed: 124 average time/residue: 0.3818 time to fit residues: 83.1676 Evaluate side-chains 98 residues out of total 3705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 79 time to evaluate : 3.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain M residue 58 ILE Chi-restraints excluded: chain M residue 100 TYR Chi-restraints excluded: chain N residue 27 GLN Chi-restraints excluded: chain P residue 57 THR Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 36 TYR Chi-restraints excluded: chain H residue 100 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 212 optimal weight: 9.9990 chunk 118 optimal weight: 10.0000 chunk 318 optimal weight: 50.0000 chunk 260 optimal weight: 1.9990 chunk 105 optimal weight: 8.9990 chunk 383 optimal weight: 8.9990 chunk 413 optimal weight: 50.0000 chunk 341 optimal weight: 7.9990 chunk 379 optimal weight: 20.0000 chunk 130 optimal weight: 10.0000 chunk 307 optimal weight: 7.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 564 GLN ** A 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 690 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN B 804 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN B 935 GLN C 606 ASN C 690 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 29 ASN L 28 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.125 29962 Z= 0.581 Angle : 0.843 11.479 41081 Z= 0.429 Chirality : 0.052 0.364 5131 Planarity : 0.005 0.051 5382 Dihedral : 9.409 59.758 5786 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.34 % Favored : 90.59 % Rotamer: Outliers : 2.27 % Allowed : 10.16 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.13), residues: 4153 helix: 0.64 (0.19), residues: 719 sheet: -1.41 (0.16), residues: 963 loop : -1.49 (0.12), residues: 2471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A1102 HIS 0.012 0.002 HIS A1048 PHE 0.042 0.003 PHE A1089 TYR 0.033 0.003 TYR A1067 ARG 0.007 0.001 ARG B1039 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8306 Ramachandran restraints generated. 4153 Oldfield, 0 Emsley, 4153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8306 Ramachandran restraints generated. 4153 Oldfield, 0 Emsley, 4153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 3705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 77 time to evaluate : 3.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8529 (OUTLIER) cc_final: 0.8162 (mmmt) REVERT: A 338 PHE cc_start: 0.9090 (m-10) cc_final: 0.8827 (m-10) REVERT: A 869 MET cc_start: 0.8731 (OUTLIER) cc_final: 0.8446 (mtt) REVERT: A 1029 MET cc_start: 0.8855 (tpp) cc_final: 0.8555 (tpp) REVERT: A 1031 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7030 (mp0) REVERT: B 43 PHE cc_start: 0.6470 (t80) cc_final: 0.5650 (m-80) REVERT: B 902 MET cc_start: 0.9107 (tpt) cc_final: 0.8883 (mmp) REVERT: B 1101 HIS cc_start: 0.5868 (OUTLIER) cc_final: 0.4037 (m90) REVERT: M 58 ILE cc_start: 0.9323 (OUTLIER) cc_final: 0.8958 (mm) REVERT: N 27 TYR cc_start: 0.8135 (t80) cc_final: 0.7794 (t80) REVERT: N 32 TYR cc_start: 0.8397 (m-10) cc_final: 0.7899 (m-10) REVERT: O 27 TYR cc_start: 0.7585 (t80) cc_final: 0.7073 (m-80) REVERT: L 27 LEU cc_start: 0.9226 (mt) cc_final: 0.8843 (mt) outliers start: 54 outliers final: 29 residues processed: 126 average time/residue: 0.3682 time to fit residues: 80.9866 Evaluate side-chains 106 residues out of total 3705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 72 time to evaluate : 3.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain M residue 58 ILE Chi-restraints excluded: chain M residue 100 TYR Chi-restraints excluded: chain N residue 9 ASP Chi-restraints excluded: chain P residue 57 THR Chi-restraints excluded: chain O residue 36 TYR Chi-restraints excluded: chain O residue 94 LEU Chi-restraints excluded: chain H residue 100 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 378 optimal weight: 0.0270 chunk 287 optimal weight: 3.9990 chunk 198 optimal weight: 10.0000 chunk 42 optimal weight: 3.9990 chunk 182 optimal weight: 0.9980 chunk 257 optimal weight: 0.9990 chunk 384 optimal weight: 4.9990 chunk 406 optimal weight: 7.9990 chunk 200 optimal weight: 0.9990 chunk 364 optimal weight: 7.9990 chunk 109 optimal weight: 2.9990 overall best weight: 1.2044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 675 GLN A1058 HIS B 804 GLN B 907 ASN B 935 GLN C 955 ASN ** P 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 29962 Z= 0.182 Angle : 0.621 10.772 41081 Z= 0.317 Chirality : 0.046 0.348 5131 Planarity : 0.004 0.056 5382 Dihedral : 7.861 59.119 5781 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.30 % Favored : 92.66 % Rotamer: Outliers : 1.59 % Allowed : 11.16 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.13), residues: 4153 helix: 1.37 (0.20), residues: 718 sheet: -1.25 (0.16), residues: 958 loop : -1.30 (0.13), residues: 2477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 104 HIS 0.002 0.001 HIS A 207 PHE 0.024 0.001 PHE C 220 TYR 0.019 0.001 TYR A 904 ARG 0.003 0.000 ARG C 905 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8306 Ramachandran restraints generated. 4153 Oldfield, 0 Emsley, 4153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8306 Ramachandran restraints generated. 4153 Oldfield, 0 Emsley, 4153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 3705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 83 time to evaluate : 3.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8480 (OUTLIER) cc_final: 0.8185 (mmmt) REVERT: A 338 PHE cc_start: 0.9112 (m-10) cc_final: 0.8829 (m-10) REVERT: A 902 MET cc_start: 0.8656 (tpp) cc_final: 0.8439 (tpp) REVERT: A 913 GLN cc_start: 0.7976 (OUTLIER) cc_final: 0.7726 (pt0) REVERT: B 43 PHE cc_start: 0.6446 (t80) cc_final: 0.5753 (m-80) REVERT: B 287 ASP cc_start: 0.8184 (t0) cc_final: 0.7587 (m-30) REVERT: B 486 TYR cc_start: 0.7353 (t80) cc_final: 0.6994 (t80) REVERT: B 489 TYR cc_start: 0.8750 (m-80) cc_final: 0.8490 (p90) REVERT: B 543 PHE cc_start: 0.7367 (t80) cc_final: 0.7141 (t80) REVERT: B 1101 HIS cc_start: 0.5750 (OUTLIER) cc_final: 0.3768 (m90) REVERT: C 374 PHE cc_start: 0.8729 (m-10) cc_final: 0.8474 (m-10) REVERT: C 1106 GLN cc_start: 0.8035 (OUTLIER) cc_final: 0.7789 (pt0) REVERT: M 58 ILE cc_start: 0.9292 (OUTLIER) cc_final: 0.8981 (mm) REVERT: N 27 TYR cc_start: 0.7829 (t80) cc_final: 0.7440 (t80) REVERT: N 32 TYR cc_start: 0.8144 (m-10) cc_final: 0.7532 (m-10) REVERT: O 4 MET cc_start: -0.0525 (tpp) cc_final: -0.0784 (ttm) REVERT: O 27 TYR cc_start: 0.7502 (t80) cc_final: 0.6802 (m-80) REVERT: O 92 TYR cc_start: 0.4002 (t80) cc_final: 0.3725 (t80) REVERT: L 27 LEU cc_start: 0.9187 (mt) cc_final: 0.8774 (mt) outliers start: 38 outliers final: 21 residues processed: 114 average time/residue: 0.3668 time to fit residues: 74.1485 Evaluate side-chains 99 residues out of total 3705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 73 time to evaluate : 3.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain M residue 58 ILE Chi-restraints excluded: chain M residue 100 TYR Chi-restraints excluded: chain N residue 9 ASP Chi-restraints excluded: chain O residue 36 TYR Chi-restraints excluded: chain O residue 94 LEU Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 4 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 338 optimal weight: 10.0000 chunk 231 optimal weight: 10.0000 chunk 5 optimal weight: 4.9990 chunk 302 optimal weight: 50.0000 chunk 167 optimal weight: 6.9990 chunk 347 optimal weight: 50.0000 chunk 281 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 207 optimal weight: 0.0170 chunk 365 optimal weight: 40.0000 chunk 102 optimal weight: 9.9990 overall best weight: 5.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1011 GLN B 690 GLN B 804 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN B 935 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.098 29962 Z= 0.419 Angle : 0.690 9.773 41081 Z= 0.350 Chirality : 0.047 0.351 5131 Planarity : 0.005 0.053 5382 Dihedral : 7.571 56.128 5781 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.55 % Favored : 91.40 % Rotamer: Outliers : 2.18 % Allowed : 11.58 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.13), residues: 4153 helix: 1.25 (0.20), residues: 719 sheet: -1.35 (0.16), residues: 965 loop : -1.35 (0.13), residues: 2469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A1102 HIS 0.008 0.002 HIS C1048 PHE 0.030 0.002 PHE B 559 TYR 0.028 0.002 TYR A1067 ARG 0.005 0.000 ARG B1039 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8306 Ramachandran restraints generated. 4153 Oldfield, 0 Emsley, 4153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8306 Ramachandran restraints generated. 4153 Oldfield, 0 Emsley, 4153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 3705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 76 time to evaluate : 3.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 869 MET cc_start: 0.8694 (OUTLIER) cc_final: 0.8473 (mtt) REVERT: B 43 PHE cc_start: 0.6595 (t80) cc_final: 0.5867 (m-80) REVERT: B 287 ASP cc_start: 0.8236 (t0) cc_final: 0.7616 (m-30) REVERT: B 486 TYR cc_start: 0.7459 (t80) cc_final: 0.7104 (t80) REVERT: B 489 TYR cc_start: 0.8660 (m-80) cc_final: 0.8376 (p90) REVERT: B 543 PHE cc_start: 0.7606 (t80) cc_final: 0.7378 (t80) REVERT: B 1101 HIS cc_start: 0.5933 (OUTLIER) cc_final: 0.3925 (m90) REVERT: C 1106 GLN cc_start: 0.8298 (OUTLIER) cc_final: 0.8008 (pt0) REVERT: M 58 ILE cc_start: 0.9269 (OUTLIER) cc_final: 0.8959 (mt) REVERT: N 27 TYR cc_start: 0.8094 (t80) cc_final: 0.7728 (t80) REVERT: N 32 TYR cc_start: 0.8316 (m-10) cc_final: 0.7783 (m-10) REVERT: O 27 TYR cc_start: 0.7504 (t80) cc_final: 0.6935 (m-80) REVERT: L 27 LEU cc_start: 0.9205 (mt) cc_final: 0.8773 (mt) outliers start: 52 outliers final: 33 residues processed: 119 average time/residue: 0.3991 time to fit residues: 83.9340 Evaluate side-chains 112 residues out of total 3705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 75 time to evaluate : 3.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain M residue 58 ILE Chi-restraints excluded: chain M residue 100 TYR Chi-restraints excluded: chain N residue 9 ASP Chi-restraints excluded: chain O residue 36 TYR Chi-restraints excluded: chain O residue 94 LEU Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 94 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 136 optimal weight: 30.0000 chunk 366 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 238 optimal weight: 0.9990 chunk 100 optimal weight: 5.9990 chunk 407 optimal weight: 40.0000 chunk 338 optimal weight: 0.0670 chunk 188 optimal weight: 0.8980 chunk 33 optimal weight: 50.0000 chunk 134 optimal weight: 1.9990 chunk 213 optimal weight: 6.9990 overall best weight: 0.9924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 907 ASN C 901 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 29962 Z= 0.168 Angle : 0.585 10.079 41081 Z= 0.296 Chirality : 0.045 0.348 5131 Planarity : 0.004 0.058 5382 Dihedral : 7.092 55.225 5781 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.13 % Favored : 92.82 % Rotamer: Outliers : 1.55 % Allowed : 12.30 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.13), residues: 4153 helix: 1.62 (0.20), residues: 717 sheet: -1.21 (0.16), residues: 961 loop : -1.18 (0.13), residues: 2475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 104 HIS 0.002 0.001 HIS C1048 PHE 0.017 0.001 PHE C 220 TYR 0.019 0.001 TYR A 904 ARG 0.002 0.000 ARG C 905 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8306 Ramachandran restraints generated. 4153 Oldfield, 0 Emsley, 4153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8306 Ramachandran restraints generated. 4153 Oldfield, 0 Emsley, 4153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 3705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 82 time to evaluate : 3.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8473 (OUTLIER) cc_final: 0.8231 (mmmt) REVERT: A 913 GLN cc_start: 0.7874 (OUTLIER) cc_final: 0.7489 (pt0) REVERT: B 43 PHE cc_start: 0.6453 (t80) cc_final: 0.5884 (m-80) REVERT: B 287 ASP cc_start: 0.8195 (t0) cc_final: 0.7670 (m-30) REVERT: B 486 TYR cc_start: 0.7469 (t80) cc_final: 0.7112 (t80) REVERT: B 614 ASP cc_start: 0.8151 (t70) cc_final: 0.7536 (t0) REVERT: B 1101 HIS cc_start: 0.5607 (OUTLIER) cc_final: 0.3474 (m90) REVERT: C 374 PHE cc_start: 0.8634 (m-10) cc_final: 0.8391 (m-10) REVERT: C 912 THR cc_start: 0.8331 (OUTLIER) cc_final: 0.8029 (p) REVERT: M 58 ILE cc_start: 0.9244 (mm) cc_final: 0.8950 (mm) REVERT: N 32 TYR cc_start: 0.8194 (m-10) cc_final: 0.7916 (m-10) REVERT: O 4 MET cc_start: 0.0272 (OUTLIER) cc_final: -0.0688 (ptm) REVERT: O 27 TYR cc_start: 0.7522 (t80) cc_final: 0.7145 (m-80) REVERT: L 27 LEU cc_start: 0.9166 (mt) cc_final: 0.8649 (mt) outliers start: 37 outliers final: 24 residues processed: 113 average time/residue: 0.3658 time to fit residues: 73.1614 Evaluate side-chains 106 residues out of total 3705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 77 time to evaluate : 3.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain M residue 100 TYR Chi-restraints excluded: chain N residue 9 ASP Chi-restraints excluded: chain O residue 4 MET Chi-restraints excluded: chain O residue 36 TYR Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 94 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 392 optimal weight: 40.0000 chunk 45 optimal weight: 7.9990 chunk 232 optimal weight: 8.9990 chunk 297 optimal weight: 50.0000 chunk 230 optimal weight: 30.0000 chunk 342 optimal weight: 40.0000 chunk 227 optimal weight: 30.0000 chunk 405 optimal weight: 50.0000 chunk 253 optimal weight: 2.9990 chunk 247 optimal weight: 3.9990 chunk 187 optimal weight: 8.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 42 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.119 29962 Z= 0.545 Angle : 0.752 9.915 41081 Z= 0.379 Chirality : 0.049 0.349 5131 Planarity : 0.005 0.053 5382 Dihedral : 7.378 56.503 5779 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.05 % Favored : 90.87 % Rotamer: Outliers : 2.52 % Allowed : 12.34 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.13), residues: 4153 helix: 1.21 (0.20), residues: 716 sheet: -1.41 (0.16), residues: 981 loop : -1.33 (0.13), residues: 2456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A1102 HIS 0.013 0.002 HIS C1048 PHE 0.035 0.003 PHE B 559 TYR 0.032 0.002 TYR A1067 ARG 0.006 0.001 ARG B1107 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8306 Ramachandran restraints generated. 4153 Oldfield, 0 Emsley, 4153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8306 Ramachandran restraints generated. 4153 Oldfield, 0 Emsley, 4153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 3705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 77 time to evaluate : 3.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8550 (OUTLIER) cc_final: 0.8232 (mmmt) REVERT: A 869 MET cc_start: 0.8720 (OUTLIER) cc_final: 0.8476 (mtt) REVERT: B 43 PHE cc_start: 0.6642 (t80) cc_final: 0.5971 (m-80) REVERT: B 287 ASP cc_start: 0.8294 (t0) cc_final: 0.7706 (m-30) REVERT: B 1101 HIS cc_start: 0.5882 (OUTLIER) cc_final: 0.3919 (m90) REVERT: C 912 THR cc_start: 0.8305 (OUTLIER) cc_final: 0.7805 (p) REVERT: C 1106 GLN cc_start: 0.8324 (OUTLIER) cc_final: 0.8106 (pt0) REVERT: M 58 ILE cc_start: 0.9259 (mm) cc_final: 0.8978 (mm) REVERT: M 100 LEU cc_start: 0.7789 (mm) cc_final: 0.7408 (tt) REVERT: N 4 MET cc_start: 0.7727 (mpp) cc_final: 0.7464 (mpp) REVERT: N 32 TYR cc_start: 0.8422 (m-10) cc_final: 0.8073 (m-10) REVERT: O 4 MET cc_start: 0.0370 (OUTLIER) cc_final: -0.0562 (ptp) REVERT: O 27 TYR cc_start: 0.7509 (t80) cc_final: 0.7109 (m-80) REVERT: L 27 LEU cc_start: 0.9202 (mt) cc_final: 0.8699 (mt) outliers start: 60 outliers final: 38 residues processed: 128 average time/residue: 0.3794 time to fit residues: 85.0608 Evaluate side-chains 122 residues out of total 3705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 78 time to evaluate : 3.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain M residue 100 TYR Chi-restraints excluded: chain N residue 9 ASP Chi-restraints excluded: chain O residue 4 MET Chi-restraints excluded: chain O residue 36 TYR Chi-restraints excluded: chain O residue 94 LEU Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 42 GLN Chi-restraints excluded: chain L residue 94 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 251 optimal weight: 3.9990 chunk 162 optimal weight: 0.8980 chunk 242 optimal weight: 5.9990 chunk 122 optimal weight: 30.0000 chunk 79 optimal weight: 4.9990 chunk 78 optimal weight: 0.8980 chunk 257 optimal weight: 0.9980 chunk 276 optimal weight: 0.9980 chunk 200 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 318 optimal weight: 10.0000 overall best weight: 1.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B 907 ASN C 895 GLN C 907 ASN L 42 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 29962 Z= 0.206 Angle : 0.599 12.423 41081 Z= 0.303 Chirality : 0.045 0.345 5131 Planarity : 0.004 0.058 5382 Dihedral : 6.994 56.107 5779 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.32 % Favored : 92.61 % Rotamer: Outliers : 2.01 % Allowed : 13.18 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.13), residues: 4153 helix: 1.59 (0.20), residues: 708 sheet: -1.30 (0.16), residues: 984 loop : -1.19 (0.13), residues: 2461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 104 HIS 0.004 0.001 HIS C1048 PHE 0.015 0.001 PHE C 238 TYR 0.018 0.001 TYR A1067 ARG 0.006 0.000 ARG C 577 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8306 Ramachandran restraints generated. 4153 Oldfield, 0 Emsley, 4153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8306 Ramachandran restraints generated. 4153 Oldfield, 0 Emsley, 4153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 3705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 79 time to evaluate : 3.399 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: A 41 LYS cc_start: 0.8494 (OUTLIER) cc_final: 0.8260 (mmmt) REVERT: A 869 MET cc_start: 0.8552 (OUTLIER) cc_final: 0.8329 (mtt) REVERT: B 43 PHE cc_start: 0.6389 (t80) cc_final: 0.5854 (m-80) REVERT: B 287 ASP cc_start: 0.8173 (t0) cc_final: 0.7668 (m-30) REVERT: B 486 TYR cc_start: 0.7651 (t80) cc_final: 0.7411 (t80) REVERT: B 489 TYR cc_start: 0.8668 (m-80) cc_final: 0.8455 (p90) REVERT: B 614 ASP cc_start: 0.8155 (t70) cc_final: 0.7544 (t0) REVERT: B 1101 HIS cc_start: 0.5646 (OUTLIER) cc_final: 0.3572 (m90) REVERT: C 912 THR cc_start: 0.8256 (OUTLIER) cc_final: 0.7676 (p) REVERT: C 1106 GLN cc_start: 0.8175 (OUTLIER) cc_final: 0.7879 (pt0) REVERT: M 58 ILE cc_start: 0.9248 (mm) cc_final: 0.8982 (mm) REVERT: N 32 TYR cc_start: 0.8273 (m-10) cc_final: 0.7954 (m-10) REVERT: O 4 MET cc_start: -0.0001 (OUTLIER) cc_final: -0.0851 (ptt) REVERT: O 27 TYR cc_start: 0.7484 (t80) cc_final: 0.7165 (m-80) REVERT: L 27 LEU cc_start: 0.9167 (mt) cc_final: 0.8590 (mt) outliers start: 48 outliers final: 32 residues processed: 119 average time/residue: 0.3612 time to fit residues: 76.5229 Evaluate side-chains 117 residues out of total 3705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 79 time to evaluate : 3.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain M residue 100 TYR Chi-restraints excluded: chain O residue 4 MET Chi-restraints excluded: chain O residue 36 TYR Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 42 GLN Chi-restraints excluded: chain L residue 94 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 369 optimal weight: 50.0000 chunk 388 optimal weight: 40.0000 chunk 354 optimal weight: 40.0000 chunk 378 optimal weight: 50.0000 chunk 227 optimal weight: 20.0000 chunk 164 optimal weight: 0.8980 chunk 296 optimal weight: 5.9990 chunk 116 optimal weight: 0.0870 chunk 341 optimal weight: 50.0000 chunk 357 optimal weight: 30.0000 chunk 376 optimal weight: 20.0000 overall best weight: 9.3968 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN L 42 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.3659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.145 29962 Z= 0.740 Angle : 0.879 13.601 41081 Z= 0.444 Chirality : 0.052 0.348 5131 Planarity : 0.006 0.060 5382 Dihedral : 7.686 59.965 5779 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.94 % Favored : 90.01 % Rotamer: Outliers : 2.22 % Allowed : 13.18 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.13), residues: 4153 helix: 0.87 (0.19), residues: 702 sheet: -1.64 (0.16), residues: 1007 loop : -1.47 (0.13), residues: 2444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 64 HIS 0.018 0.003 HIS C1048 PHE 0.047 0.004 PHE A1089 TYR 0.040 0.003 TYR B1067 ARG 0.007 0.001 ARG B1107 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8306 Ramachandran restraints generated. 4153 Oldfield, 0 Emsley, 4153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8306 Ramachandran restraints generated. 4153 Oldfield, 0 Emsley, 4153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 3705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 79 time to evaluate : 3.638 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: A 41 LYS cc_start: 0.8586 (OUTLIER) cc_final: 0.8223 (mmmt) REVERT: B 43 PHE cc_start: 0.6554 (t80) cc_final: 0.5847 (m-80) REVERT: B 287 ASP cc_start: 0.8338 (t0) cc_final: 0.7669 (m-30) REVERT: B 1101 HIS cc_start: 0.6639 (OUTLIER) cc_final: 0.4932 (m90) REVERT: C 63 THR cc_start: 0.8127 (OUTLIER) cc_final: 0.7837 (p) REVERT: C 912 THR cc_start: 0.8296 (OUTLIER) cc_final: 0.7871 (p) REVERT: M 58 ILE cc_start: 0.9271 (mm) cc_final: 0.8974 (mm) REVERT: N 32 TYR cc_start: 0.8514 (m-10) cc_final: 0.8139 (m-10) REVERT: O 4 MET cc_start: 0.0161 (OUTLIER) cc_final: -0.0699 (ptt) REVERT: O 27 TYR cc_start: 0.7467 (t80) cc_final: 0.7093 (m-80) REVERT: H 64 GLN cc_start: 0.8383 (OUTLIER) cc_final: 0.7819 (pp30) REVERT: L 27 LEU cc_start: 0.9158 (mt) cc_final: 0.8661 (mt) outliers start: 53 outliers final: 39 residues processed: 126 average time/residue: 0.3473 time to fit residues: 77.3646 Evaluate side-chains 121 residues out of total 3705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 76 time to evaluate : 3.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain M residue 100 TYR Chi-restraints excluded: chain N residue 9 ASP Chi-restraints excluded: chain O residue 4 MET Chi-restraints excluded: chain O residue 36 TYR Chi-restraints excluded: chain O residue 94 LEU Chi-restraints excluded: chain H residue 64 GLN Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 42 GLN Chi-restraints excluded: chain L residue 94 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 248 optimal weight: 0.9990 chunk 399 optimal weight: 9.9990 chunk 244 optimal weight: 4.9990 chunk 189 optimal weight: 0.7980 chunk 277 optimal weight: 0.9980 chunk 419 optimal weight: 9.9990 chunk 386 optimal weight: 50.0000 chunk 333 optimal weight: 40.0000 chunk 34 optimal weight: 50.0000 chunk 257 optimal weight: 0.9980 chunk 204 optimal weight: 20.0000 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 901 GLN B 907 ASN C1106 GLN L 42 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.3643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 29962 Z= 0.222 Angle : 0.612 9.578 41081 Z= 0.310 Chirality : 0.046 0.339 5131 Planarity : 0.004 0.058 5382 Dihedral : 7.050 59.725 5777 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.34 % Favored : 92.58 % Rotamer: Outliers : 1.80 % Allowed : 13.55 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.13), residues: 4153 helix: 1.52 (0.20), residues: 696 sheet: -1.49 (0.16), residues: 994 loop : -1.24 (0.13), residues: 2463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 104 HIS 0.004 0.001 HIS C1101 PHE 0.018 0.001 PHE C 220 TYR 0.019 0.001 TYR A1067 ARG 0.003 0.000 ARG B1039 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8306 Ramachandran restraints generated. 4153 Oldfield, 0 Emsley, 4153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8306 Ramachandran restraints generated. 4153 Oldfield, 0 Emsley, 4153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 3705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 82 time to evaluate : 3.553 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: A 41 LYS cc_start: 0.8497 (OUTLIER) cc_final: 0.8251 (mmmt) REVERT: A 869 MET cc_start: 0.8532 (OUTLIER) cc_final: 0.8328 (mtt) REVERT: B 43 PHE cc_start: 0.6230 (t80) cc_final: 0.5751 (m-80) REVERT: B 287 ASP cc_start: 0.8184 (t0) cc_final: 0.7659 (m-30) REVERT: B 1101 HIS cc_start: 0.5764 (OUTLIER) cc_final: 0.3777 (m90) REVERT: C 912 THR cc_start: 0.8090 (OUTLIER) cc_final: 0.7877 (p) REVERT: M 58 ILE cc_start: 0.9264 (mm) cc_final: 0.9004 (mm) REVERT: N 32 TYR cc_start: 0.8300 (m-10) cc_final: 0.7956 (m-10) REVERT: O 4 MET cc_start: -0.0459 (ttm) cc_final: -0.1160 (ptt) REVERT: O 27 TYR cc_start: 0.7418 (t80) cc_final: 0.7101 (m-80) REVERT: L 27 LEU cc_start: 0.9215 (mt) cc_final: 0.8931 (mt) outliers start: 43 outliers final: 34 residues processed: 118 average time/residue: 0.3607 time to fit residues: 75.2251 Evaluate side-chains 117 residues out of total 3705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 79 time to evaluate : 3.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain N residue 9 ASP Chi-restraints excluded: chain O residue 36 TYR Chi-restraints excluded: chain O residue 94 LEU Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 42 GLN Chi-restraints excluded: chain L residue 94 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 265 optimal weight: 2.9990 chunk 355 optimal weight: 20.0000 chunk 102 optimal weight: 5.9990 chunk 307 optimal weight: 30.0000 chunk 49 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 334 optimal weight: 9.9990 chunk 139 optimal weight: 7.9990 chunk 343 optimal weight: 20.0000 chunk 42 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 901 GLN B 907 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.081530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.055574 restraints weight = 141199.196| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 3.83 r_work: 0.3212 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.3646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.243 29962 Z= 0.281 Angle : 0.731 59.200 41081 Z= 0.399 Chirality : 0.046 0.342 5131 Planarity : 0.005 0.143 5382 Dihedral : 7.051 59.766 5777 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.51 % Favored : 92.42 % Rotamer: Outliers : 1.55 % Allowed : 13.85 % Favored : 84.60 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.13), residues: 4153 helix: 1.52 (0.20), residues: 696 sheet: -1.49 (0.16), residues: 996 loop : -1.23 (0.13), residues: 2461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 104 HIS 0.005 0.001 HIS C1048 PHE 0.018 0.001 PHE B1052 TYR 0.020 0.001 TYR A1067 ARG 0.003 0.000 ARG B1039 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5065.78 seconds wall clock time: 92 minutes 52.26 seconds (5572.26 seconds total)