Starting phenix.real_space_refine on Thu Feb 22 07:48:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lrt_23499/02_2024/7lrt_23499.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lrt_23499/02_2024/7lrt_23499.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lrt_23499/02_2024/7lrt_23499.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lrt_23499/02_2024/7lrt_23499.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lrt_23499/02_2024/7lrt_23499.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lrt_23499/02_2024/7lrt_23499.pdb" } resolution = 3.54 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= 0.012 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 148 5.16 5 C 21214 2.51 5 N 5485 2.21 5 O 6618 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 46": "OE1" <-> "OE2" Residue "D TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 574": "OD1" <-> "OD2" Residue "A TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 867": "OD1" <-> "OD2" Residue "B PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 868": "OE1" <-> "OE2" Residue "B TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 465": "OE1" <-> "OE2" Residue "C TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 33465 Number of models: 1 Model: "" Number of chains: 34 Chain: "F" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 946 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 119} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "G" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 825 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 100} Chain: "H" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 946 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 119} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "L" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 825 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 100} Chain: "D" Number of atoms: 1625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1625 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 203} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "E" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1636 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 200} Chain: "A" Number of atoms: 8494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1085, 8494 Classifications: {'peptide': 1085} Link IDs: {'PTRANS': 58, 'TRANS': 1026} Chain breaks: 4 Chain: "B" Number of atoms: 8515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1088, 8515 Classifications: {'peptide': 1088} Link IDs: {'PTRANS': 59, 'TRANS': 1028} Chain breaks: 5 Chain: "C" Number of atoms: 8516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1088, 8516 Classifications: {'peptide': 1088} Link IDs: {'PTRANS': 59, 'TRANS': 1028} Chain breaks: 4 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: "M" 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: "N" 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: "O" 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: "P" 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: "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: 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: "S" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "T" 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: "U" 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: "V" 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: "W" 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: "X" 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: "Y" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "Z" 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: 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: "b" 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: "c" 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: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" 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 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 15.97, per 1000 atoms: 0.48 Number of scatterers: 33465 At special positions: 0 Unit cell: (157.32, 162.45, 267.615, 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 148 16.00 O 6618 8.00 N 5485 7.00 C 21214 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=53, symmetry=0 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.03 Simple disulfide: pdb=" SG CYS F 97 " - pdb=" SG CYS F 100B" distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 97 " - pdb=" SG CYS H 100B" distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 97 " - pdb=" SG CYS D 100B" distance=2.03 Simple disulfide: pdb=" SG CYS D 140 " - pdb=" SG CYS D 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 134 " - pdb=" SG CYS E 194 " distance=2.03 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 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=2.02 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=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 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 ALPHA1-3 " BMA S 3 " - " MAN S 4 " " BMA Y 3 " - " MAN Y 4 " " BMA e 3 " - " MAN e 4 " ALPHA1-6 " BMA S 3 " - " MAN S 5 " " BMA Y 3 " - " MAN Y 5 " " BMA e 3 " - " MAN e 5 " BETA1-4 " 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 M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " NAG-ASN " NAG A1301 " - " ASN A 282 " " NAG A1302 " - " ASN A 657 " " NAG A1303 " - " ASN A 616 " " NAG A1304 " - " ASN A 801 " " NAG A1305 " - " ASN A1074 " " NAG A1306 " - " ASN A 61 " " NAG A1307 " - " ASN A 234 " " NAG A1308 " - " ASN A 165 " " NAG A1309 " - " ASN A 603 " " NAG A1310 " - " ASN A 149 " " NAG B1301 " - " ASN B 282 " " NAG B1302 " - " ASN B 657 " " NAG B1303 " - " ASN B 616 " " NAG B1304 " - " ASN B 709 " " NAG B1305 " - " ASN B1074 " " NAG B1306 " - " ASN B 603 " " NAG B1307 " - " ASN B 17 " " NAG C1301 " - " ASN C 282 " " NAG C1302 " - " ASN C 657 " " NAG C1303 " - " ASN C 616 " " NAG C1304 " - " ASN C 709 " " NAG C1305 " - " ASN C1074 " " NAG C1306 " - " ASN C 61 " " NAG C1307 " - " ASN C 234 " " NAG C1308 " - " ASN C 603 " " NAG C1309 " - " ASN C 165 " " NAG C1310 " - " ASN C 17 " " NAG I 1 " - " ASN F 96 " " NAG J 1 " - " ASN H 96 " " NAG K 1 " - " ASN D 96 " " NAG M 1 " - " ASN A 331 " " NAG N 1 " - " ASN A1134 " " NAG O 1 " - " ASN A1098 " " NAG P 1 " - " ASN A 717 " " NAG Q 1 " - " ASN A 709 " " NAG R 1 " - " ASN A 17 " " NAG S 1 " - " ASN A 343 " " NAG T 1 " - " ASN B1134 " " NAG U 1 " - " ASN B1098 " " NAG V 1 " - " ASN B 717 " " NAG W 1 " - " ASN B 801 " " NAG X 1 " - " ASN B 331 " " NAG Y 1 " - " ASN B 343 " " NAG Z 1 " - " ASN C 331 " " NAG a 1 " - " ASN C1134 " " NAG b 1 " - " ASN C1098 " " NAG c 1 " - " ASN C 717 " " NAG d 1 " - " ASN C 801 " " NAG e 1 " - " ASN C 343 " Time building additional restraints: 13.78 Conformation dependent library (CDL) restraints added in 5.9 seconds 8212 Ramachandran restraints generated. 4106 Oldfield, 0 Emsley, 4106 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7750 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 78 sheets defined 18.9% alpha, 24.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.23 Creating SS restraints... Processing helix chain 'F' and resid 83 through 87 removed outlier: 3.714A pdb=" N THR F 87 " --> pdb=" O SER F 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.821A pdb=" N THR H 87 " --> pdb=" O SER H 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 87 removed outlier: 3.509A pdb=" N THR D 87 " --> pdb=" O SER D 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 126 removed outlier: 3.531A pdb=" N GLN E 124 " --> pdb=" O SER E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 202 removed outlier: 4.097A pdb=" N SER E 202 " --> pdb=" O GLN E 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.778A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.734A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 506 removed outlier: 3.899A pdb=" N GLN A 506 " --> pdb=" O VAL A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 638 removed outlier: 3.640A pdb=" N THR A 638 " --> pdb=" O VAL A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.592A pdb=" N ILE A 742 " --> pdb=" O CYS A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.804A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LYS A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.236A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN A 919 " --> pdb=" O VAL A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.759A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 945 removed outlier: 4.484A pdb=" N LEU A 945 " --> pdb=" O PRO A 942 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 942 through 945' Processing helix chain 'A' and resid 947 through 965 removed outlier: 3.725A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.758A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU A 984 " --> pdb=" O ILE A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 5.457A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1149 removed outlier: 4.167A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE A1148 " --> pdb=" O GLU A1144 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.724A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 371 removed outlier: 4.055A pdb=" N SER B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 410 removed outlier: 3.899A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 506 removed outlier: 3.693A pdb=" N GLN B 506 " --> pdb=" O VAL B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 623 Proline residue: B 621 - end of helix Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.695A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N GLN B 774 " --> pdb=" O ILE B 770 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 908 removed outlier: 3.574A pdb=" N TYR B 904 " --> pdb=" O MET B 900 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.519A pdb=" N GLU B 918 " --> pdb=" O ASN B 914 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.863A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.612A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.603A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 5.358A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR B 998 " --> pdb=" O ASP B 994 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY B 999 " --> pdb=" O ARG B 995 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1149 removed outlier: 4.307A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) 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 371 removed outlier: 3.789A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N SER C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 409 removed outlier: 3.803A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 506 removed outlier: 3.921A pdb=" N GLN C 506 " --> pdb=" O VAL C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 618 No H-bonds generated for 'chain 'C' and resid 616 through 618' Processing helix chain 'C' and resid 619 through 624 removed outlier: 3.876A pdb=" N ALA C 623 " --> pdb=" O GLU C 619 " (cutoff:3.500A) Processing helix chain 'C' and resid 632 through 636 Processing helix chain 'C' and resid 737 through 743 removed outlier: 3.637A pdb=" N TYR C 741 " --> pdb=" O ASP C 737 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N CYS C 743 " --> pdb=" O THR C 739 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.687A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE C 770 " --> pdb=" O ALA C 766 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.743A pdb=" N GLY C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.898A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 902 Processing helix chain 'C' and resid 906 through 910 removed outlier: 3.628A pdb=" N GLY C 910 " --> pdb=" O ASN C 907 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.971A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 946 through 965 removed outlier: 4.142A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.622A pdb=" N LEU C 984 " --> pdb=" O ILE C 980 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1034 removed outlier: 4.922A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU C1034 " --> pdb=" O SER C1030 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1148 removed outlier: 4.099A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'F' and resid 3 through 6 removed outlier: 3.512A pdb=" N LEU F 82 " --> pdb=" O VAL F 18 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 10 through 12 Processing sheet with id=AA3, first strand: chain 'F' and resid 33 through 36 Processing sheet with id=AA4, first strand: chain 'F' and resid 93 through 94 Processing sheet with id=AA5, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.249A pdb=" N LEU G 11 " --> pdb=" O GLU G 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'G' and resid 20 through 22 Processing sheet with id=AA7, first strand: chain 'G' and resid 45 through 49 removed outlier: 6.756A pdb=" N TRP G 35 " --> pdb=" O LEU G 47 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N TYR G 49 " --> pdb=" O LEU G 33 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LEU G 33 " --> pdb=" O TYR G 49 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL G 85 " --> pdb=" O GLN G 38 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 3 through 5 removed outlier: 4.366A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N SER H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL H 5 " --> pdb=" O LYS H 23 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU H 82 " --> pdb=" O VAL H 18 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AB1, first strand: chain 'H' and resid 33 through 36 removed outlier: 3.816A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 93 through 94 Processing sheet with id=AB3, first strand: chain 'L' and resid 10 through 12 Processing sheet with id=AB4, first strand: chain 'L' and resid 21 through 22 Processing sheet with id=AB5, first strand: chain 'L' and resid 45 through 49 removed outlier: 6.565A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL L 85 " --> pdb=" O GLN L 38 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 3 through 6 removed outlier: 3.605A pdb=" N GLN D 3 " --> pdb=" O SER D 25 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER D 25 " --> pdb=" O GLN D 3 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 10 through 12 removed outlier: 4.067A pdb=" N VAL D 37 " --> pdb=" O TYR D 91 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 10 through 12 Processing sheet with id=AB9, first strand: chain 'D' and resid 120 through 124 removed outlier: 6.137A pdb=" N TYR D 176 " --> pdb=" O ASP D 144 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL D 181 " --> pdb=" O HIS D 164 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 120 through 124 removed outlier: 6.137A pdb=" N TYR D 176 " --> pdb=" O ASP D 144 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER D 177 " --> pdb=" O VAL D 169 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 10 through 12 removed outlier: 4.090A pdb=" N ILE E 48 " --> pdb=" O TRP E 35 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N GLN E 37 " --> pdb=" O LEU E 46 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N LEU E 46 " --> pdb=" O GLN E 37 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 20 through 22 Processing sheet with id=AC4, first strand: chain 'E' and resid 114 through 118 removed outlier: 3.941A pdb=" N VAL E 133 " --> pdb=" O PHE E 118 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N TYR E 173 " --> pdb=" O ASN E 138 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 145 through 150 removed outlier: 4.165A pdb=" N LYS E 145 " --> pdb=" O THR E 197 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR E 197 " --> pdb=" O LYS E 145 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N CYS E 194 " --> pdb=" O LYS E 207 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N LYS E 207 " --> pdb=" O CYS E 194 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N VAL E 196 " --> pdb=" O VAL E 205 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N VAL E 205 " --> pdb=" O VAL E 196 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 28 through 30 removed outlier: 3.599A pdb=" N GLU A 96 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LYS A 187 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.709A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.583A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.963A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 83 through 85 Processing sheet with id=AC9, first strand: chain 'A' and resid 128 through 129 Processing sheet with id=AD1, first strand: chain 'A' and resid 133 through 140 removed outlier: 8.361A pdb=" N CYS A 136 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 10.176A pdb=" N SER A 162 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 9.743A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG A 158 " --> pdb=" O PHE A 140 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 143 through 145 Processing sheet with id=AD3, first strand: chain 'A' and resid 311 through 314 Processing sheet with id=AD4, first strand: chain 'A' and resid 318 through 319 Processing sheet with id=AD5, first strand: chain 'A' and resid 325 through 326 removed outlier: 3.542A pdb=" N VAL A 539 " --> pdb=" O GLY A 550 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.616A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N GLY A 431 " --> pdb=" O TYR A 380 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N TYR A 380 " --> pdb=" O GLY A 431 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N VAL A 433 " --> pdb=" O LYS A 378 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AD8, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AD9, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.800A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.538A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'A' and resid 735 through 736 Processing sheet with id=AE3, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AE4, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AE5, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AE6, first strand: chain 'B' and resid 27 through 30 removed outlier: 4.173A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 36 through 37 removed outlier: 6.776A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.521A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 9.667A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N GLU B 96 " --> pdb=" O ASN B 188 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.944A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 66 through 67 removed outlier: 4.176A pdb=" N ALA B 67 " --> pdb=" O ALA B 263 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AF2, first strand: chain 'B' and resid 127 through 129 Processing sheet with id=AF3, first strand: chain 'B' and resid 153 through 163 removed outlier: 6.700A pdb=" N MET B 153 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N GLY B 142 " --> pdb=" O MET B 153 " (cutoff:3.500A) removed outlier: 8.994A pdb=" N SER B 155 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 10.992A pdb=" N PHE B 140 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 10.171A pdb=" N PHE B 157 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 11.493A pdb=" N ASP B 138 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'B' and resid 311 through 319 removed outlier: 3.712A pdb=" N THR B 315 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLN B 613 " --> pdb=" O GLY B 594 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'B' and resid 325 through 326 Processing sheet with id=AF6, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.944A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE B 402 " --> pdb=" O TYR B 508 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TYR B 508 " --> pdb=" O ILE B 402 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AF8, first strand: chain 'B' and resid 453 through 454 Processing sheet with id=AF9, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AG1, first strand: chain 'B' and resid 576 through 577 Processing sheet with id=AG2, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.904A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N TYR B 695 " --> pdb=" O CYS B 671 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.495A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG3 Processing sheet with id=AG4, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.682A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'B' and resid 735 through 736 Processing sheet with id=AG6, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.672A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'B' and resid 1094 through 1096 Processing sheet with id=AG8, first strand: chain 'C' and resid 29 through 30 Processing sheet with id=AG9, first strand: chain 'C' and resid 36 through 37 removed outlier: 7.317A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG9 Processing sheet with id=AH1, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.040A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'C' and resid 66 through 68 removed outlier: 3.649A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'C' and resid 83 through 85 removed outlier: 14.487A pdb=" N PHE C 238 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 12.169A pdb=" N ASN C 137 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 9.344A pdb=" N THR C 240 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N LEU C 242 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG C 246 " --> pdb=" O VAL C 143 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 11.700A pdb=" N ASP C 138 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 9.629A pdb=" N PHE C 157 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 10.933A pdb=" N PHE C 140 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 8.938A pdb=" N SER C 155 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N GLY C 142 " --> pdb=" O MET C 153 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N MET C 153 " --> pdb=" O GLY C 142 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N TYR C 144 " --> pdb=" O SER C 151 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N SER C 151 " --> pdb=" O TYR C 144 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'C' and resid 83 through 85 removed outlier: 4.045A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'C' and resid 310 through 319 removed outlier: 5.815A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLN C 613 " --> pdb=" O GLY C 594 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'C' and resid 356 through 358 removed outlier: 3.946A pdb=" N ARG C 509 " --> pdb=" O TRP C 436 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'C' and resid 356 through 358 removed outlier: 4.180A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AH9, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AI1, first strand: chain 'C' and resid 539 through 542 removed outlier: 4.065A pdb=" N THR C 588 " --> pdb=" O VAL C 551 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'C' and resid 654 through 660 removed outlier: 6.161A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.526A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 8.683A pdb=" N VAL C 656 " --> pdb=" O THR C 696 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.823A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AI5, first strand: chain 'C' and resid 1081 through 1083 Processing sheet with id=AI6, first strand: chain 'C' and resid 1094 through 1097 1032 hydrogen bonds defined for protein. 2778 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: 15.04 Time building geometry restraints manager: 15.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10570 1.34 - 1.46: 8490 1.46 - 1.58: 14977 1.58 - 1.70: 0 1.70 - 1.83: 190 Bond restraints: 34227 Sorted by residual: bond pdb=" C1 NAG U 2 " pdb=" O5 NAG U 2 " ideal model delta sigma weight residual 1.406 1.464 -0.058 2.00e-02 2.50e+03 8.49e+00 bond pdb=" C1 NAG X 1 " pdb=" O5 NAG X 1 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 6.11e+00 bond pdb=" C TYR B 505 " pdb=" N GLN B 506 " ideal model delta sigma weight residual 1.330 1.363 -0.033 1.47e-02 4.63e+03 5.05e+00 bond pdb=" C1 BMA e 3 " pdb=" C2 BMA e 3 " ideal model delta sigma weight residual 1.519 1.556 -0.037 2.00e-02 2.50e+03 3.34e+00 bond pdb=" C1 BMA J 3 " pdb=" C2 BMA J 3 " ideal model delta sigma weight residual 1.519 1.554 -0.035 2.00e-02 2.50e+03 3.07e+00 ... (remaining 34222 not shown) Histogram of bond angle deviations from ideal: 98.94 - 105.97: 799 105.97 - 113.00: 18926 113.00 - 120.03: 11124 120.03 - 127.06: 15387 127.06 - 134.09: 348 Bond angle restraints: 46584 Sorted by residual: angle pdb=" N VAL B 635 " pdb=" CA VAL B 635 " pdb=" C VAL B 635 " ideal model delta sigma weight residual 113.71 106.72 6.99 9.50e-01 1.11e+00 5.42e+01 angle pdb=" C PRO C 330 " pdb=" N ASN C 331 " pdb=" CA ASN C 331 " ideal model delta sigma weight residual 121.54 128.39 -6.85 1.91e+00 2.74e-01 1.29e+01 angle pdb=" N ILE F 48 " pdb=" CA ILE F 48 " pdb=" C ILE F 48 " ideal model delta sigma weight residual 111.90 109.00 2.90 8.10e-01 1.52e+00 1.28e+01 angle pdb=" N THR A 236 " pdb=" CA THR A 236 " pdb=" C THR A 236 " ideal model delta sigma weight residual 114.75 110.87 3.88 1.26e+00 6.30e-01 9.46e+00 angle pdb=" CA GLY A 502 " pdb=" C GLY A 502 " pdb=" N VAL A 503 " ideal model delta sigma weight residual 114.23 116.93 -2.70 8.80e-01 1.29e+00 9.43e+00 ... (remaining 46579 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.87: 19993 22.87 - 45.73: 1203 45.73 - 68.60: 178 68.60 - 91.47: 83 91.47 - 114.34: 45 Dihedral angle restraints: 21502 sinusoidal: 9442 harmonic: 12060 Sorted by residual: dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 88 " pdb=" CB CYS L 88 " ideal model delta sinusoidal sigma weight residual 93.00 179.47 -86.47 1 1.00e+01 1.00e-02 9.01e+01 dihedral pdb=" CB CYS G 23 " pdb=" SG CYS G 23 " pdb=" SG CYS G 88 " pdb=" CB CYS G 88 " ideal model delta sinusoidal sigma weight residual 93.00 159.39 -66.39 1 1.00e+01 1.00e-02 5.76e+01 dihedral pdb=" CB CYS B 336 " pdb=" SG CYS B 336 " pdb=" SG CYS B 361 " pdb=" CB CYS B 361 " ideal model delta sinusoidal sigma weight residual -86.00 -149.92 63.92 1 1.00e+01 1.00e-02 5.38e+01 ... (remaining 21499 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 5170 0.096 - 0.192: 318 0.192 - 0.288: 12 0.288 - 0.384: 1 0.384 - 0.481: 1 Chirality restraints: 5502 Sorted by residual: chirality pdb=" C1 NAG M 1 " pdb=" ND2 ASN A 331 " pdb=" C2 NAG M 1 " pdb=" O5 NAG M 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.77e+00 chirality pdb=" C1 NAG C1308 " pdb=" ND2 ASN C 603 " pdb=" C2 NAG C1308 " pdb=" O5 NAG C1308 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.87e+00 chirality pdb=" C5 BMA S 3 " pdb=" C4 BMA S 3 " pdb=" C6 BMA S 3 " pdb=" O5 BMA S 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.87e+00 ... (remaining 5499 not shown) Planarity restraints: 5951 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE C 329 " -0.080 5.00e-02 4.00e+02 1.21e-01 2.35e+01 pdb=" N PRO C 330 " 0.210 5.00e-02 4.00e+02 pdb=" CA PRO C 330 " -0.064 5.00e-02 4.00e+02 pdb=" CD PRO C 330 " -0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 104 " -0.031 2.00e-02 2.50e+03 2.66e-02 1.77e+01 pdb=" CG TRP C 104 " 0.073 2.00e-02 2.50e+03 pdb=" CD1 TRP C 104 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP C 104 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 104 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP C 104 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 104 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 104 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 104 " -0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP C 104 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 331 " 0.036 2.00e-02 2.50e+03 3.47e-02 1.50e+01 pdb=" CG ASN A 331 " -0.034 2.00e-02 2.50e+03 pdb=" OD1 ASN A 331 " 0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN A 331 " -0.045 2.00e-02 2.50e+03 pdb=" C1 NAG M 1 " 0.039 2.00e-02 2.50e+03 ... (remaining 5948 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 1104 2.70 - 3.25: 32684 3.25 - 3.80: 49705 3.80 - 4.35: 61477 4.35 - 4.90: 104894 Nonbonded interactions: 249864 Sorted by model distance: nonbonded pdb=" OH TYR B 453 " pdb=" OE1 GLN B 493 " model vdw 2.146 2.440 nonbonded pdb=" OG1 THR C1116 " pdb=" OD1 ASP C1118 " model vdw 2.175 2.440 nonbonded pdb=" OG SER A 438 " pdb=" O PRO A 507 " model vdw 2.177 2.440 nonbonded pdb=" O6 NAG U 1 " pdb=" O3 NAG U 2 " model vdw 2.189 2.440 nonbonded pdb=" O GLY A 880 " pdb=" OG SER A 884 " model vdw 2.210 2.440 ... (remaining 249859 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 14 through 1149 or resid 1301 through 1307)) selection = (chain 'B' and (resid 14 through 623 or resid 633 through 1149 or resid 1301 thr \ ough 1307)) selection = (chain 'C' and (resid 14 through 623 or resid 633 through 1149 or resid 1301 thr \ ough 1307)) } ncs_group { reference = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'Z' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' } ncs_group { reference = chain 'S' selection = chain 'Y' selection = chain 'e' } 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 group one per residue 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: 7.780 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: 0.040 Extract box with map and model: 29.200 Check model and map are aligned: 0.520 Set scattering table: 0.310 Process input model: 87.770 Find NCS groups from input model: 2.410 Set up NCS constraints: 0.440 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 131.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 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 : 0.005 0.075 34227 Z= 0.330 Angle : 0.690 8.385 46584 Z= 0.347 Chirality : 0.048 0.481 5502 Planarity : 0.005 0.121 5902 Dihedral : 15.670 114.337 13593 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.87 % Favored : 92.84 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.13), residues: 4106 helix: 1.94 (0.21), residues: 604 sheet: -0.60 (0.16), residues: 1068 loop : -1.96 (0.12), residues: 2434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.002 TRP C 104 HIS 0.003 0.001 HIS B 66 PHE 0.034 0.002 PHE C 329 TYR 0.024 0.001 TYR A 904 ARG 0.007 0.000 ARG B 357 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8212 Ramachandran restraints generated. 4106 Oldfield, 0 Emsley, 4106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8212 Ramachandran restraints generated. 4106 Oldfield, 0 Emsley, 4106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 3622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 190 time to evaluate : 3.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 103 LYS cc_start: 0.6038 (tttp) cc_final: 0.5666 (tmtt) REVERT: E 107 LYS cc_start: 0.6934 (tptp) cc_final: 0.6586 (mmmm) REVERT: A 456 PHE cc_start: 0.7881 (m-80) cc_final: 0.7432 (m-80) REVERT: A 1002 GLN cc_start: 0.8434 (tm-30) cc_final: 0.8167 (tm-30) REVERT: B 517 LEU cc_start: 0.9282 (tp) cc_final: 0.8767 (tp) REVERT: C 79 PHE cc_start: 0.7528 (t80) cc_final: 0.7294 (t80) REVERT: C 495 TYR cc_start: 0.5639 (m-10) cc_final: 0.5281 (m-10) outliers start: 0 outliers final: 0 residues processed: 190 average time/residue: 0.5069 time to fit residues: 152.5063 Evaluate side-chains 120 residues out of total 3622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 4.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 346 optimal weight: 0.8980 chunk 310 optimal weight: 9.9990 chunk 172 optimal weight: 3.9990 chunk 106 optimal weight: 0.0770 chunk 209 optimal weight: 7.9990 chunk 166 optimal weight: 2.9990 chunk 321 optimal weight: 7.9990 chunk 124 optimal weight: 30.0000 chunk 195 optimal weight: 6.9990 chunk 239 optimal weight: 30.0000 chunk 372 optimal weight: 3.9990 overall best weight: 2.3944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 43 GLN ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 487 ASN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.0943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 34227 Z= 0.298 Angle : 0.622 10.103 46584 Z= 0.313 Chirality : 0.045 0.238 5502 Planarity : 0.004 0.127 5902 Dihedral : 10.890 105.697 6198 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.04 % Favored : 92.69 % Rotamer: Outliers : 0.39 % Allowed : 6.41 % Favored : 93.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % 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: -1.34 (0.13), residues: 4106 helix: 2.00 (0.21), residues: 630 sheet: -0.58 (0.16), residues: 1050 loop : -1.92 (0.12), residues: 2426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP C 104 HIS 0.003 0.001 HIS A 66 PHE 0.021 0.002 PHE B 906 TYR 0.022 0.001 TYR A 904 ARG 0.007 0.000 ARG D 83 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8212 Ramachandran restraints generated. 4106 Oldfield, 0 Emsley, 4106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8212 Ramachandran restraints generated. 4106 Oldfield, 0 Emsley, 4106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 3622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 128 time to evaluate : 4.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 456 PHE cc_start: 0.7695 (m-80) cc_final: 0.7427 (m-80) REVERT: A 1002 GLN cc_start: 0.8457 (tm-30) cc_final: 0.8069 (tm-30) REVERT: C 177 MET cc_start: 0.4792 (mtt) cc_final: 0.3664 (ptp) outliers start: 14 outliers final: 12 residues processed: 134 average time/residue: 0.4669 time to fit residues: 105.4429 Evaluate side-chains 129 residues out of total 3622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 117 time to evaluate : 4.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 70 ASP Chi-restraints excluded: chain G residue 71 PHE Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1148 PHE Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 206 optimal weight: 8.9990 chunk 115 optimal weight: 0.7980 chunk 309 optimal weight: 7.9990 chunk 253 optimal weight: 0.9990 chunk 102 optimal weight: 9.9990 chunk 372 optimal weight: 4.9990 chunk 402 optimal weight: 0.8980 chunk 332 optimal weight: 1.9990 chunk 369 optimal weight: 0.6980 chunk 127 optimal weight: 6.9990 chunk 299 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 99 ASN ** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 606 ASN C 69 HIS C1106 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.1224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.082 34227 Z= 0.161 Angle : 0.547 9.395 46584 Z= 0.274 Chirality : 0.043 0.233 5502 Planarity : 0.004 0.119 5902 Dihedral : 8.890 96.773 6198 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.21 % Favored : 93.52 % Rotamer: Outliers : 0.66 % Allowed : 9.78 % Favored : 89.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % 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: -1.14 (0.13), residues: 4106 helix: 2.40 (0.21), residues: 621 sheet: -0.40 (0.16), residues: 1039 loop : -1.86 (0.12), residues: 2446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 104 HIS 0.002 0.000 HIS B1048 PHE 0.017 0.001 PHE E 116 TYR 0.022 0.001 TYR A 904 ARG 0.003 0.000 ARG F 71 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8212 Ramachandran restraints generated. 4106 Oldfield, 0 Emsley, 4106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8212 Ramachandran restraints generated. 4106 Oldfield, 0 Emsley, 4106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 3622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 134 time to evaluate : 3.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 73 MET cc_start: -0.1056 (mmt) cc_final: -0.1300 (mmt) REVERT: H 2 MET cc_start: 0.2265 (tpt) cc_final: 0.1713 (tpt) REVERT: D 2 MET cc_start: 0.2205 (tmm) cc_final: 0.1463 (tmm) REVERT: D 90 TYR cc_start: 0.9303 (m-80) cc_final: 0.8976 (m-80) REVERT: A 456 PHE cc_start: 0.7588 (m-80) cc_final: 0.7293 (m-80) REVERT: A 1002 GLN cc_start: 0.8342 (tm-30) cc_final: 0.7932 (tm-30) REVERT: C 177 MET cc_start: 0.4483 (mtt) cc_final: 0.4266 (mtt) REVERT: C 489 TYR cc_start: 0.6413 (m-80) cc_final: 0.6175 (m-80) REVERT: C 495 TYR cc_start: 0.4762 (m-80) cc_final: 0.4451 (m-10) REVERT: C 1031 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.7300 (mp0) outliers start: 24 outliers final: 12 residues processed: 151 average time/residue: 0.4643 time to fit residues: 117.1154 Evaluate side-chains 136 residues out of total 3622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 123 time to evaluate : 3.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 71 PHE Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1148 PHE Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 368 optimal weight: 0.0570 chunk 280 optimal weight: 3.9990 chunk 193 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 chunk 178 optimal weight: 0.0050 chunk 250 optimal weight: 5.9990 chunk 374 optimal weight: 4.9990 chunk 396 optimal weight: 1.9990 chunk 195 optimal weight: 6.9990 chunk 354 optimal weight: 6.9990 chunk 106 optimal weight: 0.4980 overall best weight: 0.7114 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN ** D 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.080 34227 Z= 0.146 Angle : 0.526 9.485 46584 Z= 0.263 Chirality : 0.042 0.238 5502 Planarity : 0.004 0.113 5902 Dihedral : 7.657 91.453 6198 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.55 % Favored : 93.18 % Rotamer: Outliers : 0.83 % Allowed : 11.96 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.13), residues: 4106 helix: 2.60 (0.21), residues: 622 sheet: -0.33 (0.16), residues: 1060 loop : -1.79 (0.12), residues: 2424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 104 HIS 0.002 0.000 HIS A 66 PHE 0.021 0.001 PHE C 855 TYR 0.031 0.001 TYR A 904 ARG 0.005 0.000 ARG D 83 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8212 Ramachandran restraints generated. 4106 Oldfield, 0 Emsley, 4106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8212 Ramachandran restraints generated. 4106 Oldfield, 0 Emsley, 4106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 3622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 127 time to evaluate : 3.629 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 73 MET cc_start: -0.1078 (mmt) cc_final: -0.1703 (mmt) REVERT: H 2 MET cc_start: 0.2383 (tpt) cc_final: 0.1894 (tpt) REVERT: H 38 ARG cc_start: 0.4418 (ttp-170) cc_final: 0.3712 (tmt170) REVERT: D 2 MET cc_start: 0.2402 (tmm) cc_final: 0.1535 (tmm) REVERT: D 90 TYR cc_start: 0.9363 (m-80) cc_final: 0.9061 (m-80) REVERT: E 173 TYR cc_start: 0.4884 (m-80) cc_final: 0.4675 (m-80) REVERT: A 449 TYR cc_start: 0.8512 (m-80) cc_final: 0.8118 (m-80) REVERT: A 456 PHE cc_start: 0.7584 (m-80) cc_final: 0.7287 (m-80) REVERT: A 1002 GLN cc_start: 0.8317 (tm-30) cc_final: 0.7897 (tm-30) REVERT: C 177 MET cc_start: 0.4197 (mtt) cc_final: 0.3964 (mtt) REVERT: C 489 TYR cc_start: 0.6340 (m-80) cc_final: 0.6088 (m-80) REVERT: C 495 TYR cc_start: 0.4752 (m-80) cc_final: 0.4453 (m-10) outliers start: 30 outliers final: 14 residues processed: 149 average time/residue: 0.4499 time to fit residues: 112.1366 Evaluate side-chains 134 residues out of total 3622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 120 time to evaluate : 4.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 70 ASP Chi-restraints excluded: chain G residue 71 PHE Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1148 PHE Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 330 optimal weight: 0.9990 chunk 224 optimal weight: 5.9990 chunk 5 optimal weight: 30.0000 chunk 295 optimal weight: 0.9980 chunk 163 optimal weight: 4.9990 chunk 338 optimal weight: 8.9990 chunk 273 optimal weight: 6.9990 chunk 0 optimal weight: 40.0000 chunk 202 optimal weight: 4.9990 chunk 355 optimal weight: 0.0010 chunk 100 optimal weight: 7.9990 overall best weight: 2.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 189 HIS ** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 34227 Z= 0.293 Angle : 0.575 9.366 46584 Z= 0.289 Chirality : 0.043 0.231 5502 Planarity : 0.004 0.118 5902 Dihedral : 7.405 90.007 6198 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.89 % Favored : 92.86 % Rotamer: Outliers : 1.08 % Allowed : 13.10 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % 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: -1.06 (0.13), residues: 4106 helix: 2.40 (0.21), residues: 631 sheet: -0.41 (0.16), residues: 1068 loop : -1.80 (0.12), residues: 2407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 104 HIS 0.003 0.001 HIS A 66 PHE 0.019 0.001 PHE A 238 TYR 0.022 0.001 TYR C 904 ARG 0.003 0.000 ARG D 83 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8212 Ramachandran restraints generated. 4106 Oldfield, 0 Emsley, 4106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8212 Ramachandran restraints generated. 4106 Oldfield, 0 Emsley, 4106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 3622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 116 time to evaluate : 3.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 73 MET cc_start: -0.1004 (mmt) cc_final: -0.1621 (mmt) REVERT: H 2 MET cc_start: 0.2463 (tpt) cc_final: 0.2038 (tpt) REVERT: D 2 MET cc_start: 0.2115 (OUTLIER) cc_final: 0.1279 (tmm) REVERT: D 90 TYR cc_start: 0.9376 (m-80) cc_final: 0.9088 (m-80) REVERT: E 173 TYR cc_start: 0.4925 (m-80) cc_final: 0.4703 (m-80) REVERT: A 456 PHE cc_start: 0.7607 (m-80) cc_final: 0.7334 (m-80) REVERT: A 1002 GLN cc_start: 0.8435 (tm-30) cc_final: 0.8017 (tm-30) REVERT: B 392 PHE cc_start: 0.8847 (m-80) cc_final: 0.8529 (m-80) REVERT: C 177 MET cc_start: 0.4348 (mtt) cc_final: 0.3997 (mtt) REVERT: C 489 TYR cc_start: 0.6319 (m-80) cc_final: 0.6070 (m-80) REVERT: C 1031 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.7415 (mp0) outliers start: 39 outliers final: 21 residues processed: 146 average time/residue: 0.4515 time to fit residues: 110.7496 Evaluate side-chains 135 residues out of total 3622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 112 time to evaluate : 3.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 70 ASP Chi-restraints excluded: chain G residue 71 PHE Chi-restraints excluded: chain D residue 2 MET Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1148 PHE Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 133 optimal weight: 50.0000 chunk 356 optimal weight: 0.8980 chunk 78 optimal weight: 4.9990 chunk 232 optimal weight: 7.9990 chunk 97 optimal weight: 1.9990 chunk 396 optimal weight: 3.9990 chunk 329 optimal weight: 5.9990 chunk 183 optimal weight: 3.9990 chunk 32 optimal weight: 30.0000 chunk 131 optimal weight: 5.9990 chunk 208 optimal weight: 7.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN D 39 GLN ** D 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 38 GLN ** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 GLN C 370 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 34227 Z= 0.372 Angle : 0.623 9.261 46584 Z= 0.315 Chirality : 0.044 0.225 5502 Planarity : 0.004 0.123 5902 Dihedral : 7.334 88.217 6198 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.67 % Favored : 92.06 % Rotamer: Outliers : 1.49 % Allowed : 13.73 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % 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: -1.17 (0.13), residues: 4106 helix: 2.14 (0.21), residues: 637 sheet: -0.51 (0.16), residues: 1070 loop : -1.82 (0.12), residues: 2399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 104 HIS 0.003 0.001 HIS B 49 PHE 0.026 0.002 PHE C 855 TYR 0.023 0.001 TYR C 904 ARG 0.005 0.000 ARG D 83 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8212 Ramachandran restraints generated. 4106 Oldfield, 0 Emsley, 4106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8212 Ramachandran restraints generated. 4106 Oldfield, 0 Emsley, 4106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 3622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 116 time to evaluate : 3.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 38 ARG cc_start: 0.4655 (ttp-170) cc_final: 0.3879 (tmt170) REVERT: D 2 MET cc_start: 0.2007 (OUTLIER) cc_final: 0.1092 (tmm) REVERT: D 80 MET cc_start: 0.3010 (tpt) cc_final: 0.2800 (tpt) REVERT: D 83 ARG cc_start: 0.6317 (ptt-90) cc_final: 0.5840 (pmt-80) REVERT: D 90 TYR cc_start: 0.9419 (m-80) cc_final: 0.9198 (m-80) REVERT: E 173 TYR cc_start: 0.4916 (m-80) cc_final: 0.4705 (m-80) REVERT: A 449 TYR cc_start: 0.8546 (m-80) cc_final: 0.8213 (m-80) REVERT: A 456 PHE cc_start: 0.7587 (m-80) cc_final: 0.7340 (m-80) REVERT: A 1002 GLN cc_start: 0.8508 (tm-30) cc_final: 0.8072 (tm-30) REVERT: B 392 PHE cc_start: 0.9025 (m-80) cc_final: 0.8709 (m-80) REVERT: B 1017 GLU cc_start: 0.8477 (tm-30) cc_final: 0.8249 (tm-30) REVERT: C 177 MET cc_start: 0.4507 (mtt) cc_final: 0.3924 (mtt) REVERT: C 489 TYR cc_start: 0.6269 (m-80) cc_final: 0.6054 (m-80) REVERT: C 1031 GLU cc_start: 0.8689 (OUTLIER) cc_final: 0.7392 (mp0) outliers start: 54 outliers final: 34 residues processed: 158 average time/residue: 0.4480 time to fit residues: 118.4858 Evaluate side-chains 147 residues out of total 3622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 111 time to evaluate : 3.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 71 PHE Chi-restraints excluded: chain D residue 2 MET Chi-restraints excluded: chain D residue 66 ARG Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 914 ASN Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1148 PHE Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 382 optimal weight: 0.8980 chunk 44 optimal weight: 30.0000 chunk 226 optimal weight: 7.9990 chunk 289 optimal weight: 0.8980 chunk 224 optimal weight: 0.9980 chunk 333 optimal weight: 6.9990 chunk 221 optimal weight: 1.9990 chunk 395 optimal weight: 0.8980 chunk 247 optimal weight: 9.9990 chunk 240 optimal weight: 10.0000 chunk 182 optimal weight: 1.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 34227 Z= 0.178 Angle : 0.542 9.413 46584 Z= 0.273 Chirality : 0.043 0.233 5502 Planarity : 0.004 0.117 5902 Dihedral : 6.917 85.274 6198 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.33 % Favored : 93.40 % Rotamer: Outliers : 1.16 % Allowed : 14.48 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.13), residues: 4106 helix: 2.57 (0.21), residues: 619 sheet: -0.41 (0.16), residues: 1087 loop : -1.75 (0.12), residues: 2400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 104 HIS 0.003 0.000 HIS C1101 PHE 0.012 0.001 PHE A 238 TYR 0.024 0.001 TYR A 451 ARG 0.003 0.000 ARG D 83 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8212 Ramachandran restraints generated. 4106 Oldfield, 0 Emsley, 4106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8212 Ramachandran restraints generated. 4106 Oldfield, 0 Emsley, 4106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 3622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 123 time to evaluate : 4.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 73 MET cc_start: -0.0764 (mmt) cc_final: -0.1382 (mmt) REVERT: H 38 ARG cc_start: 0.4488 (ttp-170) cc_final: 0.3703 (tmt170) REVERT: D 2 MET cc_start: 0.2038 (OUTLIER) cc_final: 0.1115 (tmm) REVERT: D 90 TYR cc_start: 0.9432 (m-80) cc_final: 0.9218 (m-80) REVERT: E 173 TYR cc_start: 0.4993 (m-80) cc_final: 0.4775 (m-80) REVERT: A 449 TYR cc_start: 0.8510 (m-80) cc_final: 0.8091 (m-10) REVERT: A 456 PHE cc_start: 0.7541 (m-80) cc_final: 0.7271 (m-80) REVERT: A 1002 GLN cc_start: 0.8380 (tm-30) cc_final: 0.7929 (tm-30) REVERT: B 392 PHE cc_start: 0.8971 (m-80) cc_final: 0.8576 (m-80) REVERT: C 63 THR cc_start: 0.8046 (OUTLIER) cc_final: 0.7769 (m) REVERT: C 104 TRP cc_start: 0.8684 (m-90) cc_final: 0.8298 (m-10) REVERT: C 177 MET cc_start: 0.4428 (mtt) cc_final: 0.3849 (mtt) REVERT: C 489 TYR cc_start: 0.6281 (m-80) cc_final: 0.6067 (m-80) REVERT: C 1031 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.7441 (mp0) outliers start: 42 outliers final: 30 residues processed: 154 average time/residue: 0.4693 time to fit residues: 119.9754 Evaluate side-chains 150 residues out of total 3622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 117 time to evaluate : 3.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 71 PHE Chi-restraints excluded: chain D residue 2 MET Chi-restraints excluded: chain D residue 66 ARG Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1148 PHE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 244 optimal weight: 0.0050 chunk 157 optimal weight: 2.9990 chunk 236 optimal weight: 20.0000 chunk 119 optimal weight: 3.9990 chunk 77 optimal weight: 0.0370 chunk 76 optimal weight: 40.0000 chunk 251 optimal weight: 6.9990 chunk 269 optimal weight: 0.0980 chunk 195 optimal weight: 6.9990 chunk 36 optimal weight: 8.9990 chunk 310 optimal weight: 3.9990 overall best weight: 1.4276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 105 GLN ** D 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 644 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 34227 Z= 0.200 Angle : 0.546 11.317 46584 Z= 0.274 Chirality : 0.043 0.244 5502 Planarity : 0.004 0.114 5902 Dihedral : 6.790 83.653 6198 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.48 % Favored : 93.28 % Rotamer: Outliers : 1.46 % Allowed : 14.59 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.13), residues: 4106 helix: 2.66 (0.21), residues: 618 sheet: -0.37 (0.16), residues: 1083 loop : -1.72 (0.12), residues: 2405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 104 HIS 0.001 0.000 HIS A1058 PHE 0.027 0.001 PHE C 855 TYR 0.020 0.001 TYR A 904 ARG 0.006 0.000 ARG L 45 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8212 Ramachandran restraints generated. 4106 Oldfield, 0 Emsley, 4106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8212 Ramachandran restraints generated. 4106 Oldfield, 0 Emsley, 4106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 3622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 120 time to evaluate : 3.490 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: F 73 MET cc_start: -0.0986 (mmt) cc_final: -0.1617 (mmt) REVERT: G 2 ILE cc_start: 0.3257 (OUTLIER) cc_final: 0.3006 (tt) REVERT: H 38 ARG cc_start: 0.4486 (ttp-170) cc_final: 0.3706 (tmt170) REVERT: D 2 MET cc_start: 0.2061 (OUTLIER) cc_final: 0.1125 (tmm) REVERT: E 173 TYR cc_start: 0.5008 (m-80) cc_final: 0.4749 (m-80) REVERT: A 449 TYR cc_start: 0.8509 (m-80) cc_final: 0.8080 (m-10) REVERT: A 456 PHE cc_start: 0.7531 (m-80) cc_final: 0.7267 (m-80) REVERT: A 1002 GLN cc_start: 0.8378 (tm-30) cc_final: 0.7933 (tm-30) REVERT: B 392 PHE cc_start: 0.8970 (m-80) cc_final: 0.8568 (m-80) REVERT: C 63 THR cc_start: 0.8023 (OUTLIER) cc_final: 0.7731 (m) REVERT: C 104 TRP cc_start: 0.8678 (m-90) cc_final: 0.8288 (m-10) REVERT: C 177 MET cc_start: 0.4499 (mtt) cc_final: 0.4059 (mtt) REVERT: C 489 TYR cc_start: 0.6286 (m-80) cc_final: 0.6078 (m-80) REVERT: C 1031 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.7474 (mp0) outliers start: 53 outliers final: 37 residues processed: 159 average time/residue: 0.4631 time to fit residues: 121.7991 Evaluate side-chains 158 residues out of total 3622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 117 time to evaluate : 3.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 2 ILE Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 71 PHE Chi-restraints excluded: chain D residue 2 MET Chi-restraints excluded: chain D residue 66 ARG Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1148 PHE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 359 optimal weight: 2.9990 chunk 378 optimal weight: 0.4980 chunk 345 optimal weight: 20.0000 chunk 368 optimal weight: 6.9990 chunk 221 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 chunk 289 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 332 optimal weight: 4.9990 chunk 348 optimal weight: 5.9990 chunk 366 optimal weight: 2.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 34227 Z= 0.262 Angle : 0.576 15.662 46584 Z= 0.287 Chirality : 0.043 0.233 5502 Planarity : 0.004 0.114 5902 Dihedral : 6.789 82.414 6198 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.92 % Favored : 92.84 % Rotamer: Outliers : 1.49 % Allowed : 14.62 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.13), residues: 4106 helix: 2.60 (0.21), residues: 618 sheet: -0.41 (0.16), residues: 1081 loop : -1.73 (0.12), residues: 2407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 104 HIS 0.003 0.001 HIS C1101 PHE 0.018 0.001 PHE A 238 TYR 0.022 0.001 TYR A 904 ARG 0.004 0.000 ARG C1107 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8212 Ramachandran restraints generated. 4106 Oldfield, 0 Emsley, 4106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8212 Ramachandran restraints generated. 4106 Oldfield, 0 Emsley, 4106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 3622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 117 time to evaluate : 3.701 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: F 73 MET cc_start: -0.0962 (mmt) cc_final: -0.1595 (mmt) REVERT: G 2 ILE cc_start: 0.3354 (OUTLIER) cc_final: 0.3117 (tt) REVERT: H 38 ARG cc_start: 0.4547 (ttp-170) cc_final: 0.3737 (tmt170) REVERT: D 2 MET cc_start: 0.2050 (OUTLIER) cc_final: 0.1686 (tmm) REVERT: A 456 PHE cc_start: 0.7526 (m-80) cc_final: 0.7271 (m-80) REVERT: A 1002 GLN cc_start: 0.8417 (tm-30) cc_final: 0.7973 (tm-30) REVERT: B 392 PHE cc_start: 0.8996 (m-80) cc_final: 0.8586 (m-80) REVERT: C 63 THR cc_start: 0.8032 (OUTLIER) cc_final: 0.7727 (m) REVERT: C 104 TRP cc_start: 0.8669 (m-90) cc_final: 0.8293 (m-10) REVERT: C 177 MET cc_start: 0.4498 (mtt) cc_final: 0.4000 (mtt) REVERT: C 489 TYR cc_start: 0.6370 (m-80) cc_final: 0.6168 (m-80) REVERT: C 1031 GLU cc_start: 0.8664 (OUTLIER) cc_final: 0.7469 (mp0) outliers start: 54 outliers final: 41 residues processed: 155 average time/residue: 0.4936 time to fit residues: 126.8440 Evaluate side-chains 160 residues out of total 3622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 115 time to evaluate : 3.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 2 ILE Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 71 PHE Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain D residue 2 MET Chi-restraints excluded: chain D residue 66 ARG Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1148 PHE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 241 optimal weight: 40.0000 chunk 389 optimal weight: 3.9990 chunk 237 optimal weight: 9.9990 chunk 184 optimal weight: 0.8980 chunk 270 optimal weight: 1.9990 chunk 408 optimal weight: 2.9990 chunk 375 optimal weight: 1.9990 chunk 325 optimal weight: 30.0000 chunk 33 optimal weight: 6.9990 chunk 251 optimal weight: 5.9990 chunk 199 optimal weight: 10.0000 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 197 ASN ** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 34227 Z= 0.287 Angle : 0.587 13.795 46584 Z= 0.293 Chirality : 0.043 0.232 5502 Planarity : 0.004 0.116 5902 Dihedral : 6.806 81.045 6198 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.89 % Favored : 92.86 % Rotamer: Outliers : 1.35 % Allowed : 14.89 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % 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: -1.03 (0.13), residues: 4106 helix: 2.39 (0.21), residues: 626 sheet: -0.43 (0.16), residues: 1070 loop : -1.73 (0.12), residues: 2410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 886 HIS 0.002 0.001 HIS C1048 PHE 0.020 0.001 PHE A 238 TYR 0.023 0.001 TYR A 904 ARG 0.006 0.000 ARG C1107 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8212 Ramachandran restraints generated. 4106 Oldfield, 0 Emsley, 4106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8212 Ramachandran restraints generated. 4106 Oldfield, 0 Emsley, 4106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 3622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 119 time to evaluate : 3.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 73 MET cc_start: -0.0955 (mmt) cc_final: -0.1599 (mmt) REVERT: G 2 ILE cc_start: 0.3466 (OUTLIER) cc_final: 0.3240 (tt) REVERT: H 38 ARG cc_start: 0.4584 (ttp-170) cc_final: 0.3780 (tmt170) REVERT: H 108 MET cc_start: 0.7583 (mtm) cc_final: 0.7368 (mmt) REVERT: D 2 MET cc_start: 0.2020 (OUTLIER) cc_final: 0.1506 (tmm) REVERT: A 456 PHE cc_start: 0.7518 (m-80) cc_final: 0.7271 (m-80) REVERT: A 1002 GLN cc_start: 0.8442 (tm-30) cc_final: 0.7988 (tm-30) REVERT: B 392 PHE cc_start: 0.8979 (m-80) cc_final: 0.8608 (m-80) REVERT: C 63 THR cc_start: 0.8042 (OUTLIER) cc_final: 0.7751 (m) REVERT: C 104 TRP cc_start: 0.8697 (m-90) cc_final: 0.8374 (m-10) REVERT: C 132 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.8183 (pm20) REVERT: C 177 MET cc_start: 0.4597 (mtt) cc_final: 0.4054 (mtt) REVERT: C 1031 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.7497 (mp0) outliers start: 49 outliers final: 39 residues processed: 151 average time/residue: 0.4742 time to fit residues: 119.7946 Evaluate side-chains 159 residues out of total 3622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 115 time to evaluate : 3.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 2 ILE Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 71 PHE Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain D residue 2 MET Chi-restraints excluded: chain D residue 66 ARG Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1148 PHE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 258 optimal weight: 0.9980 chunk 346 optimal weight: 7.9990 chunk 99 optimal weight: 5.9990 chunk 299 optimal weight: 0.6980 chunk 48 optimal weight: 6.9990 chunk 90 optimal weight: 5.9990 chunk 325 optimal weight: 30.0000 chunk 136 optimal weight: 0.0980 chunk 334 optimal weight: 3.9990 chunk 41 optimal weight: 10.0000 chunk 60 optimal weight: 5.9990 overall best weight: 2.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 197 ASN ** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.106142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.066135 restraints weight = 154294.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.067860 restraints weight = 75626.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.068318 restraints weight = 45895.666| |-----------------------------------------------------------------------------| r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 34227 Z= 0.287 Angle : 0.585 13.744 46584 Z= 0.292 Chirality : 0.043 0.232 5502 Planarity : 0.004 0.116 5902 Dihedral : 6.786 81.360 6198 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.16 % Favored : 92.62 % Rotamer: Outliers : 1.33 % Allowed : 15.17 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % 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: -1.02 (0.13), residues: 4106 helix: 2.40 (0.21), residues: 625 sheet: -0.42 (0.16), residues: 1060 loop : -1.73 (0.12), residues: 2421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 886 HIS 0.003 0.001 HIS C1101 PHE 0.019 0.001 PHE A 238 TYR 0.022 0.001 TYR A 904 ARG 0.006 0.000 ARG C1107 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6495.43 seconds wall clock time: 120 minutes 34.29 seconds (7234.29 seconds total)