Starting phenix.real_space_refine on Sat Nov 18 22:00:09 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m6f_23694/11_2023/7m6f_23694_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m6f_23694/11_2023/7m6f_23694.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m6f_23694/11_2023/7m6f_23694.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m6f_23694/11_2023/7m6f_23694.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m6f_23694/11_2023/7m6f_23694_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m6f_23694/11_2023/7m6f_23694_neut.pdb" } resolution = 3.9 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= 0.016 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 106 5.16 5 C 15415 2.51 5 N 4144 2.21 5 O 4639 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1017": "OE1" <-> "OE2" Residue "A TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 979": "OD1" <-> "OD2" Residue "B TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1139": "OD1" <-> "OD2" Residue "E PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 614": "OD1" <-> "OD2" Residue "E PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 24304 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 7064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 998, 7064 Classifications: {'peptide': 998} Incomplete info: {'truncation_to_alanine': 244} Link IDs: {'PTRANS': 53, 'TRANS': 944} Chain breaks: 7 Unresolved non-hydrogen bonds: 747 Unresolved non-hydrogen angles: 959 Unresolved non-hydrogen dihedrals: 582 Unresolved non-hydrogen chiralities: 75 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 2, 'TYR:plan': 9, 'ASN:plan1': 29, 'ASP:plan': 25, 'PHE:plan': 8, 'GLU:plan': 17, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 437 Chain: "B" Number of atoms: 7026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 998, 7026 Classifications: {'peptide': 998} Incomplete info: {'truncation_to_alanine': 255} Link IDs: {'PTRANS': 53, 'TRANS': 944} Chain breaks: 7 Unresolved non-hydrogen bonds: 788 Unresolved non-hydrogen angles: 1010 Unresolved non-hydrogen dihedrals: 620 Unresolved non-hydrogen chiralities: 77 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 2, 'TYR:plan': 10, 'ASN:plan1': 29, 'ASP:plan': 25, 'PHE:plan': 10, 'GLU:plan': 18, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 460 Chain: "C" Number of atoms: 596 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 118, 591 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 93} Link IDs: {'PTRANS': 8, 'TRANS': 109} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 337 Unresolved non-hydrogen angles: 441 Unresolved non-hydrogen dihedrals: 289 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 6, 'ASN:plan1': 4, 'TRP:plan': 4, 'ASP:plan': 7, 'PHE:plan': 4, 'GLU:plan': 3, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 197 Conformer: "B" Number of residues, atoms: 118, 591 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 93} Link IDs: {'PTRANS': 8, 'TRANS': 109} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 337 Unresolved non-hydrogen angles: 441 Unresolved non-hydrogen dihedrals: 289 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 6, 'ASN:plan1': 4, 'TRP:plan': 4, 'ASP:plan': 7, 'PHE:plan': 4, 'GLU:plan': 3, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 197 bond proxies already assigned to first conformer: 589 Chain: "D" Number of atoms: 538 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 108, 529 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 84} Link IDs: {'PTRANS': 7, 'TRANS': 100} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 289 Unresolved non-hydrogen angles: 378 Unresolved non-hydrogen dihedrals: 248 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 4, 'TYR:plan': 7, 'ASN:plan1': 3, 'TRP:plan': 2, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 162 Conformer: "B" Number of residues, atoms: 108, 529 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 84} Link IDs: {'PTRANS': 7, 'TRANS': 100} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 289 Unresolved non-hydrogen angles: 378 Unresolved non-hydrogen dihedrals: 248 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 4, 'TYR:plan': 7, 'ASN:plan1': 3, 'TRP:plan': 2, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 162 bond proxies already assigned to first conformer: 518 Chain: "E" Number of atoms: 7064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 998, 7064 Classifications: {'peptide': 998} Incomplete info: {'truncation_to_alanine': 244} Link IDs: {'PTRANS': 53, 'TRANS': 944} Chain breaks: 7 Unresolved non-hydrogen bonds: 747 Unresolved non-hydrogen angles: 959 Unresolved non-hydrogen dihedrals: 582 Unresolved non-hydrogen chiralities: 75 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 2, 'TYR:plan': 9, 'ASN:plan1': 29, 'ASP:plan': 25, 'PHE:plan': 8, 'GLU:plan': 17, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 437 Chain: "H" Number of atoms: 596 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 118, 591 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 93} Link IDs: {'PTRANS': 8, 'TRANS': 109} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 337 Unresolved non-hydrogen angles: 441 Unresolved non-hydrogen dihedrals: 289 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 6, 'ASN:plan1': 4, 'TRP:plan': 4, 'ASP:plan': 7, 'PHE:plan': 4, 'GLU:plan': 3, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 197 Conformer: "B" Number of residues, atoms: 118, 591 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 93} Link IDs: {'PTRANS': 8, 'TRANS': 109} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 337 Unresolved non-hydrogen angles: 441 Unresolved non-hydrogen dihedrals: 289 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 6, 'ASN:plan1': 4, 'TRP:plan': 4, 'ASP:plan': 7, 'PHE:plan': 4, 'GLU:plan': 3, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 197 bond proxies already assigned to first conformer: 589 Chain: "L" Number of atoms: 538 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 108, 529 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 84} Link IDs: {'PTRANS': 7, 'TRANS': 100} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 289 Unresolved non-hydrogen angles: 378 Unresolved non-hydrogen dihedrals: 248 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 4, 'TYR:plan': 7, 'ASN:plan1': 3, 'TRP:plan': 2, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 162 Conformer: "B" Number of residues, atoms: 108, 529 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 84} Link IDs: {'PTRANS': 7, 'TRANS': 100} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 289 Unresolved non-hydrogen angles: 378 Unresolved non-hydrogen dihedrals: 248 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 4, 'TYR:plan': 7, 'ASN:plan1': 3, 'TRP:plan': 2, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 162 bond proxies already assigned to first conformer: 518 Chain: "F" 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 chiralities: 2 Chain: "G" 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 chiralities: 2 Chain: "I" 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 chiralities: 2 Chain: "K" 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 chiralities: 2 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 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 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 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 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 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 chiralities: 2 Chain: "S" 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 chiralities: 2 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 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 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 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 chiralities: 2 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Chain: "E" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N ASER C 17 " occ=0.35 ... (8 atoms not shown) pdb=" CB BSER C 17 " occ=0.65 residue: pdb=" N AARG D 54 " occ=0.46 ... (8 atoms not shown) pdb=" CB BARG D 54 " occ=0.54 residue: pdb=" N ASER H 17 " occ=0.35 ... (8 atoms not shown) pdb=" CB BSER H 17 " occ=0.65 residue: pdb=" N AARG L 54 " occ=0.46 ... (8 atoms not shown) pdb=" CB BARG L 54 " occ=0.54 Time building chain proxies: 14.71, per 1000 atoms: 0.61 Number of scatterers: 24304 At special positions: 0 Unit cell: (132.088, 134.695, 208.56, 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 106 16.00 O 4639 8.00 N 4144 7.00 C 15415 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 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=2.04 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=2.03 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=2.04 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 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=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 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=2.02 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 166 " distance=2.03 Simple disulfide: pdb=" SG CYS E 291 " - pdb=" SG CYS E 301 " distance=2.03 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.03 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.03 Simple disulfide: pdb=" SG CYS E 538 " - pdb=" SG CYS E 590 " distance=2.03 Simple disulfide: pdb=" SG CYS E 617 " - pdb=" SG CYS E 649 " distance=2.03 Simple disulfide: pdb=" SG CYS E 662 " - pdb=" SG CYS E 671 " distance=2.03 Simple disulfide: pdb=" SG CYS E 738 " - pdb=" SG CYS E 760 " distance=2.04 Simple disulfide: pdb=" SG CYS E 743 " - pdb=" SG CYS E 749 " distance=2.03 Simple disulfide: pdb=" SG CYS E1032 " - pdb=" SG CYS E1043 " distance=2.03 Simple disulfide: pdb=" SG CYS E1082 " - pdb=" SG CYS E1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " 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 Atom "HETATM23574 O5 NAG N 1 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG K 1 " - " NAG K 2 " " 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 T 1 " - " NAG T 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " NAG-ASN " NAG A1301 " - " ASN A 603 " " NAG A1302 " - " ASN A 657 " " NAG A1303 " - " ASN A1074 " " NAG A1304 " - " ASN A 61 " " NAG A1305 " - " ASN A 616 " " NAG A1306 " - " ASN A 122 " " NAG A1307 " - " ASN A 165 " " NAG A1308 " - " ASN A 234 " " NAG A1309 " - " ASN A 331 " " NAG A1310 " - " ASN A 282 " " NAG A1311 " - " ASN A 709 " " NAG B1301 " - " ASN B 282 " " NAG B1302 " - " ASN B 603 " " NAG B1303 " - " ASN B 657 " " NAG B1304 " - " ASN B1074 " " NAG B1305 " - " ASN B 61 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 122 " " NAG B1308 " - " ASN B 165 " " NAG B1309 " - " ASN B 234 " " NAG B1310 " - " ASN B 331 " " NAG B1311 " - " ASN B 709 " " NAG E1301 " - " ASN E 282 " " NAG E1302 " - " ASN E 603 " " NAG E1303 " - " ASN E 657 " " NAG E1304 " - " ASN E1074 " " NAG E1305 " - " ASN E 61 " " NAG E1306 " - " ASN E 122 " " NAG E1307 " - " ASN E 165 " " NAG E1308 " - " ASN E 234 " " NAG E1309 " - " ASN E 331 " " NAG E1310 " - " ASN E 709 " " NAG E1311 " - " ASN E 616 " " NAG F 1 " - " ASN A1098 " " NAG G 1 " - " ASN E1098 " " NAG I 1 " - " ASN A 717 " " NAG K 1 " - " ASN A1134 " " NAG M 1 " - " ASN A 343 " " NAG N 1 " - " ASN A 801 " " NAG O 1 " - " ASN B 717 " " NAG P 1 " - " ASN B1098 " " NAG Q 1 " - " ASN B1134 " " NAG R 1 " - " ASN B 343 " " NAG S 1 " - " ASN B 801 " " NAG T 1 " - " ASN E 717 " " NAG V 1 " - " ASN E1134 " " NAG W 1 " - " ASN E 343 " " NAG X 1 " - " ASN E 801 " Time building additional restraints: 11.14 Conformation dependent library (CDL) restraints added in 5.8 seconds 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6418 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 57 sheets defined 23.2% alpha, 27.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.19 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.861A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.064A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 390 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.137A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.642A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 753 Processing helix chain 'A' and resid 754 through 757 Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.701A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.332A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 967 removed outlier: 3.575A pdb=" N SER A 967 " --> pdb=" O VAL A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 5.040A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1145 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 351 through 353 No H-bonds generated for 'chain 'B' and resid 351 through 353' Processing helix chain 'B' and resid 364 through 371 removed outlier: 4.108A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 390 Processing helix chain 'B' and resid 404 through 408 removed outlier: 4.485A pdb=" N ARG B 408 " --> pdb=" O GLY B 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 404 through 408' Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.504A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 753 Processing helix chain 'B' and resid 754 through 757 Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.698A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.727A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.573A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 967 Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.560A pdb=" N LEU B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.982A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 Processing helix chain 'E' and resid 294 through 304 Processing helix chain 'E' and resid 338 through 343 Processing helix chain 'E' and resid 349 through 353 removed outlier: 3.832A pdb=" N TRP E 353 " --> pdb=" O VAL E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 364 through 371 removed outlier: 4.074A pdb=" N LEU E 368 " --> pdb=" O ASP E 364 " (cutoff:3.500A) Processing helix chain 'E' and resid 386 through 390 Processing helix chain 'E' and resid 405 through 410 removed outlier: 4.219A pdb=" N ARG E 408 " --> pdb=" O ASP E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 422 Processing helix chain 'E' and resid 438 through 443 removed outlier: 3.580A pdb=" N SER E 443 " --> pdb=" O ASN E 439 " (cutoff:3.500A) Processing helix chain 'E' and resid 502 through 505 Processing helix chain 'E' and resid 737 through 743 Processing helix chain 'E' and resid 746 through 753 Processing helix chain 'E' and resid 754 through 757 Processing helix chain 'E' and resid 758 through 783 removed outlier: 3.644A pdb=" N ASP E 775 " --> pdb=" O ALA E 771 " (cutoff:3.500A) Processing helix chain 'E' and resid 816 through 825 Processing helix chain 'E' and resid 866 through 885 Processing helix chain 'E' and resid 897 through 908 Processing helix chain 'E' and resid 912 through 919 removed outlier: 4.376A pdb=" N LEU E 916 " --> pdb=" O THR E 912 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TYR E 917 " --> pdb=" O GLN E 913 " (cutoff:3.500A) Processing helix chain 'E' and resid 919 through 941 removed outlier: 3.518A pdb=" N GLN E 935 " --> pdb=" O ILE E 931 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP E 936 " --> pdb=" O GLY E 932 " (cutoff:3.500A) Processing helix chain 'E' and resid 945 through 967 Processing helix chain 'E' and resid 976 through 984 Processing helix chain 'E' and resid 985 through 1033 removed outlier: 5.048A pdb=" N VAL E 991 " --> pdb=" O PRO E 987 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN E 992 " --> pdb=" O GLU E 988 " (cutoff:3.500A) Processing helix chain 'E' and resid 1140 through 1145 Processing helix chain 'H' and resid 83 through 87 removed outlier: 4.053A pdb=" N THR H 87 " --> pdb=" O PRO H 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 27B through 31 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.514A pdb=" N GLU L 83 " --> pdb=" O ALA L 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 3.547A pdb=" N VAL A 62 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU A 189 " --> pdb=" O THR A 208 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.377A pdb=" N ASP E 574 " --> pdb=" O ILE E 587 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N GLU E 324 " --> pdb=" O ASN E 540 " (cutoff:3.500A) removed outlier: 8.651A pdb=" N ASN E 542 " --> pdb=" O GLU E 324 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N ILE E 326 " --> pdb=" O ASN E 542 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 7.473A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.854A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TRP A 104 " --> pdb=" O ILE A 119 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE A 119 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N VAL A 126 " --> pdb=" O TYR A 170 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N TYR A 170 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N CYS A 136 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N TYR A 160 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ASP A 138 " --> pdb=" O ARG A 158 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N ARG A 158 " --> pdb=" O ASP A 138 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.967A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.352A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.578A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.303A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.270A pdb=" N TYR A 660 " --> pdb=" O SER A 698 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.578A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.531A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 728 removed outlier: 5.907A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.549A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.423A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 30 removed outlier: 7.733A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU B 189 " --> pdb=" O THR B 208 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 48 through 55 removed outlier: 7.975A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.563A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N TRP B 104 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE B 119 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 11.174A pdb=" N VAL B 126 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 9.508A pdb=" N GLU B 169 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.104A pdb=" N ILE B 128 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N THR B 167 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N VAL B 130 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N ASN B 165 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 12.391A pdb=" N ASP B 138 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 11.745A pdb=" N PHE B 157 " --> pdb=" O ASP B 138 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.819A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 325 through 328 removed outlier: 4.837A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 348 through 349 removed outlier: 7.279A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 9.590A pdb=" N ARG B 403 " --> pdb=" O ALA B 348 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 348 through 349 removed outlier: 7.279A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 9.590A pdb=" N ARG B 403 " --> pdb=" O ALA B 348 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA B 435 " --> pdb=" O THR B 376 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N THR B 376 " --> pdb=" O ALA B 435 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 361 through 362 removed outlier: 7.001A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC9, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.588A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.886A pdb=" N ALA B 701 " --> pdb=" O ILE E 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.541A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 718 through 728 removed outlier: 3.514A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.440A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.223A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 3 through 7 removed outlier: 3.565A pdb=" N LEU C 18 " --> pdb=" O MET C 82 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 11 through 12 Processing sheet with id=AD9, first strand: chain 'C' and resid 57 through 58 removed outlier: 5.786A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 9 through 11 removed outlier: 7.083A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 19 through 24 removed outlier: 3.882A pdb=" N VAL D 19 " --> pdb=" O ILE D 75 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE D 75 " --> pdb=" O VAL D 19 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 89 through 91 Processing sheet with id=AE4, first strand: chain 'E' and resid 28 through 30 removed outlier: 3.786A pdb=" N VAL E 62 " --> pdb=" O THR E 29 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N ASN E 61 " --> pdb=" O TYR E 269 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N TYR E 269 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA E 93 " --> pdb=" O TYR E 266 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N PHE E 201 " --> pdb=" O ASP E 228 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ASP E 228 " --> pdb=" O PHE E 201 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ILE E 203 " --> pdb=" O LEU E 226 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 48 through 55 removed outlier: 3.732A pdb=" N ASP E 53 " --> pdb=" O ARG E 273 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG E 273 " --> pdb=" O ASP E 53 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLN E 271 " --> pdb=" O PHE E 55 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N THR E 274 " --> pdb=" O ASP E 290 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N ASP E 290 " --> pdb=" O THR E 274 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N LEU E 276 " --> pdb=" O ALA E 288 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ALA E 288 " --> pdb=" O LEU E 276 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N LYS E 278 " --> pdb=" O THR E 286 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 84 through 85 removed outlier: 6.454A pdb=" N ARG E 102 " --> pdb=" O ASN E 121 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL E 120 " --> pdb=" O VAL E 127 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ASN E 122 " --> pdb=" O ASN E 125 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N VAL E 126 " --> pdb=" O TYR E 170 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N TYR E 170 " --> pdb=" O VAL E 126 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE E 128 " --> pdb=" O PHE E 168 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N PHE E 168 " --> pdb=" O ILE E 128 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N VAL E 130 " --> pdb=" O CYS E 166 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N CYS E 166 " --> pdb=" O VAL E 130 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER E 162 " --> pdb=" O GLN E 134 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N CYS E 136 " --> pdb=" O TYR E 160 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N TYR E 160 " --> pdb=" O CYS E 136 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ASP E 138 " --> pdb=" O ARG E 158 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N ARG E 158 " --> pdb=" O ASP E 138 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 311 through 319 removed outlier: 5.649A pdb=" N ILE E 312 " --> pdb=" O THR E 599 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N THR E 599 " --> pdb=" O ILE E 312 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N GLN E 314 " --> pdb=" O VAL E 597 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL E 597 " --> pdb=" O GLN E 314 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N GLY E 594 " --> pdb=" O GLN E 613 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 354 through 358 removed outlier: 4.067A pdb=" N ASN E 354 " --> pdb=" O SER E 399 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N SER E 399 " --> pdb=" O ASN E 354 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS E 356 " --> pdb=" O ALA E 397 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AF1, first strand: chain 'E' and resid 473 through 474 removed outlier: 3.609A pdb=" N TYR E 473 " --> pdb=" O TYR E 489 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYR E 489 " --> pdb=" O TYR E 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'E' and resid 654 through 655 removed outlier: 6.683A pdb=" N ILE E 670 " --> pdb=" O ILE E 666 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 711 through 715 Processing sheet with id=AF4, first strand: chain 'E' and resid 718 through 728 removed outlier: 5.880A pdb=" N TYR E1067 " --> pdb=" O HIS E1048 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N HIS E1048 " --> pdb=" O TYR E1067 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 733 through 736 removed outlier: 4.504A pdb=" N LYS E 733 " --> pdb=" O LEU E 861 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 1120 through 1125 removed outlier: 4.251A pdb=" N ALA E1087 " --> pdb=" O SER E1123 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AF8, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AF9, first strand: chain 'H' and resid 57 through 58 removed outlier: 5.786A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'L' and resid 9 through 11 removed outlier: 7.082A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'L' and resid 19 through 22 removed outlier: 3.883A pdb=" N VAL L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE L 75 " --> pdb=" O VAL L 19 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'L' and resid 89 through 90 1113 hydrogen bonds defined for protein. 3019 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 12.53 Time building geometry restraints manager: 11.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7542 1.33 - 1.46: 6324 1.46 - 1.59: 10797 1.59 - 1.72: 0 1.72 - 1.84: 130 Bond restraints: 24793 Sorted by residual: bond pdb=" C1 NAG N 2 " pdb=" O5 NAG N 2 " ideal model delta sigma weight residual 1.406 1.523 -0.117 2.00e-02 2.50e+03 3.40e+01 bond pdb=" C1 NAG W 1 " pdb=" O5 NAG W 1 " ideal model delta sigma weight residual 1.406 1.484 -0.078 2.00e-02 2.50e+03 1.51e+01 bond pdb=" C1 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.406 1.478 -0.072 2.00e-02 2.50e+03 1.31e+01 bond pdb=" N ASN A 282 " pdb=" CA ASN A 282 " ideal model delta sigma weight residual 1.456 1.498 -0.043 1.33e-02 5.65e+03 1.03e+01 bond pdb=" N GLN D 17 " pdb=" CA GLN D 17 " ideal model delta sigma weight residual 1.454 1.491 -0.037 1.17e-02 7.31e+03 9.88e+00 ... (remaining 24788 not shown) Histogram of bond angle deviations from ideal: 84.66 - 94.54: 2 94.54 - 104.42: 505 104.42 - 114.29: 14660 114.29 - 124.17: 18314 124.17 - 134.05: 520 Bond angle restraints: 34001 Sorted by residual: angle pdb=" C ASN A 709 " pdb=" CA ASN A 709 " pdb=" CB ASN A 709 " ideal model delta sigma weight residual 109.95 84.66 25.29 1.99e+00 2.53e-01 1.61e+02 angle pdb=" C ASN E 343 " pdb=" CA ASN E 343 " pdb=" CB ASN E 343 " ideal model delta sigma weight residual 111.02 123.08 -12.06 1.61e+00 3.86e-01 5.61e+01 angle pdb=" N ASN A 709 " pdb=" CA ASN A 709 " pdb=" CB ASN A 709 " ideal model delta sigma weight residual 110.41 120.86 -10.45 1.68e+00 3.54e-01 3.87e+01 angle pdb=" CG ARG B 273 " pdb=" CD ARG B 273 " pdb=" NE ARG B 273 " ideal model delta sigma weight residual 112.00 99.01 12.99 2.20e+00 2.07e-01 3.49e+01 angle pdb=" CA ASN A 709 " pdb=" CB ASN A 709 " pdb=" CG ASN A 709 " ideal model delta sigma weight residual 112.60 118.44 -5.84 1.00e+00 1.00e+00 3.41e+01 ... (remaining 33996 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 13574 17.92 - 35.84: 412 35.84 - 53.76: 91 53.76 - 71.68: 25 71.68 - 89.60: 22 Dihedral angle restraints: 14124 sinusoidal: 4170 harmonic: 9954 Sorted by residual: dihedral pdb=" C ASN A 709 " pdb=" N ASN A 709 " pdb=" CA ASN A 709 " pdb=" CB ASN A 709 " ideal model delta harmonic sigma weight residual -122.60 -98.28 -24.32 0 2.50e+00 1.60e-01 9.47e+01 dihedral pdb=" CB CYS B 291 " pdb=" SG CYS B 291 " pdb=" SG CYS B 301 " pdb=" CB CYS B 301 " ideal model delta sinusoidal sigma weight residual 93.00 175.66 -82.66 1 1.00e+01 1.00e-02 8.37e+01 dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual -86.00 -152.16 66.16 1 1.00e+01 1.00e-02 5.72e+01 ... (remaining 14121 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.264: 4183 0.264 - 0.528: 15 0.528 - 0.791: 3 0.791 - 1.055: 0 1.055 - 1.319: 2 Chirality restraints: 4203 Sorted by residual: chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-02 2.50e+03 8.52e+01 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-02 2.50e+03 4.82e+01 chirality pdb=" C4 NAG N 1 " pdb=" C3 NAG N 1 " pdb=" C5 NAG N 1 " pdb=" O4 NAG N 1 " both_signs ideal model delta sigma weight residual False -2.53 -1.21 -1.32 2.00e-01 2.50e+01 4.35e+01 ... (remaining 4200 not shown) Planarity restraints: 4487 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG G 1 " 0.184 2.00e-02 2.50e+03 1.53e-01 2.93e+02 pdb=" C7 NAG G 1 " -0.052 2.00e-02 2.50e+03 pdb=" C8 NAG G 1 " 0.134 2.00e-02 2.50e+03 pdb=" N2 NAG G 1 " -0.250 2.00e-02 2.50e+03 pdb=" O7 NAG G 1 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 1 " -0.154 2.00e-02 2.50e+03 1.28e-01 2.05e+02 pdb=" C7 NAG F 1 " 0.043 2.00e-02 2.50e+03 pdb=" C8 NAG F 1 " -0.114 2.00e-02 2.50e+03 pdb=" N2 NAG F 1 " 0.207 2.00e-02 2.50e+03 pdb=" O7 NAG F 1 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG G 2 " -0.145 2.00e-02 2.50e+03 1.19e-01 1.78e+02 pdb=" C7 NAG G 2 " 0.040 2.00e-02 2.50e+03 pdb=" C8 NAG G 2 " -0.108 2.00e-02 2.50e+03 pdb=" N2 NAG G 2 " 0.191 2.00e-02 2.50e+03 pdb=" O7 NAG G 2 " 0.022 2.00e-02 2.50e+03 ... (remaining 4484 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.48: 104 2.48 - 3.08: 16669 3.08 - 3.69: 35195 3.69 - 4.29: 49399 4.29 - 4.90: 82499 Nonbonded interactions: 183866 Sorted by model distance: nonbonded pdb=" OH TYR A 421 " pdb=" CG PRO H 53 " model vdw 1.869 3.440 nonbonded pdb=" OH TYR A 421 " pdb=" CD PRO H 53 " model vdw 1.875 3.440 nonbonded pdb=" OH TYR A 421 " pdb=" N GLY H 54 " model vdw 1.925 2.520 nonbonded pdb=" OH TYR A 421 " pdb=" CB PRO H 53 " model vdw 2.019 3.440 nonbonded pdb=" OD1 ASN B 122 " pdb=" N2 NAG B1307 " model vdw 2.079 2.520 ... (remaining 183861 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 59 or (resid 60 and (name N or name CA or name \ C or name O or name CB )) or resid 61 through 166 or (resid 167 through 188 and \ (name N or name CA or name C or name O or name CB )) or resid 189 through 374 or \ (resid 375 through 378 and (name N or name CA or name C or name O or name CB )) \ or resid 379 through 920 or (resid 921 and (name N or name CA or name C or name \ O or name CB )) or resid 922 through 1145 or resid 1301 through 1311)) selection = (chain 'B' and (resid 27 through 510 or (resid 511 through 512 and (name N or na \ me CA or name C or name O or name CB )) or resid 513 through 1145 or resid 1301 \ through 1311)) selection = (chain 'E' and (resid 27 through 59 or (resid 60 and (name N or name CA or name \ C or name O or name CB )) or resid 61 through 166 or (resid 167 through 188 and \ (name N or name CA or name C or name O or name CB )) or resid 189 through 374 or \ (resid 375 through 378 and (name N or name CA or name C or name O or name CB )) \ or resid 379 through 920 or (resid 921 and (name N or name CA or name C or name \ O or name CB )) or resid 922 through 1145 or resid 1301 through 1311)) } ncs_group { reference = (chain 'C' and (resid 2 through 16 or resid 18 through 116)) selection = (chain 'H' and (resid 2 through 16 or resid 18 through 116)) } ncs_group { reference = (chain 'D' and (resid 3 through 9 or resid 12 through 19 or resid 21 through 53 \ or resid 55 through 106)) selection = (chain 'L' and (resid 3 through 9 or resid 12 through 19 or resid 21 through 53 \ or resid 55 through 106)) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'V' selection = chain 'W' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.18 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: 4.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 17.700 Check model and map are aligned: 0.360 Set scattering table: 0.220 Process input model: 73.590 Find NCS groups from input model: 1.650 Set up NCS constraints: 0.310 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:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 100.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 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 : 0.006 0.117 24793 Z= 0.422 Angle : 1.003 25.286 34001 Z= 0.579 Chirality : 0.069 1.319 4203 Planarity : 0.006 0.153 4439 Dihedral : 10.466 89.597 7583 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.90 % Favored : 96.07 % Rotamer: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.14), residues: 3402 helix: 0.98 (0.19), residues: 628 sheet: 0.62 (0.19), residues: 737 loop : 0.00 (0.13), residues: 2037 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 199 time to evaluate : 2.665 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 199 average time/residue: 0.3095 time to fit residues: 104.8353 Evaluate side-chains 94 residues out of total 2991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 2.772 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.8309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 286 optimal weight: 0.5980 chunk 256 optimal weight: 40.0000 chunk 142 optimal weight: 0.2980 chunk 87 optimal weight: 5.9990 chunk 173 optimal weight: 3.9990 chunk 137 optimal weight: 1.9990 chunk 265 optimal weight: 0.9990 chunk 102 optimal weight: 9.9990 chunk 161 optimal weight: 0.9980 chunk 197 optimal weight: 8.9990 chunk 307 optimal weight: 5.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 926 GLN B 49 HIS B 641 ASN B1002 GLN B1135 ASN ** E 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 804 GLN E 935 GLN ** E 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1005 GLN E1135 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 24793 Z= 0.212 Angle : 0.659 11.914 34001 Z= 0.336 Chirality : 0.050 0.520 4203 Planarity : 0.004 0.059 4439 Dihedral : 4.478 24.744 3605 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.42 % Favored : 97.52 % Rotamer: Outliers : 1.05 % Allowed : 5.99 % Favored : 92.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.14), residues: 3402 helix: 2.04 (0.19), residues: 661 sheet: 0.79 (0.19), residues: 760 loop : -0.03 (0.14), residues: 1981 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 2991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 126 time to evaluate : 2.783 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 11 residues processed: 138 average time/residue: 0.2975 time to fit residues: 74.7081 Evaluate side-chains 104 residues out of total 2991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 93 time to evaluate : 2.784 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2425 time to fit residues: 8.6024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 171 optimal weight: 5.9990 chunk 95 optimal weight: 0.9990 chunk 256 optimal weight: 0.6980 chunk 209 optimal weight: 30.0000 chunk 84 optimal weight: 2.9990 chunk 308 optimal weight: 7.9990 chunk 333 optimal weight: 50.0000 chunk 274 optimal weight: 7.9990 chunk 305 optimal weight: 0.6980 chunk 105 optimal weight: 0.8980 chunk 247 optimal weight: 30.0000 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1010 GLN E 641 ASN ** E 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1135 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 24793 Z= 0.208 Angle : 0.576 8.980 34001 Z= 0.290 Chirality : 0.048 0.604 4203 Planarity : 0.004 0.049 4439 Dihedral : 4.102 22.723 3605 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.68 % Allowed : 8.73 % Favored : 90.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.14), residues: 3402 helix: 2.28 (0.20), residues: 664 sheet: 0.60 (0.18), residues: 755 loop : -0.06 (0.14), residues: 1983 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 2991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 108 time to evaluate : 2.871 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 5 residues processed: 118 average time/residue: 0.2966 time to fit residues: 63.4971 Evaluate side-chains 89 residues out of total 2991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 84 time to evaluate : 2.839 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2238 time to fit residues: 6.4250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 304 optimal weight: 5.9990 chunk 231 optimal weight: 10.0000 chunk 160 optimal weight: 10.0000 chunk 34 optimal weight: 9.9990 chunk 147 optimal weight: 0.7980 chunk 207 optimal weight: 5.9990 chunk 309 optimal weight: 1.9990 chunk 327 optimal weight: 10.0000 chunk 161 optimal weight: 0.9980 chunk 293 optimal weight: 6.9990 chunk 88 optimal weight: 0.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 926 GLN A1106 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN E 641 ASN ** E 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 901 GLN E1135 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 24793 Z= 0.259 Angle : 0.596 8.970 34001 Z= 0.301 Chirality : 0.048 0.626 4203 Planarity : 0.004 0.050 4439 Dihedral : 4.121 21.319 3605 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.63 % Allowed : 9.10 % Favored : 89.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.14), residues: 3402 helix: 2.16 (0.20), residues: 655 sheet: 0.38 (0.17), residues: 820 loop : -0.16 (0.14), residues: 1927 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 2991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 94 time to evaluate : 2.999 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 14 residues processed: 116 average time/residue: 0.2935 time to fit residues: 61.9444 Evaluate side-chains 89 residues out of total 2991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 75 time to evaluate : 3.010 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 14 outliers final: 1 residues processed: 14 average time/residue: 0.2283 time to fit residues: 9.8087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 272 optimal weight: 6.9990 chunk 186 optimal weight: 6.9990 chunk 4 optimal weight: 5.9990 chunk 243 optimal weight: 5.9990 chunk 135 optimal weight: 40.0000 chunk 279 optimal weight: 3.9990 chunk 226 optimal weight: 40.0000 chunk 0 optimal weight: 10.0000 chunk 167 optimal weight: 4.9990 chunk 294 optimal weight: 0.6980 chunk 82 optimal weight: 7.9990 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 949 GLN B 953 ASN B1002 GLN B1088 HIS B1135 ASN ** E 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1005 GLN E1135 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.4424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.132 24793 Z= 0.456 Angle : 0.733 13.821 34001 Z= 0.370 Chirality : 0.051 0.571 4203 Planarity : 0.005 0.047 4439 Dihedral : 4.712 24.381 3605 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.79 % Allowed : 10.09 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.14), residues: 3402 helix: 1.59 (0.20), residues: 671 sheet: 0.09 (0.17), residues: 817 loop : -0.34 (0.14), residues: 1914 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 2991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 79 time to evaluate : 2.818 Fit side-chains revert: symmetry clash outliers start: 34 outliers final: 15 residues processed: 104 average time/residue: 0.3079 time to fit residues: 58.0474 Evaluate side-chains 85 residues out of total 2991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 70 time to evaluate : 2.742 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 15 outliers final: 1 residues processed: 15 average time/residue: 0.2368 time to fit residues: 10.4985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 68.2141 > 50: distance: 24 - 94: 34.823 distance: 47 - 61: 36.563 distance: 53 - 61: 35.021 distance: 62 - 65: 41.834 distance: 63 - 64: 17.306 distance: 63 - 66: 39.068 distance: 66 - 67: 18.006 distance: 67 - 68: 5.615 distance: 67 - 70: 53.408 distance: 68 - 69: 30.482 distance: 68 - 71: 46.506 distance: 71 - 72: 3.982 distance: 72 - 73: 11.843 distance: 72 - 75: 32.379 distance: 73 - 74: 26.037 distance: 73 - 76: 12.910 distance: 76 - 77: 21.197 distance: 77 - 78: 18.230 distance: 77 - 80: 21.253 distance: 78 - 79: 9.465 distance: 78 - 81: 25.693 distance: 81 - 82: 21.174 distance: 82 - 83: 6.993 distance: 82 - 85: 20.361 distance: 83 - 84: 49.060 distance: 83 - 89: 13.795 distance: 85 - 86: 9.032 distance: 86 - 87: 20.345 distance: 86 - 88: 14.794 distance: 88 - 122: 22.908 distance: 89 - 90: 27.677 distance: 90 - 91: 35.204 distance: 90 - 93: 11.046 distance: 91 - 92: 34.198 distance: 91 - 95: 13.424 distance: 93 - 94: 12.594 distance: 95 - 96: 43.066 distance: 96 - 97: 45.880 distance: 96 - 99: 15.989 distance: 97 - 98: 36.408 distance: 101 - 104: 33.420 distance: 102 - 105: 5.310 distance: 105 - 106: 40.597 distance: 106 - 107: 21.719 distance: 106 - 109: 46.178 distance: 107 - 108: 6.554 distance: 107 - 110: 58.489 distance: 110 - 111: 38.469 distance: 111 - 112: 55.805 distance: 111 - 114: 19.551 distance: 112 - 115: 35.179