Starting phenix.real_space_refine on Tue Mar 19 22:16:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k4n_22668/03_2024/7k4n_22668.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k4n_22668/03_2024/7k4n_22668.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k4n_22668/03_2024/7k4n_22668.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k4n_22668/03_2024/7k4n_22668.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k4n_22668/03_2024/7k4n_22668.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k4n_22668/03_2024/7k4n_22668.pdb" } resolution = 3.3 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= 0.003 sd= 0.044 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 120 5.16 5 C 16036 2.51 5 N 4351 2.21 5 O 4846 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 808": "OD1" <-> "OD2" Residue "A TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1111": "OE1" <-> "OE2" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 808": "OD1" <-> "OD2" Residue "B TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1111": "OE1" <-> "OE2" Residue "B PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 808": "OD1" <-> "OD2" Residue "E TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 1111": "OE1" <-> "OE2" Residue "E PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 25353 Number of models: 1 Model: "" Number of chains: 27 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: "H" Number of atoms: 598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 598 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 94} Link IDs: {'PTRANS': 3, 'TRANS': 116} Unresolved non-hydrogen bonds: 338 Unresolved non-hydrogen angles: 440 Unresolved non-hydrogen dihedrals: 289 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 4, 'TYR:plan': 5, 'ASN:plan1': 2, 'TRP:plan': 4, 'HIS:plan': 1, 'PHE:plan': 4, 'GLU:plan': 5, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 201 Chain: "L" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 504 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 75} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 93} Chain breaks: 1 Unresolved non-hydrogen bonds: 276 Unresolved non-hydrogen angles: 361 Unresolved non-hydrogen dihedrals: 231 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 8, 'TYR:plan': 6, 'TRP:plan': 2, 'ASP:plan': 3, 'PHE:plan': 4, 'GLU:plan': 3, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 167 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: 598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 598 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 94} Link IDs: {'PTRANS': 3, 'TRANS': 116} Unresolved non-hydrogen bonds: 338 Unresolved non-hydrogen angles: 440 Unresolved non-hydrogen dihedrals: 289 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 4, 'TYR:plan': 5, 'ASN:plan1': 2, 'TRP:plan': 4, 'HIS:plan': 1, 'PHE:plan': 4, 'GLU:plan': 5, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 201 Chain: "D" Number of atoms: 506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 506 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 74} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 93} Chain breaks: 1 Unresolved non-hydrogen bonds: 274 Unresolved non-hydrogen angles: 358 Unresolved non-hydrogen dihedrals: 230 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 8, 'TYR:plan': 6, 'TRP:plan': 2, 'ASP:plan': 3, 'PHE:plan': 4, 'GLU:plan': 3, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 167 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: "F" Number of atoms: 598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 598 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 94} Link IDs: {'PTRANS': 3, 'TRANS': 116} Unresolved non-hydrogen bonds: 338 Unresolved non-hydrogen angles: 440 Unresolved non-hydrogen dihedrals: 289 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 4, 'TYR:plan': 5, 'ASN:plan1': 2, 'TRP:plan': 4, 'HIS:plan': 1, 'PHE:plan': 4, 'GLU:plan': 5, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 201 Chain: "G" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 513 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 73} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 93} Chain breaks: 1 Unresolved non-hydrogen bonds: 267 Unresolved non-hydrogen angles: 350 Unresolved non-hydrogen dihedrals: 224 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 8, 'TYR:plan': 6, 'TRP:plan': 2, 'ASP:plan': 2, 'PHE:plan': 4, 'GLU:plan': 3, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 159 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" 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: "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 dihedrals: 6 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 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: 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: "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: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 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 dihedrals: 33 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 dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 13.97, per 1000 atoms: 0.55 Number of scatterers: 25353 At special positions: 0 Unit cell: (129.15, 132.3, 219.45, 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 120 16.00 O 4846 8.00 N 4351 7.00 C 16036 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, 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=2.02 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=2.09 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=2.04 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=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.09 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.02 Simple disulfide: pdb=" SG CYS H 101 " - pdb=" SG CYS H 106 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " 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=2.02 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=2.09 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=2.04 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.09 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.02 Simple disulfide: pdb=" SG CYS C 101 " - pdb=" SG CYS C 106 " distance=2.04 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 89 " 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=2.02 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=2.09 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=2.04 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=2.04 Simple disulfide: pdb=" SG CYS E 662 " - pdb=" SG CYS E 671 " distance=2.04 Simple disulfide: pdb=" SG CYS E 738 " - pdb=" SG CYS E 760 " distance=2.09 Simple disulfide: pdb=" SG CYS E 743 " - pdb=" SG CYS E 749 " distance=2.04 Simple disulfide: pdb=" SG CYS E1032 " - pdb=" SG CYS E1043 " distance=2.02 Simple disulfide: pdb=" SG CYS E1082 " - pdb=" SG CYS E1126 " distance=2.02 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.02 Simple disulfide: pdb=" SG CYS F 101 " - pdb=" SG CYS F 106 " distance=2.04 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 89 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 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 U 1 " - " NAG U 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 282 " " NAG A1302 " - " ASN A 603 " " NAG A1303 " - " ASN A 657 " " NAG A1304 " - " ASN A1074 " " NAG A1305 " - " ASN A 61 " " NAG A1306 " - " ASN A 616 " " NAG A1307 " - " ASN A 122 " " NAG A1308 " - " ASN A 165 " " NAG A1309 " - " ASN A 234 " " NAG A1310 " - " ASN A 331 " " 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 616 " " NAG E1307 " - " ASN E 122 " " NAG E1308 " - " ASN E 165 " " NAG E1309 " - " ASN E 234 " " NAG E1310 " - " ASN E 331 " " NAG E1311 " - " ASN E 709 " " NAG I 1 " - " ASN A 717 " " NAG J 1 " - " ASN A1098 " " 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 U 1 " - " ASN E1098 " " NAG V 1 " - " ASN E1134 " " NAG W 1 " - " ASN E 343 " " NAG X 1 " - " ASN E 801 " Time building additional restraints: 10.46 Conformation dependent library (CDL) restraints added in 4.9 seconds 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6798 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 63 sheets defined 23.2% alpha, 31.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.20 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 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.217A 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: 4.248A 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 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: 3.839A 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 913 through 919 Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 967 Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.997A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1145 Processing helix chain 'H' and resid 28 through 31 Processing helix chain 'H' and resid 64 through 66 No H-bonds generated for 'chain 'H' and resid 64 through 66' Processing helix chain 'H' and resid 74 through 76 No H-bonds generated for 'chain 'H' and resid 74 through 76' Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'L' and resid 30 through 32 No H-bonds generated for 'chain 'L' and resid 30 through 32' Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.817A pdb=" N PHE L 84 " --> pdb=" O PRO L 81 " (cutoff:3.500A) 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: 4.217A 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 405 through 410 removed outlier: 4.248A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 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: 3.839A 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 Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 967 Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.997A 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 'C' and resid 28 through 31 Processing helix chain 'C' and resid 64 through 66 No H-bonds generated for 'chain 'C' and resid 64 through 66' Processing helix chain 'C' and resid 74 through 76 No H-bonds generated for 'chain 'C' and resid 74 through 76' Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'D' and resid 30 through 32 No H-bonds generated for 'chain 'D' and resid 30 through 32' Processing helix chain 'D' and resid 80 through 84 removed outlier: 3.817A pdb=" N PHE D 84 " --> pdb=" O PRO D 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 304 Processing helix chain 'E' and resid 338 through 343 Processing helix chain 'E' and resid 351 through 353 No H-bonds generated for 'chain 'E' and resid 351 through 353' Processing helix chain 'E' and resid 364 through 371 removed outlier: 4.217A 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: 4.247A 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 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: 3.839A 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 913 through 919 Processing helix chain 'E' and resid 919 through 941 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: 4.997A pdb=" N VAL E 991 " --> pdb=" O PRO E 987 " (cutoff:3.500A) Processing helix chain 'E' and resid 1140 through 1145 Processing helix chain 'F' and resid 28 through 31 Processing helix chain 'F' and resid 64 through 66 No H-bonds generated for 'chain 'F' and resid 64 through 66' Processing helix chain 'F' and resid 74 through 76 No H-bonds generated for 'chain 'F' and resid 74 through 76' Processing helix chain 'F' and resid 87 through 91 Processing helix chain 'G' and resid 30 through 32 No H-bonds generated for 'chain 'G' and resid 30 through 32' Processing helix chain 'G' and resid 80 through 84 removed outlier: 3.817A pdb=" N PHE G 84 " --> pdb=" O PRO G 81 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 7.937A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.522A pdb=" N ALA E 575 " --> pdb=" O GLY E 566 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N ASP E 574 " --> pdb=" O ILE E 587 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLU E 324 " --> pdb=" O CYS E 538 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 7.398A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.955A 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: 6.010A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASN A 122 " --> pdb=" O ASN A 125 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N VAL A 126 " --> pdb=" O TYR A 170 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N TYR A 170 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N CYS A 136 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N TYR A 160 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ASP A 138 " --> pdb=" O ARG A 158 " (cutoff:3.500A) removed outlier: 7.366A 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: 5.281A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.363A 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: 4.054A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 348 through 349 removed outlier: 7.180A pdb=" N ALA A 348 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 9.569A pdb=" N ARG A 403 " --> pdb=" O ALA A 348 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 348 through 349 removed outlier: 7.180A pdb=" N ALA A 348 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 9.569A pdb=" N ARG A 403 " --> pdb=" O ALA A 348 " (cutoff:3.500A) 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: 6.654A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.775A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.534A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 728 removed outlier: 5.876A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.406A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.525A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AC1, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.646A pdb=" N GLU H 10 " --> pdb=" O THR H 120 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.646A pdb=" N GLU H 10 " --> pdb=" O THR H 120 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 101 through 102 Processing sheet with id=AC4, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AC5, first strand: chain 'L' and resid 54 through 55 removed outlier: 6.557A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N TYR L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N LEU L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR L 99 " --> pdb=" O GLN L 91 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 28 through 30 removed outlier: 7.937A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 48 through 55 removed outlier: 7.398A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.011A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASN B 122 " --> pdb=" O ASN B 125 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N VAL B 126 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N TYR B 170 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ILE B 128 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N PHE B 168 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N VAL B 130 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N CYS B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N CYS B 136 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N TYR B 160 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ASP B 138 " --> pdb=" O ARG B 158 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N ARG B 158 " --> pdb=" O ASP B 138 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.281A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 324 through 328 removed outlier: 4.054A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N PHE B 565 " --> pdb=" O PHE E 43 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 348 through 349 removed outlier: 7.181A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 9.569A pdb=" N ARG B 403 " --> pdb=" O ALA B 348 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 348 through 349 removed outlier: 7.181A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 9.569A pdb=" N ARG B 403 " --> pdb=" O ALA B 348 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD5, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD6, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.654A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.776A pdb=" N ALA B 701 " --> pdb=" O ILE E 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.535A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.876A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.406A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.524A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 3 through 6 Processing sheet with id=AE4, first strand: chain 'C' and resid 10 through 11 removed outlier: 6.646A pdb=" N GLU C 10 " --> pdb=" O THR C 120 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 10 through 11 removed outlier: 6.646A pdb=" N GLU C 10 " --> pdb=" O THR C 120 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 101 through 102 Processing sheet with id=AE7, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AE8, first strand: chain 'D' and resid 54 through 55 removed outlier: 6.555A pdb=" N TRP D 36 " --> pdb=" O LEU D 48 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N TYR D 50 " --> pdb=" O LEU D 34 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LEU D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR D 99 " --> pdb=" O GLN D 91 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 28 through 30 removed outlier: 7.938A pdb=" N ASN E 61 " --> pdb=" O TYR E 269 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N TYR E 269 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N PHE E 201 " --> pdb=" O ASP E 228 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ASP E 228 " --> pdb=" O PHE E 201 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ILE E 203 " --> pdb=" O LEU E 226 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 48 through 55 removed outlier: 7.398A pdb=" N THR E 274 " --> pdb=" O ASP E 290 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N ASP E 290 " --> pdb=" O THR E 274 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LEU E 276 " --> pdb=" O ALA E 288 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ALA E 288 " --> pdb=" O LEU E 276 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N LYS E 278 " --> pdb=" O THR E 286 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 84 through 85 removed outlier: 6.010A pdb=" N ARG E 102 " --> pdb=" O ASN E 121 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASN E 122 " --> pdb=" O ASN E 125 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N VAL E 126 " --> pdb=" O TYR E 170 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N TYR E 170 " --> pdb=" O VAL E 126 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ILE E 128 " --> pdb=" O PHE E 168 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N PHE E 168 " --> pdb=" O ILE E 128 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N VAL E 130 " --> pdb=" O CYS E 166 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N CYS E 166 " --> pdb=" O VAL E 130 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER E 162 " --> pdb=" O GLN E 134 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N CYS E 136 " --> pdb=" O TYR E 160 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N TYR E 160 " --> pdb=" O CYS E 136 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ASP E 138 " --> pdb=" O ARG E 158 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N ARG E 158 " --> pdb=" O ASP E 138 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 311 through 319 removed outlier: 5.282A pdb=" N ILE E 312 " --> pdb=" O THR E 599 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N THR E 599 " --> pdb=" O ILE E 312 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N GLN E 314 " --> pdb=" O VAL E 597 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL E 597 " --> pdb=" O GLN E 314 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N GLY E 594 " --> pdb=" O GLN E 613 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 348 through 349 removed outlier: 7.180A pdb=" N ALA E 348 " --> pdb=" O VAL E 401 " (cutoff:3.500A) removed outlier: 9.569A pdb=" N ARG E 403 " --> pdb=" O ALA E 348 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 348 through 349 removed outlier: 7.180A pdb=" N ALA E 348 " --> pdb=" O VAL E 401 " (cutoff:3.500A) removed outlier: 9.569A pdb=" N ARG E 403 " --> pdb=" O ALA E 348 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AF7, first strand: chain 'E' and resid 473 through 474 Processing sheet with id=AF8, first strand: chain 'E' and resid 654 through 655 removed outlier: 6.654A pdb=" N ILE E 670 " --> pdb=" O ILE E 666 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'E' and resid 711 through 715 removed outlier: 3.534A pdb=" N ALA E1078 " --> pdb=" O PHE E1095 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N PHE E1095 " --> pdb=" O ALA E1078 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'E' and resid 718 through 728 removed outlier: 5.877A pdb=" N TYR E1067 " --> pdb=" O HIS E1048 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N HIS E1048 " --> pdb=" O TYR E1067 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'E' and resid 733 through 736 removed outlier: 4.407A pdb=" N LYS E 733 " --> pdb=" O LEU E 861 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'E' and resid 1120 through 1125 removed outlier: 4.525A pdb=" N ALA E1087 " --> pdb=" O SER E1123 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'F' and resid 3 through 6 Processing sheet with id=AG5, first strand: chain 'F' and resid 10 through 11 removed outlier: 6.646A pdb=" N GLU F 10 " --> pdb=" O THR F 120 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'F' and resid 10 through 11 removed outlier: 6.646A pdb=" N GLU F 10 " --> pdb=" O THR F 120 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'F' and resid 101 through 102 Processing sheet with id=AG8, first strand: chain 'G' and resid 4 through 7 Processing sheet with id=AG9, first strand: chain 'G' and resid 54 through 55 removed outlier: 6.557A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N TYR G 50 " --> pdb=" O LEU G 34 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N LEU G 34 " --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR G 99 " --> pdb=" O GLN G 91 " (cutoff:3.500A) 1260 hydrogen bonds defined for protein. 3366 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: 13.83 Time building geometry restraints manager: 11.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 6976 1.33 - 1.46: 7413 1.46 - 1.59: 11303 1.59 - 1.73: 6 1.73 - 1.86: 144 Bond restraints: 25842 Sorted by residual: bond pdb=" CB LEU E1145 " pdb=" CG LEU E1145 " ideal model delta sigma weight residual 1.530 1.618 -0.088 2.00e-02 2.50e+03 1.94e+01 bond pdb=" CB LEU B1145 " pdb=" CG LEU B1145 " ideal model delta sigma weight residual 1.530 1.617 -0.087 2.00e-02 2.50e+03 1.91e+01 bond pdb=" CB LEU A1145 " pdb=" CG LEU A1145 " ideal model delta sigma weight residual 1.530 1.617 -0.087 2.00e-02 2.50e+03 1.90e+01 bond pdb=" CB ASN B 914 " pdb=" CG ASN B 914 " ideal model delta sigma weight residual 1.516 1.423 0.093 2.50e-02 1.60e+03 1.39e+01 bond pdb=" CB ASN A 914 " pdb=" CG ASN A 914 " ideal model delta sigma weight residual 1.516 1.423 0.093 2.50e-02 1.60e+03 1.39e+01 ... (remaining 25837 not shown) Histogram of bond angle deviations from ideal: 98.14 - 105.31: 741 105.31 - 112.49: 13147 112.49 - 119.67: 8035 119.67 - 126.84: 13412 126.84 - 134.02: 112 Bond angle restraints: 35447 Sorted by residual: angle pdb=" C GLY H 8 " pdb=" N PRO H 9 " pdb=" CA PRO H 9 " ideal model delta sigma weight residual 120.03 128.09 -8.06 9.90e-01 1.02e+00 6.63e+01 angle pdb=" C GLY F 8 " pdb=" N PRO F 9 " pdb=" CA PRO F 9 " ideal model delta sigma weight residual 120.03 128.05 -8.02 9.90e-01 1.02e+00 6.56e+01 angle pdb=" C GLY C 8 " pdb=" N PRO C 9 " pdb=" CA PRO C 9 " ideal model delta sigma weight residual 120.03 128.05 -8.02 9.90e-01 1.02e+00 6.56e+01 angle pdb=" C LEU A 861 " pdb=" N PRO A 862 " pdb=" CA PRO A 862 " ideal model delta sigma weight residual 119.66 125.33 -5.67 7.20e-01 1.93e+00 6.20e+01 angle pdb=" C LEU E 861 " pdb=" N PRO E 862 " pdb=" CA PRO E 862 " ideal model delta sigma weight residual 119.66 125.30 -5.64 7.20e-01 1.93e+00 6.13e+01 ... (remaining 35442 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 15509 17.58 - 35.16: 484 35.16 - 52.75: 47 52.75 - 70.33: 34 70.33 - 87.91: 18 Dihedral angle restraints: 16092 sinusoidal: 5569 harmonic: 10523 Sorted by residual: 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 -147.04 61.04 1 1.00e+01 1.00e-02 4.95e+01 dihedral pdb=" CB CYS E 538 " pdb=" SG CYS E 538 " pdb=" SG CYS E 590 " pdb=" CB CYS E 590 " ideal model delta sinusoidal sigma weight residual -86.00 -147.02 61.02 1 1.00e+01 1.00e-02 4.95e+01 dihedral pdb=" CB CYS B 538 " pdb=" SG CYS B 538 " pdb=" SG CYS B 590 " pdb=" CB CYS B 590 " ideal model delta sinusoidal sigma weight residual -86.00 -147.01 61.01 1 1.00e+01 1.00e-02 4.95e+01 ... (remaining 16089 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 3108 0.078 - 0.156: 930 0.156 - 0.234: 185 0.234 - 0.312: 96 0.312 - 0.390: 75 Chirality restraints: 4394 Sorted by residual: chirality pdb=" C1 NAG Q 2 " pdb=" O4 NAG Q 1 " pdb=" C2 NAG Q 2 " pdb=" O5 NAG Q 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.56 0.16 2.00e-02 2.50e+03 6.18e+01 chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.56 0.16 2.00e-02 2.50e+03 6.02e+01 chirality pdb=" C1 NAG V 2 " pdb=" O4 NAG V 1 " pdb=" C2 NAG V 2 " pdb=" O5 NAG V 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.55 0.15 2.00e-02 2.50e+03 5.94e+01 ... (remaining 4391 not shown) Planarity restraints: 4693 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B1134 " 0.023 2.00e-02 2.50e+03 2.45e-02 7.52e+00 pdb=" CG ASN B1134 " -0.007 2.00e-02 2.50e+03 pdb=" OD1 ASN B1134 " -0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN B1134 " -0.039 2.00e-02 2.50e+03 pdb=" C1 NAG Q 1 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E1134 " 0.023 2.00e-02 2.50e+03 2.45e-02 7.50e+00 pdb=" CG ASN E1134 " -0.007 2.00e-02 2.50e+03 pdb=" OD1 ASN E1134 " -0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN E1134 " -0.039 2.00e-02 2.50e+03 pdb=" C1 NAG V 1 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A1134 " 0.023 2.00e-02 2.50e+03 2.45e-02 7.47e+00 pdb=" CG ASN A1134 " -0.007 2.00e-02 2.50e+03 pdb=" OD1 ASN A1134 " -0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN A1134 " -0.039 2.00e-02 2.50e+03 pdb=" C1 NAG K 1 " 0.030 2.00e-02 2.50e+03 ... (remaining 4690 not shown) Histogram of nonbonded interaction distances: 2.43 - 2.93: 11044 2.93 - 3.42: 22347 3.42 - 3.91: 40399 3.91 - 4.41: 44581 4.41 - 4.90: 75440 Nonbonded interactions: 193811 Sorted by model distance: nonbonded pdb=" OD2 ASP E 808 " pdb=" NZ LYS E 811 " model vdw 2.431 2.520 nonbonded pdb=" OD2 ASP A 808 " pdb=" NZ LYS A 811 " model vdw 2.431 2.520 nonbonded pdb=" OD2 ASP B 808 " pdb=" NZ LYS B 811 " model vdw 2.432 2.520 nonbonded pdb=" NZ LYS A1028 " pdb=" O PHE A1042 " model vdw 2.453 2.520 nonbonded pdb=" NZ LYS B1028 " pdb=" O PHE B1042 " model vdw 2.453 2.520 ... (remaining 193806 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' selection = chain 'F' selection = chain 'H' } ncs_group { reference = (chain 'D' and ((resid 2 through 7 and (name N or name CA or name C or name O or \ name CB )) or resid 8 through 104)) selection = (chain 'G' and (resid 2 through 60 or (resid 61 through 64 and (name N or name C \ A or name C or name O or name CB )) or resid 65 through 104)) selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'J' 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 'U' 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 27.300 Check model and map are aligned: 0.360 Set scattering table: 0.230 Process input model: 71.700 Find NCS groups from input model: 1.910 Set up NCS constraints: 0.330 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: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 111.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.101 25842 Z= 0.909 Angle : 1.412 8.089 35447 Z= 0.960 Chirality : 0.094 0.390 4394 Planarity : 0.005 0.041 4645 Dihedral : 9.342 87.908 9150 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 0.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: 0.95 (0.13), residues: 3588 helix: 0.56 (0.18), residues: 672 sheet: 1.10 (0.16), residues: 933 loop : 0.56 (0.14), residues: 1983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.006 TRP B1102 HIS 0.005 0.002 HIS A1083 PHE 0.021 0.003 PHE B 58 TYR 0.028 0.004 TYR B 495 ARG 0.005 0.001 ARG B 102 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 3177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 358 time to evaluate : 2.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 377 PHE cc_start: 0.5886 (t80) cc_final: 0.5670 (t80) REVERT: A 423 TYR cc_start: 0.6877 (t80) cc_final: 0.6340 (t80) REVERT: A 734 THR cc_start: 0.8866 (m) cc_final: 0.8543 (p) REVERT: A 875 SER cc_start: 0.8675 (t) cc_final: 0.8199 (p) REVERT: B 61 ASN cc_start: 0.5844 (t0) cc_final: 0.5422 (p0) REVERT: B 734 THR cc_start: 0.8977 (m) cc_final: 0.8677 (p) REVERT: B 875 SER cc_start: 0.8674 (t) cc_final: 0.8208 (p) REVERT: E 61 ASN cc_start: 0.6186 (t0) cc_final: 0.5778 (p0) outliers start: 0 outliers final: 0 residues processed: 358 average time/residue: 0.3721 time to fit residues: 206.5590 Evaluate side-chains 165 residues out of total 3177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 2.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 306 optimal weight: 0.5980 chunk 275 optimal weight: 0.0000 chunk 152 optimal weight: 0.7980 chunk 93 optimal weight: 0.9990 chunk 185 optimal weight: 0.6980 chunk 146 optimal weight: 0.9990 chunk 284 optimal weight: 0.9980 chunk 110 optimal weight: 8.9990 chunk 173 optimal weight: 0.7980 chunk 211 optimal weight: 0.6980 chunk 329 optimal weight: 0.7980 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 207 HIS A 957 GLN A1005 GLN A1010 GLN B 207 HIS B 957 GLN B1005 GLN B1010 GLN ** E 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 762 GLN E 957 GLN E1010 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 25842 Z= 0.246 Angle : 0.579 8.039 35447 Z= 0.311 Chirality : 0.047 0.251 4394 Planarity : 0.004 0.035 4645 Dihedral : 5.115 42.149 5118 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.04 % Allowed : 6.32 % Favored : 92.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: 1.41 (0.14), residues: 3588 helix: 2.11 (0.19), residues: 645 sheet: 1.22 (0.16), residues: 978 loop : 0.48 (0.14), residues: 1965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 104 HIS 0.003 0.001 HIS A1064 PHE 0.026 0.002 PHE A 59 TYR 0.017 0.001 TYR A 265 ARG 0.007 0.000 ARG A 237 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 3177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 188 time to evaluate : 2.769 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 734 THR cc_start: 0.8908 (m) cc_final: 0.8685 (p) REVERT: B 61 ASN cc_start: 0.6382 (t0) cc_final: 0.5821 (p0) REVERT: B 875 SER cc_start: 0.8792 (t) cc_final: 0.8363 (p) REVERT: B 904 TYR cc_start: 0.7901 (m-10) cc_final: 0.7359 (m-10) REVERT: E 61 ASN cc_start: 0.6196 (t0) cc_final: 0.5845 (p0) REVERT: E 342 PHE cc_start: 0.7894 (m-80) cc_final: 0.7517 (m-80) REVERT: E 423 TYR cc_start: 0.5367 (t80) cc_final: 0.5068 (t80) REVERT: E 875 SER cc_start: 0.8657 (t) cc_final: 0.8314 (p) outliers start: 20 outliers final: 12 residues processed: 203 average time/residue: 0.3102 time to fit residues: 107.2182 Evaluate side-chains 155 residues out of total 3177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 143 time to evaluate : 2.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 764 ASN Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain E residue 191 GLU Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 645 THR Chi-restraints excluded: chain E residue 723 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 183 optimal weight: 0.2980 chunk 102 optimal weight: 20.0000 chunk 274 optimal weight: 2.9990 chunk 224 optimal weight: 40.0000 chunk 90 optimal weight: 0.5980 chunk 330 optimal weight: 0.8980 chunk 356 optimal weight: 50.0000 chunk 294 optimal weight: 0.9980 chunk 327 optimal weight: 1.9990 chunk 112 optimal weight: 40.0000 chunk 264 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 957 GLN A1071 GLN B 901 GLN B1071 GLN E 317 ASN E 957 GLN E1071 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 25842 Z= 0.273 Angle : 0.525 8.725 35447 Z= 0.279 Chirality : 0.046 0.228 4394 Planarity : 0.004 0.037 4645 Dihedral : 4.522 48.539 5118 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.50 % Allowed : 7.98 % Favored : 90.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.14), residues: 3588 helix: 2.18 (0.20), residues: 663 sheet: 0.97 (0.16), residues: 972 loop : 0.37 (0.14), residues: 1953 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 886 HIS 0.005 0.001 HIS B1064 PHE 0.015 0.002 PHE E 898 TYR 0.016 0.001 TYR E 380 ARG 0.003 0.001 ARG B 328 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 3177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 143 time to evaluate : 2.852 Fit side-chains REVERT: A 306 PHE cc_start: 0.8546 (OUTLIER) cc_final: 0.7951 (t80) REVERT: A 734 THR cc_start: 0.8970 (m) cc_final: 0.8660 (p) REVERT: B 61 ASN cc_start: 0.6212 (t0) cc_final: 0.5713 (p0) REVERT: B 875 SER cc_start: 0.8784 (t) cc_final: 0.8411 (p) REVERT: E 61 ASN cc_start: 0.6367 (t0) cc_final: 0.6007 (p0) REVERT: E 306 PHE cc_start: 0.8345 (OUTLIER) cc_final: 0.7583 (t80) REVERT: E 342 PHE cc_start: 0.7935 (m-80) cc_final: 0.7579 (m-80) REVERT: E 423 TYR cc_start: 0.5679 (t80) cc_final: 0.5330 (t80) REVERT: E 900 MET cc_start: 0.8168 (mtp) cc_final: 0.7915 (mtp) outliers start: 29 outliers final: 16 residues processed: 164 average time/residue: 0.3140 time to fit residues: 88.7021 Evaluate side-chains 145 residues out of total 3177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 127 time to evaluate : 2.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 764 ASN Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain E residue 191 GLU Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 306 PHE Chi-restraints excluded: chain E residue 590 CYS Chi-restraints excluded: chain E residue 645 THR Chi-restraints excluded: chain E residue 723 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 326 optimal weight: 4.9990 chunk 248 optimal weight: 0.7980 chunk 171 optimal weight: 0.0370 chunk 36 optimal weight: 4.9990 chunk 157 optimal weight: 20.0000 chunk 221 optimal weight: 50.0000 chunk 331 optimal weight: 0.6980 chunk 350 optimal weight: 40.0000 chunk 173 optimal weight: 0.8980 chunk 314 optimal weight: 0.9980 chunk 94 optimal weight: 0.1980 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 957 GLN B 957 GLN E 317 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 25842 Z= 0.196 Angle : 0.481 8.061 35447 Z= 0.252 Chirality : 0.045 0.193 4394 Planarity : 0.004 0.046 4645 Dihedral : 4.180 44.872 5118 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.55 % Allowed : 9.17 % Favored : 89.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.14), residues: 3588 helix: 2.33 (0.20), residues: 663 sheet: 0.77 (0.16), residues: 993 loop : 0.38 (0.14), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 886 HIS 0.002 0.001 HIS B1064 PHE 0.019 0.001 PHE A 377 TYR 0.016 0.001 TYR E 365 ARG 0.002 0.000 ARG A 237 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 3177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 140 time to evaluate : 3.158 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 306 PHE cc_start: 0.8573 (OUTLIER) cc_final: 0.7947 (t80) REVERT: A 734 THR cc_start: 0.8931 (m) cc_final: 0.8611 (p) REVERT: B 61 ASN cc_start: 0.6214 (t0) cc_final: 0.5679 (p0) REVERT: B 875 SER cc_start: 0.8777 (t) cc_final: 0.8420 (p) REVERT: E 61 ASN cc_start: 0.6324 (t0) cc_final: 0.5908 (p0) REVERT: E 306 PHE cc_start: 0.8384 (OUTLIER) cc_final: 0.7650 (t80) REVERT: E 342 PHE cc_start: 0.7914 (m-80) cc_final: 0.7542 (m-80) REVERT: E 423 TYR cc_start: 0.5758 (t80) cc_final: 0.5304 (t80) REVERT: E 900 MET cc_start: 0.8115 (mtp) cc_final: 0.7900 (mtp) outliers start: 30 outliers final: 18 residues processed: 162 average time/residue: 0.3157 time to fit residues: 88.6219 Evaluate side-chains 154 residues out of total 3177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 134 time to evaluate : 2.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 764 ASN Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 306 PHE Chi-restraints excluded: chain E residue 590 CYS Chi-restraints excluded: chain E residue 645 THR Chi-restraints excluded: chain E residue 723 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 292 optimal weight: 2.9990 chunk 199 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 261 optimal weight: 0.8980 chunk 144 optimal weight: 2.9990 chunk 299 optimal weight: 2.9990 chunk 242 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 179 optimal weight: 0.9980 chunk 314 optimal weight: 0.9980 chunk 88 optimal weight: 0.9980 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 957 GLN B 540 ASN E 901 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 25842 Z= 0.312 Angle : 0.522 8.041 35447 Z= 0.271 Chirality : 0.046 0.194 4394 Planarity : 0.004 0.039 4645 Dihedral : 4.244 35.475 5118 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.66 % Allowed : 9.02 % Favored : 89.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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 (0.14), residues: 3588 helix: 2.27 (0.20), residues: 666 sheet: 0.63 (0.16), residues: 1005 loop : 0.27 (0.14), residues: 1917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 886 HIS 0.005 0.001 HIS B1058 PHE 0.019 0.002 PHE A 377 TYR 0.013 0.001 TYR B1067 ARG 0.003 0.001 ARG A 905 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 3177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 132 time to evaluate : 2.901 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 306 PHE cc_start: 0.8596 (OUTLIER) cc_final: 0.7875 (t80) REVERT: B 61 ASN cc_start: 0.6280 (t0) cc_final: 0.5819 (p0) REVERT: E 61 ASN cc_start: 0.6450 (t0) cc_final: 0.6152 (p0) REVERT: E 306 PHE cc_start: 0.8472 (OUTLIER) cc_final: 0.7647 (t80) REVERT: E 900 MET cc_start: 0.8230 (mtp) cc_final: 0.8029 (mtp) outliers start: 32 outliers final: 23 residues processed: 157 average time/residue: 0.3014 time to fit residues: 84.3279 Evaluate side-chains 149 residues out of total 3177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 124 time to evaluate : 2.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 306 PHE Chi-restraints excluded: chain E residue 590 CYS Chi-restraints excluded: chain E residue 645 THR Chi-restraints excluded: chain E residue 723 THR Chi-restraints excluded: chain E residue 902 MET Chi-restraints excluded: chain E residue 1104 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 118 optimal weight: 7.9990 chunk 315 optimal weight: 0.0980 chunk 69 optimal weight: 0.9980 chunk 206 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 351 optimal weight: 50.0000 chunk 291 optimal weight: 2.9990 chunk 162 optimal weight: 5.9990 chunk 29 optimal weight: 6.9990 chunk 116 optimal weight: 30.0000 chunk 184 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 GLN A 957 GLN E 957 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.3318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 25842 Z= 0.309 Angle : 0.517 7.456 35447 Z= 0.267 Chirality : 0.046 0.189 4394 Planarity : 0.004 0.037 4645 Dihedral : 4.182 30.232 5118 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.81 % Allowed : 9.17 % Favored : 89.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: 1.00 (0.14), residues: 3588 helix: 2.21 (0.20), residues: 666 sheet: 0.61 (0.16), residues: 993 loop : 0.24 (0.14), residues: 1929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 886 HIS 0.004 0.001 HIS B1058 PHE 0.018 0.002 PHE E 374 TYR 0.014 0.001 TYR A1067 ARG 0.003 0.000 ARG A 905 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 3177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 126 time to evaluate : 2.974 Fit side-chains revert: symmetry clash REVERT: A 306 PHE cc_start: 0.8613 (OUTLIER) cc_final: 0.7857 (t80) REVERT: B 61 ASN cc_start: 0.6304 (t0) cc_final: 0.5846 (p0) REVERT: E 61 ASN cc_start: 0.6503 (t0) cc_final: 0.5973 (p0) REVERT: E 306 PHE cc_start: 0.8465 (OUTLIER) cc_final: 0.7647 (t80) REVERT: E 900 MET cc_start: 0.8257 (mtp) cc_final: 0.8053 (mtp) outliers start: 35 outliers final: 30 residues processed: 154 average time/residue: 0.2991 time to fit residues: 81.7821 Evaluate side-chains 145 residues out of total 3177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 113 time to evaluate : 2.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 764 ASN Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 306 PHE Chi-restraints excluded: chain E residue 590 CYS Chi-restraints excluded: chain E residue 645 THR Chi-restraints excluded: chain E residue 723 THR Chi-restraints excluded: chain E residue 902 MET Chi-restraints excluded: chain E residue 1104 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 338 optimal weight: 0.9990 chunk 39 optimal weight: 20.0000 chunk 200 optimal weight: 3.9990 chunk 256 optimal weight: 7.9990 chunk 198 optimal weight: 0.4980 chunk 295 optimal weight: 0.7980 chunk 196 optimal weight: 0.0970 chunk 349 optimal weight: 40.0000 chunk 218 optimal weight: 1.9990 chunk 213 optimal weight: 0.7980 chunk 161 optimal weight: 8.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 907 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.3418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25842 Z= 0.226 Angle : 0.485 7.282 35447 Z= 0.251 Chirality : 0.045 0.235 4394 Planarity : 0.004 0.038 4645 Dihedral : 4.020 35.436 5118 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.81 % Allowed : 9.53 % Favored : 88.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: 1.08 (0.14), residues: 3588 helix: 2.47 (0.20), residues: 648 sheet: 0.65 (0.16), residues: 987 loop : 0.24 (0.14), residues: 1953 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 436 HIS 0.003 0.001 HIS B1064 PHE 0.014 0.001 PHE B 898 TYR 0.014 0.001 TYR A 380 ARG 0.006 0.000 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 3177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 119 time to evaluate : 3.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 PHE cc_start: 0.8593 (OUTLIER) cc_final: 0.7891 (t80) REVERT: B 61 ASN cc_start: 0.6276 (t0) cc_final: 0.5811 (p0) REVERT: B 697 MET cc_start: 0.7663 (ptm) cc_final: 0.7449 (ptp) REVERT: E 61 ASN cc_start: 0.6358 (t0) cc_final: 0.5915 (p0) REVERT: E 104 TRP cc_start: 0.7679 (m-90) cc_final: 0.7476 (m-90) REVERT: E 306 PHE cc_start: 0.8430 (OUTLIER) cc_final: 0.7620 (t80) outliers start: 35 outliers final: 26 residues processed: 148 average time/residue: 0.3038 time to fit residues: 80.9462 Evaluate side-chains 141 residues out of total 3177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 113 time to evaluate : 2.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 306 PHE Chi-restraints excluded: chain E residue 590 CYS Chi-restraints excluded: chain E residue 645 THR Chi-restraints excluded: chain E residue 723 THR Chi-restraints excluded: chain E residue 902 MET Chi-restraints excluded: chain E residue 1104 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 216 optimal weight: 0.9990 chunk 139 optimal weight: 0.9990 chunk 208 optimal weight: 0.9990 chunk 105 optimal weight: 50.0000 chunk 68 optimal weight: 0.0570 chunk 67 optimal weight: 0.8980 chunk 222 optimal weight: 8.9990 chunk 238 optimal weight: 50.0000 chunk 172 optimal weight: 0.8980 chunk 32 optimal weight: 10.0000 chunk 275 optimal weight: 20.0000 overall best weight: 0.7702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.3521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 25842 Z= 0.262 Angle : 0.496 7.151 35447 Z= 0.256 Chirality : 0.045 0.188 4394 Planarity : 0.004 0.037 4645 Dihedral : 4.031 31.726 5118 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.87 % Allowed : 9.69 % Favored : 88.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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 (0.14), residues: 3588 helix: 2.44 (0.20), residues: 648 sheet: 0.64 (0.16), residues: 987 loop : 0.23 (0.15), residues: 1953 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 353 HIS 0.003 0.001 HIS B1058 PHE 0.019 0.001 PHE A 168 TYR 0.014 0.001 TYR A1067 ARG 0.005 0.000 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 3177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 116 time to evaluate : 2.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 PHE cc_start: 0.8579 (OUTLIER) cc_final: 0.7828 (t80) REVERT: B 61 ASN cc_start: 0.6247 (t0) cc_final: 0.5786 (p0) REVERT: B 697 MET cc_start: 0.7624 (ptm) cc_final: 0.7407 (ptp) REVERT: E 61 ASN cc_start: 0.6388 (t0) cc_final: 0.6063 (p0) REVERT: E 104 TRP cc_start: 0.7662 (m-90) cc_final: 0.7446 (m-90) REVERT: E 306 PHE cc_start: 0.8462 (OUTLIER) cc_final: 0.7646 (t80) outliers start: 36 outliers final: 29 residues processed: 146 average time/residue: 0.2948 time to fit residues: 76.7253 Evaluate side-chains 143 residues out of total 3177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 112 time to evaluate : 2.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 764 ASN Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 306 PHE Chi-restraints excluded: chain E residue 590 CYS Chi-restraints excluded: chain E residue 645 THR Chi-restraints excluded: chain E residue 723 THR Chi-restraints excluded: chain E residue 902 MET Chi-restraints excluded: chain E residue 1104 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 318 optimal weight: 0.7980 chunk 335 optimal weight: 0.9990 chunk 305 optimal weight: 2.9990 chunk 326 optimal weight: 0.8980 chunk 196 optimal weight: 0.6980 chunk 142 optimal weight: 0.5980 chunk 256 optimal weight: 10.0000 chunk 100 optimal weight: 0.5980 chunk 294 optimal weight: 0.1980 chunk 308 optimal weight: 0.6980 chunk 324 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25842 Z= 0.204 Angle : 0.471 8.941 35447 Z= 0.243 Chirality : 0.044 0.203 4394 Planarity : 0.003 0.038 4645 Dihedral : 3.874 33.879 5118 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.81 % Allowed : 9.84 % Favored : 88.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: 1.10 (0.14), residues: 3588 helix: 2.39 (0.20), residues: 666 sheet: 0.72 (0.16), residues: 972 loop : 0.23 (0.15), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 436 HIS 0.002 0.001 HIS B1064 PHE 0.026 0.001 PHE A 377 TYR 0.014 0.001 TYR A1067 ARG 0.005 0.000 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 3177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 122 time to evaluate : 2.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 PHE cc_start: 0.8613 (OUTLIER) cc_final: 0.7900 (t80) REVERT: B 61 ASN cc_start: 0.6274 (t0) cc_final: 0.5816 (p0) REVERT: B 697 MET cc_start: 0.7615 (ptm) cc_final: 0.7390 (ptp) REVERT: E 61 ASN cc_start: 0.6344 (t0) cc_final: 0.6107 (p0) REVERT: E 104 TRP cc_start: 0.7661 (m-90) cc_final: 0.7437 (m-90) REVERT: E 306 PHE cc_start: 0.8432 (OUTLIER) cc_final: 0.7672 (t80) outliers start: 35 outliers final: 29 residues processed: 152 average time/residue: 0.2927 time to fit residues: 78.0205 Evaluate side-chains 144 residues out of total 3177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 113 time to evaluate : 2.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 306 PHE Chi-restraints excluded: chain E residue 590 CYS Chi-restraints excluded: chain E residue 645 THR Chi-restraints excluded: chain E residue 723 THR Chi-restraints excluded: chain E residue 902 MET Chi-restraints excluded: chain E residue 1104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 214 optimal weight: 0.1980 chunk 344 optimal weight: 20.0000 chunk 210 optimal weight: 0.3980 chunk 163 optimal weight: 7.9990 chunk 239 optimal weight: 0.5980 chunk 361 optimal weight: 0.9990 chunk 332 optimal weight: 0.0980 chunk 287 optimal weight: 1.9990 chunk 29 optimal weight: 7.9990 chunk 222 optimal weight: 20.0000 chunk 176 optimal weight: 0.8980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.3670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25842 Z= 0.175 Angle : 0.468 8.806 35447 Z= 0.242 Chirality : 0.044 0.186 4394 Planarity : 0.003 0.037 4645 Dihedral : 3.791 30.473 5118 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.81 % Allowed : 9.95 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: 1.12 (0.14), residues: 3588 helix: 2.45 (0.20), residues: 666 sheet: 0.74 (0.16), residues: 972 loop : 0.22 (0.15), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 436 HIS 0.002 0.000 HIS B1064 PHE 0.018 0.001 PHE A 168 TYR 0.013 0.001 TYR A1067 ARG 0.005 0.000 ARG A 102 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 3177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 116 time to evaluate : 3.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 PHE cc_start: 0.8635 (OUTLIER) cc_final: 0.7956 (t80) REVERT: B 61 ASN cc_start: 0.6267 (t0) cc_final: 0.5805 (p0) REVERT: B 697 MET cc_start: 0.7534 (ptm) cc_final: 0.7289 (ptp) REVERT: B 875 SER cc_start: 0.8763 (t) cc_final: 0.8404 (p) REVERT: B 1029 MET cc_start: 0.8337 (tpp) cc_final: 0.7889 (ttm) REVERT: E 61 ASN cc_start: 0.6368 (t0) cc_final: 0.5915 (p0) REVERT: E 104 TRP cc_start: 0.7617 (m-90) cc_final: 0.7396 (m-90) REVERT: E 306 PHE cc_start: 0.8410 (OUTLIER) cc_final: 0.7649 (t80) outliers start: 35 outliers final: 28 residues processed: 146 average time/residue: 0.2940 time to fit residues: 75.3066 Evaluate side-chains 145 residues out of total 3177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 115 time to evaluate : 2.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 764 ASN Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 306 PHE Chi-restraints excluded: chain E residue 590 CYS Chi-restraints excluded: chain E residue 645 THR Chi-restraints excluded: chain E residue 723 THR Chi-restraints excluded: chain E residue 1104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 228 optimal weight: 50.0000 chunk 306 optimal weight: 0.9990 chunk 88 optimal weight: 0.9980 chunk 265 optimal weight: 2.9990 chunk 42 optimal weight: 7.9990 chunk 80 optimal weight: 1.9990 chunk 288 optimal weight: 3.9990 chunk 120 optimal weight: 40.0000 chunk 296 optimal weight: 2.9990 chunk 36 optimal weight: 30.0000 chunk 53 optimal weight: 0.7980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 907 ASN E 907 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.144939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.097923 restraints weight = 45892.031| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.61 r_work: 0.3023 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.3801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 25842 Z= 0.475 Angle : 0.585 8.526 35447 Z= 0.299 Chirality : 0.048 0.191 4394 Planarity : 0.004 0.037 4645 Dihedral : 4.446 34.434 5118 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.97 % Allowed : 10.05 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.14), residues: 3588 helix: 1.83 (0.20), residues: 684 sheet: 0.54 (0.16), residues: 1005 loop : 0.04 (0.15), residues: 1899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 353 HIS 0.006 0.002 HIS B1058 PHE 0.017 0.002 PHE E 86 TYR 0.017 0.002 TYR A1067 ARG 0.005 0.001 ARG A 905 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4804.92 seconds wall clock time: 87 minutes 37.68 seconds (5257.68 seconds total)