Starting phenix.real_space_refine on Mon Aug 25 21:26:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ndc_12283/08_2025/7ndc_12283.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ndc_12283/08_2025/7ndc_12283.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ndc_12283/08_2025/7ndc_12283.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ndc_12283/08_2025/7ndc_12283.map" model { file = "/net/cci-nas-00/data/ceres_data/7ndc_12283/08_2025/7ndc_12283.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ndc_12283/08_2025/7ndc_12283.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.002 sd= 0.021 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 135 5.16 5 C 19449 2.51 5 N 5079 2.21 5 O 5982 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30645 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 8314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8314 Classifications: {'peptide': 1063} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 53, 'TRANS': 1009} Chain breaks: 5 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 8314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8314 Classifications: {'peptide': 1063} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 53, 'TRANS': 1009} Chain breaks: 5 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 8314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8314 Classifications: {'peptide': 1063} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 53, 'TRANS': 1009} Chain breaks: 5 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 6 Chain: "D" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 856 Classifications: {'peptide': 115} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 112} Chain breaks: 1 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 2, 'TYR:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "E" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 793 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "F" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 856 Classifications: {'peptide': 115} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 112} Chain breaks: 1 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 2, 'TYR:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "G" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 793 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "H" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 856 Classifications: {'peptide': 115} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 112} Chain breaks: 1 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 2, 'TYR:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "L" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 793 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 12 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: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 7.20, per 1000 atoms: 0.23 Number of scatterers: 30645 At special positions: 0 Unit cell: (168.92, 183.68, 188.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 135 16.00 O 5982 8.00 N 5079 7.00 C 19449 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 89 " distance=2.04 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 89 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 61 " " NAG A1302 " - " ASN A 282 " " NAG A1303 " - " ASN A 603 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 657 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A1074 " " NAG A1308 " - " ASN A 165 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 282 " " NAG B1303 " - " ASN B 603 " " NAG B1304 " - " ASN B 616 " " NAG B1305 " - " ASN B 657 " " NAG B1306 " - " ASN B 709 " " NAG B1307 " - " ASN B1074 " " NAG B1308 " - " ASN B 165 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 603 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 657 " " NAG C1306 " - " ASN C 709 " " NAG C1307 " - " ASN C1074 " " NAG C1308 " - " ASN C 165 " " NAG I 1 " - " ASN A 234 " " NAG J 1 " - " ASN A 717 " " NAG K 1 " - " ASN A 801 " " NAG M 1 " - " ASN A1098 " " NAG N 1 " - " ASN A1134 " " NAG O 1 " - " ASN B 234 " " NAG P 1 " - " ASN B 717 " " NAG Q 1 " - " ASN B 801 " " NAG R 1 " - " ASN B1098 " " NAG S 1 " - " ASN B1134 " " NAG T 1 " - " ASN C 234 " " NAG U 1 " - " ASN C 717 " " NAG V 1 " - " ASN C 801 " " NAG W 1 " - " ASN C1098 " " NAG X 1 " - " ASN C1134 " Time building additional restraints: 2.30 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 715.3 nanoseconds 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7158 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 60 sheets defined 22.6% alpha, 32.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.61 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 364 through 371 removed outlier: 3.783A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.409A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.634A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.656A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.131A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.891A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.615A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 3.959A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (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 364 through 371 removed outlier: 3.782A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.409A 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 removed outlier: 3.634A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.657A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.130A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.892A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.615A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 3.959A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 364 through 371 removed outlier: 3.782A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.409A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.635A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.656A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.130A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.891A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.615A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 3.959A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 32 Processing helix chain 'D' and resid 62 through 65 removed outlier: 3.594A pdb=" N LYS D 65 " --> pdb=" O ASP D 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 62 through 65' Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'E' and resid 29 through 32 removed outlier: 3.993A pdb=" N ASN E 32 " --> pdb=" O ILE E 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 29 through 32' Processing helix chain 'E' and resid 80 through 84 Processing helix chain 'F' and resid 28 through 32 Processing helix chain 'F' and resid 62 through 65 removed outlier: 3.593A pdb=" N LYS F 65 " --> pdb=" O ASP F 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 62 through 65' Processing helix chain 'F' and resid 87 through 91 Processing helix chain 'G' and resid 29 through 32 removed outlier: 3.994A pdb=" N ASN G 32 " --> pdb=" O ILE G 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 29 through 32' Processing helix chain 'G' and resid 80 through 84 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 62 through 65 removed outlier: 3.593A pdb=" N LYS H 65 " --> pdb=" O ASP H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 62 through 65' Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'L' and resid 29 through 32 removed outlier: 3.993A pdb=" N ASN L 32 " --> pdb=" O ILE L 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 29 through 32' Processing helix chain 'L' and resid 80 through 84 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.541A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU A 96 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.931A pdb=" N PHE A 43 " --> pdb=" O ARG C 567 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.622A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N VAL A 126 " --> pdb=" O TYR A 170 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N TYR A 170 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.353A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.671A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.185A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.815A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.411A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 3.751A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 3.751A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB6, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.422A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.540A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU B 96 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 48 through 55 Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.621A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N VAL B 126 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N TYR B 170 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ILE B 128 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N PHE B 168 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N VAL B 130 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N CYS B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.353A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.671A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.185A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC6, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC7, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.815A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.441A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 3.751A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 3.751A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD3, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.420A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 27 through 31 removed outlier: 3.540A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU C 96 " --> pdb=" O ASN C 188 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 48 through 55 Processing sheet with id=AD6, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.622A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N VAL C 126 " --> pdb=" O TYR C 170 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N TYR C 170 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ILE C 128 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N PHE C 168 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N VAL C 130 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N CYS C 166 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N SER C 162 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.353A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.184A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE1, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE2, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.816A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 711 through 728 removed outlier: 3.751A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 711 through 728 removed outlier: 3.751A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE6, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.422A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AE8, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.249A pdb=" N GLY D 10 " --> pdb=" O THR D 120 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.249A pdb=" N GLY D 10 " --> pdb=" O THR D 120 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL D 112 " --> pdb=" O LYS D 98 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AF2, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.518A pdb=" N LEU E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N TYR E 50 " --> pdb=" O LEU E 34 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N TRP E 36 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 10 through 13 Processing sheet with id=AF4, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AF5, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.249A pdb=" N GLY F 10 " --> pdb=" O THR F 120 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.249A pdb=" N GLY F 10 " --> pdb=" O THR F 120 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL F 112 " --> pdb=" O LYS F 98 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'G' and resid 4 through 7 Processing sheet with id=AF8, first strand: chain 'G' and resid 10 through 13 removed outlier: 6.517A pdb=" N LEU G 34 " --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N TYR G 50 " --> pdb=" O LEU G 34 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'G' and resid 10 through 13 Processing sheet with id=AG1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AG2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.249A pdb=" N GLY H 10 " --> pdb=" O THR H 120 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.249A pdb=" N GLY H 10 " --> pdb=" O THR H 120 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL H 112 " --> pdb=" O LYS H 98 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AG5, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.517A pdb=" N LEU L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N TYR L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'L' and resid 10 through 13 1265 hydrogen bonds defined for protein. 3381 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: 6.93 Time building geometry restraints manager: 2.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 9804 1.35 - 1.47: 7981 1.47 - 1.59: 13373 1.59 - 1.71: 0 1.71 - 1.83: 174 Bond restraints: 31332 Sorted by residual: bond pdb=" C1 NAG A1308 " pdb=" O5 NAG A1308 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.66e+00 bond pdb=" C1 NAG C1308 " pdb=" O5 NAG C1308 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.58e+00 bond pdb=" C1 NAG O 2 " pdb=" O5 NAG O 2 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.52e+00 bond pdb=" C1 NAG T 2 " pdb=" O5 NAG T 2 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.39e+00 bond pdb=" C1 NAG B1308 " pdb=" O5 NAG B1308 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.36e+00 ... (remaining 31327 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.34: 41122 1.34 - 2.69: 1207 2.69 - 4.03: 236 4.03 - 5.37: 20 5.37 - 6.71: 21 Bond angle restraints: 42606 Sorted by residual: angle pdb=" CA PRO A 527 " pdb=" N PRO A 527 " pdb=" CD PRO A 527 " ideal model delta sigma weight residual 112.00 106.14 5.86 1.40e+00 5.10e-01 1.75e+01 angle pdb=" CA PRO C 527 " pdb=" N PRO C 527 " pdb=" CD PRO C 527 " ideal model delta sigma weight residual 112.00 106.16 5.84 1.40e+00 5.10e-01 1.74e+01 angle pdb=" CA PRO B 527 " pdb=" N PRO B 527 " pdb=" CD PRO B 527 " ideal model delta sigma weight residual 112.00 106.20 5.80 1.40e+00 5.10e-01 1.71e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 114.28 -3.58 1.22e+00 6.72e-01 8.60e+00 angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 114.23 -3.53 1.22e+00 6.72e-01 8.35e+00 ... (remaining 42601 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.44: 18113 17.44 - 34.88: 879 34.88 - 52.31: 229 52.31 - 69.75: 75 69.75 - 87.19: 27 Dihedral angle restraints: 19323 sinusoidal: 8157 harmonic: 11166 Sorted by residual: dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual -86.00 -165.19 79.19 1 1.00e+01 1.00e-02 7.80e+01 dihedral pdb=" CB CYS C1032 " pdb=" SG CYS C1032 " pdb=" SG CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sinusoidal sigma weight residual -86.00 -165.19 79.19 1 1.00e+01 1.00e-02 7.80e+01 dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual -86.00 -165.16 79.16 1 1.00e+01 1.00e-02 7.79e+01 ... (remaining 19320 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 4004 0.054 - 0.108: 814 0.108 - 0.161: 108 0.161 - 0.215: 6 0.215 - 0.269: 3 Chirality restraints: 4935 Sorted by residual: chirality pdb=" C1 NAG C1308 " pdb=" ND2 ASN C 165 " pdb=" C2 NAG C1308 " pdb=" O5 NAG C1308 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" C1 NAG B1308 " pdb=" ND2 ASN B 165 " pdb=" C2 NAG B1308 " pdb=" O5 NAG B1308 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" C1 NAG A1308 " pdb=" ND2 ASN A 165 " pdb=" C2 NAG A1308 " pdb=" O5 NAG A1308 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.75e+00 ... (remaining 4932 not shown) Planarity restraints: 5490 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 526 " 0.086 5.00e-02 4.00e+02 1.27e-01 2.57e+01 pdb=" N PRO A 527 " -0.219 5.00e-02 4.00e+02 pdb=" CA PRO A 527 " 0.065 5.00e-02 4.00e+02 pdb=" CD PRO A 527 " 0.068 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 526 " 0.086 5.00e-02 4.00e+02 1.27e-01 2.57e+01 pdb=" N PRO B 527 " -0.219 5.00e-02 4.00e+02 pdb=" CA PRO B 527 " 0.066 5.00e-02 4.00e+02 pdb=" CD PRO B 527 " 0.068 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 526 " 0.086 5.00e-02 4.00e+02 1.27e-01 2.57e+01 pdb=" N PRO C 527 " -0.219 5.00e-02 4.00e+02 pdb=" CA PRO C 527 " 0.065 5.00e-02 4.00e+02 pdb=" CD PRO C 527 " 0.068 5.00e-02 4.00e+02 ... (remaining 5487 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 509 2.67 - 3.23: 28194 3.23 - 3.79: 46148 3.79 - 4.34: 63992 4.34 - 4.90: 106438 Nonbonded interactions: 245281 Sorted by model distance: nonbonded pdb=" NZ LYS B 147 " pdb=" OD1 ASN H 57 " model vdw 2.118 3.120 nonbonded pdb=" OE2 GLU A 516 " pdb=" OH TYR B 200 " model vdw 2.167 3.040 nonbonded pdb=" OH TYR A 200 " pdb=" OE2 GLU C 516 " model vdw 2.195 3.040 nonbonded pdb=" OE2 GLU B 516 " pdb=" OH TYR C 200 " model vdw 2.220 3.040 nonbonded pdb=" OG1 THR B 109 " pdb=" OD1 ASP B 111 " model vdw 2.237 3.040 ... (remaining 245276 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.270 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 27.290 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.070 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 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 : 0.003 0.086 31434 Z= 0.158 Angle : 0.569 6.713 42864 Z= 0.297 Chirality : 0.044 0.269 4935 Planarity : 0.005 0.127 5451 Dihedral : 11.857 87.188 12021 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.37 % Allowed : 4.02 % Favored : 95.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.43 (0.13), residues: 3798 helix: 0.44 (0.18), residues: 744 sheet: 0.23 (0.15), residues: 1020 loop : -0.80 (0.13), residues: 2034 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 24 TYR 0.011 0.001 TYR L 37 PHE 0.009 0.001 PHE C 888 TRP 0.009 0.001 TRP C 258 HIS 0.007 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00332 (31332) covalent geometry : angle 0.55955 (42606) SS BOND : bond 0.00250 ( 48) SS BOND : angle 1.03406 ( 96) hydrogen bonds : bond 0.18492 ( 1229) hydrogen bonds : angle 7.83445 ( 3381) link_BETA1-4 : bond 0.00217 ( 15) link_BETA1-4 : angle 0.80548 ( 45) link_NAG-ASN : bond 0.00179 ( 39) link_NAG-ASN : angle 1.87247 ( 117) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 426 time to evaluate : 1.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.8773 (p90) cc_final: 0.8380 (p90) REVERT: A 285 ILE cc_start: 0.8894 (mt) cc_final: 0.8635 (mt) REVERT: A 380 TYR cc_start: 0.8492 (m-80) cc_final: 0.7963 (m-80) REVERT: A 732 THR cc_start: 0.9242 (m) cc_final: 0.9026 (p) REVERT: A 736 VAL cc_start: 0.9222 (t) cc_final: 0.8799 (p) REVERT: A 740 MET cc_start: 0.8509 (ttt) cc_final: 0.8240 (ttm) REVERT: A 990 GLU cc_start: 0.9173 (mt-10) cc_final: 0.8724 (pt0) REVERT: A 1023 ASN cc_start: 0.8816 (m-40) cc_final: 0.8497 (t0) REVERT: B 92 PHE cc_start: 0.8736 (t80) cc_final: 0.6941 (t80) REVERT: B 104 TRP cc_start: 0.7903 (m-90) cc_final: 0.7137 (m-90) REVERT: B 201 PHE cc_start: 0.8946 (t80) cc_final: 0.8267 (t80) REVERT: B 238 PHE cc_start: 0.8734 (p90) cc_final: 0.8457 (p90) REVERT: B 285 ILE cc_start: 0.8854 (mt) cc_final: 0.8555 (mt) REVERT: B 297 SER cc_start: 0.8481 (m) cc_final: 0.8130 (p) REVERT: B 380 TYR cc_start: 0.8442 (m-80) cc_final: 0.7893 (m-80) REVERT: B 402 ILE cc_start: 0.8493 (pt) cc_final: 0.8169 (pt) REVERT: B 610 VAL cc_start: 0.9528 (t) cc_final: 0.9282 (p) REVERT: B 724 THR cc_start: 0.9186 (m) cc_final: 0.8884 (p) REVERT: B 740 MET cc_start: 0.8478 (ttt) cc_final: 0.8267 (ttt) REVERT: B 990 GLU cc_start: 0.8942 (mt-10) cc_final: 0.8493 (pt0) REVERT: B 994 ASP cc_start: 0.8984 (m-30) cc_final: 0.8636 (m-30) REVERT: C 92 PHE cc_start: 0.8560 (t80) cc_final: 0.7140 (t80) REVERT: C 104 TRP cc_start: 0.7968 (m-90) cc_final: 0.7264 (m-90) REVERT: C 285 ILE cc_start: 0.8943 (mt) cc_final: 0.8679 (mt) REVERT: C 297 SER cc_start: 0.8474 (m) cc_final: 0.8195 (p) REVERT: C 380 TYR cc_start: 0.8602 (m-80) cc_final: 0.8319 (m-80) REVERT: C 724 THR cc_start: 0.9326 (m) cc_final: 0.9009 (p) REVERT: C 732 THR cc_start: 0.9144 (m) cc_final: 0.8857 (p) REVERT: C 736 VAL cc_start: 0.9073 (t) cc_final: 0.8639 (p) REVERT: C 869 MET cc_start: 0.8600 (mtt) cc_final: 0.8142 (mtp) REVERT: C 870 ILE cc_start: 0.9473 (mm) cc_final: 0.9272 (pt) REVERT: C 884 SER cc_start: 0.8742 (p) cc_final: 0.8279 (m) REVERT: C 990 GLU cc_start: 0.9226 (mt-10) cc_final: 0.8959 (pt0) REVERT: C 1023 ASN cc_start: 0.8664 (m-40) cc_final: 0.8360 (t0) REVERT: C 1029 MET cc_start: 0.9060 (tpp) cc_final: 0.8404 (tpp) outliers start: 12 outliers final: 0 residues processed: 438 average time/residue: 0.1743 time to fit residues: 123.6169 Evaluate side-chains 195 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 0.5980 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 6.9990 chunk 298 optimal weight: 0.8980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 GLN A1005 GLN B 321 GLN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN C 321 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.134255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.083921 restraints weight = 110226.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.083881 restraints weight = 70786.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.085148 restraints weight = 43802.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.085252 restraints weight = 32994.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.085518 restraints weight = 32618.964| |-----------------------------------------------------------------------------| r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.109 31434 Z= 0.228 Angle : 0.660 15.481 42864 Z= 0.341 Chirality : 0.045 0.272 4935 Planarity : 0.005 0.151 5451 Dihedral : 6.658 59.876 5289 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.15 % Allowed : 1.89 % Favored : 97.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.13), residues: 3798 helix: 1.16 (0.20), residues: 729 sheet: 0.32 (0.15), residues: 996 loop : -0.46 (0.13), residues: 2073 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 357 TYR 0.032 0.002 TYR B 200 PHE 0.027 0.002 PHE B 377 TRP 0.024 0.001 TRP B 64 HIS 0.012 0.002 HIS D 35 Details of bonding type rmsd covalent geometry : bond 0.00515 (31332) covalent geometry : angle 0.64750 (42606) SS BOND : bond 0.00680 ( 48) SS BOND : angle 1.62014 ( 96) hydrogen bonds : bond 0.04850 ( 1229) hydrogen bonds : angle 6.24324 ( 3381) link_BETA1-4 : bond 0.00381 ( 15) link_BETA1-4 : angle 1.02132 ( 45) link_NAG-ASN : bond 0.00412 ( 39) link_NAG-ASN : angle 2.08930 ( 117) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 252 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.8894 (p90) cc_final: 0.8605 (p90) REVERT: A 380 TYR cc_start: 0.8828 (m-80) cc_final: 0.8230 (m-80) REVERT: A 732 THR cc_start: 0.9233 (m) cc_final: 0.8915 (p) REVERT: A 900 MET cc_start: 0.8967 (mmm) cc_final: 0.8763 (mmt) REVERT: A 902 MET cc_start: 0.9378 (mmm) cc_final: 0.8995 (tpp) REVERT: A 936 ASP cc_start: 0.9031 (t0) cc_final: 0.8734 (t0) REVERT: A 968 SER cc_start: 0.9488 (m) cc_final: 0.9162 (p) REVERT: A 990 GLU cc_start: 0.9385 (mt-10) cc_final: 0.9044 (pt0) REVERT: B 92 PHE cc_start: 0.8801 (t80) cc_final: 0.8539 (t80) REVERT: B 238 PHE cc_start: 0.9029 (p90) cc_final: 0.8548 (p90) REVERT: B 297 SER cc_start: 0.8742 (m) cc_final: 0.8327 (p) REVERT: B 380 TYR cc_start: 0.8971 (m-80) cc_final: 0.8143 (m-80) REVERT: B 402 ILE cc_start: 0.8663 (pt) cc_final: 0.8370 (pt) REVERT: B 610 VAL cc_start: 0.9638 (t) cc_final: 0.9353 (p) REVERT: B 731 MET cc_start: 0.8871 (ptm) cc_final: 0.8609 (ptp) REVERT: B 737 ASP cc_start: 0.8671 (t70) cc_final: 0.7938 (p0) REVERT: B 740 MET cc_start: 0.8594 (ttt) cc_final: 0.7495 (ttt) REVERT: B 869 MET cc_start: 0.8733 (mtm) cc_final: 0.8289 (mtp) REVERT: B 936 ASP cc_start: 0.8878 (t0) cc_final: 0.8593 (t0) REVERT: B 990 GLU cc_start: 0.9222 (mt-10) cc_final: 0.9011 (pt0) REVERT: C 92 PHE cc_start: 0.9046 (t80) cc_final: 0.8779 (t80) REVERT: C 238 PHE cc_start: 0.8955 (p90) cc_final: 0.8329 (p90) REVERT: C 297 SER cc_start: 0.8865 (m) cc_final: 0.8458 (p) REVERT: C 380 TYR cc_start: 0.8902 (m-80) cc_final: 0.8507 (m-80) REVERT: C 387 LEU cc_start: 0.9402 (mt) cc_final: 0.9155 (mt) REVERT: C 402 ILE cc_start: 0.8609 (pt) cc_final: 0.8372 (pt) REVERT: C 731 MET cc_start: 0.9109 (ptm) cc_final: 0.8839 (ptp) REVERT: C 732 THR cc_start: 0.8817 (m) cc_final: 0.8558 (p) REVERT: C 740 MET cc_start: 0.8601 (ttt) cc_final: 0.8389 (ttt) REVERT: C 764 ASN cc_start: 0.8944 (t0) cc_final: 0.8511 (t0) REVERT: C 773 GLU cc_start: 0.8659 (tt0) cc_final: 0.7680 (tm-30) REVERT: C 869 MET cc_start: 0.8943 (mtt) cc_final: 0.8302 (mtp) REVERT: C 870 ILE cc_start: 0.9472 (mm) cc_final: 0.9267 (mt) REVERT: C 884 SER cc_start: 0.8790 (p) cc_final: 0.8502 (m) REVERT: C 900 MET cc_start: 0.8472 (tpp) cc_final: 0.8216 (tpp) REVERT: C 936 ASP cc_start: 0.8928 (t0) cc_final: 0.8688 (t0) REVERT: C 1029 MET cc_start: 0.9007 (tpp) cc_final: 0.7900 (tpp) REVERT: C 1050 MET cc_start: 0.8784 (ptp) cc_final: 0.8449 (ptm) REVERT: D 110 MET cc_start: 0.5290 (mmp) cc_final: 0.4507 (mmp) REVERT: F 110 MET cc_start: 0.5570 (mmp) cc_final: 0.4645 (mmp) REVERT: H 110 MET cc_start: 0.5794 (mmp) cc_final: 0.5081 (mmp) outliers start: 5 outliers final: 1 residues processed: 257 average time/residue: 0.1678 time to fit residues: 71.6262 Evaluate side-chains 182 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 181 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 213 optimal weight: 0.0770 chunk 190 optimal weight: 0.7980 chunk 238 optimal weight: 8.9990 chunk 38 optimal weight: 9.9990 chunk 28 optimal weight: 3.9990 chunk 275 optimal weight: 0.9990 chunk 225 optimal weight: 20.0000 chunk 278 optimal weight: 0.6980 chunk 173 optimal weight: 0.9990 chunk 200 optimal weight: 0.6980 chunk 77 optimal weight: 0.4980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN A 955 ASN A1005 GLN B1005 GLN C 901 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.142865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.096900 restraints weight = 109992.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.095046 restraints weight = 75643.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.095023 restraints weight = 49061.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.095402 restraints weight = 52525.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.095665 restraints weight = 41202.391| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 31434 Z= 0.119 Angle : 0.542 15.900 42864 Z= 0.281 Chirality : 0.043 0.258 4935 Planarity : 0.004 0.039 5451 Dihedral : 5.895 59.864 5289 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.09 % Allowed : 1.22 % Favored : 98.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.30 (0.13), residues: 3798 helix: 1.62 (0.20), residues: 702 sheet: 0.43 (0.15), residues: 1020 loop : -0.37 (0.14), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 273 TYR 0.014 0.001 TYR A 904 PHE 0.021 0.001 PHE A 194 TRP 0.020 0.001 TRP A 104 HIS 0.006 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00266 (31332) covalent geometry : angle 0.52911 (42606) SS BOND : bond 0.00386 ( 48) SS BOND : angle 1.83640 ( 96) hydrogen bonds : bond 0.03983 ( 1229) hydrogen bonds : angle 5.65526 ( 3381) link_BETA1-4 : bond 0.00434 ( 15) link_BETA1-4 : angle 0.95784 ( 45) link_NAG-ASN : bond 0.00296 ( 39) link_NAG-ASN : angle 1.55785 ( 117) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 232 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.8020 (m-10) cc_final: 0.7682 (m-10) REVERT: A 388 ASN cc_start: 0.8008 (p0) cc_final: 0.7327 (m-40) REVERT: A 773 GLU cc_start: 0.8096 (tt0) cc_final: 0.7754 (tm-30) REVERT: A 802 PHE cc_start: 0.8669 (m-80) cc_final: 0.8438 (m-10) REVERT: A 936 ASP cc_start: 0.8968 (t0) cc_final: 0.8628 (t0) REVERT: A 968 SER cc_start: 0.9441 (m) cc_final: 0.9161 (p) REVERT: A 984 LEU cc_start: 0.8596 (mm) cc_final: 0.7877 (tp) REVERT: A 990 GLU cc_start: 0.9365 (mt-10) cc_final: 0.9006 (pt0) REVERT: B 92 PHE cc_start: 0.8646 (t80) cc_final: 0.7227 (t80) REVERT: B 104 TRP cc_start: 0.8469 (m-90) cc_final: 0.7646 (m-10) REVERT: B 238 PHE cc_start: 0.9084 (p90) cc_final: 0.8751 (p90) REVERT: B 297 SER cc_start: 0.8716 (m) cc_final: 0.8284 (p) REVERT: B 380 TYR cc_start: 0.8932 (m-80) cc_final: 0.8465 (m-80) REVERT: B 387 LEU cc_start: 0.9425 (mt) cc_final: 0.9180 (mt) REVERT: B 388 ASN cc_start: 0.7781 (p0) cc_final: 0.7188 (m-40) REVERT: B 610 VAL cc_start: 0.9585 (t) cc_final: 0.9279 (p) REVERT: B 731 MET cc_start: 0.8695 (ptm) cc_final: 0.8364 (ptp) REVERT: B 737 ASP cc_start: 0.8550 (t70) cc_final: 0.7940 (p0) REVERT: B 740 MET cc_start: 0.8632 (ttt) cc_final: 0.7507 (ttt) REVERT: B 773 GLU cc_start: 0.8472 (tt0) cc_final: 0.7622 (tm-30) REVERT: B 869 MET cc_start: 0.8779 (mtm) cc_final: 0.8349 (mtp) REVERT: B 936 ASP cc_start: 0.8921 (t0) cc_final: 0.8702 (t0) REVERT: B 990 GLU cc_start: 0.9258 (mt-10) cc_final: 0.8999 (pt0) REVERT: C 92 PHE cc_start: 0.9162 (t80) cc_final: 0.8721 (t80) REVERT: C 104 TRP cc_start: 0.8507 (m-90) cc_final: 0.7953 (m-90) REVERT: C 223 LEU cc_start: 0.8792 (mp) cc_final: 0.8304 (mp) REVERT: C 238 PHE cc_start: 0.9011 (p90) cc_final: 0.8618 (p90) REVERT: C 297 SER cc_start: 0.8794 (m) cc_final: 0.8393 (p) REVERT: C 387 LEU cc_start: 0.9346 (mt) cc_final: 0.8932 (mt) REVERT: C 388 ASN cc_start: 0.8567 (p0) cc_final: 0.8114 (m-40) REVERT: C 402 ILE cc_start: 0.8661 (pt) cc_final: 0.8395 (pt) REVERT: C 414 GLN cc_start: 0.8632 (mm-40) cc_final: 0.7935 (tm-30) REVERT: C 731 MET cc_start: 0.8968 (ptm) cc_final: 0.8620 (ptp) REVERT: C 732 THR cc_start: 0.8869 (m) cc_final: 0.8636 (p) REVERT: C 764 ASN cc_start: 0.8936 (t0) cc_final: 0.8480 (t0) REVERT: C 869 MET cc_start: 0.8832 (mtt) cc_final: 0.8399 (mtp) REVERT: C 884 SER cc_start: 0.8615 (p) cc_final: 0.8357 (m) REVERT: C 936 ASP cc_start: 0.8934 (t0) cc_final: 0.8686 (t0) REVERT: C 1029 MET cc_start: 0.8941 (tpp) cc_final: 0.7952 (tpp) REVERT: D 110 MET cc_start: 0.5218 (mmp) cc_final: 0.4310 (mmp) REVERT: F 110 MET cc_start: 0.5850 (mmp) cc_final: 0.4891 (mmp) REVERT: H 110 MET cc_start: 0.5605 (mmp) cc_final: 0.4876 (mmp) outliers start: 3 outliers final: 0 residues processed: 235 average time/residue: 0.1640 time to fit residues: 63.2816 Evaluate side-chains 164 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 370 optimal weight: 7.9990 chunk 252 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 163 optimal weight: 0.8980 chunk 316 optimal weight: 0.6980 chunk 106 optimal weight: 30.0000 chunk 101 optimal weight: 0.7980 chunk 29 optimal weight: 7.9990 chunk 21 optimal weight: 1.9990 chunk 300 optimal weight: 3.9990 chunk 253 optimal weight: 10.0000 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN A1005 GLN B 901 GLN C 239 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.133220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.084811 restraints weight = 108778.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.083535 restraints weight = 69771.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.083692 restraints weight = 50409.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.084245 restraints weight = 45615.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.084307 restraints weight = 39966.397| |-----------------------------------------------------------------------------| r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 31434 Z= 0.161 Angle : 0.553 12.673 42864 Z= 0.286 Chirality : 0.043 0.243 4935 Planarity : 0.004 0.041 5451 Dihedral : 5.529 59.669 5289 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.12 % Allowed : 1.61 % Favored : 98.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.14), residues: 3798 helix: 1.48 (0.20), residues: 702 sheet: 0.48 (0.15), residues: 1023 loop : -0.29 (0.14), residues: 2073 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 403 TYR 0.018 0.001 TYR A1067 PHE 0.032 0.001 PHE C 135 TRP 0.008 0.001 TRP B 64 HIS 0.006 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00364 (31332) covalent geometry : angle 0.54351 (42606) SS BOND : bond 0.00341 ( 48) SS BOND : angle 1.47575 ( 96) hydrogen bonds : bond 0.04017 ( 1229) hydrogen bonds : angle 5.54486 ( 3381) link_BETA1-4 : bond 0.00282 ( 15) link_BETA1-4 : angle 1.03843 ( 45) link_NAG-ASN : bond 0.00285 ( 39) link_NAG-ASN : angle 1.51111 ( 117) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 215 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.7656 (m-90) cc_final: 0.7328 (m-10) REVERT: A 153 MET cc_start: 0.7174 (ptp) cc_final: 0.6875 (ptm) REVERT: A 388 ASN cc_start: 0.7842 (p0) cc_final: 0.7331 (m-40) REVERT: A 773 GLU cc_start: 0.8137 (tt0) cc_final: 0.7634 (tm-30) REVERT: A 936 ASP cc_start: 0.8943 (t0) cc_final: 0.8609 (t0) REVERT: A 968 SER cc_start: 0.9410 (m) cc_final: 0.9088 (p) REVERT: A 990 GLU cc_start: 0.9313 (mt-10) cc_final: 0.8968 (pt0) REVERT: B 92 PHE cc_start: 0.8384 (t80) cc_final: 0.6980 (t80) REVERT: B 104 TRP cc_start: 0.8186 (m-90) cc_final: 0.7402 (m-90) REVERT: B 153 MET cc_start: 0.6431 (ptp) cc_final: 0.6158 (ptm) REVERT: B 238 PHE cc_start: 0.8930 (p90) cc_final: 0.8648 (p90) REVERT: B 297 SER cc_start: 0.8720 (m) cc_final: 0.8358 (p) REVERT: B 387 LEU cc_start: 0.9331 (mt) cc_final: 0.8987 (mt) REVERT: B 388 ASN cc_start: 0.7651 (p0) cc_final: 0.7135 (m-40) REVERT: B 402 ILE cc_start: 0.8434 (pt) cc_final: 0.8213 (pt) REVERT: B 610 VAL cc_start: 0.9576 (t) cc_final: 0.9332 (p) REVERT: B 731 MET cc_start: 0.8755 (ptm) cc_final: 0.8473 (ptp) REVERT: B 737 ASP cc_start: 0.8521 (t70) cc_final: 0.7929 (p0) REVERT: B 740 MET cc_start: 0.8550 (ttt) cc_final: 0.7347 (ttt) REVERT: B 773 GLU cc_start: 0.8490 (tt0) cc_final: 0.7875 (tm-30) REVERT: B 869 MET cc_start: 0.8748 (mtm) cc_final: 0.8445 (mtp) REVERT: B 936 ASP cc_start: 0.8914 (t0) cc_final: 0.8634 (t0) REVERT: B 968 SER cc_start: 0.9226 (m) cc_final: 0.8990 (t) REVERT: B 990 GLU cc_start: 0.9187 (mt-10) cc_final: 0.8971 (pt0) REVERT: C 104 TRP cc_start: 0.7829 (m-90) cc_final: 0.6792 (m-10) REVERT: C 238 PHE cc_start: 0.8701 (p90) cc_final: 0.8481 (p90) REVERT: C 297 SER cc_start: 0.8843 (m) cc_final: 0.8418 (p) REVERT: C 387 LEU cc_start: 0.9280 (mt) cc_final: 0.8975 (mt) REVERT: C 388 ASN cc_start: 0.8569 (p0) cc_final: 0.8293 (m-40) REVERT: C 402 ILE cc_start: 0.8517 (pt) cc_final: 0.8270 (pt) REVERT: C 414 GLN cc_start: 0.8781 (mm-40) cc_final: 0.8075 (tm-30) REVERT: C 731 MET cc_start: 0.9017 (ptm) cc_final: 0.8654 (ptp) REVERT: C 732 THR cc_start: 0.8910 (m) cc_final: 0.8655 (p) REVERT: C 764 ASN cc_start: 0.8988 (t0) cc_final: 0.8587 (t0) REVERT: C 869 MET cc_start: 0.8866 (mtt) cc_final: 0.8410 (mtp) REVERT: C 1029 MET cc_start: 0.8824 (tpp) cc_final: 0.7781 (tpp) REVERT: D 83 MET cc_start: -0.6933 (mmt) cc_final: -0.8263 (mtt) REVERT: D 110 MET cc_start: 0.5612 (mmp) cc_final: 0.4804 (mmp) REVERT: F 83 MET cc_start: -0.6834 (mmt) cc_final: -0.8271 (mtt) REVERT: F 110 MET cc_start: 0.5942 (mmp) cc_final: 0.4921 (mmp) REVERT: H 110 MET cc_start: 0.5536 (mmp) cc_final: 0.4695 (mmp) outliers start: 4 outliers final: 0 residues processed: 218 average time/residue: 0.1779 time to fit residues: 64.4665 Evaluate side-chains 153 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 1.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 326 optimal weight: 50.0000 chunk 155 optimal weight: 1.9990 chunk 248 optimal weight: 2.9990 chunk 209 optimal weight: 1.9990 chunk 367 optimal weight: 6.9990 chunk 317 optimal weight: 0.1980 chunk 362 optimal weight: 0.2980 chunk 244 optimal weight: 10.0000 chunk 130 optimal weight: 8.9990 chunk 69 optimal weight: 2.9990 chunk 176 optimal weight: 0.5980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN D 35 HIS F 35 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.133225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.084577 restraints weight = 110215.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.084001 restraints weight = 73198.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.083511 restraints weight = 51690.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.084103 restraints weight = 48699.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.084123 restraints weight = 43157.794| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 31434 Z= 0.134 Angle : 0.522 13.550 42864 Z= 0.270 Chirality : 0.043 0.209 4935 Planarity : 0.003 0.044 5451 Dihedral : 5.095 59.361 5289 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.03 % Allowed : 1.31 % Favored : 98.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.14), residues: 3798 helix: 1.47 (0.20), residues: 702 sheet: 0.54 (0.15), residues: 1023 loop : -0.24 (0.14), residues: 2073 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1039 TYR 0.016 0.001 TYR B 904 PHE 0.021 0.001 PHE C 906 TRP 0.008 0.001 TRP C 104 HIS 0.006 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00302 (31332) covalent geometry : angle 0.51169 (42606) SS BOND : bond 0.00407 ( 48) SS BOND : angle 1.24622 ( 96) hydrogen bonds : bond 0.03780 ( 1229) hydrogen bonds : angle 5.36988 ( 3381) link_BETA1-4 : bond 0.00343 ( 15) link_BETA1-4 : angle 1.00979 ( 45) link_NAG-ASN : bond 0.00313 ( 39) link_NAG-ASN : angle 1.73141 ( 117) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 210 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.7875 (m-90) cc_final: 0.7443 (m-10) REVERT: A 153 MET cc_start: 0.7132 (ptp) cc_final: 0.6758 (ptm) REVERT: A 201 PHE cc_start: 0.8827 (t80) cc_final: 0.8553 (t80) REVERT: A 388 ASN cc_start: 0.7949 (p0) cc_final: 0.7357 (m-40) REVERT: A 902 MET cc_start: 0.9393 (mmm) cc_final: 0.9043 (mmt) REVERT: A 936 ASP cc_start: 0.9059 (t0) cc_final: 0.8697 (t0) REVERT: A 968 SER cc_start: 0.9444 (m) cc_final: 0.9087 (p) REVERT: A 990 GLU cc_start: 0.9374 (mt-10) cc_final: 0.8993 (pt0) REVERT: B 60 SER cc_start: 0.8821 (t) cc_final: 0.8544 (p) REVERT: B 92 PHE cc_start: 0.8679 (t80) cc_final: 0.7330 (t80) REVERT: B 104 TRP cc_start: 0.8374 (m-90) cc_final: 0.7526 (m-90) REVERT: B 153 MET cc_start: 0.6682 (ptp) cc_final: 0.6414 (ptm) REVERT: B 238 PHE cc_start: 0.9049 (p90) cc_final: 0.8684 (p90) REVERT: B 297 SER cc_start: 0.8651 (m) cc_final: 0.8249 (p) REVERT: B 387 LEU cc_start: 0.9269 (mt) cc_final: 0.8995 (mt) REVERT: B 388 ASN cc_start: 0.7807 (p0) cc_final: 0.7247 (m-40) REVERT: B 392 PHE cc_start: 0.8741 (m-80) cc_final: 0.7930 (m-80) REVERT: B 402 ILE cc_start: 0.8487 (pt) cc_final: 0.8248 (pt) REVERT: B 414 GLN cc_start: 0.8846 (mm-40) cc_final: 0.8332 (tm-30) REVERT: B 610 VAL cc_start: 0.9565 (t) cc_final: 0.9333 (p) REVERT: B 731 MET cc_start: 0.8746 (ptm) cc_final: 0.8426 (ptp) REVERT: B 737 ASP cc_start: 0.8433 (t70) cc_final: 0.7893 (p0) REVERT: B 740 MET cc_start: 0.8522 (ttt) cc_final: 0.7479 (ttt) REVERT: B 773 GLU cc_start: 0.8495 (tt0) cc_final: 0.7823 (tm-30) REVERT: B 869 MET cc_start: 0.8624 (mtm) cc_final: 0.8412 (mtp) REVERT: B 902 MET cc_start: 0.9489 (mmm) cc_final: 0.9022 (mmm) REVERT: B 936 ASP cc_start: 0.8969 (t0) cc_final: 0.8670 (t0) REVERT: B 990 GLU cc_start: 0.9227 (mt-10) cc_final: 0.8979 (pt0) REVERT: C 92 PHE cc_start: 0.8853 (t80) cc_final: 0.8292 (t80) REVERT: C 104 TRP cc_start: 0.8020 (m-90) cc_final: 0.7572 (m-90) REVERT: C 238 PHE cc_start: 0.8829 (p90) cc_final: 0.8572 (p90) REVERT: C 297 SER cc_start: 0.8865 (m) cc_final: 0.8421 (p) REVERT: C 387 LEU cc_start: 0.9337 (mt) cc_final: 0.8959 (mt) REVERT: C 388 ASN cc_start: 0.8624 (p0) cc_final: 0.8297 (m-40) REVERT: C 402 ILE cc_start: 0.8607 (pt) cc_final: 0.8325 (pt) REVERT: C 414 GLN cc_start: 0.8862 (mm-40) cc_final: 0.8096 (tm-30) REVERT: C 731 MET cc_start: 0.9018 (ptm) cc_final: 0.8649 (ptp) REVERT: C 732 THR cc_start: 0.8938 (m) cc_final: 0.8665 (p) REVERT: C 764 ASN cc_start: 0.8977 (t0) cc_final: 0.8575 (t0) REVERT: C 869 MET cc_start: 0.8905 (mtt) cc_final: 0.8460 (mtp) REVERT: C 900 MET cc_start: 0.8917 (mmm) cc_final: 0.8523 (tpp) REVERT: D 83 MET cc_start: -0.6727 (mmt) cc_final: -0.8309 (mtt) REVERT: D 110 MET cc_start: 0.5273 (mmp) cc_final: 0.4357 (mmp) REVERT: F 83 MET cc_start: -0.6468 (mmt) cc_final: -0.8140 (mtt) REVERT: F 110 MET cc_start: 0.5899 (mmp) cc_final: 0.4858 (mmp) REVERT: H 110 MET cc_start: 0.5616 (mmp) cc_final: 0.4768 (mmp) outliers start: 1 outliers final: 0 residues processed: 211 average time/residue: 0.1728 time to fit residues: 60.8141 Evaluate side-chains 158 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 290 optimal weight: 1.9990 chunk 152 optimal weight: 20.0000 chunk 69 optimal weight: 0.9980 chunk 245 optimal weight: 2.9990 chunk 296 optimal weight: 0.6980 chunk 350 optimal weight: 50.0000 chunk 304 optimal weight: 1.9990 chunk 250 optimal weight: 10.0000 chunk 129 optimal weight: 20.0000 chunk 299 optimal weight: 2.9990 chunk 121 optimal weight: 7.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 655 HIS A 955 ASN A1005 GLN A1119 ASN B 239 GLN B 655 HIS B 913 GLN B1010 GLN B1119 ASN C 613 GLN C 655 HIS C1119 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.133598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.082481 restraints weight = 106241.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.079717 restraints weight = 79255.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.080068 restraints weight = 56891.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.080243 restraints weight = 49669.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.080419 restraints weight = 42077.718| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 31434 Z= 0.199 Angle : 0.573 12.741 42864 Z= 0.295 Chirality : 0.043 0.232 4935 Planarity : 0.004 0.053 5451 Dihedral : 4.901 58.300 5289 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.03 % Allowed : 1.13 % Favored : 98.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.30 (0.14), residues: 3798 helix: 1.20 (0.20), residues: 702 sheet: 0.56 (0.16), residues: 975 loop : -0.27 (0.14), residues: 2121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A1107 TYR 0.023 0.001 TYR A1067 PHE 0.019 0.002 PHE A 927 TRP 0.008 0.001 TRP B 104 HIS 0.007 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00446 (31332) covalent geometry : angle 0.56399 (42606) SS BOND : bond 0.00385 ( 48) SS BOND : angle 1.43699 ( 96) hydrogen bonds : bond 0.04115 ( 1229) hydrogen bonds : angle 5.46742 ( 3381) link_BETA1-4 : bond 0.00298 ( 15) link_BETA1-4 : angle 1.12466 ( 45) link_NAG-ASN : bond 0.00342 ( 39) link_NAG-ASN : angle 1.51488 ( 117) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 200 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.7855 (m-90) cc_final: 0.7574 (m-10) REVERT: A 153 MET cc_start: 0.7665 (ptp) cc_final: 0.7333 (ptm) REVERT: A 201 PHE cc_start: 0.9117 (t80) cc_final: 0.8596 (t80) REVERT: A 388 ASN cc_start: 0.7887 (p0) cc_final: 0.7249 (m-40) REVERT: A 773 GLU cc_start: 0.8194 (tt0) cc_final: 0.7513 (tm-30) REVERT: A 902 MET cc_start: 0.9484 (mmm) cc_final: 0.9097 (mmt) REVERT: A 936 ASP cc_start: 0.9075 (t0) cc_final: 0.8722 (t0) REVERT: A 968 SER cc_start: 0.9431 (m) cc_final: 0.9104 (t) REVERT: A 990 GLU cc_start: 0.9386 (mt-10) cc_final: 0.9004 (pt0) REVERT: B 60 SER cc_start: 0.8813 (t) cc_final: 0.8572 (t) REVERT: B 104 TRP cc_start: 0.8338 (m-90) cc_final: 0.7654 (m-90) REVERT: B 153 MET cc_start: 0.6692 (ptp) cc_final: 0.6411 (ptm) REVERT: B 238 PHE cc_start: 0.9117 (p90) cc_final: 0.8782 (p90) REVERT: B 297 SER cc_start: 0.8814 (m) cc_final: 0.8412 (p) REVERT: B 387 LEU cc_start: 0.9333 (mt) cc_final: 0.9006 (mt) REVERT: B 388 ASN cc_start: 0.7993 (p0) cc_final: 0.7370 (m-40) REVERT: B 392 PHE cc_start: 0.8764 (m-80) cc_final: 0.8056 (m-80) REVERT: B 414 GLN cc_start: 0.8915 (mm-40) cc_final: 0.8388 (tm-30) REVERT: B 610 VAL cc_start: 0.9601 (t) cc_final: 0.9383 (p) REVERT: B 731 MET cc_start: 0.8837 (ptm) cc_final: 0.8473 (ptp) REVERT: B 737 ASP cc_start: 0.8540 (t70) cc_final: 0.7896 (p0) REVERT: B 740 MET cc_start: 0.8400 (ttt) cc_final: 0.7204 (ttt) REVERT: B 773 GLU cc_start: 0.8460 (tt0) cc_final: 0.7686 (tm-30) REVERT: B 869 MET cc_start: 0.8840 (mtm) cc_final: 0.8429 (mtp) REVERT: B 900 MET cc_start: 0.8667 (mmt) cc_final: 0.8214 (mmt) REVERT: B 902 MET cc_start: 0.9649 (mmm) cc_final: 0.9283 (mmm) REVERT: B 936 ASP cc_start: 0.9075 (t0) cc_final: 0.8754 (t0) REVERT: B 968 SER cc_start: 0.9159 (m) cc_final: 0.8903 (t) REVERT: C 104 TRP cc_start: 0.8141 (m-90) cc_final: 0.7520 (m-90) REVERT: C 297 SER cc_start: 0.8894 (m) cc_final: 0.8430 (p) REVERT: C 377 PHE cc_start: 0.8691 (t80) cc_final: 0.8441 (t80) REVERT: C 387 LEU cc_start: 0.9446 (mt) cc_final: 0.9053 (mt) REVERT: C 388 ASN cc_start: 0.8598 (p0) cc_final: 0.8177 (m-40) REVERT: C 402 ILE cc_start: 0.8597 (pt) cc_final: 0.8315 (pt) REVERT: C 414 GLN cc_start: 0.8896 (mm-40) cc_final: 0.8136 (tm-30) REVERT: C 731 MET cc_start: 0.9039 (ptm) cc_final: 0.8672 (ptp) REVERT: C 732 THR cc_start: 0.9000 (m) cc_final: 0.8747 (p) REVERT: C 764 ASN cc_start: 0.9125 (t0) cc_final: 0.8726 (t0) REVERT: C 869 MET cc_start: 0.9021 (mtt) cc_final: 0.8580 (mtp) REVERT: C 1029 MET cc_start: 0.9068 (tpp) cc_final: 0.7799 (tpp) REVERT: D 83 MET cc_start: -0.6743 (mmt) cc_final: -0.8207 (mtt) REVERT: D 110 MET cc_start: 0.5383 (mmp) cc_final: 0.4517 (mmp) REVERT: F 83 MET cc_start: -0.6272 (mmt) cc_final: -0.7835 (mtt) REVERT: F 110 MET cc_start: 0.5496 (mmp) cc_final: 0.4632 (mmp) REVERT: H 110 MET cc_start: 0.5894 (mmp) cc_final: 0.5075 (mmp) outliers start: 1 outliers final: 0 residues processed: 201 average time/residue: 0.1701 time to fit residues: 57.6304 Evaluate side-chains 144 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 65.9403 > 50: distance: 33 - 196: 37.311 distance: 36 - 193: 35.832 distance: 45 - 181: 33.969 distance: 48 - 178: 26.563 distance: 59 - 163: 11.792 distance: 62 - 160: 29.451 distance: 116 - 189: 30.580 distance: 119 - 186: 17.015 distance: 126 - 174: 36.026 distance: 129 - 171: 28.106 distance: 136 - 155: 36.374 distance: 139 - 152: 24.950 distance: 147 - 152: 21.925 distance: 152 - 153: 9.837 distance: 153 - 154: 20.358 distance: 153 - 156: 5.300 distance: 154 - 155: 11.965 distance: 154 - 160: 4.337 distance: 156 - 157: 18.109 distance: 157 - 158: 16.439 distance: 157 - 159: 7.844 distance: 160 - 161: 11.680 distance: 161 - 162: 26.185 distance: 161 - 164: 11.193 distance: 162 - 163: 3.103 distance: 162 - 171: 19.963 distance: 164 - 165: 27.484 distance: 165 - 167: 16.353 distance: 166 - 168: 27.712 distance: 167 - 169: 12.868 distance: 168 - 170: 3.487 distance: 169 - 170: 10.220 distance: 171 - 172: 19.823 distance: 172 - 173: 8.866 distance: 172 - 175: 8.887 distance: 173 - 174: 27.283 distance: 175 - 176: 32.883 distance: 175 - 177: 41.576 distance: 178 - 179: 11.216 distance: 179 - 180: 32.270 distance: 179 - 182: 9.768 distance: 180 - 181: 6.198 distance: 180 - 186: 15.788 distance: 182 - 183: 36.840 distance: 183 - 184: 11.912 distance: 183 - 185: 19.062 distance: 186 - 187: 15.575 distance: 187 - 188: 9.309 distance: 187 - 190: 29.341 distance: 188 - 189: 43.123 distance: 188 - 193: 3.279 distance: 193 - 194: 13.992 distance: 194 - 195: 25.110 distance: 194 - 197: 22.782 distance: 197 - 198: 22.741 distance: 197 - 199: 9.925 distance: 198 - 200: 4.006 distance: 201 - 202: 7.662 distance: 202 - 203: 12.159 distance: 202 - 205: 32.180 distance: 203 - 204: 15.818 distance: 203 - 207: 20.537 distance: 205 - 206: 10.044 distance: 207 - 208: 13.718 distance: 208 - 209: 17.182 distance: 208 - 211: 8.527 distance: 209 - 210: 26.211 distance: 209 - 218: 49.614 distance: 211 - 212: 20.776 distance: 212 - 213: 27.229 distance: 213 - 214: 7.831 distance: 214 - 215: 32.945 distance: 215 - 216: 13.585 distance: 215 - 217: 25.254 distance: 218 - 219: 26.528 distance: 219 - 220: 21.540 distance: 219 - 222: 22.705 distance: 220 - 226: 40.295 distance: 222 - 223: 11.653 distance: 223 - 224: 40.374 distance: 223 - 225: 30.193 distance: 226 - 227: 34.379 distance: 227 - 228: 11.045 distance: 227 - 230: 43.126 distance: 228 - 229: 5.295 distance: 228 - 235: 28.942 distance: 229 - 249: 29.951 distance: 230 - 231: 16.785 distance: 231 - 232: 53.538 distance: 232 - 233: 47.504 distance: 232 - 234: 3.375