Starting phenix.real_space_refine on Mon Sep 14 04:47:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6wps_21864/09_2026/6wps_21864.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wps_21864/09_2026/6wps_21864.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6wps_21864/09_2026/6wps_21864.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wps_21864/09_2026/6wps_21864.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6wps_21864/09_2026/6wps_21864.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6wps_21864/09_2026/6wps_21864.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6wps_21864/09_2026/6wps_21864.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wps_21864/09_2026/6wps_21864.map" } resolution = 3.1 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= 0.004 sd= 0.066 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 117 5.16 5 C 17909 2.51 5 N 4593 2.21 5 O 5497 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 200 residue(s): 0.14s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 28116 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 7386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 955, 7386 Classifications: {'peptide': 955} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 45, 'TRANS': 909} Chain breaks: 13 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 8, 'ASN:plan1': 2, 'ARG:plan': 2, 'GLU:plan': 5} Unresolved non-hydrogen planarities: 68 Chain: "H" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 937 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 3, 'TRANS': 119} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "L" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 706 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 5, 'TRANS': 96} Chain breaks: 1 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 3, 'GLN:plan1': 2, 'ASP:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "B" Number of atoms: 7395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 955, 7395 Classifications: {'peptide': 955} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 45, 'TRANS': 909} Chain breaks: 13 Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 7, 'ASN:plan1': 2, 'ARG:plan': 2, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 61 Chain: "C" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 937 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 3, 'TRANS': 119} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "D" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 706 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 5, 'TRANS': 96} Chain breaks: 1 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 3, 'GLN:plan1': 2, 'ASP:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "E" Number of atoms: 7395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 955, 7395 Classifications: {'peptide': 955} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 45, 'TRANS': 909} Chain breaks: 13 Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 7, 'ASN:plan1': 2, 'ARG:plan': 2, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 61 Chain: "F" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 937 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 3, 'TRANS': 119} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "G" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 706 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 5, 'TRANS': 96} Chain breaks: 1 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 3, 'GLN:plan1': 2, 'ASP:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Chain: "E" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 5.37, per 1000 atoms: 0.19 Number of scatterers: 28116 At special positions: 0 Unit cell: (148.05, 144.9, 179.55, 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 117 16.00 O 5497 8.00 N 4593 7.00 C 17909 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.09 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.23 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.02 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 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 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.09 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.23 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.02 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 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=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 89 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 166 " distance=2.03 Simple disulfide: pdb=" SG CYS E 291 " - pdb=" SG CYS E 301 " distance=2.02 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.02 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.10 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.23 Simple disulfide: pdb=" SG CYS E 538 " - pdb=" SG CYS E 590 " distance=2.02 Simple disulfide: pdb=" SG CYS E 617 " - pdb=" SG CYS E 649 " distance=2.03 Simple disulfide: pdb=" SG CYS E 662 " - pdb=" SG CYS E 671 " distance=2.04 Simple disulfide: pdb=" SG CYS E 738 " - pdb=" SG CYS E 760 " distance=2.03 Simple disulfide: pdb=" SG CYS E 743 " - pdb=" SG CYS E 749 " distance=2.03 Simple disulfide: pdb=" SG CYS E1032 " - pdb=" SG CYS E1043 " distance=2.02 Simple disulfide: pdb=" SG CYS E1082 " - pdb=" SG CYS E1126 " distance=2.02 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 89 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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 ALPHA1-3 " BMA N 3 " - " MAN N 4 " " BMA S 3 " - " MAN S 4 " " BMA X 3 " - " MAN X 4 " ALPHA1-6 " BMA N 3 " - " MAN N 5 " " BMA S 3 " - " MAN S 5 " " BMA X 3 " - " MAN X 5 " 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 N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " BETA1-6 " NAG N 1 " - " FUC N 6 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG S 1 " - " FUC S 6 " " NAG X 1 " - " FUC X 6 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 234 " " NAG A1304 " - " ASN A 282 " " NAG A1305 " - " ASN A 331 " " NAG A1306 " - " ASN A 603 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 709 " " NAG A1314 " - " ASN A1074 " " NAG A1319 " - " ASN A 165 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 234 " " NAG B1304 " - " ASN B 282 " " NAG B1305 " - " ASN B 331 " " NAG B1306 " - " ASN B 603 " " NAG B1307 " - " ASN B 616 " " NAG B1308 " - " ASN B 657 " " NAG B1309 " - " ASN B 709 " " NAG B1314 " - " ASN B1074 " " NAG B1319 " - " ASN B 165 " " NAG E1301 " - " ASN E 61 " " NAG E1302 " - " ASN E 122 " " NAG E1303 " - " ASN E 234 " " NAG E1304 " - " ASN E 282 " " NAG E1305 " - " ASN E 331 " " NAG E1306 " - " ASN E 603 " " NAG E1307 " - " ASN E 616 " " NAG E1308 " - " ASN E 657 " " NAG E1309 " - " ASN E 709 " " NAG E1314 " - " ASN E1074 " " NAG E1319 " - " ASN E 165 " " NAG I 1 " - " ASN A 717 " " NAG J 1 " - " ASN A 801 " " NAG K 1 " - " ASN A1098 " " NAG M 1 " - " ASN A1134 " " NAG N 1 " - " ASN A 343 " " NAG O 1 " - " ASN B 717 " " NAG P 1 " - " ASN B 801 " " NAG Q 1 " - " ASN B1098 " " NAG R 1 " - " ASN B1134 " " NAG S 1 " - " ASN B 343 " " NAG T 1 " - " ASN E 717 " " NAG U 1 " - " ASN E 801 " " NAG V 1 " - " ASN E1098 " " NAG W 1 " - " ASN E1134 " " NAG X 1 " - " ASN E 343 " Time building additional restraints: 2.20 Conformation dependent library (CDL) restraints added in 883.3 milliseconds 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6576 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 69 sheets defined 21.8% alpha, 36.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.27 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.359A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) 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 759 removed outlier: 6.935A pdb=" N SER A 758 " --> pdb=" O GLN A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 783 removed outlier: 3.541A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 3.975A 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 removed outlier: 3.541A pdb=" N GLY A 885 " --> pdb=" O THR A 881 " (cutoff:3.500A) 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: 4.196A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.530A pdb=" N SER A 940 " --> pdb=" O ASP A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.993A 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: 5.038A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.770A pdb=" N PHE L 84 " --> pdb=" O PRO L 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 351 through 353 No H-bonds generated for 'chain 'B' and resid 351 through 353' Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.359A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) 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 759 removed outlier: 6.935A pdb=" N SER B 758 " --> pdb=" O GLN B 755 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 783 removed outlier: 3.541A pdb=" N GLN B 774 " --> pdb=" O ILE B 770 " (cutoff:3.500A) removed outlier: 3.975A 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 removed outlier: 3.540A pdb=" N GLY B 885 " --> pdb=" O THR B 881 " (cutoff:3.500A) 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: 4.196A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.530A pdb=" N SER B 940 " --> pdb=" O ASP B 936 " (cutoff:3.500A) 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: 3.993A 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: 5.038A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 32 Processing helix chain 'C' and resid 62 through 65 Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'D' and resid 80 through 84 removed outlier: 3.770A pdb=" N PHE D 84 " --> pdb=" O PRO D 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 303 Processing helix chain 'E' and resid 338 through 343 Processing helix chain 'E' and resid 351 through 353 No H-bonds generated for 'chain 'E' and resid 351 through 353' Processing helix chain 'E' and resid 365 through 371 Processing helix chain 'E' and resid 405 through 410 removed outlier: 4.359A pdb=" N ARG E 408 " --> pdb=" O ASP E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 737 through 743 Processing helix chain 'E' and resid 746 through 754 Processing helix chain 'E' and resid 755 through 759 removed outlier: 6.935A pdb=" N SER E 758 " --> pdb=" O GLN E 755 " (cutoff:3.500A) Processing helix chain 'E' and resid 760 through 783 removed outlier: 3.541A pdb=" N GLN E 774 " --> pdb=" O ILE E 770 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ASP E 775 " --> pdb=" O ALA E 771 " (cutoff:3.500A) Processing helix chain 'E' and resid 816 through 824 Processing helix chain 'E' and resid 866 through 885 removed outlier: 3.542A pdb=" N GLY E 885 " --> pdb=" O THR E 881 " (cutoff:3.500A) Processing helix chain 'E' and resid 886 through 891 Processing helix chain 'E' and resid 897 through 908 Processing helix chain 'E' and resid 912 through 919 removed outlier: 4.196A pdb=" N LEU E 916 " --> pdb=" O THR E 912 " (cutoff:3.500A) Processing helix chain 'E' and resid 919 through 941 removed outlier: 3.530A pdb=" N SER E 940 " --> pdb=" O ASP E 936 " (cutoff:3.500A) Processing helix chain 'E' and resid 942 through 944 No H-bonds generated for 'chain 'E' and resid 942 through 944' Processing helix chain 'E' and resid 945 through 965 removed outlier: 3.993A pdb=" N VAL E 951 " --> pdb=" O LYS E 947 " (cutoff:3.500A) Processing helix chain 'E' and resid 966 through 968 No H-bonds generated for 'chain 'E' and resid 966 through 968' Processing helix chain 'E' and resid 976 through 982 Processing helix chain 'E' and resid 985 through 1033 removed outlier: 5.038A pdb=" N VAL E 991 " --> pdb=" O PRO E 987 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 32 Processing helix chain 'F' and resid 62 through 65 Processing helix chain 'F' and resid 87 through 91 Processing helix chain 'G' and resid 80 through 84 removed outlier: 3.769A pdb=" N PHE G 84 " --> pdb=" O PRO G 81 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 7.866A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.368A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.489A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 4.091A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 7.399A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 removed outlier: 6.661A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 83 through 85 removed outlier: 6.736A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASN A 122 " --> pdb=" O ASN A 125 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.287A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.423A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N PHE A 565 " --> pdb=" O PHE E 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 348 through 349 removed outlier: 7.160A pdb=" N ALA A 348 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 9.460A pdb=" N ARG A 403 " --> pdb=" O ALA A 348 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 348 through 349 removed outlier: 7.160A pdb=" N ALA A 348 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 9.460A pdb=" N ARG A 403 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.294A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.898A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N TYR A 660 " --> pdb=" O SER A 698 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.898A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.651A pdb=" N ALA A 701 " --> pdb=" O ILE E 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.466A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.466A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB9, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AC1, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.836A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AC3, first strand: chain 'H' and resid 10 through 11 removed outlier: 7.079A pdb=" N GLU H 10 " --> pdb=" O THR H 124 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 10 through 11 removed outlier: 7.079A pdb=" N GLU H 10 " --> pdb=" O THR H 124 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASN H 116 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 4 through 5 Processing sheet with id=AC6, first strand: chain 'L' and resid 10 through 11 removed outlier: 6.412A pdb=" N LEU L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N TYR L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 10 through 11 Processing sheet with id=AC8, first strand: chain 'B' and resid 28 through 30 removed outlier: 7.866A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.368A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.489A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 42 through 43 removed outlier: 4.091A pdb=" N ALA E 575 " --> pdb=" O GLY E 566 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ASP E 574 " --> pdb=" O ILE E 587 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N GLU E 324 " --> pdb=" O CYS E 538 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 47 through 55 removed outlier: 7.399A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 83 through 85 removed outlier: 6.660A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 83 through 85 removed outlier: 6.736A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASN B 122 " --> pdb=" O ASN B 125 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.288A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 348 through 349 removed outlier: 7.161A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 9.460A pdb=" N ARG B 403 " --> pdb=" O ALA B 348 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 348 through 349 removed outlier: 7.161A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 9.460A pdb=" N ARG B 403 " --> pdb=" O ALA B 348 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.294A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AD9, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.898A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N TYR B 660 " --> pdb=" O SER B 698 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.898A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.467A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.467A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AE5, first strand: chain 'B' and resid 787 through 788 Processing sheet with id=AE6, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.837A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 3 through 6 Processing sheet with id=AE8, first strand: chain 'C' and resid 10 through 11 removed outlier: 7.078A pdb=" N GLU C 10 " --> pdb=" O THR C 124 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ILE C 34 " --> pdb=" O TRP C 50 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N TRP C 50 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 10 through 11 removed outlier: 7.078A pdb=" N GLU C 10 " --> pdb=" O THR C 124 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASN C 116 " --> pdb=" O ARG C 98 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 4 through 5 Processing sheet with id=AF2, first strand: chain 'D' and resid 10 through 11 removed outlier: 6.413A pdb=" N LEU D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N TYR D 50 " --> pdb=" O LEU D 34 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N TRP D 36 " --> pdb=" O LEU D 48 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 10 through 11 Processing sheet with id=AF4, first strand: chain 'E' and resid 28 through 30 removed outlier: 7.866A pdb=" N ASN E 61 " --> pdb=" O TYR E 269 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N TYR E 269 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N SER E 205 " --> pdb=" O PRO E 225 " (cutoff:3.500A) removed outlier: 9.368A pdb=" N HIS E 207 " --> pdb=" O LEU E 223 " (cutoff:3.500A) removed outlier: 9.488A pdb=" N LEU E 223 " --> pdb=" O HIS E 207 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N VAL E 36 " --> pdb=" O LEU E 223 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 47 through 55 removed outlier: 7.399A pdb=" N THR E 274 " --> pdb=" O ASP E 290 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N ASP E 290 " --> pdb=" O THR E 274 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N LEU E 276 " --> pdb=" O ALA E 288 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ALA E 288 " --> pdb=" O LEU E 276 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N LYS E 278 " --> pdb=" O THR E 286 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 83 through 85 removed outlier: 6.661A pdb=" N LEU E 141 " --> pdb=" O LEU E 244 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 83 through 85 removed outlier: 6.736A pdb=" N ALA E 243 " --> pdb=" O ILE E 101 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ILE E 101 " --> pdb=" O ALA E 243 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N ARG E 102 " --> pdb=" O ASN E 121 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASN E 122 " --> pdb=" O ASN E 125 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N PHE E 168 " --> pdb=" O VAL E 130 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 311 through 319 removed outlier: 5.288A pdb=" N ILE E 312 " --> pdb=" O THR E 599 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N THR E 599 " --> pdb=" O ILE E 312 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N GLN E 314 " --> pdb=" O VAL E 597 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL E 597 " --> pdb=" O GLN E 314 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N GLY E 594 " --> pdb=" O GLN E 613 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'E' and resid 348 through 349 removed outlier: 7.160A pdb=" N ALA E 348 " --> pdb=" O VAL E 401 " (cutoff:3.500A) removed outlier: 9.459A pdb=" N ARG E 403 " --> pdb=" O ALA E 348 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'E' and resid 348 through 349 removed outlier: 7.160A pdb=" N ALA E 348 " --> pdb=" O VAL E 401 " (cutoff:3.500A) removed outlier: 9.459A pdb=" N ARG E 403 " --> pdb=" O ALA E 348 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASN E 394 " --> pdb=" O GLU E 516 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'E' and resid 361 through 362 removed outlier: 6.293A pdb=" N CYS E 361 " --> pdb=" O CYS E 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG2 Processing sheet with id=AG3, first strand: chain 'E' and resid 452 through 453 Processing sheet with id=AG4, first strand: chain 'E' and resid 654 through 655 removed outlier: 5.899A pdb=" N GLU E 654 " --> pdb=" O ALA E 694 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N THR E 696 " --> pdb=" O GLU E 654 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N TYR E 660 " --> pdb=" O SER E 698 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG4 Processing sheet with id=AG5, first strand: chain 'E' and resid 654 through 655 removed outlier: 5.899A pdb=" N GLU E 654 " --> pdb=" O ALA E 694 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N THR E 696 " --> pdb=" O GLU E 654 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ILE E 670 " --> pdb=" O ILE E 666 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'E' and resid 711 through 728 removed outlier: 6.466A pdb=" N SER E 711 " --> pdb=" O THR E1076 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N THR E1076 " --> pdb=" O SER E 711 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ALA E 713 " --> pdb=" O ASN E1074 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ASN E1074 " --> pdb=" O ALA E 713 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N GLU E1072 " --> pdb=" O PRO E 715 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ASN E 717 " --> pdb=" O ALA E1070 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N TYR E1067 " --> pdb=" O HIS E1048 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N HIS E1048 " --> pdb=" O TYR E1067 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'E' and resid 711 through 728 removed outlier: 6.466A pdb=" N SER E 711 " --> pdb=" O THR E1076 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N THR E1076 " --> pdb=" O SER E 711 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ALA E 713 " --> pdb=" O ASN E1074 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ASN E1074 " --> pdb=" O ALA E 713 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N GLU E1072 " --> pdb=" O PRO E 715 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ASN E 717 " --> pdb=" O ALA E1070 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ALA E1078 " --> pdb=" O PHE E1095 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N PHE E1095 " --> pdb=" O ALA E1078 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'E' and resid 734 through 736 Processing sheet with id=AG9, first strand: chain 'E' and resid 1120 through 1125 removed outlier: 4.836A pdb=" N ALA E1087 " --> pdb=" O SER E1123 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'F' and resid 3 through 6 Processing sheet with id=AH2, first strand: chain 'F' and resid 10 through 11 removed outlier: 7.079A pdb=" N GLU F 10 " --> pdb=" O THR F 124 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ILE F 34 " --> pdb=" O TRP F 50 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N TRP F 50 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N TRP F 36 " --> pdb=" O MET F 48 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'F' and resid 10 through 11 removed outlier: 7.079A pdb=" N GLU F 10 " --> pdb=" O THR F 124 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASN F 116 " --> pdb=" O ARG F 98 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'G' and resid 4 through 5 Processing sheet with id=AH5, first strand: chain 'G' and resid 10 through 11 removed outlier: 6.413A pdb=" N LEU G 34 " --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N TYR G 50 " --> pdb=" O LEU G 34 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'G' and resid 10 through 11 1242 hydrogen bonds defined for protein. 3312 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: 7.33 Time building geometry restraints manager: 2.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 7795 1.33 - 1.48: 8760 1.48 - 1.62: 11999 1.62 - 1.76: 9 1.76 - 1.90: 150 Bond restraints: 28713 Sorted by residual: bond pdb=" NE ARG A 454 " pdb=" CZ ARG A 454 " ideal model delta sigma weight residual 1.326 1.379 -0.053 1.10e-02 8.26e+03 2.29e+01 bond pdb=" NE ARG B 454 " pdb=" CZ ARG B 454 " ideal model delta sigma weight residual 1.326 1.379 -0.053 1.10e-02 8.26e+03 2.29e+01 bond pdb=" NE ARG E 454 " pdb=" CZ ARG E 454 " ideal model delta sigma weight residual 1.326 1.378 -0.052 1.10e-02 8.26e+03 2.28e+01 bond pdb=" CB ILE B 468 " pdb=" CG1 ILE B 468 " ideal model delta sigma weight residual 1.530 1.622 -0.092 2.00e-02 2.50e+03 2.14e+01 bond pdb=" CB ILE A 468 " pdb=" CG1 ILE A 468 " ideal model delta sigma weight residual 1.530 1.622 -0.092 2.00e-02 2.50e+03 2.13e+01 ... (remaining 28708 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 32852 1.73 - 3.46: 5287 3.46 - 5.18: 709 5.18 - 6.91: 212 6.91 - 8.64: 18 Bond angle restraints: 39078 Sorted by residual: angle pdb=" C ILE G 59 " pdb=" N PRO G 60 " pdb=" CA PRO G 60 " ideal model delta sigma weight residual 119.78 127.24 -7.46 1.03e+00 9.43e-01 5.25e+01 angle pdb=" C ILE D 59 " pdb=" N PRO D 60 " pdb=" CA PRO D 60 " ideal model delta sigma weight residual 119.78 127.22 -7.44 1.03e+00 9.43e-01 5.22e+01 angle pdb=" C ILE L 59 " pdb=" N PRO L 60 " pdb=" CA PRO L 60 " ideal model delta sigma weight residual 119.78 127.22 -7.44 1.03e+00 9.43e-01 5.22e+01 angle pdb=" C ASP E 808 " pdb=" N PRO E 809 " pdb=" CA PRO E 809 " ideal model delta sigma weight residual 119.56 126.88 -7.32 1.02e+00 9.61e-01 5.16e+01 angle pdb=" C ASP A 808 " pdb=" N PRO A 809 " pdb=" CA PRO A 809 " ideal model delta sigma weight residual 119.56 126.86 -7.30 1.02e+00 9.61e-01 5.12e+01 ... (remaining 39073 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 15684 17.58 - 35.15: 490 35.15 - 52.73: 101 52.73 - 70.31: 48 70.31 - 87.88: 21 Dihedral angle restraints: 16344 sinusoidal: 6120 harmonic: 10224 Sorted by residual: dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -153.38 67.38 1 1.00e+01 1.00e-02 5.91e+01 dihedral pdb=" CB CYS E1082 " pdb=" SG CYS E1082 " pdb=" SG CYS E1126 " pdb=" CB CYS E1126 " ideal model delta sinusoidal sigma weight residual -86.00 -153.37 67.37 1 1.00e+01 1.00e-02 5.91e+01 dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -153.37 67.37 1 1.00e+01 1.00e-02 5.91e+01 ... (remaining 16341 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 3292 0.085 - 0.169: 1048 0.169 - 0.254: 289 0.254 - 0.339: 68 0.339 - 0.423: 12 Chirality restraints: 4709 Sorted by residual: chirality pdb=" C1 NAG R 2 " pdb=" O4 NAG R 1 " pdb=" C2 NAG R 2 " pdb=" O5 NAG R 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.49 0.09 2.00e-02 2.50e+03 2.01e+01 chirality pdb=" C1 NAG M 2 " pdb=" O4 NAG M 1 " pdb=" C2 NAG M 2 " pdb=" O5 NAG M 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.49 0.09 2.00e-02 2.50e+03 1.97e+01 chirality pdb=" C1 NAG W 2 " pdb=" O4 NAG W 1 " pdb=" C2 NAG W 2 " pdb=" O5 NAG W 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.49 0.09 2.00e-02 2.50e+03 1.93e+01 ... (remaining 4706 not shown) Planarity restraints: 4951 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN E 331 " 0.046 2.00e-02 2.50e+03 4.62e-02 2.66e+01 pdb=" CG ASN E 331 " -0.029 2.00e-02 2.50e+03 pdb=" OD1 ASN E 331 " -0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN E 331 " -0.067 2.00e-02 2.50e+03 pdb=" C1 NAG E1305 " 0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 331 " 0.046 2.00e-02 2.50e+03 4.59e-02 2.64e+01 pdb=" CG ASN B 331 " -0.028 2.00e-02 2.50e+03 pdb=" OD1 ASN B 331 " -0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN B 331 " -0.067 2.00e-02 2.50e+03 pdb=" C1 NAG B1305 " 0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 331 " -0.046 2.00e-02 2.50e+03 4.58e-02 2.62e+01 pdb=" CG ASN A 331 " 0.028 2.00e-02 2.50e+03 pdb=" OD1 ASN A 331 " 0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN A 331 " 0.067 2.00e-02 2.50e+03 pdb=" C1 NAG A1305 " -0.055 2.00e-02 2.50e+03 ... (remaining 4948 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 9505 2.87 - 3.38: 24884 3.38 - 3.89: 48554 3.89 - 4.39: 55527 4.39 - 4.90: 91903 Nonbonded interactions: 230373 Sorted by model distance: nonbonded pdb=" NZ LYS B 557 " pdb=" OD2 ASP B 574 " model vdw 2.364 3.120 nonbonded pdb=" NZ LYS A 557 " pdb=" OD2 ASP A 574 " model vdw 2.364 3.120 nonbonded pdb=" NZ LYS E 557 " pdb=" OD2 ASP E 574 " model vdw 2.365 3.120 nonbonded pdb=" NH1 ARG B 346 " pdb=" OD1 ASP D 93 " model vdw 2.430 3.120 nonbonded pdb=" NH1 ARG E 346 " pdb=" OD1 ASP G 93 " model vdw 2.430 3.120 ... (remaining 230368 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 27 through 419 or (resid 420 and (name N or name CA or nam \ e C or name O or name CB )) or resid 421 through 499 or (resid 500 and (name N o \ r name CA or name C or name O or name CB )) or resid 501 through 772 or (resid 7 \ 73 and (name N or name CA or name C or name O or name CB )) or resid 774 through \ 1319)) selection = (chain 'E' and (resid 27 through 419 or (resid 420 and (name N or name CA or nam \ e C or name O or name CB )) or resid 421 through 499 or (resid 500 and (name N o \ r name CA or name C or name O or name CB )) or resid 501 through 772 or (resid 7 \ 73 and (name N or name CA or name C or name O or name CB )) or resid 774 through \ 1319)) } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' } ncs_group { reference = chain 'N' selection = chain 'S' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 26.440 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.090 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.202 28830 Z= 0.710 Angle : 1.357 9.892 39387 Z= 0.903 Chirality : 0.092 0.423 4709 Planarity : 0.005 0.028 4903 Dihedral : 10.403 87.884 9642 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 0.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.10 % Allowed : 0.82 % Favored : 99.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.67 (0.13), residues: 3438 helix: -0.00 (0.18), residues: 666 sheet: 0.96 (0.17), residues: 858 loop : 0.51 (0.14), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 509 TYR 0.037 0.005 TYR B 495 PHE 0.020 0.004 PHE B 497 TRP 0.025 0.007 TRP C 47 HIS 0.006 0.001 HIS E1048 Details of bonding type rmsd/Z covalent geometry : bond 0.01305 / 0.69 (28713) covalent geometry : angle 1.33886 / 0.90 (39078) SS BOND : bond 0.05689 / 3.62 ( 42) SS BOND : angle 3.58240 / 2.25 ( 84) hydrogen bonds : bond 0.16827 / 11.10 ( 1182) hydrogen bonds : angle 8.03509 / 5.61 ( 3312) link_ALPHA1-3 : bond 0.05488 / 2.45 ( 3) link_ALPHA1-3 : angle 2.56284 / 1.54 ( 9) link_ALPHA1-6 : bond 0.04740 / 2.11 ( 3) link_ALPHA1-6 : angle 1.76105 / 1.01 ( 9) link_BETA1-4 : bond 0.05624 / 3.14 ( 18) link_BETA1-4 : angle 3.19735 / 2.03 ( 54) link_BETA1-6 : bond 0.04228 / 1.88 ( 3) link_BETA1-6 : angle 2.12290 / 1.25 ( 9) link_NAG-ASN : bond 0.05574 / 3.50 ( 48) link_NAG-ASN : angle 2.25174 / 1.55 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 748 residues out of total 3057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 745 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 453 TYR cc_start: 0.6989 (p90) cc_final: 0.6756 (p90) REVERT: A 764 ASN cc_start: 0.8251 (m-40) cc_final: 0.7902 (m-40) REVERT: A 1105 THR cc_start: 0.7429 (t) cc_final: 0.6503 (m) REVERT: D 50 TYR cc_start: 0.8084 (p90) cc_final: 0.7884 (p90) REVERT: D 55 ARG cc_start: 0.6312 (ttm110) cc_final: 0.5866 (ttm110) REVERT: E 95 THR cc_start: 0.7552 (p) cc_final: 0.7303 (p) REVERT: E 764 ASN cc_start: 0.8225 (m-40) cc_final: 0.7903 (m-40) REVERT: G 36 TRP cc_start: 0.7775 (m100) cc_final: 0.7325 (m100) outliers start: 3 outliers final: 3 residues processed: 748 average time/residue: 0.1840 time to fit residues: 214.9987 Evaluate side-chains 399 residues out of total 3057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 396 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain E residue 603 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 0.7980 chunk 298 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 519 HIS A 914 ASN A 935 GLN A1054 GLN H 3 GLN H 39 GLN H 59 ASN B 196 ASN B 703 ASN B 764 ASN B 914 ASN B 935 GLN C 3 GLN C 39 GLN C 59 ASN E 66 HIS E 519 HIS E 914 ASN E 935 GLN E1054 GLN E1101 HIS F 3 GLN F 59 ASN F 116 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.176653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.151817 restraints weight = 40855.824| |-----------------------------------------------------------------------------| r_work (start): 0.4074 rms_B_bonded: 2.61 r_work: 0.3730 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 28830 Z= 0.179 Angle : 0.658 8.000 39387 Z= 0.346 Chirality : 0.046 0.191 4709 Planarity : 0.004 0.046 4903 Dihedral : 4.854 46.912 3768 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 2.12 % Allowed : 7.71 % Favored : 90.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.65 (0.14), residues: 3438 helix: 1.21 (0.21), residues: 645 sheet: 0.56 (0.16), residues: 930 loop : 0.20 (0.14), residues: 1863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 102 TYR 0.022 0.002 TYR G 50 PHE 0.028 0.002 PHE D 72 TRP 0.012 0.001 TRP B1102 HIS 0.010 0.001 HIS G 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.18 (28713) covalent geometry : angle 0.63800 / 0.34 (39078) SS BOND : bond 0.00684 / 0.48 ( 42) SS BOND : angle 1.75425 / 1.01 ( 84) hydrogen bonds : bond 0.04975 / 3.27 ( 1182) hydrogen bonds : angle 6.29591 / 4.36 ( 3312) link_ALPHA1-3 : bond 0.00830 / 0.38 ( 3) link_ALPHA1-3 : angle 1.51202 / 0.83 ( 9) link_ALPHA1-6 : bond 0.00753 / 0.33 ( 3) link_ALPHA1-6 : angle 1.24891 / 0.64 ( 9) link_BETA1-4 : bond 0.00490 / 0.27 ( 18) link_BETA1-4 : angle 2.00742 / 1.36 ( 54) link_BETA1-6 : bond 0.00221 / 0.10 ( 3) link_BETA1-6 : angle 1.97153 / 1.09 ( 9) link_NAG-ASN : bond 0.00540 / 0.34 ( 48) link_NAG-ASN : angle 2.04428 / 1.46 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 3057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 431 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 421 TYR cc_start: 0.4203 (OUTLIER) cc_final: 0.3205 (t80) REVERT: A 453 TYR cc_start: 0.7435 (p90) cc_final: 0.6963 (p90) REVERT: H 116 ASN cc_start: 0.7578 (m-40) cc_final: 0.7199 (m-40) REVERT: L 55 ARG cc_start: 0.7499 (mtm-85) cc_final: 0.6945 (mtm-85) REVERT: L 79 LEU cc_start: 0.5618 (OUTLIER) cc_final: 0.5413 (tp) REVERT: L 83 ASP cc_start: 0.6500 (m-30) cc_final: 0.6262 (m-30) REVERT: B 140 PHE cc_start: 0.8333 (p90) cc_final: 0.8005 (p90) REVERT: B 376 THR cc_start: 0.7750 (t) cc_final: 0.7466 (p) REVERT: B 421 TYR cc_start: 0.4350 (OUTLIER) cc_final: 0.3186 (t80) REVERT: B 808 ASP cc_start: 0.6733 (OUTLIER) cc_final: 0.6310 (m-30) REVERT: B 1138 TYR cc_start: 0.7507 (t80) cc_final: 0.7285 (m-10) REVERT: C 80 TYR cc_start: 0.7207 (m-80) cc_final: 0.7006 (m-80) REVERT: D 50 TYR cc_start: 0.8182 (p90) cc_final: 0.7748 (p90) REVERT: D 55 ARG cc_start: 0.6768 (ttm110) cc_final: 0.6514 (mtm-85) REVERT: D 72 PHE cc_start: 0.8239 (m-80) cc_final: 0.7955 (m-10) REVERT: D 73 THR cc_start: 0.7665 (p) cc_final: 0.7245 (p) REVERT: D 80 GLU cc_start: 0.7925 (tp30) cc_final: 0.7320 (mp0) REVERT: D 90 GLN cc_start: 0.7941 (OUTLIER) cc_final: 0.7523 (tt0) REVERT: E 95 THR cc_start: 0.7654 (p) cc_final: 0.7352 (p) REVERT: E 421 TYR cc_start: 0.4712 (m-80) cc_final: 0.3686 (t80) REVERT: G 55 ARG cc_start: 0.6829 (ttp-110) cc_final: 0.6267 (mtm-85) outliers start: 62 outliers final: 39 residues processed: 469 average time/residue: 0.1663 time to fit residues: 126.9109 Evaluate side-chains 392 residues out of total 3057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 348 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 302 THR Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 574 ASP Chi-restraints excluded: chain E residue 603 ASN Chi-restraints excluded: chain E residue 738 CYS Chi-restraints excluded: chain E residue 747 THR Chi-restraints excluded: chain E residue 759 PHE Chi-restraints excluded: chain E residue 761 THR Chi-restraints excluded: chain E residue 791 THR Chi-restraints excluded: chain E residue 808 ASP Chi-restraints excluded: chain E residue 980 ILE Chi-restraints excluded: chain E residue 1117 THR Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain G residue 89 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 233 optimal weight: 0.7980 chunk 129 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 chunk 173 optimal weight: 0.5980 chunk 196 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 235 optimal weight: 1.9990 chunk 152 optimal weight: 7.9990 chunk 56 optimal weight: 0.8980 chunk 204 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS A 658 ASN A 703 ASN A 935 GLN A 955 ASN H 3 GLN H 65 GLN B 207 HIS B 658 ASN B 935 GLN C 3 GLN E 207 HIS F 3 GLN F 119 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.174007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.149774 restraints weight = 41002.519| |-----------------------------------------------------------------------------| r_work (start): 0.4035 rms_B_bonded: 2.62 r_work: 0.3666 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.3264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 28830 Z= 0.180 Angle : 0.607 8.338 39387 Z= 0.315 Chirality : 0.045 0.261 4709 Planarity : 0.004 0.065 4903 Dihedral : 4.619 46.142 3768 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.64 % Allowed : 8.91 % Favored : 88.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.56 (0.14), residues: 3438 helix: 1.36 (0.21), residues: 645 sheet: 0.48 (0.16), residues: 933 loop : 0.06 (0.14), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 983 TYR 0.020 0.002 TYR B1067 PHE 0.020 0.002 PHE E 497 TRP 0.017 0.001 TRP F 105 HIS 0.008 0.001 HIS D 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.18 (28713) covalent geometry : angle 0.58662 / 0.31 (39078) SS BOND : bond 0.00578 / 0.38 ( 42) SS BOND : angle 1.89283 / 1.15 ( 84) hydrogen bonds : bond 0.04475 / 2.97 ( 1182) hydrogen bonds : angle 5.79362 / 4.02 ( 3312) link_ALPHA1-3 : bond 0.00530 / 0.23 ( 3) link_ALPHA1-3 : angle 1.38152 / 0.76 ( 9) link_ALPHA1-6 : bond 0.00932 / 0.42 ( 3) link_ALPHA1-6 : angle 1.05762 / 0.56 ( 9) link_BETA1-4 : bond 0.00552 / 0.31 ( 18) link_BETA1-4 : angle 1.57465 / 1.07 ( 54) link_BETA1-6 : bond 0.00240 / 0.11 ( 3) link_BETA1-6 : angle 1.76369 / 0.95 ( 9) link_NAG-ASN : bond 0.00476 / 0.29 ( 48) link_NAG-ASN : angle 2.00875 / 1.45 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 3057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 359 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 421 TYR cc_start: 0.4276 (OUTLIER) cc_final: 0.3198 (t80) REVERT: A 453 TYR cc_start: 0.7590 (p90) cc_final: 0.7104 (p90) REVERT: A 588 THR cc_start: 0.8114 (m) cc_final: 0.7892 (p) REVERT: A 1029 MET cc_start: 0.8787 (tpp) cc_final: 0.8243 (tpp) REVERT: H 80 TYR cc_start: 0.7272 (m-80) cc_final: 0.7044 (m-80) REVERT: H 116 ASN cc_start: 0.7686 (m-40) cc_final: 0.7292 (m-40) REVERT: L 55 ARG cc_start: 0.7497 (mtm-85) cc_final: 0.6884 (mtm-85) REVERT: L 79 LEU cc_start: 0.5364 (OUTLIER) cc_final: 0.5085 (tp) REVERT: L 83 ASP cc_start: 0.6786 (m-30) cc_final: 0.6569 (m-30) REVERT: L 90 GLN cc_start: 0.7874 (OUTLIER) cc_final: 0.7657 (tt0) REVERT: B 421 TYR cc_start: 0.4469 (OUTLIER) cc_final: 0.3156 (t80) REVERT: B 759 PHE cc_start: 0.7138 (OUTLIER) cc_final: 0.6577 (t80) REVERT: B 808 ASP cc_start: 0.6983 (OUTLIER) cc_final: 0.6518 (m-30) REVERT: B 977 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8455 (mp) REVERT: B 984 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.7904 (mt) REVERT: C 45 LEU cc_start: 0.7437 (mt) cc_final: 0.7213 (mt) REVERT: D 36 TRP cc_start: 0.8093 (m-90) cc_final: 0.7700 (m-90) REVERT: D 50 TYR cc_start: 0.8121 (p90) cc_final: 0.7824 (p90) REVERT: D 80 GLU cc_start: 0.7932 (tp30) cc_final: 0.7690 (mp0) REVERT: D 90 GLN cc_start: 0.7963 (OUTLIER) cc_final: 0.7430 (tt0) REVERT: E 95 THR cc_start: 0.7549 (p) cc_final: 0.7212 (p) REVERT: E 421 TYR cc_start: 0.4601 (m-80) cc_final: 0.3530 (t80) REVERT: E 453 TYR cc_start: 0.7268 (p90) cc_final: 0.7051 (p90) REVERT: E 904 TYR cc_start: 0.7602 (m-10) cc_final: 0.7163 (m-10) REVERT: E 1002 GLN cc_start: 0.7909 (tt0) cc_final: 0.7701 (tt0) REVERT: F 81 MET cc_start: 0.7591 (ttp) cc_final: 0.7375 (ttp) REVERT: F 116 ASN cc_start: 0.7560 (m110) cc_final: 0.7306 (m-40) outliers start: 77 outliers final: 42 residues processed: 416 average time/residue: 0.1784 time to fit residues: 122.2653 Evaluate side-chains 373 residues out of total 3057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 322 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 302 THR Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 371 SER Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 603 ASN Chi-restraints excluded: chain E residue 747 THR Chi-restraints excluded: chain E residue 752 LEU Chi-restraints excluded: chain E residue 759 PHE Chi-restraints excluded: chain E residue 791 THR Chi-restraints excluded: chain E residue 808 ASP Chi-restraints excluded: chain E residue 858 LEU Chi-restraints excluded: chain E residue 1117 THR Chi-restraints excluded: chain F residue 31 SER Chi-restraints excluded: chain F residue 121 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 139 optimal weight: 6.9990 chunk 324 optimal weight: 0.8980 chunk 204 optimal weight: 0.9980 chunk 221 optimal weight: 2.9990 chunk 206 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 165 optimal weight: 0.5980 chunk 262 optimal weight: 0.3980 chunk 227 optimal weight: 0.9980 chunk 45 optimal weight: 0.5980 chunk 40 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 3 GLN E 935 GLN E1054 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.173216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 117)---------------| | r_work = 0.3874 r_free = 0.3874 target = 0.136603 restraints weight = 41784.656| |-----------------------------------------------------------------------------| r_work (start): 0.3875 rms_B_bonded: 1.99 r_work: 0.3735 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3599 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.3573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 28830 Z= 0.136 Angle : 0.562 11.066 39387 Z= 0.290 Chirality : 0.044 0.283 4709 Planarity : 0.004 0.065 4903 Dihedral : 4.484 46.036 3768 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.19 % Allowed : 10.45 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.48 (0.14), residues: 3438 helix: 1.57 (0.21), residues: 630 sheet: 0.29 (0.16), residues: 978 loop : -0.01 (0.14), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 102 TYR 0.019 0.001 TYR A1067 PHE 0.018 0.001 PHE D 72 TRP 0.010 0.001 TRP F 105 HIS 0.006 0.001 HIS D 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (28713) covalent geometry : angle 0.53797 / 0.28 (39078) SS BOND : bond 0.00548 / 0.37 ( 42) SS BOND : angle 2.37895 / 1.27 ( 84) hydrogen bonds : bond 0.03978 / 2.64 ( 1182) hydrogen bonds : angle 5.51119 / 3.82 ( 3312) link_ALPHA1-3 : bond 0.00598 / 0.28 ( 3) link_ALPHA1-3 : angle 1.58864 / 0.86 ( 9) link_ALPHA1-6 : bond 0.00592 / 0.26 ( 3) link_ALPHA1-6 : angle 1.12866 / 0.59 ( 9) link_BETA1-4 : bond 0.00443 / 0.25 ( 18) link_BETA1-4 : angle 1.36219 / 0.94 ( 54) link_BETA1-6 : bond 0.00076 / 0.04 ( 3) link_BETA1-6 : angle 1.75652 / 0.94 ( 9) link_NAG-ASN : bond 0.00390 / 0.25 ( 48) link_NAG-ASN : angle 1.86074 / 1.34 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 3057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 353 time to evaluate : 1.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 390 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8464 (pp) REVERT: A 421 TYR cc_start: 0.4359 (OUTLIER) cc_final: 0.4087 (m-80) REVERT: A 453 TYR cc_start: 0.7728 (p90) cc_final: 0.7207 (p90) REVERT: A 588 THR cc_start: 0.7800 (m) cc_final: 0.7565 (p) REVERT: A 754 LEU cc_start: 0.8346 (mp) cc_final: 0.8114 (mp) REVERT: A 759 PHE cc_start: 0.8274 (OUTLIER) cc_final: 0.7766 (m-10) REVERT: A 1029 MET cc_start: 0.8783 (tpp) cc_final: 0.8256 (tpp) REVERT: H 80 TYR cc_start: 0.7306 (m-80) cc_final: 0.7047 (m-80) REVERT: H 98 ARG cc_start: 0.8468 (tmm-80) cc_final: 0.7810 (ttp-170) REVERT: H 116 ASN cc_start: 0.7715 (m-40) cc_final: 0.7394 (m-40) REVERT: L 55 ARG cc_start: 0.7527 (mtm-85) cc_final: 0.6892 (mtm-85) REVERT: L 72 PHE cc_start: 0.8231 (m-10) cc_final: 0.7967 (m-10) REVERT: L 79 LEU cc_start: 0.5356 (OUTLIER) cc_final: 0.5096 (tp) REVERT: L 80 GLU cc_start: 0.7460 (tp30) cc_final: 0.7204 (mp0) REVERT: L 90 GLN cc_start: 0.7953 (OUTLIER) cc_final: 0.7601 (tt0) REVERT: B 421 TYR cc_start: 0.4327 (m-80) cc_final: 0.3016 (t80) REVERT: B 759 PHE cc_start: 0.8271 (OUTLIER) cc_final: 0.7569 (t80) REVERT: B 808 ASP cc_start: 0.7110 (OUTLIER) cc_final: 0.6656 (m-30) REVERT: B 984 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.7876 (mt) REVERT: D 36 TRP cc_start: 0.8254 (m-90) cc_final: 0.7807 (m-90) REVERT: D 50 TYR cc_start: 0.8088 (p90) cc_final: 0.7743 (p90) REVERT: D 90 GLN cc_start: 0.8107 (OUTLIER) cc_final: 0.7805 (tt0) REVERT: E 95 THR cc_start: 0.7464 (p) cc_final: 0.7110 (p) REVERT: E 421 TYR cc_start: 0.4844 (m-80) cc_final: 0.3318 (t80) REVERT: E 453 TYR cc_start: 0.7243 (p90) cc_final: 0.7010 (p90) REVERT: F 98 ARG cc_start: 0.8397 (tmm-80) cc_final: 0.7792 (ttp-170) REVERT: G 80 GLU cc_start: 0.7423 (tp30) cc_final: 0.7219 (mp0) outliers start: 64 outliers final: 39 residues processed: 397 average time/residue: 0.1787 time to fit residues: 116.7090 Evaluate side-chains 360 residues out of total 3057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 312 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 371 SER Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 571 ASP Chi-restraints excluded: chain E residue 603 ASN Chi-restraints excluded: chain E residue 759 PHE Chi-restraints excluded: chain E residue 791 THR Chi-restraints excluded: chain E residue 808 ASP Chi-restraints excluded: chain E residue 858 LEU Chi-restraints excluded: chain E residue 1117 THR Chi-restraints excluded: chain E residue 1128 VAL Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain G residue 5 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 45 optimal weight: 3.9990 chunk 173 optimal weight: 0.5980 chunk 188 optimal weight: 0.9980 chunk 126 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 270 optimal weight: 6.9990 chunk 294 optimal weight: 0.7980 chunk 200 optimal weight: 2.9990 chunk 230 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 256 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 ASN L 39 GLN L 91 GLN B 519 HIS ** D 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 196 ASN E 935 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.171324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 108)---------------| | r_work = 0.3865 r_free = 0.3865 target = 0.136533 restraints weight = 41654.378| |-----------------------------------------------------------------------------| r_work (start): 0.3839 rms_B_bonded: 1.95 r_work: 0.3681 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3546 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.3908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 28830 Z= 0.155 Angle : 0.560 8.385 39387 Z= 0.287 Chirality : 0.045 0.352 4709 Planarity : 0.004 0.057 4903 Dihedral : 4.439 45.921 3768 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.81 % Allowed : 11.34 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.39 (0.14), residues: 3438 helix: 1.56 (0.21), residues: 630 sheet: 0.20 (0.15), residues: 987 loop : -0.09 (0.14), residues: 1821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 408 TYR 0.020 0.001 TYR A1067 PHE 0.018 0.002 PHE C 106 TRP 0.015 0.001 TRP C 47 HIS 0.006 0.001 HIS D 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.15 (28713) covalent geometry : angle 0.53848 / 0.28 (39078) SS BOND : bond 0.00438 / 0.29 ( 42) SS BOND : angle 2.02970 / 1.14 ( 84) hydrogen bonds : bond 0.03949 / 2.63 ( 1182) hydrogen bonds : angle 5.38579 / 3.73 ( 3312) link_ALPHA1-3 : bond 0.00365 / 0.16 ( 3) link_ALPHA1-3 : angle 1.44115 / 0.78 ( 9) link_ALPHA1-6 : bond 0.00676 / 0.30 ( 3) link_ALPHA1-6 : angle 1.12003 / 0.59 ( 9) link_BETA1-4 : bond 0.00495 / 0.29 ( 18) link_BETA1-4 : angle 1.37980 / 0.95 ( 54) link_BETA1-6 : bond 0.00181 / 0.07 ( 3) link_BETA1-6 : angle 1.71998 / 0.93 ( 9) link_NAG-ASN : bond 0.00383 / 0.25 ( 48) link_NAG-ASN : angle 1.89705 / 1.37 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 3057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 336 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 390 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8574 (pp) REVERT: A 421 TYR cc_start: 0.4554 (m-80) cc_final: 0.4308 (m-80) REVERT: A 453 TYR cc_start: 0.7775 (p90) cc_final: 0.7211 (p90) REVERT: A 588 THR cc_start: 0.7851 (m) cc_final: 0.7632 (p) REVERT: A 759 PHE cc_start: 0.8268 (OUTLIER) cc_final: 0.7827 (m-10) REVERT: A 1029 MET cc_start: 0.8848 (tpp) cc_final: 0.8357 (tpp) REVERT: H 80 TYR cc_start: 0.7329 (m-80) cc_final: 0.6906 (m-80) REVERT: H 116 ASN cc_start: 0.7728 (m-40) cc_final: 0.7328 (m-40) REVERT: L 72 PHE cc_start: 0.8271 (m-80) cc_final: 0.7950 (m-10) REVERT: L 90 GLN cc_start: 0.7906 (OUTLIER) cc_final: 0.7591 (tt0) REVERT: B 410 ILE cc_start: 0.8270 (mm) cc_final: 0.7983 (mt) REVERT: B 421 TYR cc_start: 0.4737 (m-80) cc_final: 0.3212 (t80) REVERT: B 453 TYR cc_start: 0.7453 (p90) cc_final: 0.7040 (p90) REVERT: B 493 GLN cc_start: 0.6982 (mp10) cc_final: 0.6716 (mp10) REVERT: B 646 ARG cc_start: 0.7906 (mtm-85) cc_final: 0.7695 (mtm180) REVERT: B 759 PHE cc_start: 0.8415 (OUTLIER) cc_final: 0.7825 (t80) REVERT: B 808 ASP cc_start: 0.7173 (OUTLIER) cc_final: 0.6722 (m-30) REVERT: B 984 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8003 (mt) REVERT: B 985 ASP cc_start: 0.7428 (p0) cc_final: 0.7114 (p0) REVERT: C 84 ARG cc_start: 0.6742 (mmm-85) cc_final: 0.6393 (mtm180) REVERT: D 36 TRP cc_start: 0.8239 (m-90) cc_final: 0.7815 (m-90) REVERT: D 50 TYR cc_start: 0.7995 (p90) cc_final: 0.7228 (p90) REVERT: D 90 GLN cc_start: 0.8004 (OUTLIER) cc_final: 0.7642 (tt0) REVERT: E 95 THR cc_start: 0.7533 (p) cc_final: 0.7188 (p) REVERT: E 421 TYR cc_start: 0.5087 (m-80) cc_final: 0.3461 (t80) REVERT: E 453 TYR cc_start: 0.7379 (p90) cc_final: 0.7097 (p90) REVERT: E 977 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8731 (mp) REVERT: F 98 ARG cc_start: 0.8465 (tmm-80) cc_final: 0.7888 (tmm160) REVERT: G 80 GLU cc_start: 0.7682 (tp30) cc_final: 0.7312 (mp0) outliers start: 82 outliers final: 51 residues processed: 400 average time/residue: 0.1729 time to fit residues: 114.9631 Evaluate side-chains 368 residues out of total 3057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 309 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 196 ASN Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 302 THR Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 371 SER Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 571 ASP Chi-restraints excluded: chain E residue 588 THR Chi-restraints excluded: chain E residue 603 ASN Chi-restraints excluded: chain E residue 759 PHE Chi-restraints excluded: chain E residue 791 THR Chi-restraints excluded: chain E residue 808 ASP Chi-restraints excluded: chain E residue 858 LEU Chi-restraints excluded: chain E residue 977 LEU Chi-restraints excluded: chain E residue 1072 GLU Chi-restraints excluded: chain E residue 1117 THR Chi-restraints excluded: chain E residue 1128 VAL Chi-restraints excluded: chain F residue 31 SER Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 121 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 263 optimal weight: 4.9990 chunk 266 optimal weight: 1.9990 chunk 257 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 14 optimal weight: 0.6980 chunk 167 optimal weight: 5.9990 chunk 298 optimal weight: 0.0670 chunk 238 optimal weight: 1.9990 chunk 175 optimal weight: 0.9990 chunk 312 optimal weight: 2.9990 chunk 211 optimal weight: 0.0980 overall best weight: 0.7722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 39 GLN ** D 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.170216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 123)---------------| | r_work = 0.3858 r_free = 0.3858 target = 0.135556 restraints weight = 41649.494| |-----------------------------------------------------------------------------| r_work (start): 0.3860 rms_B_bonded: 2.00 r_work: 0.3730 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3603 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.4056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 28830 Z= 0.143 Angle : 0.549 9.251 39387 Z= 0.281 Chirality : 0.044 0.335 4709 Planarity : 0.004 0.056 4903 Dihedral : 4.393 45.851 3768 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.50 % Allowed : 12.50 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.36 (0.14), residues: 3438 helix: 1.44 (0.21), residues: 651 sheet: 0.13 (0.15), residues: 993 loop : -0.04 (0.14), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 102 TYR 0.020 0.001 TYR A1067 PHE 0.014 0.001 PHE B 400 TRP 0.017 0.001 TRP F 105 HIS 0.006 0.001 HIS D 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 (28713) covalent geometry : angle 0.52637 / 0.28 (39078) SS BOND : bond 0.00420 / 0.28 ( 42) SS BOND : angle 2.12495 / 1.12 ( 84) hydrogen bonds : bond 0.03826 / 2.55 ( 1182) hydrogen bonds : angle 5.32106 / 3.69 ( 3312) link_ALPHA1-3 : bond 0.00457 / 0.21 ( 3) link_ALPHA1-3 : angle 1.49745 / 0.82 ( 9) link_ALPHA1-6 : bond 0.00656 / 0.29 ( 3) link_ALPHA1-6 : angle 1.14607 / 0.60 ( 9) link_BETA1-4 : bond 0.00422 / 0.24 ( 18) link_BETA1-4 : angle 1.34096 / 0.94 ( 54) link_BETA1-6 : bond 0.00127 / 0.06 ( 3) link_BETA1-6 : angle 1.65719 / 0.90 ( 9) link_NAG-ASN : bond 0.00368 / 0.24 ( 48) link_NAG-ASN : angle 1.87204 / 1.35 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 3057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 315 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 421 TYR cc_start: 0.4657 (m-80) cc_final: 0.4447 (m-80) REVERT: A 453 TYR cc_start: 0.7749 (p90) cc_final: 0.7191 (p90) REVERT: A 588 THR cc_start: 0.7859 (m) cc_final: 0.7638 (p) REVERT: A 759 PHE cc_start: 0.8416 (OUTLIER) cc_final: 0.7834 (m-10) REVERT: A 977 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8696 (mp) REVERT: A 1029 MET cc_start: 0.8833 (tpp) cc_final: 0.8301 (tpp) REVERT: H 80 TYR cc_start: 0.7185 (m-80) cc_final: 0.6884 (m-80) REVERT: H 116 ASN cc_start: 0.7721 (m-40) cc_final: 0.7418 (m-40) REVERT: L 72 PHE cc_start: 0.8274 (m-80) cc_final: 0.7979 (m-10) REVERT: L 90 GLN cc_start: 0.7984 (OUTLIER) cc_final: 0.7590 (tt0) REVERT: B 410 ILE cc_start: 0.8339 (mm) cc_final: 0.8076 (mt) REVERT: B 421 TYR cc_start: 0.4736 (m-80) cc_final: 0.4325 (m-80) REVERT: B 453 TYR cc_start: 0.7433 (p90) cc_final: 0.6981 (p90) REVERT: B 493 GLN cc_start: 0.6980 (mp10) cc_final: 0.6738 (mp10) REVERT: B 643 PHE cc_start: 0.8277 (t80) cc_final: 0.7928 (t80) REVERT: B 759 PHE cc_start: 0.8416 (OUTLIER) cc_final: 0.7598 (t80) REVERT: B 808 ASP cc_start: 0.7148 (OUTLIER) cc_final: 0.6713 (m-30) REVERT: B 984 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8175 (mt) REVERT: C 84 ARG cc_start: 0.6871 (mmm-85) cc_final: 0.6555 (mtt180) REVERT: D 36 TRP cc_start: 0.8217 (m-90) cc_final: 0.7815 (m-90) REVERT: D 50 TYR cc_start: 0.7992 (p90) cc_final: 0.7108 (p90) REVERT: D 90 GLN cc_start: 0.7976 (OUTLIER) cc_final: 0.7485 (tt0) REVERT: E 95 THR cc_start: 0.7583 (p) cc_final: 0.7247 (p) REVERT: E 421 TYR cc_start: 0.5129 (m-80) cc_final: 0.3467 (t80) REVERT: E 453 TYR cc_start: 0.7401 (p90) cc_final: 0.7137 (p90) REVERT: E 977 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8713 (mp) REVERT: E 993 ILE cc_start: 0.9260 (OUTLIER) cc_final: 0.9021 (mp) REVERT: F 98 ARG cc_start: 0.8444 (tmm-80) cc_final: 0.7833 (tmm160) REVERT: F 116 ASN cc_start: 0.7701 (m110) cc_final: 0.7499 (m-40) REVERT: G 80 GLU cc_start: 0.7642 (tp30) cc_final: 0.7429 (mp0) outliers start: 73 outliers final: 49 residues processed: 371 average time/residue: 0.1706 time to fit residues: 105.1477 Evaluate side-chains 356 residues out of total 3057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 298 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 302 THR Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 371 SER Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 571 ASP Chi-restraints excluded: chain E residue 588 THR Chi-restraints excluded: chain E residue 603 ASN Chi-restraints excluded: chain E residue 743 CYS Chi-restraints excluded: chain E residue 747 THR Chi-restraints excluded: chain E residue 752 LEU Chi-restraints excluded: chain E residue 759 PHE Chi-restraints excluded: chain E residue 791 THR Chi-restraints excluded: chain E residue 808 ASP Chi-restraints excluded: chain E residue 977 LEU Chi-restraints excluded: chain E residue 993 ILE Chi-restraints excluded: chain E residue 1117 THR Chi-restraints excluded: chain E residue 1128 VAL Chi-restraints excluded: chain F residue 31 SER Chi-restraints excluded: chain F residue 101 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 131 optimal weight: 0.2980 chunk 52 optimal weight: 0.7980 chunk 310 optimal weight: 0.6980 chunk 75 optimal weight: 0.0870 chunk 6 optimal weight: 3.9990 chunk 276 optimal weight: 3.9990 chunk 235 optimal weight: 0.8980 chunk 163 optimal weight: 0.4980 chunk 147 optimal weight: 4.9990 chunk 32 optimal weight: 10.0000 chunk 285 optimal weight: 0.0570 overall best weight: 0.3276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 91 GLN E 965 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.171880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.146683 restraints weight = 41600.708| |-----------------------------------------------------------------------------| r_work (start): 0.4031 rms_B_bonded: 2.92 r_work: 0.3652 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.4181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 28830 Z= 0.104 Angle : 0.510 7.496 39387 Z= 0.264 Chirality : 0.043 0.389 4709 Planarity : 0.004 0.054 4903 Dihedral : 4.251 45.505 3768 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.02 % Allowed : 13.46 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.46 (0.14), residues: 3438 helix: 1.56 (0.21), residues: 657 sheet: 0.26 (0.15), residues: 1005 loop : -0.05 (0.14), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 102 TYR 0.020 0.001 TYR C 95 PHE 0.015 0.001 PHE B 400 TRP 0.020 0.001 TRP F 105 HIS 0.005 0.000 HIS D 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.10 (28713) covalent geometry : angle 0.49119 / 0.26 (39078) SS BOND : bond 0.00413 / 0.28 ( 42) SS BOND : angle 1.83008 / 1.00 ( 84) hydrogen bonds : bond 0.03558 / 2.37 ( 1182) hydrogen bonds : angle 5.20283 / 3.61 ( 3312) link_ALPHA1-3 : bond 0.00422 / 0.19 ( 3) link_ALPHA1-3 : angle 1.48177 / 0.81 ( 9) link_ALPHA1-6 : bond 0.00539 / 0.24 ( 3) link_ALPHA1-6 : angle 1.24275 / 0.66 ( 9) link_BETA1-4 : bond 0.00458 / 0.24 ( 18) link_BETA1-4 : angle 1.21561 / 0.86 ( 54) link_BETA1-6 : bond 0.00106 / 0.05 ( 3) link_BETA1-6 : angle 1.46583 / 0.79 ( 9) link_NAG-ASN : bond 0.00345 / 0.23 ( 48) link_NAG-ASN : angle 1.71174 / 1.23 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 3057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 347 time to evaluate : 1.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 453 TYR cc_start: 0.7754 (p90) cc_final: 0.7230 (p90) REVERT: A 588 THR cc_start: 0.7827 (m) cc_final: 0.7617 (p) REVERT: A 759 PHE cc_start: 0.8310 (OUTLIER) cc_final: 0.7620 (m-10) REVERT: A 1029 MET cc_start: 0.8787 (tpp) cc_final: 0.8215 (tpp) REVERT: H 116 ASN cc_start: 0.7671 (m-40) cc_final: 0.7341 (m-40) REVERT: L 72 PHE cc_start: 0.8193 (m-80) cc_final: 0.7953 (m-10) REVERT: L 90 GLN cc_start: 0.7912 (OUTLIER) cc_final: 0.7578 (tt0) REVERT: B 410 ILE cc_start: 0.8327 (mm) cc_final: 0.8042 (mt) REVERT: B 421 TYR cc_start: 0.4732 (m-80) cc_final: 0.4329 (m-80) REVERT: B 453 TYR cc_start: 0.7420 (p90) cc_final: 0.7097 (p90) REVERT: B 759 PHE cc_start: 0.7237 (OUTLIER) cc_final: 0.6834 (t80) REVERT: B 808 ASP cc_start: 0.7045 (OUTLIER) cc_final: 0.6678 (m-30) REVERT: B 984 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8128 (mt) REVERT: C 80 TYR cc_start: 0.7037 (m-80) cc_final: 0.6565 (m-80) REVERT: C 84 ARG cc_start: 0.6963 (mmm-85) cc_final: 0.6699 (mtm180) REVERT: D 36 TRP cc_start: 0.8290 (m-90) cc_final: 0.7845 (m-90) REVERT: D 50 TYR cc_start: 0.7907 (p90) cc_final: 0.7330 (p90) REVERT: D 90 GLN cc_start: 0.8008 (OUTLIER) cc_final: 0.7777 (tt0) REVERT: E 95 THR cc_start: 0.7445 (p) cc_final: 0.7096 (p) REVERT: E 453 TYR cc_start: 0.7365 (p90) cc_final: 0.7059 (p90) REVERT: E 977 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8722 (mp) REVERT: F 98 ARG cc_start: 0.8453 (tmm-80) cc_final: 0.7895 (tmm160) outliers start: 59 outliers final: 39 residues processed: 392 average time/residue: 0.1648 time to fit residues: 107.0768 Evaluate side-chains 351 residues out of total 3057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 305 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 371 SER Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 603 ASN Chi-restraints excluded: chain E residue 752 LEU Chi-restraints excluded: chain E residue 759 PHE Chi-restraints excluded: chain E residue 791 THR Chi-restraints excluded: chain E residue 808 ASP Chi-restraints excluded: chain E residue 977 LEU Chi-restraints excluded: chain E residue 1117 THR Chi-restraints excluded: chain E residue 1128 VAL Chi-restraints excluded: chain F residue 101 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 327 optimal weight: 0.9980 chunk 222 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 251 optimal weight: 0.9980 chunk 243 optimal weight: 0.7980 chunk 192 optimal weight: 6.9990 chunk 267 optimal weight: 2.9990 chunk 288 optimal weight: 3.9990 chunk 90 optimal weight: 0.1980 chunk 342 optimal weight: 8.9990 chunk 334 optimal weight: 0.1980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1002 GLN A1101 HIS H 119 GLN L 39 GLN D 39 GLN ** D 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 965 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.171926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.144673 restraints weight = 42068.532| |-----------------------------------------------------------------------------| r_work (start): 0.3989 rms_B_bonded: 3.11 r_work: 0.3646 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.4300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 28830 Z= 0.129 Angle : 0.531 7.791 39387 Z= 0.273 Chirality : 0.044 0.329 4709 Planarity : 0.004 0.047 4903 Dihedral : 4.260 45.306 3768 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.92 % Allowed : 13.87 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.42 (0.14), residues: 3438 helix: 1.49 (0.21), residues: 660 sheet: 0.24 (0.15), residues: 1008 loop : -0.06 (0.15), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 102 TYR 0.019 0.001 TYR A1067 PHE 0.015 0.001 PHE E 168 TRP 0.019 0.001 TRP F 105 HIS 0.006 0.001 HIS D 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (28713) covalent geometry : angle 0.51094 / 0.27 (39078) SS BOND : bond 0.00453 / 0.31 ( 42) SS BOND : angle 1.93299 / 1.09 ( 84) hydrogen bonds : bond 0.03636 / 2.42 ( 1182) hydrogen bonds : angle 5.20396 / 3.61 ( 3312) link_ALPHA1-3 : bond 0.00415 / 0.19 ( 3) link_ALPHA1-3 : angle 1.49057 / 0.81 ( 9) link_ALPHA1-6 : bond 0.00616 / 0.27 ( 3) link_ALPHA1-6 : angle 1.19171 / 0.63 ( 9) link_BETA1-4 : bond 0.00418 / 0.22 ( 18) link_BETA1-4 : angle 1.26248 / 0.89 ( 54) link_BETA1-6 : bond 0.00184 / 0.08 ( 3) link_BETA1-6 : angle 1.49805 / 0.81 ( 9) link_NAG-ASN : bond 0.00344 / 0.23 ( 48) link_NAG-ASN : angle 1.77507 / 1.28 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 3057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 315 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 453 TYR cc_start: 0.7730 (p90) cc_final: 0.7207 (p90) REVERT: A 588 THR cc_start: 0.7838 (m) cc_final: 0.7637 (p) REVERT: A 759 PHE cc_start: 0.8378 (OUTLIER) cc_final: 0.7675 (m-10) REVERT: A 977 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8681 (mp) REVERT: A 1029 MET cc_start: 0.8814 (tpp) cc_final: 0.8249 (tpp) REVERT: H 116 ASN cc_start: 0.7744 (m-40) cc_final: 0.7404 (m-40) REVERT: L 72 PHE cc_start: 0.8173 (m-80) cc_final: 0.7937 (m-10) REVERT: L 90 GLN cc_start: 0.7893 (OUTLIER) cc_final: 0.7623 (tt0) REVERT: B 421 TYR cc_start: 0.4626 (m-80) cc_final: 0.4218 (m-80) REVERT: B 453 TYR cc_start: 0.7437 (p90) cc_final: 0.7135 (p90) REVERT: B 759 PHE cc_start: 0.7863 (OUTLIER) cc_final: 0.7303 (t80) REVERT: B 984 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8287 (mt) REVERT: C 80 TYR cc_start: 0.7030 (m-80) cc_final: 0.6562 (m-80) REVERT: C 84 ARG cc_start: 0.7090 (mmm-85) cc_final: 0.6766 (mtm180) REVERT: D 88 TYR cc_start: 0.7234 (m-80) cc_final: 0.7002 (m-80) REVERT: D 90 GLN cc_start: 0.8105 (OUTLIER) cc_final: 0.7825 (tt0) REVERT: E 95 THR cc_start: 0.7509 (p) cc_final: 0.7153 (p) REVERT: E 421 TYR cc_start: 0.4957 (m-80) cc_final: 0.3311 (t80) REVERT: E 453 TYR cc_start: 0.7399 (p90) cc_final: 0.7129 (p90) REVERT: E 977 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8699 (mp) REVERT: E 993 ILE cc_start: 0.9336 (OUTLIER) cc_final: 0.9095 (mp) outliers start: 56 outliers final: 41 residues processed: 360 average time/residue: 0.1706 time to fit residues: 101.5043 Evaluate side-chains 351 residues out of total 3057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 302 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 371 SER Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 603 ASN Chi-restraints excluded: chain E residue 752 LEU Chi-restraints excluded: chain E residue 759 PHE Chi-restraints excluded: chain E residue 791 THR Chi-restraints excluded: chain E residue 808 ASP Chi-restraints excluded: chain E residue 977 LEU Chi-restraints excluded: chain E residue 993 ILE Chi-restraints excluded: chain E residue 1032 CYS Chi-restraints excluded: chain E residue 1072 GLU Chi-restraints excluded: chain E residue 1117 THR Chi-restraints excluded: chain E residue 1128 VAL Chi-restraints excluded: chain F residue 31 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 72 optimal weight: 0.8980 chunk 134 optimal weight: 4.9990 chunk 184 optimal weight: 3.9990 chunk 261 optimal weight: 8.9990 chunk 288 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 222 optimal weight: 4.9990 chunk 108 optimal weight: 6.9990 chunk 114 optimal weight: 6.9990 chunk 201 optimal weight: 0.5980 chunk 60 optimal weight: 0.8980 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1002 GLN C 116 ASN ** E 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 119 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.167676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.135271 restraints weight = 42414.749| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 1.84 r_work: 0.3693 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3567 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.4578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.102 28830 Z= 0.309 Angle : 0.699 8.967 39387 Z= 0.352 Chirality : 0.050 0.366 4709 Planarity : 0.005 0.045 4903 Dihedral : 4.782 46.341 3768 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.12 % Allowed : 13.67 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.03 (0.14), residues: 3438 helix: 1.03 (0.20), residues: 657 sheet: -0.02 (0.15), residues: 966 loop : -0.33 (0.14), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 102 TYR 0.025 0.002 TYR E 265 PHE 0.027 0.002 PHE E 92 TRP 0.027 0.003 TRP F 105 HIS 0.014 0.002 HIS B 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00740 / 0.31 (28713) covalent geometry : angle 0.67217 / 0.35 (39078) SS BOND : bond 0.00524 / 0.34 ( 42) SS BOND : angle 2.39921 / 1.32 ( 84) hydrogen bonds : bond 0.04581 / 3.04 ( 1182) hydrogen bonds : angle 5.60197 / 3.89 ( 3312) link_ALPHA1-3 : bond 0.00492 / 0.22 ( 3) link_ALPHA1-3 : angle 1.55287 / 0.84 ( 9) link_ALPHA1-6 : bond 0.00880 / 0.39 ( 3) link_ALPHA1-6 : angle 1.09441 / 0.59 ( 9) link_BETA1-4 : bond 0.00491 / 0.26 ( 18) link_BETA1-4 : angle 1.89065 / 1.26 ( 54) link_BETA1-6 : bond 0.00205 / 0.07 ( 3) link_BETA1-6 : angle 1.95074 / 1.09 ( 9) link_NAG-ASN : bond 0.00508 / 0.32 ( 48) link_NAG-ASN : angle 2.44398 / 1.78 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 3057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 308 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 453 TYR cc_start: 0.7746 (p90) cc_final: 0.7089 (p90) REVERT: A 505 TYR cc_start: 0.6908 (t80) cc_final: 0.6302 (t80) REVERT: A 586 ASP cc_start: 0.7816 (m-30) cc_final: 0.7484 (t0) REVERT: A 588 THR cc_start: 0.8145 (m) cc_final: 0.7898 (p) REVERT: A 759 PHE cc_start: 0.8527 (OUTLIER) cc_final: 0.7797 (m-10) REVERT: A 1029 MET cc_start: 0.8930 (tpp) cc_final: 0.8398 (tpp) REVERT: H 116 ASN cc_start: 0.7836 (m-40) cc_final: 0.7537 (m-40) REVERT: L 80 GLU cc_start: 0.6198 (mp0) cc_final: 0.5946 (mp0) REVERT: L 90 GLN cc_start: 0.8082 (OUTLIER) cc_final: 0.7677 (tt0) REVERT: B 453 TYR cc_start: 0.7548 (p90) cc_final: 0.7182 (p90) REVERT: B 759 PHE cc_start: 0.8196 (OUTLIER) cc_final: 0.7507 (t80) REVERT: B 984 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8416 (mt) REVERT: C 57 ASN cc_start: 0.7952 (t0) cc_final: 0.7326 (m110) REVERT: C 84 ARG cc_start: 0.7172 (mmm-85) cc_final: 0.6800 (mtm180) REVERT: D 90 GLN cc_start: 0.8211 (OUTLIER) cc_final: 0.7848 (tt0) REVERT: E 95 THR cc_start: 0.7990 (p) cc_final: 0.7724 (p) REVERT: E 453 TYR cc_start: 0.7605 (p90) cc_final: 0.7217 (p90) REVERT: E 977 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8730 (mp) REVERT: E 993 ILE cc_start: 0.9362 (OUTLIER) cc_final: 0.9154 (mp) outliers start: 62 outliers final: 46 residues processed: 360 average time/residue: 0.1684 time to fit residues: 100.3592 Evaluate side-chains 347 residues out of total 3057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 294 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 302 THR Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 371 SER Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 588 THR Chi-restraints excluded: chain E residue 603 ASN Chi-restraints excluded: chain E residue 747 THR Chi-restraints excluded: chain E residue 752 LEU Chi-restraints excluded: chain E residue 791 THR Chi-restraints excluded: chain E residue 808 ASP Chi-restraints excluded: chain E residue 859 THR Chi-restraints excluded: chain E residue 977 LEU Chi-restraints excluded: chain E residue 993 ILE Chi-restraints excluded: chain E residue 1072 GLU Chi-restraints excluded: chain E residue 1117 THR Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 31 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 130 optimal weight: 0.7980 chunk 197 optimal weight: 1.9990 chunk 243 optimal weight: 0.9980 chunk 71 optimal weight: 0.0980 chunk 236 optimal weight: 0.9990 chunk 99 optimal weight: 0.9980 chunk 325 optimal weight: 0.9990 chunk 161 optimal weight: 5.9990 chunk 245 optimal weight: 3.9990 chunk 326 optimal weight: 0.5980 chunk 90 optimal weight: 0.4980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1002 GLN B1101 HIS G 91 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.169253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.142798 restraints weight = 41820.499| |-----------------------------------------------------------------------------| r_work (start): 0.3981 rms_B_bonded: 3.07 r_work: 0.3622 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.4606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 28830 Z= 0.131 Angle : 0.556 8.085 39387 Z= 0.285 Chirality : 0.044 0.320 4709 Planarity : 0.004 0.047 4903 Dihedral : 4.454 45.970 3768 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.51 % Allowed : 14.59 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.14 (0.14), residues: 3438 helix: 1.25 (0.21), residues: 657 sheet: 0.09 (0.16), residues: 936 loop : -0.26 (0.14), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 102 TYR 0.024 0.001 TYR D 50 PHE 0.018 0.001 PHE L 72 TRP 0.026 0.001 TRP F 105 HIS 0.006 0.001 HIS D 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (28713) covalent geometry : angle 0.53528 / 0.28 (39078) SS BOND : bond 0.00412 / 0.27 ( 42) SS BOND : angle 1.82650 / 1.02 ( 84) hydrogen bonds : bond 0.03741 / 2.49 ( 1182) hydrogen bonds : angle 5.34678 / 3.71 ( 3312) link_ALPHA1-3 : bond 0.00432 / 0.20 ( 3) link_ALPHA1-3 : angle 1.50782 / 0.83 ( 9) link_ALPHA1-6 : bond 0.00565 / 0.25 ( 3) link_ALPHA1-6 : angle 1.19669 / 0.63 ( 9) link_BETA1-4 : bond 0.00427 / 0.24 ( 18) link_BETA1-4 : angle 1.34137 / 0.95 ( 54) link_BETA1-6 : bond 0.00330 / 0.14 ( 3) link_BETA1-6 : angle 1.45813 / 0.80 ( 9) link_NAG-ASN : bond 0.00337 / 0.24 ( 48) link_NAG-ASN : angle 1.95090 / 1.40 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 3057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 314 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 414 GLN cc_start: 0.7651 (tp40) cc_final: 0.7448 (tp40) REVERT: A 453 TYR cc_start: 0.7729 (p90) cc_final: 0.7089 (p90) REVERT: A 505 TYR cc_start: 0.6971 (t80) cc_final: 0.6283 (t80) REVERT: A 584 ILE cc_start: 0.8592 (mm) cc_final: 0.8201 (mm) REVERT: A 759 PHE cc_start: 0.8352 (OUTLIER) cc_final: 0.7513 (m-10) REVERT: A 977 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8656 (mp) REVERT: A 1029 MET cc_start: 0.8843 (tpp) cc_final: 0.8317 (tpp) REVERT: H 116 ASN cc_start: 0.7837 (m-40) cc_final: 0.7448 (m-40) REVERT: L 80 GLU cc_start: 0.6191 (mp0) cc_final: 0.5951 (mp0) REVERT: L 90 GLN cc_start: 0.8020 (OUTLIER) cc_final: 0.7618 (tt0) REVERT: B 453 TYR cc_start: 0.7567 (p90) cc_final: 0.7214 (p90) REVERT: B 759 PHE cc_start: 0.7903 (OUTLIER) cc_final: 0.7351 (t80) REVERT: B 984 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8389 (mt) REVERT: C 80 TYR cc_start: 0.7015 (m-80) cc_final: 0.6695 (m-80) REVERT: C 84 ARG cc_start: 0.7028 (mmm-85) cc_final: 0.6640 (mtt180) REVERT: D 90 GLN cc_start: 0.8051 (OUTLIER) cc_final: 0.7740 (tt0) REVERT: E 95 THR cc_start: 0.7827 (p) cc_final: 0.7493 (p) REVERT: E 453 TYR cc_start: 0.7563 (p90) cc_final: 0.7164 (p90) REVERT: E 977 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8687 (mp) REVERT: E 993 ILE cc_start: 0.9338 (OUTLIER) cc_final: 0.9111 (mp) outliers start: 44 outliers final: 32 residues processed: 352 average time/residue: 0.1666 time to fit residues: 97.1159 Evaluate side-chains 343 residues out of total 3057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 303 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 371 SER Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 603 ASN Chi-restraints excluded: chain E residue 752 LEU Chi-restraints excluded: chain E residue 791 THR Chi-restraints excluded: chain E residue 808 ASP Chi-restraints excluded: chain E residue 977 LEU Chi-restraints excluded: chain E residue 993 ILE Chi-restraints excluded: chain E residue 1117 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 104 optimal weight: 7.9990 chunk 191 optimal weight: 0.5980 chunk 99 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 269 optimal weight: 8.9990 chunk 6 optimal weight: 0.9980 chunk 59 optimal weight: 0.5980 chunk 53 optimal weight: 3.9990 chunk 176 optimal weight: 0.7980 chunk 237 optimal weight: 3.9990 chunk 341 optimal weight: 10.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1002 GLN H 3 GLN E 655 HIS ** E1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.168868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 99)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.134646 restraints weight = 41787.553| |-----------------------------------------------------------------------------| r_work (start): 0.3852 rms_B_bonded: 1.97 r_work: 0.3708 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3580 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.4685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 28830 Z= 0.144 Angle : 0.556 7.680 39387 Z= 0.284 Chirality : 0.044 0.291 4709 Planarity : 0.004 0.045 4903 Dihedral : 4.379 45.609 3768 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.47 % Allowed : 14.66 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.17 (0.14), residues: 3438 helix: 1.31 (0.21), residues: 657 sheet: 0.08 (0.15), residues: 966 loop : -0.23 (0.14), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 102 TYR 0.024 0.001 TYR D 50 PHE 0.016 0.001 PHE E 168 TRP 0.022 0.001 TRP C 47 HIS 0.007 0.001 HIS D 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.14 (28713) covalent geometry : angle 0.53604 / 0.28 (39078) SS BOND : bond 0.00413 / 0.27 ( 42) SS BOND : angle 1.74643 / 0.97 ( 84) hydrogen bonds : bond 0.03768 / 2.52 ( 1182) hydrogen bonds : angle 5.28068 / 3.66 ( 3312) link_ALPHA1-3 : bond 0.00401 / 0.18 ( 3) link_ALPHA1-3 : angle 1.51948 / 0.82 ( 9) link_ALPHA1-6 : bond 0.00615 / 0.27 ( 3) link_ALPHA1-6 : angle 1.18355 / 0.62 ( 9) link_BETA1-4 : bond 0.00438 / 0.23 ( 18) link_BETA1-4 : angle 1.35221 / 0.95 ( 54) link_BETA1-6 : bond 0.00289 / 0.14 ( 3) link_BETA1-6 : angle 1.47169 / 0.81 ( 9) link_NAG-ASN : bond 0.00346 / 0.24 ( 48) link_NAG-ASN : angle 1.91554 / 1.39 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7835.30 seconds wall clock time: 134 minutes 49.06 seconds (8089.06 seconds total)