Starting phenix.real_space_refine on Thu Mar 5 15:32:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6m15_30037/03_2026/6m15_30037_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6m15_30037/03_2026/6m15_30037.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6m15_30037/03_2026/6m15_30037_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6m15_30037/03_2026/6m15_30037_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6m15_30037/03_2026/6m15_30037.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6m15_30037/03_2026/6m15_30037.map" } resolution = 2.38 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= 0.000 sd= 0.008 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 129 5.16 5 C 14889 2.51 5 N 3840 2.21 5 O 4613 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23471 Number of models: 1 Model: "" Number of chains: 30 Chain: "B" Number of atoms: 7467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 965, 7467 Classifications: {'peptide': 965} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 925} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 3, 'ARG:plan': 2, 'GLN:plan1': 2, 'TYR:plan': 2, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 53 Chain: "A" Number of atoms: 7467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 965, 7467 Classifications: {'peptide': 965} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 925} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 3, 'ARG:plan': 2, 'GLN:plan1': 2, 'TYR:plan': 2, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 53 Chain: "C" Number of atoms: 7467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 965, 7467 Classifications: {'peptide': 965} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 925} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 3, 'ARG:plan': 2, 'GLN:plan1': 2, 'TYR:plan': 2, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 53 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Chain: "C" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Time building chain proxies: 5.55, per 1000 atoms: 0.24 Number of scatterers: 23471 At special positions: 0 Unit cell: (132.625, 126.259, 162.333, 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 129 16.00 O 4613 8.00 N 3840 7.00 C 14889 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS B 17 " - pdb=" SG CYS B 56 " distance=2.03 Simple disulfide: pdb=" SG CYS B 124 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS B 234 " - pdb=" SG CYS B 244 " distance=2.02 Simple disulfide: pdb=" SG CYS B 277 " - pdb=" SG CYS B 300 " distance=2.03 Simple disulfide: pdb=" SG CYS B 285 " - pdb=" SG CYS B 290 " distance=2.03 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 369 " distance=2.03 Simple disulfide: pdb=" SG CYS B 341 " - pdb=" SG CYS B 397 " distance=2.04 Simple disulfide: pdb=" SG CYS B 409 " - pdb=" SG CYS B 458 " distance=2.05 Simple disulfide: pdb=" SG CYS B 482 " - pdb=" SG CYS B 509 " distance=2.02 Simple disulfide: pdb=" SG CYS B 524 " - pdb=" SG CYS B 533 " distance=2.03 Simple disulfide: pdb=" SG CYS B 590 " - pdb=" SG CYS B 612 " distance=2.03 Simple disulfide: pdb=" SG CYS B 595 " - pdb=" SG CYS B 601 " distance=2.03 Simple disulfide: pdb=" SG CYS B 696 " - pdb=" SG CYS B 706 " distance=2.04 Simple disulfide: pdb=" SG CYS B 884 " - pdb=" SG CYS B 895 " distance=2.03 Simple disulfide: pdb=" SG CYS B 934 " - pdb=" SG CYS B 943 " distance=2.03 Simple disulfide: pdb=" SG CYS A 17 " - pdb=" SG CYS A 56 " distance=2.03 Simple disulfide: pdb=" SG CYS A 124 " - pdb=" SG CYS A 149 " distance=2.03 Simple disulfide: pdb=" SG CYS A 234 " - pdb=" SG CYS A 244 " distance=2.02 Simple disulfide: pdb=" SG CYS A 277 " - pdb=" SG CYS A 300 " distance=2.03 Simple disulfide: pdb=" SG CYS A 285 " - pdb=" SG CYS A 290 " distance=2.03 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 369 " distance=2.03 Simple disulfide: pdb=" SG CYS A 341 " - pdb=" SG CYS A 397 " distance=2.04 Simple disulfide: pdb=" SG CYS A 409 " - pdb=" SG CYS A 458 " distance=2.05 Simple disulfide: pdb=" SG CYS A 482 " - pdb=" SG CYS A 509 " distance=2.02 Simple disulfide: pdb=" SG CYS A 524 " - pdb=" SG CYS A 533 " distance=2.03 Simple disulfide: pdb=" SG CYS A 590 " - pdb=" SG CYS A 612 " distance=2.03 Simple disulfide: pdb=" SG CYS A 595 " - pdb=" SG CYS A 601 " distance=2.03 Simple disulfide: pdb=" SG CYS A 696 " - pdb=" SG CYS A 706 " distance=2.04 Simple disulfide: pdb=" SG CYS A 884 " - pdb=" SG CYS A 895 " distance=2.03 Simple disulfide: pdb=" SG CYS A 934 " - pdb=" SG CYS A 943 " distance=2.03 Simple disulfide: pdb=" SG CYS C 17 " - pdb=" SG CYS C 56 " distance=2.03 Simple disulfide: pdb=" SG CYS C 124 " - pdb=" SG CYS C 149 " distance=2.03 Simple disulfide: pdb=" SG CYS C 234 " - pdb=" SG CYS C 244 " distance=2.02 Simple disulfide: pdb=" SG CYS C 277 " - pdb=" SG CYS C 300 " distance=2.03 Simple disulfide: pdb=" SG CYS C 285 " - pdb=" SG CYS C 290 " distance=2.03 Simple disulfide: pdb=" SG CYS C 331 " - pdb=" SG CYS C 369 " distance=2.03 Simple disulfide: pdb=" SG CYS C 341 " - pdb=" SG CYS C 397 " distance=2.04 Simple disulfide: pdb=" SG CYS C 409 " - pdb=" SG CYS C 458 " distance=2.05 Simple disulfide: pdb=" SG CYS C 482 " - pdb=" SG CYS C 509 " distance=2.02 Simple disulfide: pdb=" SG CYS C 524 " - pdb=" SG CYS C 533 " distance=2.03 Simple disulfide: pdb=" SG CYS C 590 " - pdb=" SG CYS C 612 " distance=2.03 Simple disulfide: pdb=" SG CYS C 595 " - pdb=" SG CYS C 601 " distance=2.03 Simple disulfide: pdb=" SG CYS C 696 " - pdb=" SG CYS C 706 " distance=2.04 Simple disulfide: pdb=" SG CYS C 884 " - pdb=" SG CYS C 895 " distance=2.03 Simple disulfide: pdb=" SG CYS C 934 " - pdb=" SG CYS C 943 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " NAG-ASN " NAG A1203 " - " ASN A 985 " " NAG A1204 " - " ASN A 37 " " NAG A1207 " - " ASN A 118 " " NAG A1210 " - " ASN A 273 " " NAG A1213 " - " ASN A 356 " " NAG A1214 " - " ASN A 427 " " NAG A1218 " - " ASN A 523 " " NAG A1221 " - " ASN A 922 " " NAG B1203 " - " ASN B 985 " " NAG B1204 " - " ASN B 37 " " NAG B1207 " - " ASN B 118 " " NAG B1210 " - " ASN B 273 " " NAG B1213 " - " ASN B 356 " " NAG B1214 " - " ASN B 427 " " NAG B1218 " - " ASN B 523 " " NAG B1221 " - " ASN B 922 " " NAG C1203 " - " ASN C 985 " " NAG C1204 " - " ASN C 37 " " NAG C1207 " - " ASN C 118 " " NAG C1210 " - " ASN C 273 " " NAG C1213 " - " ASN C 356 " " NAG C1214 " - " ASN C 427 " " NAG C1218 " - " ASN C 523 " " NAG C1221 " - " ASN C 922 " " NAG D 1 " - " ASN B 955 " " NAG E 1 " - " ASN B 102 " " NAG F 1 " - " ASN B 152 " " NAG G 1 " - " ASN B 303 " " NAG H 1 " - " ASN B 501 " " NAG I 1 " - " ASN B 652 " " NAG J 1 " - " ASN B 971 " " NAG K 1 " - " ASN A 955 " " NAG L 1 " - " ASN A 102 " " NAG M 1 " - " ASN A 152 " " NAG N 1 " - " ASN A 303 " " NAG O 1 " - " ASN A 501 " " NAG P 1 " - " ASN A 652 " " NAG Q 1 " - " ASN A 971 " " NAG R 1 " - " ASN C 955 " " NAG S 1 " - " ASN C 102 " " NAG T 1 " - " ASN C 152 " " NAG U 1 " - " ASN C 303 " " NAG V 1 " - " ASN C 501 " " NAG W 1 " - " ASN C 652 " " NAG X 1 " - " ASN C 971 " Time building additional restraints: 1.80 Conformation dependent library (CDL) restraints added in 974.0 milliseconds 5754 Ramachandran restraints generated. 2877 Oldfield, 0 Emsley, 2877 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5352 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 36 sheets defined 25.0% alpha, 28.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'B' and resid 21 through 29 removed outlier: 3.776A pdb=" N ASN B 26 " --> pdb=" O ARG B 23 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY B 27 " --> pdb=" O LEU B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 52 No H-bonds generated for 'chain 'B' and resid 50 through 52' Processing helix chain 'B' and resid 237 through 247 removed outlier: 3.542A pdb=" N LEU B 242 " --> pdb=" O PHE B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 308 removed outlier: 3.550A pdb=" N THR B 308 " --> pdb=" O THR B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 316 removed outlier: 3.955A pdb=" N TYR B 315 " --> pdb=" O LEU B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 319 No H-bonds generated for 'chain 'B' and resid 317 through 319' Processing helix chain 'B' and resid 483 through 488 Processing helix chain 'B' and resid 497 through 501 removed outlier: 3.580A pdb=" N ASN B 501 " --> pdb=" O PRO B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 589 through 595 Processing helix chain 'B' and resid 598 through 603 Processing helix chain 'B' and resid 604 through 608 removed outlier: 3.502A pdb=" N ARG B 607 " --> pdb=" O LEU B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 610 through 638 removed outlier: 3.583A pdb=" N ARG B 620 " --> pdb=" O GLU B 616 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY B 632 " --> pdb=" O SER B 628 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 681 Processing helix chain 'B' and resid 688 through 700 Processing helix chain 'B' and resid 721 through 725 Processing helix chain 'B' and resid 749 through 761 Processing helix chain 'B' and resid 768 through 785 Processing helix chain 'B' and resid 786 through 789 Processing helix chain 'B' and resid 794 through 817 removed outlier: 3.623A pdb=" N VAL B 803 " --> pdb=" O ALA B 799 " (cutoff:3.500A) Processing helix chain 'B' and resid 828 through 836 Processing helix chain 'B' and resid 837 through 885 removed outlier: 4.364A pdb=" N ASN B 872 " --> pdb=" O ALA B 868 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG B 875 " --> pdb=" O ARG B 871 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 29 removed outlier: 3.776A pdb=" N ASN A 26 " --> pdb=" O ARG A 23 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY A 27 " --> pdb=" O LEU A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 52 No H-bonds generated for 'chain 'A' and resid 50 through 52' Processing helix chain 'A' and resid 237 through 247 removed outlier: 3.543A pdb=" N LEU A 242 " --> pdb=" O PHE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 308 removed outlier: 3.550A pdb=" N THR A 308 " --> pdb=" O THR A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 316 removed outlier: 3.955A pdb=" N TYR A 315 " --> pdb=" O LEU A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 319 No H-bonds generated for 'chain 'A' and resid 317 through 319' Processing helix chain 'A' and resid 483 through 488 Processing helix chain 'A' and resid 497 through 501 removed outlier: 3.581A pdb=" N ASN A 501 " --> pdb=" O PRO A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 595 Processing helix chain 'A' and resid 598 through 603 Processing helix chain 'A' and resid 604 through 608 removed outlier: 3.501A pdb=" N ARG A 607 " --> pdb=" O LEU A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 638 removed outlier: 3.583A pdb=" N ARG A 620 " --> pdb=" O GLU A 616 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY A 632 " --> pdb=" O SER A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 681 Processing helix chain 'A' and resid 688 through 700 Processing helix chain 'A' and resid 721 through 725 Processing helix chain 'A' and resid 749 through 761 Processing helix chain 'A' and resid 768 through 785 Processing helix chain 'A' and resid 786 through 789 Processing helix chain 'A' and resid 794 through 817 removed outlier: 3.623A pdb=" N VAL A 803 " --> pdb=" O ALA A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 828 through 836 Processing helix chain 'A' and resid 837 through 885 removed outlier: 4.364A pdb=" N ASN A 872 " --> pdb=" O ALA A 868 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG A 875 " --> pdb=" O ARG A 871 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 29 removed outlier: 3.776A pdb=" N ASN C 26 " --> pdb=" O ARG C 23 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY C 27 " --> pdb=" O LEU C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 52 No H-bonds generated for 'chain 'C' and resid 50 through 52' Processing helix chain 'C' and resid 237 through 247 removed outlier: 3.543A pdb=" N LEU C 242 " --> pdb=" O PHE C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 308 removed outlier: 3.550A pdb=" N THR C 308 " --> pdb=" O THR C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 316 removed outlier: 3.955A pdb=" N TYR C 315 " --> pdb=" O LEU C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 319 No H-bonds generated for 'chain 'C' and resid 317 through 319' Processing helix chain 'C' and resid 483 through 488 Processing helix chain 'C' and resid 497 through 501 removed outlier: 3.580A pdb=" N ASN C 501 " --> pdb=" O PRO C 498 " (cutoff:3.500A) Processing helix chain 'C' and resid 589 through 595 Processing helix chain 'C' and resid 598 through 603 Processing helix chain 'C' and resid 604 through 608 removed outlier: 3.501A pdb=" N ARG C 607 " --> pdb=" O LEU C 604 " (cutoff:3.500A) Processing helix chain 'C' and resid 610 through 638 removed outlier: 3.583A pdb=" N ARG C 620 " --> pdb=" O GLU C 616 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY C 632 " --> pdb=" O SER C 628 " (cutoff:3.500A) Processing helix chain 'C' and resid 672 through 681 Processing helix chain 'C' and resid 688 through 700 Processing helix chain 'C' and resid 721 through 725 Processing helix chain 'C' and resid 749 through 761 Processing helix chain 'C' and resid 768 through 785 Processing helix chain 'C' and resid 786 through 789 Processing helix chain 'C' and resid 794 through 817 removed outlier: 3.623A pdb=" N VAL C 803 " --> pdb=" O ALA C 799 " (cutoff:3.500A) Processing helix chain 'C' and resid 828 through 836 Processing helix chain 'C' and resid 837 through 885 removed outlier: 4.364A pdb=" N ASN C 872 " --> pdb=" O ALA C 868 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG C 875 " --> pdb=" O ARG C 871 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 34 through 35 removed outlier: 6.829A pdb=" N GLY B 34 " --> pdb=" O TYR C 438 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LEU C 437 " --> pdb=" O LYS C 444 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N LYS C 444 " --> pdb=" O VAL C 455 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 39 through 44 removed outlier: 7.437A pdb=" N SER B 217 " --> pdb=" O TYR B 233 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N TYR B 233 " --> pdb=" O SER B 217 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LEU B 219 " --> pdb=" O TYR B 231 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N TYR B 231 " --> pdb=" O LEU B 219 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LEU B 221 " --> pdb=" O THR B 229 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 54 through 55 removed outlier: 4.022A pdb=" N TYR B 163 " --> pdb=" O THR B 76 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 64 through 68 removed outlier: 6.497A pdb=" N VAL B 119 " --> pdb=" O SER B 154 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N SER B 154 " --> pdb=" O VAL B 119 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL B 121 " --> pdb=" O ASN B 152 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASN B 152 " --> pdb=" O VAL B 121 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LEU B 123 " --> pdb=" O LEU B 150 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLU B 148 " --> pdb=" O ARG B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 254 through 260 removed outlier: 5.612A pdb=" N VAL B 255 " --> pdb=" O PHE B 467 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N PHE B 467 " --> pdb=" O VAL B 255 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N SER B 257 " --> pdb=" O VAL B 465 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL B 465 " --> pdb=" O SER B 257 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N SER B 472 " --> pdb=" O ARG B 468 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 265 through 268 removed outlier: 5.738A pdb=" N LYS B 444 " --> pdb=" O VAL B 455 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LEU B 437 " --> pdb=" O LYS B 444 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 275 through 276 removed outlier: 6.823A pdb=" N SER B 275 " --> pdb=" O VAL B 301 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N CYS B 300 " --> pdb=" O CYS B 397 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 294 through 297 removed outlier: 6.688A pdb=" N ILE B 381 " --> pdb=" O ASN B 375 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU B 368 " --> pdb=" O ASN B 332 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 514 through 521 removed outlier: 4.479A pdb=" N ARG B 544 " --> pdb=" O ALA B 516 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N ASN B 518 " --> pdb=" O ARG B 544 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N PHE B 532 " --> pdb=" O LEU B 528 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 562 through 580 removed outlier: 6.539A pdb=" N ASN B 923 " --> pdb=" O LEU B 568 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N HIS B 570 " --> pdb=" O PRO B 921 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N LEU B 572 " --> pdb=" O LEU B 919 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N LEU B 919 " --> pdb=" O LEU B 572 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU B 574 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N TYR B 917 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N GLU B 576 " --> pdb=" O PHE B 915 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N PHE B 915 " --> pdb=" O GLU B 576 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N PHE B 578 " --> pdb=" O MET B 913 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N MET B 913 " --> pdb=" O PHE B 578 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLN B 580 " --> pdb=" O GLY B 911 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N GLY B 911 " --> pdb=" O GLN B 580 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N LEU B 919 " --> pdb=" O HIS B 900 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N HIS B 900 " --> pdb=" O LEU B 919 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 562 through 580 removed outlier: 6.539A pdb=" N ASN B 923 " --> pdb=" O LEU B 568 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N HIS B 570 " --> pdb=" O PRO B 921 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N LEU B 572 " --> pdb=" O LEU B 919 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N LEU B 919 " --> pdb=" O LEU B 572 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU B 574 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N TYR B 917 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N GLU B 576 " --> pdb=" O PHE B 915 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N PHE B 915 " --> pdb=" O GLU B 576 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N PHE B 578 " --> pdb=" O MET B 913 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N MET B 913 " --> pdb=" O PHE B 578 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLN B 580 " --> pdb=" O GLY B 911 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N GLY B 911 " --> pdb=" O GLN B 580 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N THR B 930 " --> pdb=" O LEU B 951 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N LEU B 951 " --> pdb=" O THR B 930 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 585 through 588 Processing sheet with id=AB4, first strand: chain 'B' and resid 977 through 980 removed outlier: 3.725A pdb=" N CYS B 943 " --> pdb=" O VAL B 980 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 39 through 44 removed outlier: 7.437A pdb=" N SER A 217 " --> pdb=" O TYR A 233 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N TYR A 233 " --> pdb=" O SER A 217 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LEU A 219 " --> pdb=" O TYR A 231 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N TYR A 231 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LEU A 221 " --> pdb=" O THR A 229 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 54 through 55 removed outlier: 4.023A pdb=" N TYR A 163 " --> pdb=" O THR A 76 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 64 through 68 removed outlier: 6.498A pdb=" N VAL A 119 " --> pdb=" O SER A 154 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N SER A 154 " --> pdb=" O VAL A 119 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL A 121 " --> pdb=" O ASN A 152 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ASN A 152 " --> pdb=" O VAL A 121 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N LEU A 123 " --> pdb=" O LEU A 150 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLU A 148 " --> pdb=" O ARG A 125 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 254 through 260 removed outlier: 5.612A pdb=" N VAL A 255 " --> pdb=" O PHE A 467 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N PHE A 467 " --> pdb=" O VAL A 255 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N SER A 257 " --> pdb=" O VAL A 465 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL A 465 " --> pdb=" O SER A 257 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N SER A 472 " --> pdb=" O ARG A 468 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 265 through 268 removed outlier: 5.738A pdb=" N LYS A 444 " --> pdb=" O VAL A 455 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N LEU A 437 " --> pdb=" O LYS A 444 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 275 through 276 removed outlier: 6.823A pdb=" N SER A 275 " --> pdb=" O VAL A 301 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N CYS A 300 " --> pdb=" O CYS A 397 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 294 through 297 removed outlier: 6.688A pdb=" N ILE A 381 " --> pdb=" O ASN A 375 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU A 368 " --> pdb=" O ASN A 332 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 514 through 521 removed outlier: 4.480A pdb=" N ARG A 544 " --> pdb=" O ALA A 516 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N ASN A 518 " --> pdb=" O ARG A 544 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N PHE A 532 " --> pdb=" O LEU A 528 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 562 through 580 removed outlier: 6.539A pdb=" N ASN A 923 " --> pdb=" O LEU A 568 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N HIS A 570 " --> pdb=" O PRO A 921 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N LEU A 572 " --> pdb=" O LEU A 919 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N LEU A 919 " --> pdb=" O LEU A 572 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N LEU A 574 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N TYR A 917 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N GLU A 576 " --> pdb=" O PHE A 915 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N PHE A 915 " --> pdb=" O GLU A 576 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N PHE A 578 " --> pdb=" O MET A 913 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N MET A 913 " --> pdb=" O PHE A 578 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLN A 580 " --> pdb=" O GLY A 911 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N GLY A 911 " --> pdb=" O GLN A 580 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N LEU A 919 " --> pdb=" O HIS A 900 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N HIS A 900 " --> pdb=" O LEU A 919 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 562 through 580 removed outlier: 6.539A pdb=" N ASN A 923 " --> pdb=" O LEU A 568 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N HIS A 570 " --> pdb=" O PRO A 921 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N LEU A 572 " --> pdb=" O LEU A 919 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N LEU A 919 " --> pdb=" O LEU A 572 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N LEU A 574 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N TYR A 917 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N GLU A 576 " --> pdb=" O PHE A 915 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N PHE A 915 " --> pdb=" O GLU A 576 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N PHE A 578 " --> pdb=" O MET A 913 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N MET A 913 " --> pdb=" O PHE A 578 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLN A 580 " --> pdb=" O GLY A 911 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N GLY A 911 " --> pdb=" O GLN A 580 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR A 930 " --> pdb=" O LEU A 951 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N LEU A 951 " --> pdb=" O THR A 930 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 585 through 588 Processing sheet with id=AC7, first strand: chain 'A' and resid 977 through 980 removed outlier: 3.726A pdb=" N CYS A 943 " --> pdb=" O VAL A 980 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 39 through 44 removed outlier: 7.437A pdb=" N SER C 217 " --> pdb=" O TYR C 233 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N TYR C 233 " --> pdb=" O SER C 217 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LEU C 219 " --> pdb=" O TYR C 231 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N TYR C 231 " --> pdb=" O LEU C 219 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU C 221 " --> pdb=" O THR C 229 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 54 through 55 removed outlier: 4.022A pdb=" N TYR C 163 " --> pdb=" O THR C 76 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 64 through 68 removed outlier: 6.498A pdb=" N VAL C 119 " --> pdb=" O SER C 154 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N SER C 154 " --> pdb=" O VAL C 119 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL C 121 " --> pdb=" O ASN C 152 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASN C 152 " --> pdb=" O VAL C 121 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N LEU C 123 " --> pdb=" O LEU C 150 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLU C 148 " --> pdb=" O ARG C 125 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 254 through 260 removed outlier: 5.612A pdb=" N VAL C 255 " --> pdb=" O PHE C 467 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N PHE C 467 " --> pdb=" O VAL C 255 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N SER C 257 " --> pdb=" O VAL C 465 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N VAL C 465 " --> pdb=" O SER C 257 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N SER C 472 " --> pdb=" O ARG C 468 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 275 through 276 removed outlier: 6.822A pdb=" N SER C 275 " --> pdb=" O VAL C 301 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N CYS C 300 " --> pdb=" O CYS C 397 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 294 through 297 removed outlier: 6.688A pdb=" N ILE C 381 " --> pdb=" O ASN C 375 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU C 368 " --> pdb=" O ASN C 332 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 514 through 521 removed outlier: 4.480A pdb=" N ARG C 544 " --> pdb=" O ALA C 516 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N ASN C 518 " --> pdb=" O ARG C 544 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N PHE C 532 " --> pdb=" O LEU C 528 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 562 through 580 removed outlier: 6.539A pdb=" N ASN C 923 " --> pdb=" O LEU C 568 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N HIS C 570 " --> pdb=" O PRO C 921 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N LEU C 572 " --> pdb=" O LEU C 919 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N LEU C 919 " --> pdb=" O LEU C 572 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU C 574 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N TYR C 917 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N GLU C 576 " --> pdb=" O PHE C 915 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N PHE C 915 " --> pdb=" O GLU C 576 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N PHE C 578 " --> pdb=" O MET C 913 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N MET C 913 " --> pdb=" O PHE C 578 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N GLN C 580 " --> pdb=" O GLY C 911 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N GLY C 911 " --> pdb=" O GLN C 580 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N LEU C 919 " --> pdb=" O HIS C 900 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N HIS C 900 " --> pdb=" O LEU C 919 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 562 through 580 removed outlier: 6.539A pdb=" N ASN C 923 " --> pdb=" O LEU C 568 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N HIS C 570 " --> pdb=" O PRO C 921 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N LEU C 572 " --> pdb=" O LEU C 919 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N LEU C 919 " --> pdb=" O LEU C 572 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU C 574 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N TYR C 917 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N GLU C 576 " --> pdb=" O PHE C 915 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N PHE C 915 " --> pdb=" O GLU C 576 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N PHE C 578 " --> pdb=" O MET C 913 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N MET C 913 " --> pdb=" O PHE C 578 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N GLN C 580 " --> pdb=" O GLY C 911 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N GLY C 911 " --> pdb=" O GLN C 580 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N THR C 930 " --> pdb=" O LEU C 951 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N LEU C 951 " --> pdb=" O THR C 930 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 585 through 588 Processing sheet with id=AD9, first strand: chain 'C' and resid 977 through 980 removed outlier: 3.725A pdb=" N CYS C 943 " --> pdb=" O VAL C 980 " (cutoff:3.500A) 940 hydrogen bonds defined for protein. 2499 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: 4.36 Time building geometry restraints manager: 2.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 6974 1.34 - 1.47: 6652 1.47 - 1.59: 10143 1.59 - 1.72: 0 1.72 - 1.85: 168 Bond restraints: 23937 Sorted by residual: bond pdb=" C1 NAG A1217 " pdb=" O5 NAG A1217 " ideal model delta sigma weight residual 1.406 1.496 -0.090 2.00e-02 2.50e+03 2.02e+01 bond pdb=" C1 NAG B1217 " pdb=" O5 NAG B1217 " ideal model delta sigma weight residual 1.406 1.496 -0.090 2.00e-02 2.50e+03 2.02e+01 bond pdb=" C1 NAG C1217 " pdb=" O5 NAG C1217 " ideal model delta sigma weight residual 1.406 1.496 -0.090 2.00e-02 2.50e+03 2.02e+01 bond pdb=" C1 BMA Q 3 " pdb=" C2 BMA Q 3 " ideal model delta sigma weight residual 1.519 1.587 -0.068 2.00e-02 2.50e+03 1.16e+01 bond pdb=" C1 BMA X 3 " pdb=" C2 BMA X 3 " ideal model delta sigma weight residual 1.519 1.587 -0.068 2.00e-02 2.50e+03 1.16e+01 ... (remaining 23932 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 30797 2.11 - 4.22: 1603 4.22 - 6.33: 171 6.33 - 8.44: 15 8.44 - 10.55: 24 Bond angle restraints: 32610 Sorted by residual: angle pdb=" CA TYR B 91 " pdb=" CB TYR B 91 " pdb=" CG TYR B 91 " ideal model delta sigma weight residual 113.90 124.10 -10.20 1.80e+00 3.09e-01 3.21e+01 angle pdb=" CA TYR C 91 " pdb=" CB TYR C 91 " pdb=" CG TYR C 91 " ideal model delta sigma weight residual 113.90 124.10 -10.20 1.80e+00 3.09e-01 3.21e+01 angle pdb=" CA TYR A 91 " pdb=" CB TYR A 91 " pdb=" CG TYR A 91 " ideal model delta sigma weight residual 113.90 124.09 -10.19 1.80e+00 3.09e-01 3.21e+01 angle pdb=" C ASP C 339 " pdb=" N ASP C 340 " pdb=" CA ASP C 340 " ideal model delta sigma weight residual 121.54 130.52 -8.98 1.91e+00 2.74e-01 2.21e+01 angle pdb=" C ASP B 339 " pdb=" N ASP B 340 " pdb=" CA ASP B 340 " ideal model delta sigma weight residual 121.54 130.49 -8.95 1.91e+00 2.74e-01 2.20e+01 ... (remaining 32605 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.14: 14454 22.14 - 44.29: 330 44.29 - 66.43: 129 66.43 - 88.57: 42 88.57 - 110.72: 48 Dihedral angle restraints: 15003 sinusoidal: 6633 harmonic: 8370 Sorted by residual: dihedral pdb=" CB CYS C 409 " pdb=" SG CYS C 409 " pdb=" SG CYS C 458 " pdb=" CB CYS C 458 " ideal model delta sinusoidal sigma weight residual 93.00 4.26 88.74 1 1.00e+01 1.00e-02 9.39e+01 dihedral pdb=" CB CYS B 409 " pdb=" SG CYS B 409 " pdb=" SG CYS B 458 " pdb=" CB CYS B 458 " ideal model delta sinusoidal sigma weight residual 93.00 4.28 88.72 1 1.00e+01 1.00e-02 9.39e+01 dihedral pdb=" CB CYS A 409 " pdb=" SG CYS A 409 " pdb=" SG CYS A 458 " pdb=" CB CYS A 458 " ideal model delta sinusoidal sigma weight residual 93.00 4.29 88.71 1 1.00e+01 1.00e-02 9.38e+01 ... (remaining 15000 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.129: 3699 0.129 - 0.258: 177 0.258 - 0.388: 12 0.388 - 0.517: 0 0.517 - 0.646: 6 Chirality restraints: 3894 Sorted by residual: chirality pdb=" C1 NAG A1204 " pdb=" ND2 ASN A 37 " pdb=" C2 NAG A1204 " pdb=" O5 NAG A1204 " both_signs ideal model delta sigma weight residual False -2.40 -1.75 -0.65 2.00e-01 2.50e+01 1.04e+01 chirality pdb=" C1 NAG B1204 " pdb=" ND2 ASN B 37 " pdb=" C2 NAG B1204 " pdb=" O5 NAG B1204 " both_signs ideal model delta sigma weight residual False -2.40 -1.76 -0.64 2.00e-01 2.50e+01 1.04e+01 chirality pdb=" C1 NAG C1204 " pdb=" ND2 ASN C 37 " pdb=" C2 NAG C1204 " pdb=" O5 NAG C1204 " both_signs ideal model delta sigma weight residual False -2.40 -1.76 -0.64 2.00e-01 2.50e+01 1.04e+01 ... (remaining 3891 not shown) Planarity restraints: 4128 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 389 " -0.025 2.00e-02 2.50e+03 2.74e-02 1.31e+01 pdb=" CG PHE A 389 " 0.060 2.00e-02 2.50e+03 pdb=" CD1 PHE A 389 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 PHE A 389 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE A 389 " 0.013 2.00e-02 2.50e+03 pdb=" CE2 PHE A 389 " -0.009 2.00e-02 2.50e+03 pdb=" CZ PHE A 389 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 389 " 0.024 2.00e-02 2.50e+03 2.73e-02 1.31e+01 pdb=" CG PHE B 389 " -0.060 2.00e-02 2.50e+03 pdb=" CD1 PHE B 389 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 PHE B 389 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE B 389 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 PHE B 389 " 0.009 2.00e-02 2.50e+03 pdb=" CZ PHE B 389 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 389 " -0.024 2.00e-02 2.50e+03 2.72e-02 1.30e+01 pdb=" CG PHE C 389 " 0.060 2.00e-02 2.50e+03 pdb=" CD1 PHE C 389 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 PHE C 389 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE C 389 " 0.013 2.00e-02 2.50e+03 pdb=" CE2 PHE C 389 " -0.009 2.00e-02 2.50e+03 pdb=" CZ PHE C 389 " -0.008 2.00e-02 2.50e+03 ... (remaining 4125 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 619 2.69 - 3.24: 20897 3.24 - 3.80: 36560 3.80 - 4.35: 49327 4.35 - 4.90: 80692 Nonbonded interactions: 188095 Sorted by model distance: nonbonded pdb=" O ARG B 607 " pdb=" CG GLU C 820 " model vdw 2.141 3.440 nonbonded pdb=" CG GLU A 820 " pdb=" O ARG C 607 " model vdw 2.142 3.440 nonbonded pdb=" CG GLU B 820 " pdb=" O ARG A 607 " model vdw 2.148 3.440 nonbonded pdb=" OG1 THR B 31 " pdb=" O ARG B 33 " model vdw 2.335 3.040 nonbonded pdb=" OG1 THR C 31 " pdb=" O ARG C 33 " model vdw 2.336 3.040 ... (remaining 188090 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' } ncs_group { reference = chain 'J' selection = chain 'Q' 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: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 21.620 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 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 : 0.009 0.134 24051 Z= 0.399 Angle : 1.094 13.530 32907 Z= 0.587 Chirality : 0.070 0.646 3894 Planarity : 0.007 0.066 4083 Dihedral : 13.409 110.717 9516 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.12 % Allowed : 1.24 % Favored : 98.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -2.43 (0.14), residues: 2877 helix: -2.92 (0.13), residues: 645 sheet: -1.04 (0.18), residues: 747 loop : -1.19 (0.14), residues: 1485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.002 ARG C 447 TYR 0.060 0.005 TYR B 233 PHE 0.060 0.006 PHE B 389 TRP 0.031 0.004 TRP A 127 HIS 0.021 0.004 HIS C 500 Details of bonding type rmsd covalent geometry : bond 0.00904 (23937) covalent geometry : angle 1.04981 (32610) SS BOND : bond 0.00709 ( 45) SS BOND : angle 2.68855 ( 90) hydrogen bonds : bond 0.24943 ( 919) hydrogen bonds : angle 8.53657 ( 2499) link_BETA1-4 : bond 0.01782 ( 24) link_BETA1-4 : angle 3.35912 ( 72) link_NAG-ASN : bond 0.00635 ( 45) link_NAG-ASN : angle 3.82370 ( 135) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5754 Ramachandran restraints generated. 2877 Oldfield, 0 Emsley, 2877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5754 Ramachandran restraints generated. 2877 Oldfield, 0 Emsley, 2877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 357 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 122 ARG cc_start: 0.8138 (mtt180) cc_final: 0.7913 (mtm-85) REVERT: B 545 MET cc_start: 0.8491 (mtp) cc_final: 0.8246 (mtp) REVERT: A 853 MET cc_start: 0.8993 (mtp) cc_final: 0.8760 (mtm) REVERT: C 122 ARG cc_start: 0.8115 (mtt180) cc_final: 0.7827 (mtt-85) REVERT: C 754 MET cc_start: 0.8929 (mmt) cc_final: 0.8728 (mmt) outliers start: 3 outliers final: 0 residues processed: 360 average time/residue: 0.7101 time to fit residues: 287.3913 Evaluate side-chains 242 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 242 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 0.2980 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.0670 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 0.6980 overall best weight: 0.6122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 159 GLN B 210 ASN ** B 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 500 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 526 ASN B 655 GLN B 710 HIS B 810 GLN B 878 GLN B 907 ASN B 976 ASN A 99 HIS A 159 GLN A 210 ASN ** A 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 500 HIS A 526 ASN A 710 HIS A 765 GLN A 810 GLN A 907 ASN C 99 HIS C 159 GLN C 210 ASN ** C 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 378 GLN C 500 HIS C 526 ASN C 710 HIS C 766 ASN C 810 GLN C 897 GLN C 907 ASN C 976 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.132714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.103390 restraints weight = 23496.232| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 1.74 r_work: 0.2973 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 24051 Z= 0.126 Angle : 0.677 11.454 32907 Z= 0.332 Chirality : 0.048 0.412 3894 Planarity : 0.004 0.047 4083 Dihedral : 11.798 69.563 4644 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.19 % Allowed : 5.19 % Favored : 93.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -0.68 (0.15), residues: 2877 helix: 0.22 (0.19), residues: 654 sheet: -0.36 (0.19), residues: 744 loop : -0.73 (0.15), residues: 1479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 991 TYR 0.020 0.002 TYR C 91 PHE 0.017 0.001 PHE C 430 TRP 0.014 0.001 TRP B 127 HIS 0.008 0.001 HIS C 500 Details of bonding type rmsd covalent geometry : bond 0.00257 (23937) covalent geometry : angle 0.64404 (32610) SS BOND : bond 0.00319 ( 45) SS BOND : angle 2.04252 ( 90) hydrogen bonds : bond 0.05878 ( 919) hydrogen bonds : angle 5.64309 ( 2499) link_BETA1-4 : bond 0.01187 ( 24) link_BETA1-4 : angle 2.37691 ( 72) link_NAG-ASN : bond 0.00346 ( 45) link_NAG-ASN : angle 2.36617 ( 135) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5754 Ramachandran restraints generated. 2877 Oldfield, 0 Emsley, 2877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5754 Ramachandran restraints generated. 2877 Oldfield, 0 Emsley, 2877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 252 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 206 MET cc_start: 0.6824 (ttt) cc_final: 0.6434 (ttt) REVERT: B 282 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7828 (mp0) REVERT: B 405 ARG cc_start: 0.8417 (OUTLIER) cc_final: 0.8027 (ttm170) REVERT: B 459 PHE cc_start: 0.7804 (OUTLIER) cc_final: 0.6784 (m-80) REVERT: B 520 THR cc_start: 0.8580 (p) cc_final: 0.8362 (p) REVERT: B 620 ARG cc_start: 0.8692 (ttm110) cc_final: 0.8470 (ttm110) REVERT: A 405 ARG cc_start: 0.8452 (OUTLIER) cc_final: 0.7920 (ttm170) REVERT: A 459 PHE cc_start: 0.7579 (OUTLIER) cc_final: 0.6501 (m-80) REVERT: A 485 LEU cc_start: 0.8413 (mm) cc_final: 0.8069 (mt) REVERT: C 99 HIS cc_start: 0.8384 (m-70) cc_final: 0.8179 (m90) REVERT: C 161 LYS cc_start: 0.7477 (mtmt) cc_final: 0.7256 (mttm) REVERT: C 206 MET cc_start: 0.6690 (ttt) cc_final: 0.6430 (ttt) REVERT: C 330 GLU cc_start: 0.8369 (tp30) cc_final: 0.8035 (mm-30) REVERT: C 340 ASP cc_start: 0.7716 (t0) cc_final: 0.7443 (t0) REVERT: C 454 GLU cc_start: 0.9018 (OUTLIER) cc_final: 0.8626 (tt0) REVERT: C 459 PHE cc_start: 0.7762 (OUTLIER) cc_final: 0.6740 (m-80) REVERT: C 545 MET cc_start: 0.9010 (mtp) cc_final: 0.8773 (mtp) outliers start: 29 outliers final: 7 residues processed: 273 average time/residue: 0.6858 time to fit residues: 212.5679 Evaluate side-chains 247 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 233 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 405 ARG Chi-restraints excluded: chain B residue 454 GLU Chi-restraints excluded: chain B residue 459 PHE Chi-restraints excluded: chain B residue 702 GLN Chi-restraints excluded: chain A residue 405 ARG Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 459 PHE Chi-restraints excluded: chain A residue 766 ASN Chi-restraints excluded: chain C residue 454 GLU Chi-restraints excluded: chain C residue 459 PHE Chi-restraints excluded: chain C residue 546 THR Chi-restraints excluded: chain C residue 564 THR Chi-restraints excluded: chain C residue 641 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 35 optimal weight: 8.9990 chunk 112 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 87 optimal weight: 10.0000 chunk 62 optimal weight: 0.9990 chunk 229 optimal weight: 3.9990 chunk 18 optimal weight: 7.9990 chunk 36 optimal weight: 7.9990 chunk 188 optimal weight: 4.9990 chunk 94 optimal weight: 0.0570 chunk 130 optimal weight: 10.0000 overall best weight: 2.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 326 ASN ** B 500 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 655 GLN B 766 ASN A 326 ASN A 483 ASN A 765 GLN C 326 ASN C 766 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.129372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.099407 restraints weight = 23311.710| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 1.74 r_work: 0.2909 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 24051 Z= 0.178 Angle : 0.741 12.693 32907 Z= 0.364 Chirality : 0.053 0.686 3894 Planarity : 0.004 0.044 4083 Dihedral : 10.638 63.873 4644 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.69 % Allowed : 5.93 % Favored : 92.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -0.11 (0.15), residues: 2877 helix: 1.17 (0.20), residues: 654 sheet: -0.17 (0.19), residues: 744 loop : -0.52 (0.16), residues: 1479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 447 TYR 0.033 0.002 TYR A 91 PHE 0.025 0.002 PHE C 430 TRP 0.010 0.001 TRP B 127 HIS 0.008 0.002 HIS A 500 Details of bonding type rmsd covalent geometry : bond 0.00413 (23937) covalent geometry : angle 0.70344 (32610) SS BOND : bond 0.00605 ( 45) SS BOND : angle 2.64002 ( 90) hydrogen bonds : bond 0.06185 ( 919) hydrogen bonds : angle 5.59325 ( 2499) link_BETA1-4 : bond 0.01098 ( 24) link_BETA1-4 : angle 2.31992 ( 72) link_NAG-ASN : bond 0.00375 ( 45) link_NAG-ASN : angle 2.58156 ( 135) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5754 Ramachandran restraints generated. 2877 Oldfield, 0 Emsley, 2877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5754 Ramachandran restraints generated. 2877 Oldfield, 0 Emsley, 2877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 250 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 37 ASN cc_start: 0.7028 (OUTLIER) cc_final: 0.6822 (m-40) REVERT: B 122 ARG cc_start: 0.8848 (OUTLIER) cc_final: 0.8443 (mtm180) REVERT: B 206 MET cc_start: 0.6870 (ttt) cc_final: 0.6496 (ttt) REVERT: B 214 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7972 (pp20) REVERT: B 405 ARG cc_start: 0.8470 (OUTLIER) cc_final: 0.8044 (ttm170) REVERT: B 459 PHE cc_start: 0.8163 (OUTLIER) cc_final: 0.7421 (m-80) REVERT: A 405 ARG cc_start: 0.8503 (OUTLIER) cc_final: 0.7952 (ttm170) REVERT: A 459 PHE cc_start: 0.8120 (OUTLIER) cc_final: 0.7378 (m-80) REVERT: C 161 LYS cc_start: 0.7490 (mtmt) cc_final: 0.7251 (mttm) REVERT: C 206 MET cc_start: 0.6717 (ttt) cc_final: 0.6482 (ttt) REVERT: C 330 GLU cc_start: 0.8417 (tp30) cc_final: 0.8083 (mm-30) REVERT: C 459 PHE cc_start: 0.8061 (OUTLIER) cc_final: 0.7481 (m-80) REVERT: C 485 LEU cc_start: 0.7955 (mm) cc_final: 0.7710 (mt) REVERT: C 545 MET cc_start: 0.9023 (mtp) cc_final: 0.8773 (mtp) outliers start: 41 outliers final: 14 residues processed: 277 average time/residue: 0.7000 time to fit residues: 219.2519 Evaluate side-chains 262 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 240 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 ASN Chi-restraints excluded: chain B residue 122 ARG Chi-restraints excluded: chain B residue 214 GLU Chi-restraints excluded: chain B residue 405 ARG Chi-restraints excluded: chain B residue 454 GLU Chi-restraints excluded: chain B residue 458 CYS Chi-restraints excluded: chain B residue 459 PHE Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 702 GLN Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 405 ARG Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 458 CYS Chi-restraints excluded: chain A residue 459 PHE Chi-restraints excluded: chain A residue 766 ASN Chi-restraints excluded: chain C residue 23 ARG Chi-restraints excluded: chain C residue 454 GLU Chi-restraints excluded: chain C residue 459 PHE Chi-restraints excluded: chain C residue 546 THR Chi-restraints excluded: chain C residue 564 THR Chi-restraints excluded: chain C residue 641 THR Chi-restraints excluded: chain C residue 731 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 53 optimal weight: 5.9990 chunk 25 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 144 optimal weight: 0.0670 chunk 279 optimal weight: 8.9990 chunk 26 optimal weight: 5.9990 chunk 225 optimal weight: 0.1980 chunk 183 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 overall best weight: 1.8522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 500 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 655 GLN B 805 ASN A 765 GLN A 805 ASN C 99 HIS C 766 ASN C 805 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.129833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.099825 restraints weight = 23368.611| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 1.75 r_work: 0.2915 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 24051 Z= 0.161 Angle : 0.721 14.857 32907 Z= 0.353 Chirality : 0.051 0.527 3894 Planarity : 0.004 0.041 4083 Dihedral : 9.445 58.591 4644 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.61 % Allowed : 6.63 % Favored : 91.76 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 2.56 % 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: 0.21 (0.16), residues: 2877 helix: 1.57 (0.21), residues: 654 sheet: 0.12 (0.19), residues: 711 loop : -0.44 (0.16), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 447 TYR 0.028 0.002 TYR A 91 PHE 0.019 0.002 PHE B 430 TRP 0.009 0.001 TRP A 127 HIS 0.006 0.001 HIS B 500 Details of bonding type rmsd covalent geometry : bond 0.00372 (23937) covalent geometry : angle 0.68121 (32610) SS BOND : bond 0.00597 ( 45) SS BOND : angle 3.09905 ( 90) hydrogen bonds : bond 0.05716 ( 919) hydrogen bonds : angle 5.47801 ( 2499) link_BETA1-4 : bond 0.01042 ( 24) link_BETA1-4 : angle 2.17205 ( 72) link_NAG-ASN : bond 0.00509 ( 45) link_NAG-ASN : angle 2.40394 ( 135) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5754 Ramachandran restraints generated. 2877 Oldfield, 0 Emsley, 2877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5754 Ramachandran restraints generated. 2877 Oldfield, 0 Emsley, 2877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 247 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 122 ARG cc_start: 0.8839 (OUTLIER) cc_final: 0.8393 (mtm180) REVERT: B 206 MET cc_start: 0.6874 (ttt) cc_final: 0.6496 (ttt) REVERT: B 214 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7959 (pp20) REVERT: B 405 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.8082 (ttm170) REVERT: B 459 PHE cc_start: 0.8221 (OUTLIER) cc_final: 0.7557 (m-80) REVERT: B 853 MET cc_start: 0.9215 (mtm) cc_final: 0.8959 (mtm) REVERT: A 214 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.8040 (pp20) REVERT: A 279 GLN cc_start: 0.8855 (mm110) cc_final: 0.8572 (mm-40) REVERT: A 405 ARG cc_start: 0.8534 (OUTLIER) cc_final: 0.7986 (ttm170) REVERT: A 459 PHE cc_start: 0.8118 (OUTLIER) cc_final: 0.7409 (m-80) REVERT: A 721 ASP cc_start: 0.8133 (t0) cc_final: 0.7845 (t0) REVERT: C 99 HIS cc_start: 0.8432 (m-70) cc_final: 0.8085 (m90) REVERT: C 206 MET cc_start: 0.6755 (ttt) cc_final: 0.6491 (ttt) REVERT: C 454 GLU cc_start: 0.9044 (OUTLIER) cc_final: 0.8817 (tt0) REVERT: C 545 MET cc_start: 0.8990 (mtp) cc_final: 0.8671 (mtp) outliers start: 39 outliers final: 16 residues processed: 271 average time/residue: 0.6957 time to fit residues: 213.2251 Evaluate side-chains 266 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 242 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 ARG Chi-restraints excluded: chain B residue 214 GLU Chi-restraints excluded: chain B residue 405 ARG Chi-restraints excluded: chain B residue 454 GLU Chi-restraints excluded: chain B residue 458 CYS Chi-restraints excluded: chain B residue 459 PHE Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 702 GLN Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 405 ARG Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 458 CYS Chi-restraints excluded: chain A residue 459 PHE Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 766 ASN Chi-restraints excluded: chain C residue 23 ARG Chi-restraints excluded: chain C residue 454 GLU Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 546 THR Chi-restraints excluded: chain C residue 564 THR Chi-restraints excluded: chain C residue 641 THR Chi-restraints excluded: chain C residue 731 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 42 optimal weight: 5.9990 chunk 208 optimal weight: 0.1980 chunk 96 optimal weight: 10.0000 chunk 245 optimal weight: 1.9990 chunk 136 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 chunk 189 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 264 optimal weight: 4.9990 chunk 47 optimal weight: 10.0000 overall best weight: 1.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 500 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 655 GLN B 766 ASN A 765 GLN ** C 160 HIS ** 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 = 0.3476 r_free = 0.3476 target = 0.129951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.100115 restraints weight = 23141.397| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 1.73 r_work: 0.2916 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 24051 Z= 0.150 Angle : 0.690 13.319 32907 Z= 0.338 Chirality : 0.049 0.431 3894 Planarity : 0.004 0.040 4083 Dihedral : 8.950 59.442 4644 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.57 % Allowed : 7.25 % Favored : 91.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.31 (0.16), residues: 2877 helix: 1.61 (0.21), residues: 654 sheet: 0.17 (0.19), residues: 711 loop : -0.35 (0.16), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 447 TYR 0.027 0.002 TYR A 91 PHE 0.018 0.002 PHE B 430 TRP 0.009 0.001 TRP A 127 HIS 0.006 0.001 HIS B 500 Details of bonding type rmsd covalent geometry : bond 0.00340 (23937) covalent geometry : angle 0.65351 (32610) SS BOND : bond 0.00530 ( 45) SS BOND : angle 2.75384 ( 90) hydrogen bonds : bond 0.05495 ( 919) hydrogen bonds : angle 5.39673 ( 2499) link_BETA1-4 : bond 0.00995 ( 24) link_BETA1-4 : angle 2.12131 ( 72) link_NAG-ASN : bond 0.00410 ( 45) link_NAG-ASN : angle 2.33872 ( 135) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5754 Ramachandran restraints generated. 2877 Oldfield, 0 Emsley, 2877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5754 Ramachandran restraints generated. 2877 Oldfield, 0 Emsley, 2877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 251 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 122 ARG cc_start: 0.8824 (OUTLIER) cc_final: 0.8402 (mtm180) REVERT: B 206 MET cc_start: 0.6817 (ttt) cc_final: 0.6431 (ttt) REVERT: B 214 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7946 (pp20) REVERT: B 405 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.8096 (ttm170) REVERT: B 459 PHE cc_start: 0.8235 (OUTLIER) cc_final: 0.7559 (m-80) REVERT: A 214 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.8025 (pp20) REVERT: A 279 GLN cc_start: 0.8858 (mm110) cc_final: 0.8561 (mm-40) REVERT: A 405 ARG cc_start: 0.8481 (OUTLIER) cc_final: 0.7941 (ttm170) REVERT: A 459 PHE cc_start: 0.8138 (OUTLIER) cc_final: 0.7488 (m-80) REVERT: A 721 ASP cc_start: 0.8144 (t0) cc_final: 0.7840 (t0) REVERT: C 99 HIS cc_start: 0.8447 (m-70) cc_final: 0.8157 (m90) REVERT: C 206 MET cc_start: 0.6786 (ttt) cc_final: 0.6573 (ttt) REVERT: C 545 MET cc_start: 0.8925 (mtp) cc_final: 0.8660 (mtp) REVERT: C 913 MET cc_start: 0.9110 (tpp) cc_final: 0.8892 (tpp) outliers start: 38 outliers final: 16 residues processed: 278 average time/residue: 0.6930 time to fit residues: 218.2970 Evaluate side-chains 270 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 247 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 ARG Chi-restraints excluded: chain B residue 214 GLU Chi-restraints excluded: chain B residue 405 ARG Chi-restraints excluded: chain B residue 454 GLU Chi-restraints excluded: chain B residue 458 CYS Chi-restraints excluded: chain B residue 459 PHE Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 702 GLN Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 405 ARG Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 458 CYS Chi-restraints excluded: chain A residue 459 PHE Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 766 ASN Chi-restraints excluded: chain C residue 23 ARG Chi-restraints excluded: chain C residue 454 GLU Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 546 THR Chi-restraints excluded: chain C residue 564 THR Chi-restraints excluded: chain C residue 641 THR Chi-restraints excluded: chain C residue 731 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 92 optimal weight: 0.7980 chunk 206 optimal weight: 0.6980 chunk 202 optimal weight: 0.9990 chunk 130 optimal weight: 9.9990 chunk 264 optimal weight: 4.9990 chunk 269 optimal weight: 0.7980 chunk 115 optimal weight: 0.9990 chunk 215 optimal weight: 9.9990 chunk 56 optimal weight: 2.9990 chunk 191 optimal weight: 6.9990 chunk 31 optimal weight: 9.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 500 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 655 GLN B 892 ASN A 765 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.131653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.101855 restraints weight = 23341.328| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 1.75 r_work: 0.2946 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 24051 Z= 0.124 Angle : 0.650 13.582 32907 Z= 0.316 Chirality : 0.047 0.377 3894 Planarity : 0.003 0.039 4083 Dihedral : 8.531 59.858 4644 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.48 % Allowed : 7.58 % Favored : 90.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.49 (0.16), residues: 2877 helix: 1.88 (0.21), residues: 651 sheet: 0.25 (0.19), residues: 711 loop : -0.28 (0.17), residues: 1515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 247 TYR 0.021 0.001 TYR A 91 PHE 0.015 0.001 PHE B 93 TRP 0.010 0.001 TRP B 126 HIS 0.004 0.001 HIS B 500 Details of bonding type rmsd covalent geometry : bond 0.00276 (23937) covalent geometry : angle 0.61261 (32610) SS BOND : bond 0.00504 ( 45) SS BOND : angle 2.73345 ( 90) hydrogen bonds : bond 0.04885 ( 919) hydrogen bonds : angle 5.20932 ( 2499) link_BETA1-4 : bond 0.00978 ( 24) link_BETA1-4 : angle 2.03771 ( 72) link_NAG-ASN : bond 0.00427 ( 45) link_NAG-ASN : angle 2.25789 ( 135) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5754 Ramachandran restraints generated. 2877 Oldfield, 0 Emsley, 2877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5754 Ramachandran restraints generated. 2877 Oldfield, 0 Emsley, 2877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 254 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 122 ARG cc_start: 0.8801 (OUTLIER) cc_final: 0.8361 (mtm180) REVERT: B 206 MET cc_start: 0.6757 (ttt) cc_final: 0.6363 (ttt) REVERT: B 214 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7920 (pp20) REVERT: B 405 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.8089 (ttm170) REVERT: B 459 PHE cc_start: 0.8071 (OUTLIER) cc_final: 0.7390 (m-80) REVERT: B 721 ASP cc_start: 0.8158 (t0) cc_final: 0.7804 (t0) REVERT: A 214 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.8006 (pp20) REVERT: A 279 GLN cc_start: 0.8782 (mm110) cc_final: 0.8498 (mm-40) REVERT: A 405 ARG cc_start: 0.8486 (OUTLIER) cc_final: 0.7958 (ttm170) REVERT: A 459 PHE cc_start: 0.8003 (OUTLIER) cc_final: 0.7339 (m-80) REVERT: A 721 ASP cc_start: 0.8091 (t0) cc_final: 0.7761 (t0) REVERT: A 837 ASP cc_start: 0.8227 (p0) cc_final: 0.7975 (p0) REVERT: C 23 ARG cc_start: 0.7462 (OUTLIER) cc_final: 0.6930 (mmp-170) REVERT: C 99 HIS cc_start: 0.8422 (m-70) cc_final: 0.8168 (m90) REVERT: C 206 MET cc_start: 0.6767 (ttt) cc_final: 0.6500 (ttt) REVERT: C 454 GLU cc_start: 0.9030 (OUTLIER) cc_final: 0.8694 (tt0) REVERT: C 545 MET cc_start: 0.8897 (mtp) cc_final: 0.8601 (mtp) REVERT: C 721 ASP cc_start: 0.8151 (t0) cc_final: 0.7888 (t0) REVERT: C 913 MET cc_start: 0.9099 (tpp) cc_final: 0.8873 (tpp) outliers start: 36 outliers final: 12 residues processed: 277 average time/residue: 0.6782 time to fit residues: 213.2681 Evaluate side-chains 264 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 243 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 ARG Chi-restraints excluded: chain B residue 214 GLU Chi-restraints excluded: chain B residue 405 ARG Chi-restraints excluded: chain B residue 454 GLU Chi-restraints excluded: chain B residue 458 CYS Chi-restraints excluded: chain B residue 459 PHE Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 405 ARG Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 458 CYS Chi-restraints excluded: chain A residue 459 PHE Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain C residue 23 ARG Chi-restraints excluded: chain C residue 454 GLU Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 546 THR Chi-restraints excluded: chain C residue 641 THR Chi-restraints excluded: chain C residue 731 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 18 optimal weight: 8.9990 chunk 169 optimal weight: 7.9990 chunk 157 optimal weight: 1.9990 chunk 233 optimal weight: 4.9990 chunk 283 optimal weight: 6.9990 chunk 32 optimal weight: 6.9990 chunk 98 optimal weight: 9.9990 chunk 65 optimal weight: 0.9980 chunk 142 optimal weight: 1.9990 chunk 131 optimal weight: 4.9990 chunk 225 optimal weight: 0.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 500 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 655 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.129443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.099443 restraints weight = 23142.259| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 1.74 r_work: 0.2908 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.108 24051 Z= 0.178 Angle : 0.731 16.235 32907 Z= 0.362 Chirality : 0.050 0.416 3894 Planarity : 0.004 0.040 4083 Dihedral : 8.633 59.322 4644 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.28 % Allowed : 8.28 % Favored : 90.44 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 2.56 % 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: 0.40 (0.16), residues: 2877 helix: 1.72 (0.21), residues: 651 sheet: 0.21 (0.19), residues: 702 loop : -0.29 (0.16), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 247 TYR 0.031 0.002 TYR A 91 PHE 0.020 0.002 PHE C 430 TRP 0.011 0.002 TRP C 108 HIS 0.006 0.001 HIS B 500 Details of bonding type rmsd covalent geometry : bond 0.00415 (23937) covalent geometry : angle 0.68927 (32610) SS BOND : bond 0.00739 ( 45) SS BOND : angle 3.30089 ( 90) hydrogen bonds : bond 0.05792 ( 919) hydrogen bonds : angle 5.45431 ( 2499) link_BETA1-4 : bond 0.01003 ( 24) link_BETA1-4 : angle 2.11776 ( 72) link_NAG-ASN : bond 0.00399 ( 45) link_NAG-ASN : angle 2.39134 ( 135) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5754 Ramachandran restraints generated. 2877 Oldfield, 0 Emsley, 2877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5754 Ramachandran restraints generated. 2877 Oldfield, 0 Emsley, 2877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 248 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 37 ASN cc_start: 0.8276 (m-40) cc_final: 0.8058 (m-40) REVERT: B 122 ARG cc_start: 0.8850 (OUTLIER) cc_final: 0.8427 (mtm180) REVERT: B 206 MET cc_start: 0.6869 (ttt) cc_final: 0.6488 (ttt) REVERT: B 214 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7961 (pp20) REVERT: B 405 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.8108 (ttm170) REVERT: B 459 PHE cc_start: 0.8283 (OUTLIER) cc_final: 0.7713 (m-80) REVERT: B 721 ASP cc_start: 0.8300 (t0) cc_final: 0.7971 (t0) REVERT: A 214 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.8026 (pp20) REVERT: A 279 GLN cc_start: 0.8819 (mm110) cc_final: 0.8506 (mm-40) REVERT: A 405 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.7958 (ttm170) REVERT: A 459 PHE cc_start: 0.8186 (OUTLIER) cc_final: 0.7574 (m-80) REVERT: C 99 HIS cc_start: 0.8470 (m-70) cc_final: 0.8265 (m90) REVERT: C 206 MET cc_start: 0.6821 (ttt) cc_final: 0.6609 (ttt) REVERT: C 459 PHE cc_start: 0.8109 (OUTLIER) cc_final: 0.7737 (m-80) REVERT: C 545 MET cc_start: 0.8869 (mtp) cc_final: 0.8613 (mtp) REVERT: C 616 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.7226 (mp0) REVERT: C 913 MET cc_start: 0.9117 (tpp) cc_final: 0.8820 (tpp) outliers start: 31 outliers final: 16 residues processed: 267 average time/residue: 0.6625 time to fit residues: 200.8767 Evaluate side-chains 273 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 248 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 ARG Chi-restraints excluded: chain B residue 214 GLU Chi-restraints excluded: chain B residue 405 ARG Chi-restraints excluded: chain B residue 454 GLU Chi-restraints excluded: chain B residue 458 CYS Chi-restraints excluded: chain B residue 459 PHE Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 766 ASN Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 405 ARG Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 458 CYS Chi-restraints excluded: chain A residue 459 PHE Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain C residue 23 ARG Chi-restraints excluded: chain C residue 454 GLU Chi-restraints excluded: chain C residue 459 PHE Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 546 THR Chi-restraints excluded: chain C residue 564 THR Chi-restraints excluded: chain C residue 616 GLU Chi-restraints excluded: chain C residue 641 THR Chi-restraints excluded: chain C residue 731 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 40 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 chunk 247 optimal weight: 1.9990 chunk 111 optimal weight: 8.9990 chunk 43 optimal weight: 7.9990 chunk 45 optimal weight: 0.7980 chunk 189 optimal weight: 2.9990 chunk 269 optimal weight: 0.9990 chunk 185 optimal weight: 8.9990 chunk 1 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 655 GLN B 897 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.132012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.102269 restraints weight = 23257.635| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 1.75 r_work: 0.2952 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 24051 Z= 0.123 Angle : 0.649 13.696 32907 Z= 0.320 Chirality : 0.047 0.357 3894 Planarity : 0.003 0.039 4083 Dihedral : 8.184 59.615 4644 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.07 % Allowed : 8.57 % Favored : 90.36 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.58 (0.16), residues: 2877 helix: 1.95 (0.21), residues: 651 sheet: 0.32 (0.19), residues: 702 loop : -0.22 (0.17), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 982 TYR 0.019 0.001 TYR B 91 PHE 0.016 0.001 PHE B 430 TRP 0.011 0.001 TRP B 126 HIS 0.005 0.001 HIS B 500 Details of bonding type rmsd covalent geometry : bond 0.00273 (23937) covalent geometry : angle 0.61993 (32610) SS BOND : bond 0.00491 ( 45) SS BOND : angle 2.74157 ( 90) hydrogen bonds : bond 0.04823 ( 919) hydrogen bonds : angle 5.21164 ( 2499) link_BETA1-4 : bond 0.00952 ( 24) link_BETA1-4 : angle 1.97112 ( 72) link_NAG-ASN : bond 0.00292 ( 45) link_NAG-ASN : angle 1.64897 ( 135) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5754 Ramachandran restraints generated. 2877 Oldfield, 0 Emsley, 2877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5754 Ramachandran restraints generated. 2877 Oldfield, 0 Emsley, 2877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 256 time to evaluate : 0.855 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: B 122 ARG cc_start: 0.8801 (OUTLIER) cc_final: 0.8362 (mtm180) REVERT: B 206 MET cc_start: 0.6784 (ttt) cc_final: 0.6382 (ttt) REVERT: B 214 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7930 (pp20) REVERT: B 459 PHE cc_start: 0.8057 (OUTLIER) cc_final: 0.7369 (m-80) REVERT: B 721 ASP cc_start: 0.8232 (t0) cc_final: 0.7996 (t0) REVERT: A 214 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7983 (pp20) REVERT: A 279 GLN cc_start: 0.8708 (mm110) cc_final: 0.8405 (mm-40) REVERT: A 459 PHE cc_start: 0.8003 (OUTLIER) cc_final: 0.7344 (m-80) REVERT: A 721 ASP cc_start: 0.7926 (t0) cc_final: 0.7665 (t0) REVERT: A 837 ASP cc_start: 0.8236 (p0) cc_final: 0.7992 (p0) REVERT: C 23 ARG cc_start: 0.7435 (OUTLIER) cc_final: 0.6892 (mmp-170) REVERT: C 122 ARG cc_start: 0.8906 (mtt180) cc_final: 0.8666 (mtt-85) REVERT: C 206 MET cc_start: 0.6654 (ttt) cc_final: 0.6398 (ttt) REVERT: C 454 GLU cc_start: 0.9024 (OUTLIER) cc_final: 0.8667 (tt0) REVERT: C 545 MET cc_start: 0.8861 (mtp) cc_final: 0.8609 (mtp) REVERT: C 721 ASP cc_start: 0.8143 (t0) cc_final: 0.7905 (t0) REVERT: C 913 MET cc_start: 0.9129 (tpp) cc_final: 0.8895 (tpp) outliers start: 26 outliers final: 11 residues processed: 273 average time/residue: 0.6729 time to fit residues: 209.1709 Evaluate side-chains 268 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 250 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 ARG Chi-restraints excluded: chain B residue 214 GLU Chi-restraints excluded: chain B residue 454 GLU Chi-restraints excluded: chain B residue 458 CYS Chi-restraints excluded: chain B residue 459 PHE Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 458 CYS Chi-restraints excluded: chain A residue 459 PHE Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain C residue 23 ARG Chi-restraints excluded: chain C residue 454 GLU Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 546 THR Chi-restraints excluded: chain C residue 641 THR Chi-restraints excluded: chain C residue 731 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 7 optimal weight: 9.9990 chunk 286 optimal weight: 3.9990 chunk 247 optimal weight: 0.9990 chunk 265 optimal weight: 0.0470 chunk 267 optimal weight: 3.9990 chunk 74 optimal weight: 8.9990 chunk 26 optimal weight: 1.9990 chunk 195 optimal weight: 4.9990 chunk 190 optimal weight: 1.9990 chunk 192 optimal weight: 4.9990 chunk 227 optimal weight: 0.5980 overall best weight: 1.1284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 655 GLN A 765 GLN A 781 GLN C 99 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.131821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.101923 restraints weight = 23347.164| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 1.76 r_work: 0.2947 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 24051 Z= 0.132 Angle : 0.654 13.780 32907 Z= 0.324 Chirality : 0.047 0.368 3894 Planarity : 0.003 0.039 4083 Dihedral : 8.020 57.276 4644 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.28 % Allowed : 8.53 % Favored : 90.19 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.61 (0.16), residues: 2877 helix: 1.96 (0.21), residues: 651 sheet: 0.31 (0.19), residues: 711 loop : -0.18 (0.17), residues: 1515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 247 TYR 0.023 0.001 TYR A 91 PHE 0.016 0.001 PHE B 93 TRP 0.015 0.001 TRP C 108 HIS 0.004 0.001 HIS B 500 Details of bonding type rmsd covalent geometry : bond 0.00299 (23937) covalent geometry : angle 0.62341 (32610) SS BOND : bond 0.00611 ( 45) SS BOND : angle 2.84071 ( 90) hydrogen bonds : bond 0.04929 ( 919) hydrogen bonds : angle 5.22459 ( 2499) link_BETA1-4 : bond 0.00929 ( 24) link_BETA1-4 : angle 1.95316 ( 72) link_NAG-ASN : bond 0.00216 ( 45) link_NAG-ASN : angle 1.73139 ( 135) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5754 Ramachandran restraints generated. 2877 Oldfield, 0 Emsley, 2877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5754 Ramachandran restraints generated. 2877 Oldfield, 0 Emsley, 2877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 258 time to evaluate : 0.792 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: B 122 ARG cc_start: 0.8820 (OUTLIER) cc_final: 0.8404 (mtm180) REVERT: B 206 MET cc_start: 0.6784 (ttt) cc_final: 0.6385 (ttt) REVERT: B 214 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7918 (pp20) REVERT: B 459 PHE cc_start: 0.8100 (OUTLIER) cc_final: 0.7465 (m-80) REVERT: B 721 ASP cc_start: 0.8222 (t0) cc_final: 0.7982 (t0) REVERT: A 214 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7988 (pp20) REVERT: A 279 GLN cc_start: 0.8699 (mm110) cc_final: 0.8399 (mm-40) REVERT: A 405 ARG cc_start: 0.8495 (OUTLIER) cc_final: 0.7981 (ttm170) REVERT: A 459 PHE cc_start: 0.8055 (OUTLIER) cc_final: 0.7435 (m-80) REVERT: A 721 ASP cc_start: 0.7939 (t0) cc_final: 0.7628 (t0) REVERT: A 837 ASP cc_start: 0.8246 (p0) cc_final: 0.7993 (p0) REVERT: C 23 ARG cc_start: 0.7445 (OUTLIER) cc_final: 0.7000 (mmp-170) REVERT: C 99 HIS cc_start: 0.8381 (m-70) cc_final: 0.8079 (m90) REVERT: C 454 GLU cc_start: 0.9025 (OUTLIER) cc_final: 0.8683 (tt0) REVERT: C 545 MET cc_start: 0.8871 (mtp) cc_final: 0.8574 (mtp) REVERT: C 616 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.7358 (mp0) REVERT: C 721 ASP cc_start: 0.8151 (t0) cc_final: 0.7920 (t0) REVERT: C 913 MET cc_start: 0.9141 (tpp) cc_final: 0.8863 (tpp) outliers start: 31 outliers final: 12 residues processed: 277 average time/residue: 0.6540 time to fit residues: 206.3077 Evaluate side-chains 275 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 254 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 ARG Chi-restraints excluded: chain B residue 214 GLU Chi-restraints excluded: chain B residue 454 GLU Chi-restraints excluded: chain B residue 458 CYS Chi-restraints excluded: chain B residue 459 PHE Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 405 ARG Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 458 CYS Chi-restraints excluded: chain A residue 459 PHE Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain C residue 23 ARG Chi-restraints excluded: chain C residue 454 GLU Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 546 THR Chi-restraints excluded: chain C residue 616 GLU Chi-restraints excluded: chain C residue 641 THR Chi-restraints excluded: chain C residue 731 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 188 optimal weight: 0.0970 chunk 236 optimal weight: 3.9990 chunk 154 optimal weight: 0.2980 chunk 93 optimal weight: 4.9990 chunk 229 optimal weight: 5.9990 chunk 61 optimal weight: 0.9990 chunk 2 optimal weight: 10.0000 chunk 117 optimal weight: 0.5980 chunk 70 optimal weight: 0.6980 chunk 136 optimal weight: 0.8980 chunk 52 optimal weight: 6.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 512 ASN B 655 GLN A 512 ASN A 765 GLN C 512 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.134475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.104865 restraints weight = 23418.496| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 1.76 r_work: 0.2995 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 24051 Z= 0.114 Angle : 0.619 13.588 32907 Z= 0.303 Chirality : 0.046 0.338 3894 Planarity : 0.003 0.038 4083 Dihedral : 7.784 57.521 4644 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.99 % Allowed : 9.06 % Favored : 89.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.62 (0.16), residues: 2877 helix: 2.00 (0.21), residues: 657 sheet: 0.29 (0.19), residues: 696 loop : -0.18 (0.17), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 247 TYR 0.016 0.001 TYR A 634 PHE 0.020 0.001 PHE A 428 TRP 0.013 0.001 TRP A 108 HIS 0.003 0.001 HIS B 500 Details of bonding type rmsd covalent geometry : bond 0.00249 (23937) covalent geometry : angle 0.59215 (32610) SS BOND : bond 0.00493 ( 45) SS BOND : angle 2.37117 ( 90) hydrogen bonds : bond 0.04251 ( 919) hydrogen bonds : angle 5.02602 ( 2499) link_BETA1-4 : bond 0.00887 ( 24) link_BETA1-4 : angle 1.82762 ( 72) link_NAG-ASN : bond 0.00368 ( 45) link_NAG-ASN : angle 1.75214 ( 135) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5754 Ramachandran restraints generated. 2877 Oldfield, 0 Emsley, 2877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5754 Ramachandran restraints generated. 2877 Oldfield, 0 Emsley, 2877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 257 time to evaluate : 0.905 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: B 206 MET cc_start: 0.6765 (ttt) cc_final: 0.6375 (ttt) REVERT: B 214 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7889 (pp20) REVERT: B 454 GLU cc_start: 0.9015 (OUTLIER) cc_final: 0.8570 (tt0) REVERT: B 459 PHE cc_start: 0.7998 (OUTLIER) cc_final: 0.7254 (m-80) REVERT: B 721 ASP cc_start: 0.8140 (t0) cc_final: 0.7869 (t0) REVERT: A 214 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7946 (pp20) REVERT: A 279 GLN cc_start: 0.8551 (mm110) cc_final: 0.8303 (mm-40) REVERT: A 459 PHE cc_start: 0.7896 (OUTLIER) cc_final: 0.7275 (m-80) REVERT: A 721 ASP cc_start: 0.7826 (t0) cc_final: 0.7539 (t0) REVERT: A 837 ASP cc_start: 0.8021 (p0) cc_final: 0.7817 (p0) REVERT: C 23 ARG cc_start: 0.7439 (OUTLIER) cc_final: 0.6742 (mmp-170) REVERT: C 99 HIS cc_start: 0.8353 (m-70) cc_final: 0.8087 (m90) REVERT: C 454 GLU cc_start: 0.8998 (OUTLIER) cc_final: 0.8627 (tt0) REVERT: C 545 MET cc_start: 0.8856 (mtp) cc_final: 0.8553 (mtp) REVERT: C 616 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.7213 (mp0) REVERT: C 721 ASP cc_start: 0.8135 (t0) cc_final: 0.7918 (t0) REVERT: C 913 MET cc_start: 0.9152 (tpp) cc_final: 0.8853 (tpp) outliers start: 24 outliers final: 10 residues processed: 275 average time/residue: 0.6621 time to fit residues: 207.4661 Evaluate side-chains 268 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 250 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 214 GLU Chi-restraints excluded: chain B residue 454 GLU Chi-restraints excluded: chain B residue 459 PHE Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 458 CYS Chi-restraints excluded: chain A residue 459 PHE Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain C residue 23 ARG Chi-restraints excluded: chain C residue 454 GLU Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 546 THR Chi-restraints excluded: chain C residue 616 GLU Chi-restraints excluded: chain C residue 641 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 38 optimal weight: 4.9990 chunk 68 optimal weight: 7.9990 chunk 35 optimal weight: 6.9990 chunk 132 optimal weight: 8.9990 chunk 62 optimal weight: 0.9990 chunk 170 optimal weight: 7.9990 chunk 261 optimal weight: 4.9990 chunk 207 optimal weight: 5.9990 chunk 216 optimal weight: 2.9990 chunk 222 optimal weight: 8.9990 chunk 17 optimal weight: 9.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 500 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 560 ASN B 655 GLN A 892 ASN ** C 512 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 = 0.3447 r_free = 0.3447 target = 0.127710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.097544 restraints weight = 23094.223| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 1.73 r_work: 0.2878 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.146 24051 Z= 0.274 Angle : 0.859 19.147 32907 Z= 0.432 Chirality : 0.056 0.535 3894 Planarity : 0.005 0.054 4083 Dihedral : 8.690 59.921 4644 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.07 % Allowed : 9.27 % Favored : 89.66 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.30 (0.16), residues: 2877 helix: 1.64 (0.21), residues: 630 sheet: 0.13 (0.19), residues: 714 loop : -0.31 (0.16), residues: 1533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 671 TYR 0.038 0.003 TYR B 91 PHE 0.025 0.003 PHE C 430 TRP 0.015 0.002 TRP C 108 HIS 0.009 0.002 HIS B 916 Details of bonding type rmsd covalent geometry : bond 0.00653 (23937) covalent geometry : angle 0.81377 (32610) SS BOND : bond 0.00961 ( 45) SS BOND : angle 4.07194 ( 90) hydrogen bonds : bond 0.06854 ( 919) hydrogen bonds : angle 5.79179 ( 2499) link_BETA1-4 : bond 0.01042 ( 24) link_BETA1-4 : angle 2.20954 ( 72) link_NAG-ASN : bond 0.00335 ( 45) link_NAG-ASN : angle 2.51043 ( 135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9171.07 seconds wall clock time: 156 minutes 20.63 seconds (9380.63 seconds total)