Starting phenix.real_space_refine on Fri Jul 3 19:57:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7l87_23224/07_2026/7l87_23224.cif Found real_map, /net/cci-nas-00/data/ceres_data/7l87_23224/07_2026/7l87_23224.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7l87_23224/07_2026/7l87_23224.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7l87_23224/07_2026/7l87_23224.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7l87_23224/07_2026/7l87_23224.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7l87_23224/07_2026/7l87_23224.cif" model { file = "/net/cci-nas-00/data/ceres_data/7l87_23224/07_2026/7l87_23224.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7l87_23224/07_2026/7l87_23224.cif" } resolution = 3.6 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= 0.004 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 99 5.16 5 C 9809 2.51 5 N 2631 2.21 5 O 3227 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15766 Number of models: 1 Model: "" Number of chains: 53 Chain: "H" Number of atoms: 605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 605 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 121} Link IDs: {'TRANS': 120} Unresolved non-hydrogen bonds: 242 Unresolved non-hydrogen angles: 363 Unresolved non-hydrogen dihedrals: 121 Planarities with less than four sites: {'UNK:plan-1': 121} Unresolved non-hydrogen planarities: 121 Chain: "L" Number of atoms: 515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 515 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 103} Link IDs: {'TRANS': 102} Unresolved non-hydrogen bonds: 206 Unresolved non-hydrogen angles: 309 Unresolved non-hydrogen dihedrals: 103 Planarities with less than four sites: {'UNK:plan-1': 103} Unresolved non-hydrogen planarities: 103 Chain: "C" Number of atoms: 3430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3430 Classifications: {'peptide': 435} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 22, 'TRANS': 412} Chain breaks: 4 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "E" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 987 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "A" Number of atoms: 3430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3430 Classifications: {'peptide': 435} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 22, 'TRANS': 412} Chain breaks: 4 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 987 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "D" Number of atoms: 3430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3430 Classifications: {'peptide': 435} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 22, 'TRANS': 412} Chain breaks: 4 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "F" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 987 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 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 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 chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "d" 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 chiralities: 3 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 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 chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 chiralities: 2 Chain: "m" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 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 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 chiralities: 2 Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "u" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.16, per 1000 atoms: 0.20 Number of scatterers: 15766 At special positions: 0 Unit cell: (130.81, 132.87, 118.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 99 16.00 O 3227 8.00 N 2631 7.00 C 9809 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.05 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.05 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.02 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.02 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS E 605 " distance=2.04 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.03 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.04 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.04 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.02 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.02 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.02 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 74 " distance=2.04 Simple disulfide: pdb=" SG CYS D 119 " - pdb=" SG CYS D 205 " distance=2.07 Simple disulfide: pdb=" SG CYS D 126 " - pdb=" SG CYS D 196 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 157 " distance=2.03 Simple disulfide: pdb=" SG CYS D 218 " - pdb=" SG CYS D 247 " distance=2.03 Simple disulfide: pdb=" SG CYS D 228 " - pdb=" SG CYS D 239 " distance=2.03 Simple disulfide: pdb=" SG CYS D 296 " - pdb=" SG CYS D 331 " distance=2.04 Simple disulfide: pdb=" SG CYS D 378 " - pdb=" SG CYS D 445 " distance=2.03 Simple disulfide: pdb=" SG CYS D 385 " - pdb=" SG CYS D 418 " distance=2.02 Simple disulfide: pdb=" SG CYS D 501 " - pdb=" SG CYS F 605 " distance=2.02 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA M 3 " - " MAN M 4 " " BMA Z 3 " - " MAN Z 4 " " BMA m 3 " - " MAN m 4 " ALPHA1-6 " BMA Z 3 " - " MAN Z 5 " " BMA m 3 " - " MAN m 5 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " 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 Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " 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 k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " 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-ASN " NAG A 601 " - " ASN A 160 " " NAG A 602 " - " ASN A 339 " " NAG A 603 " - " ASN A 137 " " NAG A 604 " - " ASN A 355 " " NAG B 701 " - " ASN B 611 " " NAG C 601 " - " ASN C 160 " " NAG C 602 " - " ASN C 339 " " NAG C 603 " - " ASN C 355 " " NAG D 601 " - " ASN D 160 " " NAG D 602 " - " ASN D 339 " " NAG D 603 " - " ASN D 137 " " NAG E 701 " - " ASN E 611 " " NAG F 701 " - " ASN F 611 " " NAG G 1 " - " ASN C 133 " " NAG I 1 " - " ASN C 156 " " NAG J 1 " - " ASN C 197 " " NAG K 1 " - " ASN C 234 " " NAG M 1 " - " ASN C 262 " " NAG N 1 " - " ASN C 276 " " NAG O 1 " - " ASN C 295 " " NAG P 1 " - " ASN C 301 " " NAG Q 1 " - " ASN C 332 " " NAG R 1 " - " ASN C 386 " " NAG S 1 " - " ASN C 392 " " NAG T 1 " - " ASN C 448 " " NAG U 1 " - " ASN C 88 " " NAG V 1 " - " ASN A 133 " " NAG W 1 " - " ASN A 156 " " NAG X 1 " - " ASN A 197 " " NAG Y 1 " - " ASN A 234 " " NAG Z 1 " - " ASN A 262 " " NAG a 1 " - " ASN A 276 " " NAG b 1 " - " ASN A 295 " " NAG c 1 " - " ASN A 301 " " NAG d 1 " - " ASN A 332 " " NAG e 1 " - " ASN A 386 " " NAG f 1 " - " ASN A 392 " " NAG g 1 " - " ASN A 448 " " NAG h 1 " - " ASN A 88 " " NAG i 1 " - " ASN D 133 " " NAG j 1 " - " ASN D 156 " " NAG k 1 " - " ASN D 197 " " NAG l 1 " - " ASN D 234 " " NAG m 1 " - " ASN D 262 " " NAG n 1 " - " ASN D 276 " " NAG o 1 " - " ASN D 295 " " NAG p 1 " - " ASN D 301 " " NAG q 1 " - " ASN D 332 " " NAG r 1 " - " ASN D 386 " " NAG s 1 " - " ASN D 392 " " NAG t 1 " - " ASN D 448 " " NAG u 1 " - " ASN D 88 " Time building additional restraints: 1.13 Conformation dependent library (CDL) restraints added in 472.7 milliseconds 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3592 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 0 sheets defined 29.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'H' and resid 64 through 67 removed outlier: 4.429A pdb=" N UNK H 67 " --> pdb=" O UNK H 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 64 through 67' Processing helix chain 'C' and resid 70 through 74 removed outlier: 3.923A pdb=" N CYS C 74 " --> pdb=" O THR C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 117 removed outlier: 3.503A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU C 116 " --> pdb=" O TRP C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 195 through 198 Processing helix chain 'C' and resid 335 through 354 removed outlier: 3.529A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 387 through 391 Processing helix chain 'C' and resid 425 through 429 removed outlier: 3.951A pdb=" N GLN C 428 " --> pdb=" O ASN C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 484 removed outlier: 3.500A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 529 through 534 Processing helix chain 'E' and resid 536 through 542 removed outlier: 3.803A pdb=" N GLN E 540 " --> pdb=" O THR E 536 " (cutoff:3.500A) Processing helix chain 'E' and resid 571 through 596 removed outlier: 3.769A pdb=" N GLN E 575 " --> pdb=" O TRP E 571 " (cutoff:3.500A) Processing helix chain 'E' and resid 618 through 626 removed outlier: 3.990A pdb=" N ASP E 624 " --> pdb=" O SER E 620 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N MET E 626 " --> pdb=" O ILE E 622 " (cutoff:3.500A) Processing helix chain 'E' and resid 627 through 636 Processing helix chain 'E' and resid 638 through 663 Processing helix chain 'A' and resid 70 through 74 Processing helix chain 'A' and resid 98 through 115 removed outlier: 3.939A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 139 through 151 Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 335 through 354 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 390 Processing helix chain 'A' and resid 425 through 429 removed outlier: 4.457A pdb=" N GLN A 428 " --> pdb=" O ASN A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 483 removed outlier: 3.527A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 526 removed outlier: 4.310A pdb=" N ALA B 525 " --> pdb=" O PHE B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 537 through 542 Processing helix chain 'B' and resid 570 through 596 removed outlier: 3.567A pdb=" N GLN B 575 " --> pdb=" O TRP B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 625 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 661 Processing helix chain 'D' and resid 70 through 74 Processing helix chain 'D' and resid 94 through 97 Processing helix chain 'D' and resid 98 through 117 removed outlier: 4.226A pdb=" N GLU D 102 " --> pdb=" O ASN D 98 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU D 116 " --> pdb=" O TRP D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 126 Processing helix chain 'D' and resid 195 through 198 Processing helix chain 'D' and resid 335 through 354 Processing helix chain 'D' and resid 368 through 373 Processing helix chain 'D' and resid 425 through 429 removed outlier: 4.499A pdb=" N GLN D 428 " --> pdb=" O ASN D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 480 Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 542 removed outlier: 3.853A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 572 through 596 removed outlier: 3.650A pdb=" N LEU F 576 " --> pdb=" O GLY F 572 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU F 581 " --> pdb=" O GLN F 577 " (cutoff:3.500A) Processing helix chain 'F' and resid 619 through 624 Processing helix chain 'F' and resid 627 through 636 Processing helix chain 'F' and resid 638 through 664 294 hydrogen bonds defined for protein. 807 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: 2.03 Time building geometry restraints manager: 1.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 2642 1.31 - 1.45: 4825 1.45 - 1.59: 8369 1.59 - 1.73: 70 1.73 - 1.87: 128 Bond restraints: 16034 Sorted by residual: bond pdb=" NE ARG C 503 " pdb=" CZ ARG C 503 " ideal model delta sigma weight residual 1.326 1.401 -0.075 1.10e-02 8.26e+03 4.68e+01 bond pdb=" NE ARG D 503 " pdb=" CZ ARG D 503 " ideal model delta sigma weight residual 1.326 1.400 -0.074 1.10e-02 8.26e+03 4.55e+01 bond pdb=" CB LEU A 129 " pdb=" CG LEU A 129 " ideal model delta sigma weight residual 1.530 1.406 0.124 2.00e-02 2.50e+03 3.85e+01 bond pdb=" C GLN C 170 " pdb=" O GLN C 170 " ideal model delta sigma weight residual 1.235 1.166 0.069 1.13e-02 7.83e+03 3.75e+01 bond pdb=" NE1 TRP E 631 " pdb=" CE2 TRP E 631 " ideal model delta sigma weight residual 1.370 1.307 0.063 1.10e-02 8.26e+03 3.29e+01 ... (remaining 16029 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.04: 20987 4.04 - 8.08: 797 8.08 - 12.12: 23 12.12 - 16.16: 4 16.16 - 20.20: 2 Bond angle restraints: 21813 Sorted by residual: angle pdb=" C ASN D 137 " pdb=" N ILE D 138 " pdb=" CA ILE D 138 " ideal model delta sigma weight residual 120.98 134.88 -13.90 1.36e+00 5.41e-01 1.04e+02 angle pdb=" N ILE A 184 " pdb=" CA ILE A 184 " pdb=" C ILE A 184 " ideal model delta sigma weight residual 110.62 119.23 -8.61 1.02e+00 9.61e-01 7.13e+01 angle pdb=" C GLU C 492 " pdb=" N PRO C 493 " pdb=" CA PRO C 493 " ideal model delta sigma weight residual 119.56 127.21 -7.65 1.02e+00 9.61e-01 5.62e+01 angle pdb=" C CYS D 239 " pdb=" N PRO D 240 " pdb=" CA PRO D 240 " ideal model delta sigma weight residual 119.56 127.15 -7.59 1.02e+00 9.61e-01 5.53e+01 angle pdb=" N LEU B 544 " pdb=" CA LEU B 544 " pdb=" C LEU B 544 " ideal model delta sigma weight residual 110.48 99.70 10.78 1.48e+00 4.57e-01 5.31e+01 ... (remaining 21808 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 8505 17.58 - 35.15: 242 35.15 - 52.73: 66 52.73 - 70.30: 23 70.30 - 87.88: 12 Dihedral angle restraints: 8848 sinusoidal: 3333 harmonic: 5515 Sorted by residual: dihedral pdb=" CB CYS D 126 " pdb=" SG CYS D 126 " pdb=" SG CYS D 196 " pdb=" CB CYS D 196 " ideal model delta sinusoidal sigma weight residual 93.00 150.79 -57.79 1 1.00e+01 1.00e-02 4.48e+01 dihedral pdb=" CB CYS C 126 " pdb=" SG CYS C 126 " pdb=" SG CYS C 196 " pdb=" CB CYS C 196 " ideal model delta sinusoidal sigma weight residual 93.00 148.90 -55.90 1 1.00e+01 1.00e-02 4.22e+01 dihedral pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual 93.00 145.47 -52.47 1 1.00e+01 1.00e-02 3.75e+01 ... (remaining 8845 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.171: 2236 0.171 - 0.341: 447 0.341 - 0.511: 124 0.511 - 0.682: 4 0.682 - 0.852: 2 Chirality restraints: 2813 Sorted by residual: chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-02 2.50e+03 3.45e+02 chirality pdb=" C1 NAG l 2 " pdb=" O4 NAG l 1 " pdb=" C2 NAG l 2 " pdb=" O5 NAG l 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.66 0.26 2.00e-02 2.50e+03 1.63e+02 chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.49e+02 ... (remaining 2810 not shown) Planarity restraints: 2711 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG M 1 " -0.351 2.00e-02 2.50e+03 3.03e-01 1.14e+03 pdb=" C7 NAG M 1 " 0.082 2.00e-02 2.50e+03 pdb=" C8 NAG M 1 " -0.086 2.00e-02 2.50e+03 pdb=" N2 NAG M 1 " 0.536 2.00e-02 2.50e+03 pdb=" O7 NAG M 1 " -0.182 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG O 2 " 0.347 2.00e-02 2.50e+03 2.99e-01 1.12e+03 pdb=" C7 NAG O 2 " -0.084 2.00e-02 2.50e+03 pdb=" C8 NAG O 2 " 0.134 2.00e-02 2.50e+03 pdb=" N2 NAG O 2 " -0.533 2.00e-02 2.50e+03 pdb=" O7 NAG O 2 " 0.136 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 604 " -0.344 2.00e-02 2.50e+03 2.97e-01 1.11e+03 pdb=" C7 NAG A 604 " 0.079 2.00e-02 2.50e+03 pdb=" C8 NAG A 604 " -0.068 2.00e-02 2.50e+03 pdb=" N2 NAG A 604 " 0.525 2.00e-02 2.50e+03 pdb=" O7 NAG A 604 " -0.193 2.00e-02 2.50e+03 ... (remaining 2708 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 114 2.60 - 3.18: 13733 3.18 - 3.75: 22445 3.75 - 4.33: 33799 4.33 - 4.90: 51935 Nonbonded interactions: 122026 Sorted by model distance: nonbonded pdb=" NZ LYS A 502 " pdb=" O ASP F 664 " model vdw 2.027 3.120 nonbonded pdb=" O4 MAN M 4 " pdb=" O6 MAN M 4 " model vdw 2.308 3.040 nonbonded pdb=" O PHE E 522 " pdb=" NE2 GLN E 540 " model vdw 2.312 3.120 nonbonded pdb=" O SER D 463 " pdb=" OG SER D 463 " model vdw 2.354 3.040 nonbonded pdb=" OD2 ASP A 167 " pdb=" NZ LYS A 168 " model vdw 2.408 3.120 ... (remaining 122021 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 33 through 603) selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' 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' selection = chain 'X' selection = chain 'Y' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'r' selection = chain 's' selection = chain 't' selection = chain 'u' } ncs_group { reference = (chain 'H' and resid 19 through 121) selection = chain 'L' } ncs_group { reference = chain 'Q' selection = chain 'd' selection = chain 'q' } ncs_group { reference = chain 'Z' selection = chain 'm' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.320 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: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.250 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 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 : 0.023 0.132 16169 Z= 1.224 Angle : 1.810 20.202 22185 Z= 1.101 Chirality : 0.152 0.852 2813 Planarity : 0.016 0.303 2659 Dihedral : 10.191 87.876 5157 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 1.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.19), residues: 1635 helix: 0.10 (0.24), residues: 399 sheet: 1.15 (0.28), residues: 312 loop : 0.60 (0.19), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 166 TYR 0.036 0.007 TYR A 384 PHE 0.052 0.006 PHE A 159 TRP 0.046 0.008 TRP C 96 HIS 0.018 0.003 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.02255 / 1.20 (16034) covalent geometry : angle 1.76002 / 1.10 (21813) SS BOND : bond 0.00949 / 0.50 ( 33) SS BOND : angle 3.01211 / 1.59 ( 66) hydrogen bonds : bond 0.19611 / 10.79 ( 294) hydrogen bonds : angle 6.33812 / 3.14 ( 807) link_ALPHA1-3 : bond 0.06747 / 3.29 ( 3) link_ALPHA1-3 : angle 4.00087 / 1.81 ( 9) link_ALPHA1-6 : bond 0.05591 / 2.81 ( 2) link_ALPHA1-6 : angle 3.67510 / 1.67 ( 6) link_BETA1-4 : bond 0.06844 / 3.78 ( 45) link_BETA1-4 : angle 4.80772 / 2.40 ( 135) link_NAG-ASN : bond 0.07224 / 3.97 ( 52) link_NAG-ASN : angle 2.74403 / 1.35 ( 156) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 409 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 180 ASP cc_start: 0.8007 (m-30) cc_final: 0.7651 (m-30) REVERT: C 198 THR cc_start: 0.8988 (p) cc_final: 0.8633 (p) REVERT: B 632 ASP cc_start: 0.8295 (t70) cc_final: 0.8036 (t0) REVERT: B 652 GLN cc_start: 0.7854 (mt0) cc_final: 0.7515 (mt0) REVERT: B 660 LEU cc_start: 0.8970 (mt) cc_final: 0.8747 (tt) REVERT: D 122 LEU cc_start: 0.8864 (mt) cc_final: 0.8606 (mp) REVERT: F 590 GLN cc_start: 0.8927 (mm-40) cc_final: 0.8682 (mm110) outliers start: 0 outliers final: 0 residues processed: 409 average time/residue: 0.1235 time to fit residues: 72.6101 Evaluate side-chains 182 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 33 ASN C 363 GLN C 425 ASN A 99 ASN A 428 GLN D 352 HIS F 543 ASN F 570 HIS F 651 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.131676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.113789 restraints weight = 27422.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.116776 restraints weight = 15276.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.118780 restraints weight = 10335.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.119961 restraints weight = 7888.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.120923 restraints weight = 6609.899| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16169 Z= 0.154 Angle : 0.756 14.529 22185 Z= 0.349 Chirality : 0.046 0.308 2813 Planarity : 0.004 0.047 2659 Dihedral : 4.806 22.291 1992 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.94 % Allowed : 8.30 % Favored : 89.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.20), residues: 1635 helix: 1.58 (0.27), residues: 402 sheet: 1.22 (0.26), residues: 345 loop : 0.29 (0.21), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 588 TYR 0.009 0.001 TYR D 384 PHE 0.014 0.002 PHE C 176 TRP 0.020 0.002 TRP E 571 HIS 0.010 0.001 HIS F 570 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (16034) covalent geometry : angle 0.70075 / 0.34 (21813) SS BOND : bond 0.00234 / 0.12 ( 33) SS BOND : angle 0.90283 / 0.49 ( 66) hydrogen bonds : bond 0.06837 / 3.81 ( 294) hydrogen bonds : angle 4.32045 / 2.15 ( 807) link_ALPHA1-3 : bond 0.00618 / 0.32 ( 3) link_ALPHA1-3 : angle 2.01138 / 1.11 ( 9) link_ALPHA1-6 : bond 0.00581 / 0.29 ( 2) link_ALPHA1-6 : angle 1.45847 / 0.72 ( 6) link_BETA1-4 : bond 0.00503 / 0.29 ( 45) link_BETA1-4 : angle 2.37462 / 1.21 ( 135) link_NAG-ASN : bond 0.00358 / 0.21 ( 52) link_NAG-ASN : angle 2.65338 / 1.30 ( 156) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 242 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 475 MET cc_start: 0.8014 (mmm) cc_final: 0.7793 (mmm) REVERT: E 634 GLU cc_start: 0.8016 (tt0) cc_final: 0.7750 (mt-10) REVERT: A 72 HIS cc_start: 0.6492 (p-80) cc_final: 0.6291 (p-80) REVERT: A 246 GLN cc_start: 0.7004 (tp-100) cc_final: 0.6665 (tp-100) REVERT: A 384 TYR cc_start: 0.8903 (m-80) cc_final: 0.8646 (m-80) REVERT: A 475 MET cc_start: 0.8131 (mmm) cc_final: 0.7832 (mmm) REVERT: D 150 MET cc_start: 0.7746 (mmp) cc_final: 0.7400 (mmt) REVERT: D 167 ASP cc_start: 0.7471 (p0) cc_final: 0.7267 (p0) REVERT: D 308 ARG cc_start: 0.7527 (mmt180) cc_final: 0.7317 (mmt-90) REVERT: D 434 MET cc_start: 0.8067 (ttp) cc_final: 0.7856 (ttt) outliers start: 29 outliers final: 19 residues processed: 263 average time/residue: 0.1066 time to fit residues: 42.0397 Evaluate side-chains 195 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 176 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 414 ILE Chi-restraints excluded: chain C residue 455 THR Chi-restraints excluded: chain E residue 581 LEU Chi-restraints excluded: chain E residue 606 THR Chi-restraints excluded: chain E residue 612 SER Chi-restraints excluded: chain E residue 622 ILE Chi-restraints excluded: chain E residue 660 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain F residue 570 HIS Chi-restraints excluded: chain F residue 651 ASN Chi-restraints excluded: chain F residue 657 GLU Chi-restraints excluded: chain F residue 660 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 80 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 157 optimal weight: 7.9990 chunk 3 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 181 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 43 optimal weight: 0.1980 chunk 8 optimal weight: 10.0000 chunk 30 optimal weight: 0.6980 chunk 97 optimal weight: 0.7980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 99 ASN ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 425 ASN ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 543 ASN D 80 ASN F 543 ASN F 570 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.128070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.110239 restraints weight = 28405.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.113215 restraints weight = 15575.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.115189 restraints weight = 10381.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.116529 restraints weight = 7868.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.117368 restraints weight = 6442.274| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16169 Z= 0.142 Angle : 0.634 10.390 22185 Z= 0.301 Chirality : 0.043 0.248 2813 Planarity : 0.003 0.047 2659 Dihedral : 4.478 21.729 1992 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.61 % Allowed : 10.31 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.21), residues: 1635 helix: 1.68 (0.27), residues: 408 sheet: 1.15 (0.27), residues: 351 loop : 0.08 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 151 TYR 0.011 0.001 TYR D 173 PHE 0.020 0.001 PHE A 159 TRP 0.013 0.001 TRP E 571 HIS 0.013 0.001 HIS F 570 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (16034) covalent geometry : angle 0.59494 / 0.29 (21813) SS BOND : bond 0.00524 / 0.27 ( 33) SS BOND : angle 1.20661 / 0.50 ( 66) hydrogen bonds : bond 0.05573 / 3.09 ( 294) hydrogen bonds : angle 3.96807 / 2.00 ( 807) link_ALPHA1-3 : bond 0.00521 / 0.26 ( 3) link_ALPHA1-3 : angle 1.66758 / 0.87 ( 9) link_ALPHA1-6 : bond 0.00845 / 0.42 ( 2) link_ALPHA1-6 : angle 1.30770 / 0.62 ( 6) link_BETA1-4 : bond 0.00609 / 0.34 ( 45) link_BETA1-4 : angle 1.80214 / 0.91 ( 135) link_NAG-ASN : bond 0.00341 / 0.20 ( 52) link_NAG-ASN : angle 2.01752 / 1.00 ( 156) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 196 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 150 MET cc_start: 0.8752 (mtp) cc_final: 0.8480 (mtt) REVERT: C 370 GLU cc_start: 0.7963 (tt0) cc_final: 0.7758 (tt0) REVERT: C 475 MET cc_start: 0.8057 (mmm) cc_final: 0.7685 (mmm) REVERT: E 634 GLU cc_start: 0.8122 (tt0) cc_final: 0.7818 (mt-10) REVERT: A 107 ASP cc_start: 0.8532 (m-30) cc_final: 0.8165 (m-30) REVERT: A 217 TYR cc_start: 0.8769 (m-80) cc_final: 0.8553 (m-80) REVERT: A 246 GLN cc_start: 0.6870 (tp-100) cc_final: 0.6657 (tp-100) REVERT: A 475 MET cc_start: 0.8203 (mmm) cc_final: 0.7544 (mmm) REVERT: B 520 LEU cc_start: 0.8223 (mm) cc_final: 0.7763 (mt) REVERT: D 46 LYS cc_start: 0.8748 (OUTLIER) cc_final: 0.8100 (ptpt) REVERT: D 167 ASP cc_start: 0.7652 (p0) cc_final: 0.7437 (p0) REVERT: D 308 ARG cc_start: 0.7563 (mmt180) cc_final: 0.7315 (mmt-90) REVERT: D 434 MET cc_start: 0.8117 (ttp) cc_final: 0.7790 (ttt) REVERT: D 475 MET cc_start: 0.8528 (mmt) cc_final: 0.8244 (mmp) REVERT: F 542 ARG cc_start: 0.8832 (ptp90) cc_final: 0.8563 (ptt180) outliers start: 39 outliers final: 25 residues processed: 225 average time/residue: 0.1154 time to fit residues: 39.8352 Evaluate side-chains 198 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 172 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 414 ILE Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain E residue 539 VAL Chi-restraints excluded: chain E residue 581 LEU Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 605 CYS Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain E residue 612 SER Chi-restraints excluded: chain E residue 636 SER Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain F residue 570 HIS Chi-restraints excluded: chain F residue 613 SER Chi-restraints excluded: chain F residue 657 GLU Chi-restraints excluded: chain F residue 660 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 157 optimal weight: 7.9990 chunk 123 optimal weight: 5.9990 chunk 133 optimal weight: 5.9990 chunk 171 optimal weight: 9.9990 chunk 112 optimal weight: 4.9990 chunk 105 optimal weight: 0.9980 chunk 3 optimal weight: 10.0000 chunk 2 optimal weight: 20.0000 chunk 152 optimal weight: 0.9990 chunk 160 optimal weight: 9.9990 chunk 15 optimal weight: 20.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 99 ASN ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 ASN ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 543 ASN A 216 HIS D 80 ASN D 428 GLN F 543 ASN F 570 HIS F 651 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.120616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.102843 restraints weight = 28405.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.105607 restraints weight = 16435.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.107412 restraints weight = 11402.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.108665 restraints weight = 8896.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.109400 restraints weight = 7459.827| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.3717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.088 16169 Z= 0.333 Angle : 0.853 10.115 22185 Z= 0.402 Chirality : 0.050 0.231 2813 Planarity : 0.005 0.043 2659 Dihedral : 5.046 22.907 1992 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.68 % Allowed : 10.84 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.20), residues: 1635 helix: 1.19 (0.26), residues: 402 sheet: 0.91 (0.28), residues: 330 loop : -0.57 (0.20), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 588 TYR 0.029 0.003 TYR C 486 PHE 0.035 0.003 PHE A 159 TRP 0.022 0.002 TRP B 623 HIS 0.023 0.002 HIS F 570 Details of bonding type rmsd/Z covalent geometry : bond 0.00796 / 0.33 (16034) covalent geometry : angle 0.81505 / 0.39 (21813) SS BOND : bond 0.00560 / 0.30 ( 33) SS BOND : angle 1.54542 / 0.66 ( 66) hydrogen bonds : bond 0.06551 / 3.60 ( 294) hydrogen bonds : angle 4.23114 / 2.13 ( 807) link_ALPHA1-3 : bond 0.00618 / 0.32 ( 3) link_ALPHA1-3 : angle 1.75129 / 0.92 ( 9) link_ALPHA1-6 : bond 0.00814 / 0.39 ( 2) link_ALPHA1-6 : angle 1.42716 / 0.66 ( 6) link_BETA1-4 : bond 0.00609 / 0.33 ( 45) link_BETA1-4 : angle 2.06170 / 1.04 ( 135) link_NAG-ASN : bond 0.00400 / 0.22 ( 52) link_NAG-ASN : angle 2.38897 / 1.20 ( 156) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 159 time to evaluate : 0.588 Fit side-chains REVERT: C 111 LEU cc_start: 0.9174 (mt) cc_final: 0.8935 (mp) REVERT: E 654 GLU cc_start: 0.8089 (mm-30) cc_final: 0.7700 (mm-30) REVERT: A 202 THR cc_start: 0.9096 (m) cc_final: 0.8663 (p) REVERT: A 268 GLU cc_start: 0.8014 (mm-30) cc_final: 0.7580 (mm-30) REVERT: A 475 MET cc_start: 0.8314 (mmm) cc_final: 0.7720 (mmm) REVERT: B 584 GLU cc_start: 0.7902 (mt-10) cc_final: 0.7591 (mp0) REVERT: D 46 LYS cc_start: 0.8824 (OUTLIER) cc_final: 0.8565 (ptpt) REVERT: D 137 ASN cc_start: 0.7300 (OUTLIER) cc_final: 0.6953 (m-40) REVERT: D 308 ARG cc_start: 0.7491 (mmt180) cc_final: 0.7290 (mmt-90) REVERT: D 434 MET cc_start: 0.8172 (ttp) cc_final: 0.7840 (ttt) outliers start: 55 outliers final: 39 residues processed: 201 average time/residue: 0.1063 time to fit residues: 33.0353 Evaluate side-chains 182 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 141 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 414 ILE Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain E residue 539 VAL Chi-restraints excluded: chain E residue 581 LEU Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 605 CYS Chi-restraints excluded: chain E residue 606 THR Chi-restraints excluded: chain E residue 612 SER Chi-restraints excluded: chain E residue 636 SER Chi-restraints excluded: chain E residue 660 LEU Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 137 ASN Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 274 SER Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 502 LYS Chi-restraints excluded: chain F residue 573 ILE Chi-restraints excluded: chain F residue 613 SER Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 660 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 110 optimal weight: 0.6980 chunk 179 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 151 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 148 optimal weight: 0.0870 chunk 166 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 153 optimal weight: 0.9990 chunk 132 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 99 ASN C 289 ASN ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 ASN F 543 ASN F 570 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.126767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.109169 restraints weight = 27570.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.112068 restraints weight = 15633.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.114055 restraints weight = 10663.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.115315 restraints weight = 8142.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.116225 restraints weight = 6758.549| |-----------------------------------------------------------------------------| r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.3905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 16169 Z= 0.111 Angle : 0.599 9.653 22185 Z= 0.281 Chirality : 0.042 0.216 2813 Planarity : 0.003 0.043 2659 Dihedral : 4.425 21.758 1992 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.01 % Allowed : 13.52 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.21), residues: 1635 helix: 2.16 (0.27), residues: 381 sheet: 0.78 (0.26), residues: 390 loop : -0.25 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 588 TYR 0.027 0.001 TYR C 486 PHE 0.015 0.001 PHE A 159 TRP 0.010 0.001 TRP D 35 HIS 0.017 0.001 HIS F 570 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (16034) covalent geometry : angle 0.56478 / 0.27 (21813) SS BOND : bond 0.00420 / 0.26 ( 33) SS BOND : angle 1.67133 / 0.91 ( 66) hydrogen bonds : bond 0.04828 / 2.69 ( 294) hydrogen bonds : angle 3.66459 / 1.86 ( 807) link_ALPHA1-3 : bond 0.00521 / 0.26 ( 3) link_ALPHA1-3 : angle 1.52533 / 0.80 ( 9) link_ALPHA1-6 : bond 0.00702 / 0.35 ( 2) link_ALPHA1-6 : angle 1.40269 / 0.70 ( 6) link_BETA1-4 : bond 0.00511 / 0.28 ( 45) link_BETA1-4 : angle 1.49956 / 0.76 ( 135) link_NAG-ASN : bond 0.00271 / 0.16 ( 52) link_NAG-ASN : angle 1.75859 / 0.87 ( 156) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 182 time to evaluate : 0.635 Fit side-chains revert: symmetry clash REVERT: A 37 THR cc_start: 0.9087 (m) cc_final: 0.8808 (p) REVERT: A 92 GLU cc_start: 0.7855 (tp30) cc_final: 0.7465 (mm-30) REVERT: A 268 GLU cc_start: 0.8011 (mm-30) cc_final: 0.7664 (mm-30) REVERT: A 475 MET cc_start: 0.8176 (mmm) cc_final: 0.7651 (mmm) REVERT: D 46 LYS cc_start: 0.8854 (OUTLIER) cc_final: 0.8622 (ptpt) REVERT: D 137 ASN cc_start: 0.7376 (OUTLIER) cc_final: 0.7127 (m-40) REVERT: D 150 MET cc_start: 0.7540 (mmp) cc_final: 0.7338 (mmt) REVERT: D 434 MET cc_start: 0.8010 (ttp) cc_final: 0.7620 (ttt) REVERT: D 475 MET cc_start: 0.8568 (mmt) cc_final: 0.8278 (mmp) outliers start: 30 outliers final: 16 residues processed: 206 average time/residue: 0.1319 time to fit residues: 40.3689 Evaluate side-chains 174 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 156 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 289 ASN Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 414 ILE Chi-restraints excluded: chain E residue 581 LEU Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 605 CYS Chi-restraints excluded: chain E residue 636 SER Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 137 ASN Chi-restraints excluded: chain D residue 352 HIS Chi-restraints excluded: chain D residue 502 LYS Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 657 GLU Chi-restraints excluded: chain F residue 660 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 145 optimal weight: 0.0970 chunk 72 optimal weight: 8.9990 chunk 30 optimal weight: 1.9990 chunk 160 optimal weight: 0.6980 chunk 53 optimal weight: 10.0000 chunk 34 optimal weight: 2.9990 chunk 26 optimal weight: 0.4980 chunk 31 optimal weight: 0.1980 chunk 100 optimal weight: 5.9990 chunk 79 optimal weight: 8.9990 chunk 127 optimal weight: 7.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 99 ASN C 289 ASN ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 66 HIS A 258 GLN F 543 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.125801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.107764 restraints weight = 28243.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.110787 restraints weight = 15419.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.112831 restraints weight = 10259.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.114175 restraints weight = 7724.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.115122 restraints weight = 6325.717| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.4034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 16169 Z= 0.111 Angle : 0.588 10.443 22185 Z= 0.275 Chirality : 0.041 0.193 2813 Planarity : 0.003 0.051 2659 Dihedral : 4.265 24.581 1992 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.14 % Allowed : 14.19 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.21), residues: 1635 helix: 2.31 (0.27), residues: 381 sheet: 0.76 (0.27), residues: 369 loop : -0.17 (0.21), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 588 TYR 0.013 0.001 TYR A 173 PHE 0.016 0.001 PHE A 159 TRP 0.014 0.001 TRP E 571 HIS 0.004 0.001 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (16034) covalent geometry : angle 0.55507 / 0.27 (21813) SS BOND : bond 0.00450 / 0.29 ( 33) SS BOND : angle 1.79384 / 0.92 ( 66) hydrogen bonds : bond 0.04602 / 2.55 ( 294) hydrogen bonds : angle 3.60341 / 1.83 ( 807) link_ALPHA1-3 : bond 0.00515 / 0.26 ( 3) link_ALPHA1-3 : angle 1.49669 / 0.79 ( 9) link_ALPHA1-6 : bond 0.00710 / 0.35 ( 2) link_ALPHA1-6 : angle 1.40541 / 0.69 ( 6) link_BETA1-4 : bond 0.00495 / 0.27 ( 45) link_BETA1-4 : angle 1.45035 / 0.73 ( 135) link_NAG-ASN : bond 0.00202 / 0.12 ( 52) link_NAG-ASN : angle 1.66401 / 0.83 ( 156) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 170 time to evaluate : 0.594 Fit side-chains revert: symmetry clash REVERT: E 584 GLU cc_start: 0.8601 (mt-10) cc_final: 0.8347 (mt-10) REVERT: A 37 THR cc_start: 0.9120 (m) cc_final: 0.8797 (p) REVERT: A 92 GLU cc_start: 0.7803 (tp30) cc_final: 0.7435 (mm-30) REVERT: A 207 LYS cc_start: 0.7519 (pttt) cc_final: 0.7278 (tmmt) REVERT: A 268 GLU cc_start: 0.8079 (mm-30) cc_final: 0.7677 (mm-30) REVERT: D 46 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8619 (ptpp) REVERT: D 137 ASN cc_start: 0.7312 (OUTLIER) cc_final: 0.7050 (m-40) REVERT: D 434 MET cc_start: 0.8112 (ttp) cc_final: 0.7869 (ttt) REVERT: D 475 MET cc_start: 0.8568 (mmt) cc_final: 0.8248 (mmp) REVERT: F 536 THR cc_start: 0.8720 (p) cc_final: 0.8407 (t) REVERT: F 542 ARG cc_start: 0.8961 (ptp90) cc_final: 0.8697 (ptt180) REVERT: F 654 GLU cc_start: 0.8124 (tp30) cc_final: 0.7801 (tp30) outliers start: 32 outliers final: 22 residues processed: 193 average time/residue: 0.1192 time to fit residues: 34.8817 Evaluate side-chains 182 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 158 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 289 ASN Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 414 ILE Chi-restraints excluded: chain E residue 539 VAL Chi-restraints excluded: chain E residue 581 LEU Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 605 CYS Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain E residue 612 SER Chi-restraints excluded: chain E residue 636 SER Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 137 ASN Chi-restraints excluded: chain D residue 352 HIS Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 502 LYS Chi-restraints excluded: chain F residue 657 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 8 optimal weight: 9.9990 chunk 22 optimal weight: 0.9990 chunk 105 optimal weight: 5.9990 chunk 178 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 155 optimal weight: 0.9980 chunk 106 optimal weight: 2.9990 chunk 183 optimal weight: 4.9990 chunk 157 optimal weight: 7.9990 chunk 3 optimal weight: 10.0000 chunk 93 optimal weight: 0.7980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 99 ASN C 289 ASN ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 ASN D 302 ASN F 543 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.124599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.107026 restraints weight = 27787.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.109877 restraints weight = 15959.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.111814 restraints weight = 10958.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.113089 restraints weight = 8400.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.113897 restraints weight = 6984.571| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.4146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 16169 Z= 0.165 Angle : 0.631 12.751 22185 Z= 0.294 Chirality : 0.043 0.180 2813 Planarity : 0.003 0.042 2659 Dihedral : 4.325 26.977 1992 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.88 % Allowed : 14.26 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.21), residues: 1635 helix: 2.28 (0.27), residues: 381 sheet: 0.82 (0.27), residues: 360 loop : -0.36 (0.21), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 588 TYR 0.011 0.001 TYR A 173 PHE 0.020 0.002 PHE A 159 TRP 0.013 0.001 TRP E 571 HIS 0.005 0.001 HIS D 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.16 (16034) covalent geometry : angle 0.59845 / 0.29 (21813) SS BOND : bond 0.00508 / 0.32 ( 33) SS BOND : angle 1.77329 / 0.90 ( 66) hydrogen bonds : bond 0.04887 / 2.70 ( 294) hydrogen bonds : angle 3.68157 / 1.87 ( 807) link_ALPHA1-3 : bond 0.00486 / 0.25 ( 3) link_ALPHA1-3 : angle 1.53988 / 0.81 ( 9) link_ALPHA1-6 : bond 0.00707 / 0.34 ( 2) link_ALPHA1-6 : angle 1.40057 / 0.69 ( 6) link_BETA1-4 : bond 0.00491 / 0.27 ( 45) link_BETA1-4 : angle 1.52783 / 0.77 ( 135) link_NAG-ASN : bond 0.00207 / 0.12 ( 52) link_NAG-ASN : angle 1.72815 / 0.87 ( 156) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 164 time to evaluate : 0.580 Fit side-chains REVERT: E 584 GLU cc_start: 0.8622 (mt-10) cc_final: 0.8364 (mt-10) REVERT: A 268 GLU cc_start: 0.8024 (mm-30) cc_final: 0.7716 (mm-30) REVERT: B 584 GLU cc_start: 0.7852 (mt-10) cc_final: 0.7577 (mp0) REVERT: D 46 LYS cc_start: 0.8791 (OUTLIER) cc_final: 0.8541 (ptpp) REVERT: D 137 ASN cc_start: 0.7326 (OUTLIER) cc_final: 0.7066 (m-40) REVERT: D 178 ARG cc_start: 0.8621 (OUTLIER) cc_final: 0.7809 (ttm170) REVERT: D 434 MET cc_start: 0.8137 (ttp) cc_final: 0.7875 (ttt) REVERT: D 475 MET cc_start: 0.8656 (mmt) cc_final: 0.8364 (mmp) REVERT: F 536 THR cc_start: 0.8776 (p) cc_final: 0.8526 (t) REVERT: F 542 ARG cc_start: 0.8911 (ptp90) cc_final: 0.8639 (ptt180) REVERT: F 660 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8960 (tt) outliers start: 43 outliers final: 29 residues processed: 197 average time/residue: 0.1328 time to fit residues: 39.2298 Evaluate side-chains 191 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 158 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 289 ASN Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 414 ILE Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain E residue 539 VAL Chi-restraints excluded: chain E residue 543 ASN Chi-restraints excluded: chain E residue 581 LEU Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 605 CYS Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain E residue 612 SER Chi-restraints excluded: chain E residue 636 SER Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 137 ASN Chi-restraints excluded: chain D residue 178 ARG Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 352 HIS Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 502 LYS Chi-restraints excluded: chain F residue 657 GLU Chi-restraints excluded: chain F residue 660 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 71 optimal weight: 0.8980 chunk 131 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 115 optimal weight: 5.9990 chunk 140 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 180 optimal weight: 0.0470 chunk 69 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 109 optimal weight: 8.9990 overall best weight: 1.1682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 82 GLN C 99 ASN C 289 ASN ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 66 HIS F 543 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.125408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.107872 restraints weight = 27912.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.110750 restraints weight = 15904.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.112678 restraints weight = 10856.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.113979 restraints weight = 8326.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.114895 restraints weight = 6888.789| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.4251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 16169 Z= 0.128 Angle : 0.599 11.521 22185 Z= 0.280 Chirality : 0.042 0.179 2813 Planarity : 0.003 0.041 2659 Dihedral : 4.247 25.165 1992 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.48 % Allowed : 14.73 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.21), residues: 1635 helix: 2.30 (0.27), residues: 384 sheet: 0.74 (0.27), residues: 351 loop : -0.34 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 588 TYR 0.011 0.001 TYR A 173 PHE 0.017 0.001 PHE A 159 TRP 0.010 0.001 TRP C 338 HIS 0.006 0.001 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (16034) covalent geometry : angle 0.56694 / 0.27 (21813) SS BOND : bond 0.00436 / 0.27 ( 33) SS BOND : angle 1.67897 / 0.87 ( 66) hydrogen bonds : bond 0.04636 / 2.56 ( 294) hydrogen bonds : angle 3.61177 / 1.84 ( 807) link_ALPHA1-3 : bond 0.00486 / 0.25 ( 3) link_ALPHA1-3 : angle 1.50895 / 0.79 ( 9) link_ALPHA1-6 : bond 0.00687 / 0.34 ( 2) link_ALPHA1-6 : angle 1.39476 / 0.69 ( 6) link_BETA1-4 : bond 0.00481 / 0.26 ( 45) link_BETA1-4 : angle 1.47153 / 0.74 ( 135) link_NAG-ASN : bond 0.00203 / 0.12 ( 52) link_NAG-ASN : angle 1.66606 / 0.83 ( 156) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 164 time to evaluate : 0.597 Fit side-chains REVERT: C 82 GLN cc_start: 0.7920 (OUTLIER) cc_final: 0.7583 (pm20) REVERT: E 540 GLN cc_start: 0.8432 (OUTLIER) cc_final: 0.6891 (mp10) REVERT: A 268 GLU cc_start: 0.8018 (mm-30) cc_final: 0.7733 (mm-30) REVERT: D 46 LYS cc_start: 0.8766 (OUTLIER) cc_final: 0.8524 (ptpp) REVERT: D 150 MET cc_start: 0.7207 (mmt) cc_final: 0.6854 (mmt) REVERT: D 178 ARG cc_start: 0.8612 (OUTLIER) cc_final: 0.7796 (ttm170) REVERT: D 434 MET cc_start: 0.8141 (ttp) cc_final: 0.7887 (ttt) REVERT: D 475 MET cc_start: 0.8625 (mmt) cc_final: 0.8320 (mmp) REVERT: F 536 THR cc_start: 0.8737 (p) cc_final: 0.8493 (t) REVERT: F 542 ARG cc_start: 0.8913 (ptp90) cc_final: 0.8632 (ptt180) outliers start: 37 outliers final: 27 residues processed: 190 average time/residue: 0.1251 time to fit residues: 35.6734 Evaluate side-chains 189 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 158 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 82 GLN Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 414 ILE Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain E residue 539 VAL Chi-restraints excluded: chain E residue 540 GLN Chi-restraints excluded: chain E residue 543 ASN Chi-restraints excluded: chain E residue 581 LEU Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 605 CYS Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain E residue 612 SER Chi-restraints excluded: chain E residue 636 SER Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 178 ARG Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 352 HIS Chi-restraints excluded: chain D residue 502 LYS Chi-restraints excluded: chain F residue 657 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 1 optimal weight: 20.0000 chunk 171 optimal weight: 9.9990 chunk 56 optimal weight: 10.0000 chunk 33 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 134 optimal weight: 7.9990 chunk 113 optimal weight: 2.9990 chunk 115 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 10 optimal weight: 9.9990 chunk 184 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 99 ASN ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 GLN B 543 ASN D 80 ASN F 543 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.119396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.101825 restraints weight = 28512.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.104596 restraints weight = 16605.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.106434 restraints weight = 11475.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.107684 restraints weight = 8901.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.108514 restraints weight = 7427.011| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.4469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.071 16169 Z= 0.332 Angle : 0.854 10.734 22185 Z= 0.398 Chirality : 0.050 0.209 2813 Planarity : 0.005 0.040 2659 Dihedral : 4.993 27.838 1992 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.08 % Allowed : 14.46 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.20), residues: 1635 helix: 1.63 (0.27), residues: 384 sheet: 0.06 (0.26), residues: 390 loop : -0.96 (0.20), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 588 TYR 0.018 0.002 TYR A 384 PHE 0.032 0.003 PHE A 159 TRP 0.026 0.002 TRP E 571 HIS 0.007 0.002 HIS D 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00791 / 0.33 (16034) covalent geometry : angle 0.81459 / 0.39 (21813) SS BOND : bond 0.00593 / 0.34 ( 33) SS BOND : angle 2.10928 / 1.10 ( 66) hydrogen bonds : bond 0.06256 / 3.43 ( 294) hydrogen bonds : angle 4.13988 / 2.10 ( 807) link_ALPHA1-3 : bond 0.00540 / 0.27 ( 3) link_ALPHA1-3 : angle 1.70164 / 0.89 ( 9) link_ALPHA1-6 : bond 0.00747 / 0.36 ( 2) link_ALPHA1-6 : angle 1.44909 / 0.71 ( 6) link_BETA1-4 : bond 0.00571 / 0.31 ( 45) link_BETA1-4 : angle 1.94239 / 0.98 ( 135) link_NAG-ASN : bond 0.00420 / 0.23 ( 52) link_NAG-ASN : angle 2.35421 / 1.14 ( 156) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 159 time to evaluate : 0.507 Fit side-chains REVERT: C 111 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8890 (mp) REVERT: C 136 ASN cc_start: 0.7785 (OUTLIER) cc_final: 0.7393 (m-40) REVERT: E 540 GLN cc_start: 0.8730 (OUTLIER) cc_final: 0.7301 (mp10) REVERT: A 185 ASN cc_start: 0.7138 (t0) cc_final: 0.6501 (p0) REVERT: A 202 THR cc_start: 0.9187 (m) cc_final: 0.8814 (p) REVERT: A 268 GLU cc_start: 0.8087 (mm-30) cc_final: 0.7775 (mm-30) REVERT: B 520 LEU cc_start: 0.8080 (mm) cc_final: 0.7697 (mt) REVERT: B 584 GLU cc_start: 0.8016 (mp0) cc_final: 0.7619 (mp0) REVERT: D 46 LYS cc_start: 0.8835 (OUTLIER) cc_final: 0.8485 (ptpp) REVERT: D 137 ASN cc_start: 0.7532 (OUTLIER) cc_final: 0.7255 (m-40) REVERT: D 178 ARG cc_start: 0.8695 (OUTLIER) cc_final: 0.7862 (ttm170) REVERT: D 308 ARG cc_start: 0.7427 (mmt-90) cc_final: 0.7028 (mtp85) REVERT: D 434 MET cc_start: 0.8215 (ttp) cc_final: 0.7963 (ttt) REVERT: D 475 MET cc_start: 0.8817 (mmt) cc_final: 0.8504 (mmp) REVERT: F 536 THR cc_start: 0.8799 (p) cc_final: 0.8593 (t) outliers start: 46 outliers final: 32 residues processed: 195 average time/residue: 0.1229 time to fit residues: 36.3298 Evaluate side-chains 188 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 150 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 136 ASN Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 414 ILE Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain E residue 539 VAL Chi-restraints excluded: chain E residue 540 GLN Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 605 CYS Chi-restraints excluded: chain E residue 612 SER Chi-restraints excluded: chain E residue 636 SER Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 246 GLN Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 137 ASN Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 178 ARG Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 502 LYS Chi-restraints excluded: chain F residue 573 ILE Chi-restraints excluded: chain F residue 613 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 127 optimal weight: 3.9990 chunk 143 optimal weight: 1.9990 chunk 19 optimal weight: 20.0000 chunk 160 optimal weight: 6.9990 chunk 65 optimal weight: 0.4980 chunk 157 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 72 optimal weight: 4.9990 chunk 105 optimal weight: 0.9980 chunk 142 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 99 ASN ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 66 HIS ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 GLN B 543 ASN D 80 ASN F 543 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.119875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.102463 restraints weight = 28230.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.105246 restraints weight = 16254.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.107117 restraints weight = 11167.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.108356 restraints weight = 8594.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.109221 restraints weight = 7163.835| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.4481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.551 16169 Z= 0.377 Angle : 1.037 59.192 22185 Z= 0.524 Chirality : 0.058 1.809 2813 Planarity : 0.005 0.126 2659 Dihedral : 4.991 26.849 1992 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.68 % Allowed : 15.13 % Favored : 82.20 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.20), residues: 1635 helix: 1.60 (0.26), residues: 384 sheet: -0.02 (0.26), residues: 390 loop : -1.01 (0.20), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 151 TYR 0.018 0.002 TYR D 173 PHE 0.029 0.002 PHE A 159 TRP 0.024 0.002 TRP E 571 HIS 0.006 0.002 HIS D 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00814 / 0.38 (16034) covalent geometry : angle 0.99473 / 0.52 (21813) SS BOND : bond 0.00463 / 0.26 ( 33) SS BOND : angle 2.06890 / 1.07 ( 66) hydrogen bonds : bond 0.06058 / 3.33 ( 294) hydrogen bonds : angle 4.10343 / 2.08 ( 807) link_ALPHA1-3 : bond 0.00499 / 0.25 ( 3) link_ALPHA1-3 : angle 1.72017 / 0.89 ( 9) link_ALPHA1-6 : bond 0.00789 / 0.38 ( 2) link_ALPHA1-6 : angle 1.44751 / 0.71 ( 6) link_BETA1-4 : bond 0.00515 / 0.28 ( 45) link_BETA1-4 : angle 1.91588 / 0.97 ( 135) link_NAG-ASN : bond 0.00512 / 0.28 ( 52) link_NAG-ASN : angle 3.03424 / 1.39 ( 156) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 153 time to evaluate : 0.594 Fit side-chains REVERT: C 111 LEU cc_start: 0.9200 (OUTLIER) cc_final: 0.8881 (mp) REVERT: E 540 GLN cc_start: 0.8715 (OUTLIER) cc_final: 0.7283 (mp10) REVERT: A 92 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.6911 (tm-30) REVERT: A 185 ASN cc_start: 0.7124 (t0) cc_final: 0.6489 (p0) REVERT: A 202 THR cc_start: 0.9181 (m) cc_final: 0.8799 (p) REVERT: A 268 GLU cc_start: 0.8075 (mm-30) cc_final: 0.7767 (mm-30) REVERT: B 520 LEU cc_start: 0.8067 (mm) cc_final: 0.7695 (mt) REVERT: B 584 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7616 (mp0) REVERT: D 46 LYS cc_start: 0.8831 (OUTLIER) cc_final: 0.8481 (ptpp) REVERT: D 137 ASN cc_start: 0.7522 (OUTLIER) cc_final: 0.7249 (m-40) REVERT: D 178 ARG cc_start: 0.8685 (OUTLIER) cc_final: 0.7844 (ttm170) REVERT: D 308 ARG cc_start: 0.7406 (mmt-90) cc_final: 0.6998 (mtp85) REVERT: D 434 MET cc_start: 0.8200 (ttp) cc_final: 0.7938 (ttt) REVERT: D 475 MET cc_start: 0.8800 (mmt) cc_final: 0.8485 (mmp) outliers start: 40 outliers final: 30 residues processed: 185 average time/residue: 0.1182 time to fit residues: 33.1068 Evaluate side-chains 186 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 149 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 141 ASP Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 414 ILE Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain E residue 539 VAL Chi-restraints excluded: chain E residue 540 GLN Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 605 CYS Chi-restraints excluded: chain E residue 612 SER Chi-restraints excluded: chain E residue 636 SER Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 137 ASN Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 178 ARG Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 502 LYS Chi-restraints excluded: chain F residue 573 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 33 optimal weight: 0.9980 chunk 17 optimal weight: 9.9990 chunk 76 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 170 optimal weight: 0.0970 chunk 74 optimal weight: 2.9990 chunk 160 optimal weight: 7.9990 chunk 48 optimal weight: 3.9990 chunk 116 optimal weight: 8.9990 chunk 54 optimal weight: 2.9990 chunk 174 optimal weight: 0.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 99 ASN ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 66 HIS ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 543 ASN D 80 ASN F 543 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.119937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.102495 restraints weight = 28253.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.105259 restraints weight = 16292.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.107106 restraints weight = 11240.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.108253 restraints weight = 8699.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.109189 restraints weight = 7303.507| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.4491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.551 16169 Z= 0.378 Angle : 1.039 59.192 22185 Z= 0.525 Chirality : 0.058 1.809 2813 Planarity : 0.005 0.126 2659 Dihedral : 4.991 26.849 1992 Min Nonbonded Distance : 1.275 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.61 % Allowed : 15.33 % Favored : 82.06 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.20), residues: 1635 helix: 1.60 (0.26), residues: 384 sheet: -0.02 (0.26), residues: 390 loop : -1.01 (0.20), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 151 TYR 0.018 0.002 TYR D 173 PHE 0.029 0.002 PHE A 159 TRP 0.024 0.002 TRP E 571 HIS 0.006 0.002 HIS D 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00814 / 0.38 (16034) covalent geometry : angle 0.99473 / 0.52 (21813) SS BOND : bond 0.01434 / 0.76 ( 33) SS BOND : angle 2.41007 / 1.15 ( 66) hydrogen bonds : bond 0.06058 / 3.33 ( 294) hydrogen bonds : angle 4.10343 / 2.08 ( 807) link_ALPHA1-3 : bond 0.00499 / 0.25 ( 3) link_ALPHA1-3 : angle 1.72017 / 0.89 ( 9) link_ALPHA1-6 : bond 0.00789 / 0.38 ( 2) link_ALPHA1-6 : angle 1.44751 / 0.71 ( 6) link_BETA1-4 : bond 0.00515 / 0.28 ( 45) link_BETA1-4 : angle 1.91588 / 0.97 ( 135) link_NAG-ASN : bond 0.00512 / 0.28 ( 52) link_NAG-ASN : angle 3.03424 / 1.39 ( 156) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2220.34 seconds wall clock time: 39 minutes 23.89 seconds (2363.89 seconds total)