Starting phenix.real_space_refine on Tue Jul 7 03:47:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8aow_15554/07_2026/8aow_15554.cif Found real_map, /net/cci-nas-00/data/ceres_data/8aow_15554/07_2026/8aow_15554.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8aow_15554/07_2026/8aow_15554.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8aow_15554/07_2026/8aow_15554.cif" model { file = "/net/cci-nas-00/data/ceres_data/8aow_15554/07_2026/8aow_15554.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8aow_15554/07_2026/8aow_15554.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8aow_15554/07_2026/8aow_15554.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8aow_15554/07_2026/8aow_15554.map" } resolution = 2.7 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= 0.003 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: 7 Type Number sf(0) Gaussians Zn 12 6.06 5 P 36 5.49 5 Mg 24 5.21 5 S 384 5.16 5 C 27168 2.51 5 N 7548 2.21 5 O 8460 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 148 residue(s): 0.04s 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: 43632 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 3547 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 451, 3527 Classifications: {'peptide': 451} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 21, 'TRANS': 429} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 451, 3527 Classifications: {'peptide': 451} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 21, 'TRANS': 429} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 3576 Chain: "C" Number of atoms: 3547 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 451, 3527 Classifications: {'peptide': 451} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 21, 'TRANS': 429} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 451, 3527 Classifications: {'peptide': 451} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 21, 'TRANS': 429} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 3576 Chain: "E" Number of atoms: 3547 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 451, 3527 Classifications: {'peptide': 451} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 21, 'TRANS': 429} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 451, 3527 Classifications: {'peptide': 451} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 21, 'TRANS': 429} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 3576 Chain: "G" Number of atoms: 3547 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 451, 3527 Classifications: {'peptide': 451} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 21, 'TRANS': 429} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 451, 3527 Classifications: {'peptide': 451} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 21, 'TRANS': 429} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 3576 Chain: "I" Number of atoms: 3547 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 451, 3527 Classifications: {'peptide': 451} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 21, 'TRANS': 429} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 451, 3527 Classifications: {'peptide': 451} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 21, 'TRANS': 429} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 3576 Chain: "K" Number of atoms: 3547 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 451, 3527 Classifications: {'peptide': 451} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 21, 'TRANS': 429} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 451, 3527 Classifications: {'peptide': 451} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 21, 'TRANS': 429} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 3576 Chain: "M" Number of atoms: 3547 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 451, 3527 Classifications: {'peptide': 451} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 21, 'TRANS': 429} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 451, 3527 Classifications: {'peptide': 451} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 21, 'TRANS': 429} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 3576 Chain: "O" Number of atoms: 3547 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 451, 3527 Classifications: {'peptide': 451} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 21, 'TRANS': 429} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 451, 3527 Classifications: {'peptide': 451} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 21, 'TRANS': 429} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 3576 Chain: "Q" Number of atoms: 3547 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 451, 3527 Classifications: {'peptide': 451} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 21, 'TRANS': 429} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 451, 3527 Classifications: {'peptide': 451} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 21, 'TRANS': 429} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 3576 Chain: "S" Number of atoms: 3547 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 451, 3527 Classifications: {'peptide': 451} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 21, 'TRANS': 429} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 451, 3527 Classifications: {'peptide': 451} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 21, 'TRANS': 429} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 3576 Chain: "V" Number of atoms: 3547 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 451, 3527 Classifications: {'peptide': 451} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 21, 'TRANS': 429} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 451, 3527 Classifications: {'peptide': 451} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 21, 'TRANS': 429} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 3576 Chain: "X" Number of atoms: 3547 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 451, 3527 Classifications: {'peptide': 451} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 21, 'TRANS': 429} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 451, 3527 Classifications: {'peptide': 451} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 21, 'TRANS': 429} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 3576 Chain: "A" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 62 Unusual residues: {' MG': 2, ' ZN': 1, 'MGP': 1} Classifications: {'peptide': 1, 'undetermined': 4} Link IDs: {None: 4} Chain: "C" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 62 Unusual residues: {' MG': 2, ' ZN': 1, 'MGP': 1} Classifications: {'peptide': 1, 'undetermined': 4} Link IDs: {None: 4} Chain: "E" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 62 Unusual residues: {' MG': 2, ' ZN': 1, 'MGP': 1} Classifications: {'peptide': 1, 'undetermined': 4} Link IDs: {None: 4} Chain: "G" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 62 Unusual residues: {' MG': 2, ' ZN': 1, 'MGP': 1} Classifications: {'peptide': 1, 'undetermined': 4} Link IDs: {None: 4} Chain: "I" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 62 Unusual residues: {' MG': 2, ' ZN': 1, 'MGP': 1} Classifications: {'peptide': 1, 'undetermined': 4} Link IDs: {None: 4} Chain: "K" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 62 Unusual residues: {' MG': 2, ' ZN': 1, 'MGP': 1} Classifications: {'peptide': 1, 'undetermined': 4} Link IDs: {None: 4} Chain: "M" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 62 Unusual residues: {' MG': 2, ' ZN': 1, 'MGP': 1} Classifications: {'peptide': 1, 'undetermined': 4} Link IDs: {None: 4} Chain: "O" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 62 Unusual residues: {' MG': 2, ' ZN': 1, 'MGP': 1} Classifications: {'peptide': 1, 'undetermined': 4} Link IDs: {None: 4} Chain: "Q" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 62 Unusual residues: {' MG': 2, ' ZN': 1, 'MGP': 1} Classifications: {'peptide': 1, 'undetermined': 4} Link IDs: {None: 4} Chain: "S" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 62 Unusual residues: {' MG': 2, ' ZN': 1, 'MGP': 1} Classifications: {'peptide': 1, 'undetermined': 4} Link IDs: {None: 4} Chain: "V" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 62 Unusual residues: {' MG': 2, ' ZN': 1, 'MGP': 1} Classifications: {'peptide': 1, 'undetermined': 4} Link IDs: {None: 4} Chain: "X" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 62 Unusual residues: {' MG': 2, ' ZN': 1, 'MGP': 1} Classifications: {'peptide': 1, 'undetermined': 4} Link IDs: {None: 4} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "G" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "I" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "K" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "M" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "O" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "Q" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "S" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "V" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "X" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1022 SG CYS A 134 127.644 180.695 64.825 1.00 68.87 S ATOM 1074 SG CYS A 141 131.907 179.774 64.281 1.00 58.74 S ATOM 4569 SG CYS C 134 84.132 183.346 64.824 1.00 65.23 S ATOM 4621 SG CYS C 141 88.271 184.715 64.285 1.00 49.51 S ATOM 8116 SG CYS E 134 45.086 163.922 64.774 1.00 65.24 S ATOM 8168 SG CYS E 141 47.955 167.195 64.334 1.00 48.23 S ATOM 11663 SG CYS G 134 21.026 127.676 64.855 1.00 68.82 S ATOM 11715 SG CYS G 141 22.023 131.896 64.236 1.00 58.07 S ATOM 15210 SG CYS I 134 18.373 84.131 64.811 1.00 63.82 S ATOM 15262 SG CYS I 141 17.008 88.266 64.264 1.00 52.93 S ATOM 18757 SG CYS K 134 37.747 45.100 64.854 1.00 62.65 S ATOM 18809 SG CYS K 141 34.484 48.017 64.274 1.00 47.24 S ATOM 22304 SG CYS M 134 74.119 21.012 64.773 1.00 70.21 S ATOM 22356 SG CYS M 141 69.887 21.938 64.310 1.00 57.72 S ATOM 25851 SG CYS O 134 117.594 18.383 64.820 1.00 65.86 S ATOM 25903 SG CYS O 141 113.444 17.033 64.309 1.00 54.41 S ATOM 29398 SG CYS Q 134 156.633 37.757 64.814 1.00 63.13 S ATOM 29450 SG CYS Q 141 153.737 34.494 64.322 1.00 50.56 S ATOM 32945 SG CYS S 134 180.691 74.081 64.819 1.00 68.03 S ATOM 32997 SG CYS S 141 179.765 69.803 64.278 1.00 58.06 S ATOM 36492 SG CYS V 134 183.328 117.588 64.822 1.00 66.97 S ATOM 36544 SG CYS V 141 184.714 113.450 64.283 1.00 53.23 S ATOM 40039 SG CYS X 134 163.906 156.558 64.822 1.00 65.29 S ATOM 40091 SG CYS X 141 167.243 153.735 64.319 1.00 49.10 S Residues with excluded nonbonded symmetry interactions: 12 residue: pdb=" N ASER A 271 " occ=0.19 ... (10 atoms not shown) pdb=" OG BSER A 271 " occ=0.81 residue: pdb=" N ASER C 271 " occ=0.56 ... (10 atoms not shown) pdb=" OG BSER C 271 " occ=0.44 residue: pdb=" N ASER E 271 " occ=0.17 ... (10 atoms not shown) pdb=" OG BSER E 271 " occ=0.83 residue: pdb=" N ASER G 271 " occ=0.25 ... (10 atoms not shown) pdb=" OG BSER G 271 " occ=0.75 residue: pdb=" N ASER I 271 " occ=0.42 ... (10 atoms not shown) pdb=" OG BSER I 271 " occ=0.58 residue: pdb=" N ASER K 271 " occ=0.32 ... (10 atoms not shown) pdb=" OG BSER K 271 " occ=0.68 residue: pdb=" N ASER M 271 " occ=0.19 ... (10 atoms not shown) pdb=" OG BSER M 271 " occ=0.81 residue: pdb=" N ASER O 271 " occ=0.49 ... (10 atoms not shown) pdb=" OG BSER O 271 " occ=0.51 residue: pdb=" N ASER Q 271 " occ=0.31 ... (10 atoms not shown) pdb=" OG BSER Q 271 " occ=0.69 residue: pdb=" N ASER S 271 " occ=0.12 ... (10 atoms not shown) pdb=" OG BSER S 271 " occ=0.88 residue: pdb=" N ASER V 271 " occ=0.47 ... (10 atoms not shown) pdb=" OG BSER V 271 " occ=0.53 residue: pdb=" N ASER X 271 " occ=0.16 ... (10 atoms not shown) pdb=" OG BSER X 271 " occ=0.84 Time building chain proxies: 15.55, per 1000 atoms: 0.36 Number of scatterers: 43632 At special positions: 0 Unit cell: (203.038, 203.038, 94.807, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 12 29.99 S 384 16.00 P 36 15.00 Mg 24 11.99 O 8460 8.00 N 7548 7.00 C 27168 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 3.69 Conformation dependent library (CDL) restraints added in 3.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 141 " pdb="ZN ZN A1001 " - pdb=" NE2 HIS A 79 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 134 " pdb=" ZN C 602 " pdb="ZN ZN C 602 " - pdb=" NE2 HIS C 79 " pdb="ZN ZN C 602 " - pdb=" SG CYS C 141 " pdb="ZN ZN C 602 " - pdb=" SG CYS C 134 " pdb=" ZN E 602 " pdb="ZN ZN E 602 " - pdb=" SG CYS E 134 " pdb="ZN ZN E 602 " - pdb=" SG CYS E 141 " pdb="ZN ZN E 602 " - pdb=" NE2 HIS E 79 " pdb=" ZN G 602 " pdb="ZN ZN G 602 " - pdb=" SG CYS G 134 " pdb="ZN ZN G 602 " - pdb=" NE2 HIS G 79 " pdb="ZN ZN G 602 " - pdb=" SG CYS G 141 " pdb=" ZN I 602 " pdb="ZN ZN I 602 " - pdb=" SG CYS I 134 " pdb="ZN ZN I 602 " - pdb=" SG CYS I 141 " pdb="ZN ZN I 602 " - pdb=" NE2 HIS I 79 " pdb=" ZN K 602 " pdb="ZN ZN K 602 " - pdb=" SG CYS K 134 " pdb="ZN ZN K 602 " - pdb=" SG CYS K 141 " pdb="ZN ZN K 602 " - pdb=" NE2 HIS K 79 " pdb=" ZN M 602 " pdb="ZN ZN M 602 " - pdb=" SG CYS M 134 " pdb="ZN ZN M 602 " - pdb=" SG CYS M 141 " pdb="ZN ZN M 602 " - pdb=" NE2 HIS M 79 " pdb=" ZN O 602 " pdb="ZN ZN O 602 " - pdb=" SG CYS O 141 " pdb="ZN ZN O 602 " - pdb=" NE2 HIS O 79 " pdb="ZN ZN O 602 " - pdb=" SG CYS O 134 " pdb=" ZN Q 602 " pdb="ZN ZN Q 602 " - pdb=" SG CYS Q 134 " pdb="ZN ZN Q 602 " - pdb=" SG CYS Q 141 " pdb="ZN ZN Q 602 " - pdb=" NE2 HIS Q 79 " pdb=" ZN S 602 " pdb="ZN ZN S 602 " - pdb=" NE2 HIS S 79 " pdb="ZN ZN S 602 " - pdb=" SG CYS S 141 " pdb="ZN ZN S 602 " - pdb=" SG CYS S 134 " pdb=" ZN V 602 " pdb="ZN ZN V 602 " - pdb=" SG CYS V 141 " pdb="ZN ZN V 602 " - pdb=" SG CYS V 134 " pdb="ZN ZN V 602 " - pdb=" NE2 HIS V 79 " pdb=" ZN X 602 " pdb="ZN ZN X 602 " - pdb=" SG CYS X 141 " pdb="ZN ZN X 602 " - pdb=" SG CYS X 134 " pdb="ZN ZN X 602 " - pdb=" NE2 HIS X 79 " 10824 Ramachandran restraints generated. 5412 Oldfield, 0 Emsley, 5412 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10392 Finding SS restraints... Secondary structure from input PDB file: 188 helices and 60 sheets defined 34.3% alpha, 22.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'A' and resid 13 through 22 removed outlier: 3.967A pdb=" N ALA A 17 " --> pdb=" O ALA A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 55 Processing helix chain 'A' and resid 67 through 71 Processing helix chain 'A' and resid 88 through 103 Processing helix chain 'A' and resid 111 through 125 Processing helix chain 'A' and resid 157 through 167 Processing helix chain 'A' and resid 180 through 185 Processing helix chain 'A' and resid 193 through 195 No H-bonds generated for 'chain 'A' and resid 193 through 195' Processing helix chain 'A' and resid 203 through 205 No H-bonds generated for 'chain 'A' and resid 203 through 205' Processing helix chain 'A' and resid 252 through 258 removed outlier: 3.812A pdb=" N TRP A 258 " --> pdb=" O LEU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 342 Processing helix chain 'A' and resid 343 through 348 removed outlier: 3.612A pdb=" N LEU A 346 " --> pdb=" O THR A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 363 Processing helix chain 'A' and resid 380 through 382 No H-bonds generated for 'chain 'A' and resid 380 through 382' Processing helix chain 'A' and resid 383 through 404 Processing helix chain 'A' and resid 461 through 469 Processing helix chain 'C' and resid 13 through 22 removed outlier: 3.947A pdb=" N ALA C 17 " --> pdb=" O ALA C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 55 Processing helix chain 'C' and resid 67 through 71 Processing helix chain 'C' and resid 88 through 103 Processing helix chain 'C' and resid 111 through 125 Processing helix chain 'C' and resid 157 through 167 Processing helix chain 'C' and resid 180 through 185 Processing helix chain 'C' and resid 193 through 195 No H-bonds generated for 'chain 'C' and resid 193 through 195' Processing helix chain 'C' and resid 203 through 205 No H-bonds generated for 'chain 'C' and resid 203 through 205' Processing helix chain 'C' and resid 252 through 258 removed outlier: 3.854A pdb=" N TRP C 258 " --> pdb=" O LEU C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 342 Processing helix chain 'C' and resid 343 through 348 removed outlier: 3.547A pdb=" N LEU C 346 " --> pdb=" O THR C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 363 Processing helix chain 'C' and resid 380 through 382 No H-bonds generated for 'chain 'C' and resid 380 through 382' Processing helix chain 'C' and resid 383 through 404 Processing helix chain 'C' and resid 461 through 469 Processing helix chain 'E' and resid 13 through 22 removed outlier: 3.957A pdb=" N ALA E 17 " --> pdb=" O ALA E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 55 Processing helix chain 'E' and resid 67 through 71 Processing helix chain 'E' and resid 88 through 103 Processing helix chain 'E' and resid 111 through 125 Processing helix chain 'E' and resid 157 through 167 Processing helix chain 'E' and resid 180 through 185 Processing helix chain 'E' and resid 193 through 195 No H-bonds generated for 'chain 'E' and resid 193 through 195' Processing helix chain 'E' and resid 203 through 205 No H-bonds generated for 'chain 'E' and resid 203 through 205' Processing helix chain 'E' and resid 252 through 258 removed outlier: 3.852A pdb=" N TRP E 258 " --> pdb=" O LEU E 254 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 342 Processing helix chain 'E' and resid 343 through 348 removed outlier: 3.659A pdb=" N LEU E 346 " --> pdb=" O THR E 343 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 363 Processing helix chain 'E' and resid 380 through 382 No H-bonds generated for 'chain 'E' and resid 380 through 382' Processing helix chain 'E' and resid 383 through 404 Processing helix chain 'E' and resid 461 through 469 Processing helix chain 'G' and resid 13 through 22 removed outlier: 3.985A pdb=" N ALA G 17 " --> pdb=" O ALA G 13 " (cutoff:3.500A) Processing helix chain 'G' and resid 37 through 55 Processing helix chain 'G' and resid 67 through 71 Processing helix chain 'G' and resid 88 through 103 Processing helix chain 'G' and resid 111 through 125 Processing helix chain 'G' and resid 157 through 167 Processing helix chain 'G' and resid 180 through 185 Processing helix chain 'G' and resid 193 through 195 No H-bonds generated for 'chain 'G' and resid 193 through 195' Processing helix chain 'G' and resid 203 through 205 No H-bonds generated for 'chain 'G' and resid 203 through 205' Processing helix chain 'G' and resid 252 through 258 removed outlier: 3.847A pdb=" N TRP G 258 " --> pdb=" O LEU G 254 " (cutoff:3.500A) Processing helix chain 'G' and resid 335 through 342 Processing helix chain 'G' and resid 343 through 348 removed outlier: 3.590A pdb=" N LEU G 346 " --> pdb=" O THR G 343 " (cutoff:3.500A) Processing helix chain 'G' and resid 351 through 363 Processing helix chain 'G' and resid 380 through 382 No H-bonds generated for 'chain 'G' and resid 380 through 382' Processing helix chain 'G' and resid 383 through 404 Processing helix chain 'G' and resid 461 through 469 Processing helix chain 'I' and resid 13 through 22 removed outlier: 3.897A pdb=" N ALA I 17 " --> pdb=" O ALA I 13 " (cutoff:3.500A) Processing helix chain 'I' and resid 37 through 55 Processing helix chain 'I' and resid 67 through 72 removed outlier: 3.926A pdb=" N MET I 72 " --> pdb=" O ALA I 69 " (cutoff:3.500A) Processing helix chain 'I' and resid 88 through 103 Processing helix chain 'I' and resid 111 through 125 Processing helix chain 'I' and resid 157 through 167 Processing helix chain 'I' and resid 180 through 185 Processing helix chain 'I' and resid 193 through 195 No H-bonds generated for 'chain 'I' and resid 193 through 195' Processing helix chain 'I' and resid 203 through 205 No H-bonds generated for 'chain 'I' and resid 203 through 205' Processing helix chain 'I' and resid 252 through 258 removed outlier: 3.807A pdb=" N TRP I 258 " --> pdb=" O LEU I 254 " (cutoff:3.500A) Processing helix chain 'I' and resid 335 through 342 Processing helix chain 'I' and resid 343 through 348 removed outlier: 3.640A pdb=" N LEU I 346 " --> pdb=" O THR I 343 " (cutoff:3.500A) Processing helix chain 'I' and resid 351 through 363 Processing helix chain 'I' and resid 380 through 382 No H-bonds generated for 'chain 'I' and resid 380 through 382' Processing helix chain 'I' and resid 383 through 404 Processing helix chain 'I' and resid 461 through 469 Processing helix chain 'K' and resid 13 through 22 removed outlier: 4.004A pdb=" N ALA K 17 " --> pdb=" O ALA K 13 " (cutoff:3.500A) Processing helix chain 'K' and resid 37 through 55 Processing helix chain 'K' and resid 67 through 71 Processing helix chain 'K' and resid 88 through 103 Processing helix chain 'K' and resid 111 through 125 Processing helix chain 'K' and resid 157 through 167 Processing helix chain 'K' and resid 180 through 185 Processing helix chain 'K' and resid 193 through 195 No H-bonds generated for 'chain 'K' and resid 193 through 195' Processing helix chain 'K' and resid 203 through 205 No H-bonds generated for 'chain 'K' and resid 203 through 205' Processing helix chain 'K' and resid 252 through 258 removed outlier: 3.788A pdb=" N TRP K 258 " --> pdb=" O LEU K 254 " (cutoff:3.500A) Processing helix chain 'K' and resid 335 through 342 Processing helix chain 'K' and resid 343 through 348 removed outlier: 3.642A pdb=" N LEU K 346 " --> pdb=" O THR K 343 " (cutoff:3.500A) Processing helix chain 'K' and resid 351 through 363 Processing helix chain 'K' and resid 380 through 382 No H-bonds generated for 'chain 'K' and resid 380 through 382' Processing helix chain 'K' and resid 383 through 404 Processing helix chain 'K' and resid 461 through 469 Processing helix chain 'M' and resid 13 through 22 removed outlier: 3.975A pdb=" N ALA M 17 " --> pdb=" O ALA M 13 " (cutoff:3.500A) Processing helix chain 'M' and resid 37 through 55 Processing helix chain 'M' and resid 88 through 103 Processing helix chain 'M' and resid 111 through 125 Processing helix chain 'M' and resid 157 through 167 Processing helix chain 'M' and resid 180 through 185 Processing helix chain 'M' and resid 193 through 195 No H-bonds generated for 'chain 'M' and resid 193 through 195' Processing helix chain 'M' and resid 203 through 205 No H-bonds generated for 'chain 'M' and resid 203 through 205' Processing helix chain 'M' and resid 252 through 258 removed outlier: 3.843A pdb=" N TRP M 258 " --> pdb=" O LEU M 254 " (cutoff:3.500A) Processing helix chain 'M' and resid 335 through 342 Processing helix chain 'M' and resid 343 through 348 removed outlier: 3.593A pdb=" N LEU M 346 " --> pdb=" O THR M 343 " (cutoff:3.500A) Processing helix chain 'M' and resid 351 through 363 Processing helix chain 'M' and resid 380 through 382 No H-bonds generated for 'chain 'M' and resid 380 through 382' Processing helix chain 'M' and resid 383 through 404 Processing helix chain 'M' and resid 461 through 469 Processing helix chain 'O' and resid 13 through 22 removed outlier: 4.007A pdb=" N ALA O 17 " --> pdb=" O ALA O 13 " (cutoff:3.500A) Processing helix chain 'O' and resid 37 through 55 Processing helix chain 'O' and resid 67 through 71 Processing helix chain 'O' and resid 88 through 103 Processing helix chain 'O' and resid 111 through 125 Processing helix chain 'O' and resid 157 through 167 Processing helix chain 'O' and resid 180 through 185 Processing helix chain 'O' and resid 193 through 195 No H-bonds generated for 'chain 'O' and resid 193 through 195' Processing helix chain 'O' and resid 203 through 205 No H-bonds generated for 'chain 'O' and resid 203 through 205' Processing helix chain 'O' and resid 252 through 258 removed outlier: 3.795A pdb=" N TRP O 258 " --> pdb=" O LEU O 254 " (cutoff:3.500A) Processing helix chain 'O' and resid 335 through 342 Processing helix chain 'O' and resid 343 through 348 removed outlier: 3.664A pdb=" N LEU O 346 " --> pdb=" O THR O 343 " (cutoff:3.500A) Processing helix chain 'O' and resid 351 through 363 Processing helix chain 'O' and resid 380 through 382 No H-bonds generated for 'chain 'O' and resid 380 through 382' Processing helix chain 'O' and resid 383 through 404 Processing helix chain 'O' and resid 461 through 469 Processing helix chain 'Q' and resid 13 through 22 removed outlier: 3.923A pdb=" N ALA Q 17 " --> pdb=" O ALA Q 13 " (cutoff:3.500A) Processing helix chain 'Q' and resid 37 through 55 Processing helix chain 'Q' and resid 67 through 71 Processing helix chain 'Q' and resid 88 through 103 Processing helix chain 'Q' and resid 111 through 125 Processing helix chain 'Q' and resid 157 through 167 Processing helix chain 'Q' and resid 180 through 185 Processing helix chain 'Q' and resid 193 through 195 No H-bonds generated for 'chain 'Q' and resid 193 through 195' Processing helix chain 'Q' and resid 203 through 205 No H-bonds generated for 'chain 'Q' and resid 203 through 205' Processing helix chain 'Q' and resid 252 through 258 removed outlier: 3.845A pdb=" N TRP Q 258 " --> pdb=" O LEU Q 254 " (cutoff:3.500A) Processing helix chain 'Q' and resid 335 through 342 Processing helix chain 'Q' and resid 343 through 348 removed outlier: 3.640A pdb=" N LEU Q 346 " --> pdb=" O THR Q 343 " (cutoff:3.500A) Processing helix chain 'Q' and resid 351 through 363 Processing helix chain 'Q' and resid 380 through 382 No H-bonds generated for 'chain 'Q' and resid 380 through 382' Processing helix chain 'Q' and resid 383 through 404 Processing helix chain 'Q' and resid 461 through 469 Processing helix chain 'S' and resid 13 through 22 removed outlier: 3.939A pdb=" N ALA S 17 " --> pdb=" O ALA S 13 " (cutoff:3.500A) Processing helix chain 'S' and resid 37 through 55 Processing helix chain 'S' and resid 67 through 71 Processing helix chain 'S' and resid 88 through 103 Processing helix chain 'S' and resid 111 through 125 Processing helix chain 'S' and resid 157 through 167 Processing helix chain 'S' and resid 180 through 185 Processing helix chain 'S' and resid 193 through 195 No H-bonds generated for 'chain 'S' and resid 193 through 195' Processing helix chain 'S' and resid 203 through 205 No H-bonds generated for 'chain 'S' and resid 203 through 205' Processing helix chain 'S' and resid 252 through 258 removed outlier: 3.802A pdb=" N TRP S 258 " --> pdb=" O LEU S 254 " (cutoff:3.500A) Processing helix chain 'S' and resid 335 through 342 Processing helix chain 'S' and resid 343 through 348 removed outlier: 3.509A pdb=" N LEU S 346 " --> pdb=" O THR S 343 " (cutoff:3.500A) Processing helix chain 'S' and resid 351 through 363 Processing helix chain 'S' and resid 383 through 404 Processing helix chain 'S' and resid 461 through 469 Processing helix chain 'V' and resid 13 through 22 removed outlier: 3.957A pdb=" N ALA V 17 " --> pdb=" O ALA V 13 " (cutoff:3.500A) Processing helix chain 'V' and resid 37 through 55 Processing helix chain 'V' and resid 88 through 103 Processing helix chain 'V' and resid 111 through 125 Processing helix chain 'V' and resid 157 through 167 Processing helix chain 'V' and resid 180 through 185 Processing helix chain 'V' and resid 193 through 195 No H-bonds generated for 'chain 'V' and resid 193 through 195' Processing helix chain 'V' and resid 203 through 205 No H-bonds generated for 'chain 'V' and resid 203 through 205' Processing helix chain 'V' and resid 252 through 258 removed outlier: 3.840A pdb=" N TRP V 258 " --> pdb=" O LEU V 254 " (cutoff:3.500A) Processing helix chain 'V' and resid 335 through 342 Processing helix chain 'V' and resid 343 through 348 removed outlier: 3.558A pdb=" N LEU V 346 " --> pdb=" O THR V 343 " (cutoff:3.500A) Processing helix chain 'V' and resid 351 through 363 Processing helix chain 'V' and resid 380 through 382 No H-bonds generated for 'chain 'V' and resid 380 through 382' Processing helix chain 'V' and resid 383 through 404 Processing helix chain 'V' and resid 461 through 469 Processing helix chain 'X' and resid 13 through 22 removed outlier: 4.010A pdb=" N ALA X 17 " --> pdb=" O ALA X 13 " (cutoff:3.500A) Processing helix chain 'X' and resid 37 through 55 Processing helix chain 'X' and resid 67 through 71 Processing helix chain 'X' and resid 88 through 103 Processing helix chain 'X' and resid 111 through 125 Processing helix chain 'X' and resid 157 through 167 Processing helix chain 'X' and resid 180 through 185 Processing helix chain 'X' and resid 193 through 195 No H-bonds generated for 'chain 'X' and resid 193 through 195' Processing helix chain 'X' and resid 203 through 205 No H-bonds generated for 'chain 'X' and resid 203 through 205' Processing helix chain 'X' and resid 252 through 258 removed outlier: 3.876A pdb=" N TRP X 258 " --> pdb=" O LEU X 254 " (cutoff:3.500A) Processing helix chain 'X' and resid 335 through 342 Processing helix chain 'X' and resid 343 through 348 removed outlier: 3.654A pdb=" N LEU X 346 " --> pdb=" O THR X 343 " (cutoff:3.500A) Processing helix chain 'X' and resid 351 through 363 Processing helix chain 'X' and resid 383 through 404 Processing helix chain 'X' and resid 461 through 469 Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 6 removed outlier: 6.189A pdb=" N VAL A 4 " --> pdb=" O GLU A 28 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 133 through 134 removed outlier: 7.930A pdb=" N CYS A 134 " --> pdb=" O TYR A 78 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N CYS A 80 " --> pdb=" O CYS A 134 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ILE A 61 " --> pdb=" O HIS A 79 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N VAL A 81 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ASP A 63 " --> pdb=" O VAL A 81 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N GLN A 151 " --> pdb=" O ILE A 64 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N TYR A 285 " --> pdb=" O SER A 281 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N SER A 281 " --> pdb=" O TYR A 285 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL A 287 " --> pdb=" O VAL A 279 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 246 through 251 removed outlier: 6.751A pdb=" N ALA A 189 " --> pdb=" O CYS A 331 " (cutoff:3.500A) removed outlier: 9.117A pdb=" N TYR A 333 " --> pdb=" O ALA A 189 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N ALA A 191 " --> pdb=" O TYR A 333 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 303 through 308 removed outlier: 4.012A pdb=" N THR A 437 " --> pdb=" O HIS A 308 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 414 through 415 Processing sheet with id=AA6, first strand: chain 'C' and resid 4 through 6 removed outlier: 6.193A pdb=" N VAL C 4 " --> pdb=" O GLU C 28 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 133 through 134 removed outlier: 7.979A pdb=" N CYS C 134 " --> pdb=" O TYR C 78 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N CYS C 80 " --> pdb=" O CYS C 134 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ILE C 61 " --> pdb=" O HIS C 79 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N VAL C 81 " --> pdb=" O ILE C 61 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ASP C 63 " --> pdb=" O VAL C 81 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N GLN C 151 " --> pdb=" O ILE C 64 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N TYR C 285 " --> pdb=" O SER C 281 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N SER C 281 " --> pdb=" O TYR C 285 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N VAL C 287 " --> pdb=" O VAL C 279 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 246 through 251 removed outlier: 6.778A pdb=" N ALA C 189 " --> pdb=" O CYS C 331 " (cutoff:3.500A) removed outlier: 9.141A pdb=" N TYR C 333 " --> pdb=" O ALA C 189 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N ALA C 191 " --> pdb=" O TYR C 333 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 303 through 308 removed outlier: 3.897A pdb=" N THR C 437 " --> pdb=" O HIS C 308 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 414 through 415 Processing sheet with id=AB2, first strand: chain 'E' and resid 4 through 6 removed outlier: 6.164A pdb=" N VAL E 4 " --> pdb=" O GLU E 28 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'E' and resid 133 through 134 removed outlier: 7.979A pdb=" N CYS E 134 " --> pdb=" O TYR E 78 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N CYS E 80 " --> pdb=" O CYS E 134 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ILE E 61 " --> pdb=" O HIS E 79 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N VAL E 81 " --> pdb=" O ILE E 61 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ASP E 63 " --> pdb=" O VAL E 81 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N GLN E 151 " --> pdb=" O ILE E 64 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N TYR E 285 " --> pdb=" O SER E 281 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N SER E 281 " --> pdb=" O TYR E 285 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N VAL E 287 " --> pdb=" O VAL E 279 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 246 through 251 removed outlier: 6.805A pdb=" N ALA E 189 " --> pdb=" O CYS E 331 " (cutoff:3.500A) removed outlier: 9.204A pdb=" N TYR E 333 " --> pdb=" O ALA E 189 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N ALA E 191 " --> pdb=" O TYR E 333 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 303 through 308 removed outlier: 3.959A pdb=" N THR E 437 " --> pdb=" O HIS E 308 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 414 through 415 Processing sheet with id=AB7, first strand: chain 'G' and resid 4 through 6 removed outlier: 6.170A pdb=" N VAL G 4 " --> pdb=" O GLU G 28 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'G' and resid 133 through 134 removed outlier: 7.960A pdb=" N CYS G 134 " --> pdb=" O TYR G 78 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N CYS G 80 " --> pdb=" O CYS G 134 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ILE G 61 " --> pdb=" O HIS G 79 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N VAL G 81 " --> pdb=" O ILE G 61 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ASP G 63 " --> pdb=" O VAL G 81 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N GLN G 151 " --> pdb=" O ILE G 64 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N TYR G 285 " --> pdb=" O SER G 281 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N SER G 281 " --> pdb=" O TYR G 285 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N VAL G 287 " --> pdb=" O VAL G 279 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 246 through 251 removed outlier: 6.768A pdb=" N ALA G 189 " --> pdb=" O CYS G 331 " (cutoff:3.500A) removed outlier: 9.139A pdb=" N TYR G 333 " --> pdb=" O ALA G 189 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N ALA G 191 " --> pdb=" O TYR G 333 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 303 through 308 removed outlier: 3.991A pdb=" N THR G 437 " --> pdb=" O HIS G 308 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 414 through 415 Processing sheet with id=AC3, first strand: chain 'I' and resid 4 through 6 removed outlier: 6.180A pdb=" N VAL I 4 " --> pdb=" O GLU I 28 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'I' and resid 133 through 134 removed outlier: 7.917A pdb=" N CYS I 134 " --> pdb=" O TYR I 78 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N CYS I 80 " --> pdb=" O CYS I 134 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ILE I 61 " --> pdb=" O HIS I 79 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N VAL I 81 " --> pdb=" O ILE I 61 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ASP I 63 " --> pdb=" O VAL I 81 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N GLN I 151 " --> pdb=" O ILE I 64 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N TYR I 285 " --> pdb=" O SER I 281 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N SER I 281 " --> pdb=" O TYR I 285 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N VAL I 287 " --> pdb=" O VAL I 279 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 246 through 251 removed outlier: 6.761A pdb=" N ALA I 189 " --> pdb=" O CYS I 331 " (cutoff:3.500A) removed outlier: 9.141A pdb=" N TYR I 333 " --> pdb=" O ALA I 189 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N ALA I 191 " --> pdb=" O TYR I 333 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 303 through 308 removed outlier: 3.967A pdb=" N THR I 437 " --> pdb=" O HIS I 308 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 414 through 415 Processing sheet with id=AC8, first strand: chain 'K' and resid 4 through 6 removed outlier: 6.201A pdb=" N VAL K 4 " --> pdb=" O GLU K 28 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'K' and resid 133 through 134 removed outlier: 7.994A pdb=" N CYS K 134 " --> pdb=" O TYR K 78 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N CYS K 80 " --> pdb=" O CYS K 134 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ILE K 61 " --> pdb=" O HIS K 79 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N VAL K 81 " --> pdb=" O ILE K 61 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ASP K 63 " --> pdb=" O VAL K 81 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N GLN K 151 " --> pdb=" O ILE K 64 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N TYR K 285 " --> pdb=" O SER K 281 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N SER K 281 " --> pdb=" O TYR K 285 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N VAL K 287 " --> pdb=" O VAL K 279 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'K' and resid 246 through 251 removed outlier: 6.774A pdb=" N ALA K 189 " --> pdb=" O CYS K 331 " (cutoff:3.500A) removed outlier: 9.154A pdb=" N TYR K 333 " --> pdb=" O ALA K 189 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N ALA K 191 " --> pdb=" O TYR K 333 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'K' and resid 303 through 308 removed outlier: 3.969A pdb=" N THR K 437 " --> pdb=" O HIS K 308 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'K' and resid 414 through 415 Processing sheet with id=AD4, first strand: chain 'M' and resid 4 through 6 removed outlier: 6.173A pdb=" N VAL M 4 " --> pdb=" O GLU M 28 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'M' and resid 133 through 134 removed outlier: 8.006A pdb=" N CYS M 134 " --> pdb=" O TYR M 78 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N CYS M 80 " --> pdb=" O CYS M 134 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ILE M 61 " --> pdb=" O HIS M 79 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N VAL M 81 " --> pdb=" O ILE M 61 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ASP M 63 " --> pdb=" O VAL M 81 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N GLN M 151 " --> pdb=" O ILE M 64 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N TYR M 285 " --> pdb=" O SER M 281 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N SER M 281 " --> pdb=" O TYR M 285 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL M 287 " --> pdb=" O VAL M 279 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'M' and resid 246 through 251 removed outlier: 6.756A pdb=" N ALA M 189 " --> pdb=" O CYS M 331 " (cutoff:3.500A) removed outlier: 9.126A pdb=" N TYR M 333 " --> pdb=" O ALA M 189 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N ALA M 191 " --> pdb=" O TYR M 333 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'M' and resid 303 through 308 removed outlier: 4.030A pdb=" N THR M 437 " --> pdb=" O HIS M 308 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'M' and resid 414 through 415 Processing sheet with id=AD9, first strand: chain 'O' and resid 4 through 6 removed outlier: 6.197A pdb=" N VAL O 4 " --> pdb=" O GLU O 28 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'O' and resid 133 through 134 removed outlier: 7.928A pdb=" N CYS O 134 " --> pdb=" O TYR O 78 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N CYS O 80 " --> pdb=" O CYS O 134 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ILE O 61 " --> pdb=" O HIS O 79 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N VAL O 81 " --> pdb=" O ILE O 61 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ASP O 63 " --> pdb=" O VAL O 81 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N GLN O 151 " --> pdb=" O ILE O 64 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N TYR O 285 " --> pdb=" O SER O 281 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N SER O 281 " --> pdb=" O TYR O 285 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N VAL O 287 " --> pdb=" O VAL O 279 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'O' and resid 246 through 251 removed outlier: 6.776A pdb=" N ALA O 189 " --> pdb=" O CYS O 331 " (cutoff:3.500A) removed outlier: 9.166A pdb=" N TYR O 333 " --> pdb=" O ALA O 189 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N ALA O 191 " --> pdb=" O TYR O 333 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'O' and resid 303 through 308 removed outlier: 3.961A pdb=" N THR O 437 " --> pdb=" O HIS O 308 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'O' and resid 414 through 415 Processing sheet with id=AE5, first strand: chain 'Q' and resid 4 through 6 removed outlier: 6.216A pdb=" N VAL Q 4 " --> pdb=" O GLU Q 28 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'Q' and resid 133 through 134 removed outlier: 7.960A pdb=" N CYS Q 134 " --> pdb=" O TYR Q 78 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N CYS Q 80 " --> pdb=" O CYS Q 134 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ILE Q 61 " --> pdb=" O HIS Q 79 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N VAL Q 81 " --> pdb=" O ILE Q 61 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ASP Q 63 " --> pdb=" O VAL Q 81 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N GLN Q 151 " --> pdb=" O ILE Q 64 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N TYR Q 285 " --> pdb=" O SER Q 281 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N SER Q 281 " --> pdb=" O TYR Q 285 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N VAL Q 287 " --> pdb=" O VAL Q 279 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'Q' and resid 246 through 251 removed outlier: 6.772A pdb=" N ALA Q 189 " --> pdb=" O CYS Q 331 " (cutoff:3.500A) removed outlier: 9.156A pdb=" N TYR Q 333 " --> pdb=" O ALA Q 189 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N ALA Q 191 " --> pdb=" O TYR Q 333 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'Q' and resid 303 through 308 removed outlier: 3.966A pdb=" N THR Q 437 " --> pdb=" O HIS Q 308 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'Q' and resid 414 through 415 Processing sheet with id=AF1, first strand: chain 'S' and resid 4 through 6 removed outlier: 6.221A pdb=" N VAL S 4 " --> pdb=" O GLU S 28 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'S' and resid 133 through 134 removed outlier: 7.918A pdb=" N CYS S 134 " --> pdb=" O TYR S 78 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N CYS S 80 " --> pdb=" O CYS S 134 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ILE S 61 " --> pdb=" O HIS S 79 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N VAL S 81 " --> pdb=" O ILE S 61 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ASP S 63 " --> pdb=" O VAL S 81 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N GLN S 151 " --> pdb=" O ILE S 64 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N TYR S 285 " --> pdb=" O SER S 281 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N SER S 281 " --> pdb=" O TYR S 285 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N VAL S 287 " --> pdb=" O VAL S 279 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'S' and resid 246 through 251 removed outlier: 6.745A pdb=" N ALA S 189 " --> pdb=" O CYS S 331 " (cutoff:3.500A) removed outlier: 9.100A pdb=" N TYR S 333 " --> pdb=" O ALA S 189 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N ALA S 191 " --> pdb=" O TYR S 333 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'S' and resid 303 through 308 removed outlier: 3.971A pdb=" N THR S 437 " --> pdb=" O HIS S 308 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'S' and resid 414 through 415 Processing sheet with id=AF6, first strand: chain 'V' and resid 4 through 6 removed outlier: 6.174A pdb=" N VAL V 4 " --> pdb=" O GLU V 28 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF6 Processing sheet with id=AF7, first strand: chain 'V' and resid 133 through 134 removed outlier: 8.068A pdb=" N CYS V 134 " --> pdb=" O TYR V 78 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N CYS V 80 " --> pdb=" O CYS V 134 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ILE V 61 " --> pdb=" O HIS V 79 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N VAL V 81 " --> pdb=" O ILE V 61 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ASP V 63 " --> pdb=" O VAL V 81 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLN V 151 " --> pdb=" O ILE V 64 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N TYR V 285 " --> pdb=" O SER V 281 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N SER V 281 " --> pdb=" O TYR V 285 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N VAL V 287 " --> pdb=" O VAL V 279 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'V' and resid 246 through 251 removed outlier: 6.785A pdb=" N ALA V 189 " --> pdb=" O CYS V 331 " (cutoff:3.500A) removed outlier: 9.173A pdb=" N TYR V 333 " --> pdb=" O ALA V 189 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N ALA V 191 " --> pdb=" O TYR V 333 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'V' and resid 303 through 308 removed outlier: 3.948A pdb=" N THR V 437 " --> pdb=" O HIS V 308 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'V' and resid 414 through 415 Processing sheet with id=AG2, first strand: chain 'X' and resid 4 through 6 removed outlier: 6.177A pdb=" N VAL X 4 " --> pdb=" O GLU X 28 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG2 Processing sheet with id=AG3, first strand: chain 'X' and resid 133 through 134 removed outlier: 7.998A pdb=" N CYS X 134 " --> pdb=" O TYR X 78 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N CYS X 80 " --> pdb=" O CYS X 134 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ILE X 61 " --> pdb=" O HIS X 79 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N VAL X 81 " --> pdb=" O ILE X 61 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ASP X 63 " --> pdb=" O VAL X 81 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N GLN X 151 " --> pdb=" O ILE X 64 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N TYR X 285 " --> pdb=" O SER X 281 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N SER X 281 " --> pdb=" O TYR X 285 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N VAL X 287 " --> pdb=" O VAL X 279 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'X' and resid 246 through 251 removed outlier: 6.781A pdb=" N ALA X 189 " --> pdb=" O CYS X 331 " (cutoff:3.500A) removed outlier: 9.170A pdb=" N TYR X 333 " --> pdb=" O ALA X 189 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N ALA X 191 " --> pdb=" O TYR X 333 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'X' and resid 303 through 308 removed outlier: 3.981A pdb=" N THR X 437 " --> pdb=" O HIS X 308 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'X' and resid 414 through 415 1892 hydrogen bonds defined for protein. 5328 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: 11.00 Time building geometry restraints manager: 4.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.67 - 0.93: 1 0.93 - 1.18: 3 1.18 - 1.44: 18528 1.44 - 1.69: 25147 1.69 - 1.95: 565 Bond restraints: 44244 Sorted by residual: bond pdb=" CG PRO C 463 " pdb=" CD PRO C 463 " ideal model delta sigma weight residual 1.503 0.672 0.831 3.40e-02 8.65e+02 5.98e+02 bond pdb=" CG PRO S 463 " pdb=" CD PRO S 463 " ideal model delta sigma weight residual 1.503 1.102 0.401 3.40e-02 8.65e+02 1.39e+02 bond pdb=" C1' MGP G 604 " pdb=" C2' MGP G 604 " ideal model delta sigma weight residual 1.532 1.305 0.227 2.00e-02 2.50e+03 1.29e+02 bond pdb=" C1' MGP K 604 " pdb=" C2' MGP K 604 " ideal model delta sigma weight residual 1.532 1.305 0.227 2.00e-02 2.50e+03 1.29e+02 bond pdb=" C1' MGP M 604 " pdb=" C2' MGP M 604 " ideal model delta sigma weight residual 1.532 1.305 0.227 2.00e-02 2.50e+03 1.29e+02 ... (remaining 44239 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.03: 60041 10.03 - 20.05: 38 20.05 - 30.08: 3 30.08 - 40.10: 1 40.10 - 50.13: 1 Bond angle restraints: 60084 Sorted by residual: angle pdb=" N PRO C 463 " pdb=" CD PRO C 463 " pdb=" CG PRO C 463 " ideal model delta sigma weight residual 103.20 53.07 50.13 1.50e+00 4.44e-01 1.12e+03 angle pdb=" CA PRO C 463 " pdb=" CB PRO C 463 " pdb=" CG PRO C 463 " ideal model delta sigma weight residual 104.50 68.72 35.78 1.90e+00 2.77e-01 3.55e+02 angle pdb=" N PRO S 463 " pdb=" CD PRO S 463 " pdb=" CG PRO S 463 " ideal model delta sigma weight residual 103.20 80.65 22.55 1.50e+00 4.44e-01 2.26e+02 angle pdb=" N PRO G 463 " pdb=" CD PRO G 463 " pdb=" CG PRO G 463 " ideal model delta sigma weight residual 103.20 80.87 22.33 1.50e+00 4.44e-01 2.22e+02 angle pdb=" N PRO A 463 " pdb=" CD PRO A 463 " pdb=" CG PRO A 463 " ideal model delta sigma weight residual 103.20 81.60 21.60 1.50e+00 4.44e-01 2.07e+02 ... (remaining 60079 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.77: 24182 21.77 - 43.55: 2373 43.55 - 65.32: 517 65.32 - 87.09: 46 87.09 - 108.87: 2 Dihedral angle restraints: 27120 sinusoidal: 11052 harmonic: 16068 Sorted by residual: dihedral pdb=" CA PRO C 463 " pdb=" CB PRO C 463 " pdb=" CG PRO C 463 " pdb=" CD PRO C 463 " ideal model delta sinusoidal sigma weight residual -38.00 -146.87 108.87 1 2.00e+01 2.50e-03 3.18e+01 dihedral pdb=" CA ALA S 191 " pdb=" C ALA S 191 " pdb=" N TYR S 192 " pdb=" CA TYR S 192 " ideal model delta harmonic sigma weight residual 180.00 155.46 24.54 0 5.00e+00 4.00e-02 2.41e+01 dihedral pdb=" CA ALA G 191 " pdb=" C ALA G 191 " pdb=" N TYR G 192 " pdb=" CA TYR G 192 " ideal model delta harmonic sigma weight residual 180.00 156.57 23.43 0 5.00e+00 4.00e-02 2.20e+01 ... (remaining 27117 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 6134 0.083 - 0.166: 640 0.166 - 0.249: 6 0.249 - 0.332: 0 0.332 - 0.415: 12 Chirality restraints: 6792 Sorted by residual: chirality pdb=" C2' MGP G 604 " pdb=" C1' MGP G 604 " pdb=" C3' MGP G 604 " pdb=" O2' MGP G 604 " both_signs ideal model delta sigma weight residual False -2.75 -2.34 -0.41 2.00e-01 2.50e+01 4.30e+00 chirality pdb=" C2' MGP M 604 " pdb=" C1' MGP M 604 " pdb=" C3' MGP M 604 " pdb=" O2' MGP M 604 " both_signs ideal model delta sigma weight residual False -2.75 -2.34 -0.41 2.00e-01 2.50e+01 4.29e+00 chirality pdb=" C2' MGP A1003 " pdb=" C1' MGP A1003 " pdb=" C3' MGP A1003 " pdb=" O2' MGP A1003 " both_signs ideal model delta sigma weight residual False -2.75 -2.34 -0.41 2.00e-01 2.50e+01 4.28e+00 ... (remaining 6789 not shown) Planarity restraints: 7536 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE M 462 " 0.104 5.00e-02 4.00e+02 1.43e-01 3.27e+01 pdb=" N PRO M 463 " -0.246 5.00e-02 4.00e+02 pdb=" CA PRO M 463 " 0.069 5.00e-02 4.00e+02 pdb=" CD PRO M 463 " 0.074 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 462 " 0.104 5.00e-02 4.00e+02 1.43e-01 3.25e+01 pdb=" N PRO A 463 " -0.246 5.00e-02 4.00e+02 pdb=" CA PRO A 463 " 0.068 5.00e-02 4.00e+02 pdb=" CD PRO A 463 " 0.074 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE S 462 " 0.103 5.00e-02 4.00e+02 1.42e-01 3.21e+01 pdb=" N PRO S 463 " -0.244 5.00e-02 4.00e+02 pdb=" CA PRO S 463 " 0.069 5.00e-02 4.00e+02 pdb=" CD PRO S 463 " 0.073 5.00e-02 4.00e+02 ... (remaining 7533 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.48: 332 2.48 - 3.08: 28569 3.08 - 3.69: 68560 3.69 - 4.29: 107510 4.29 - 4.90: 175128 Nonbonded interactions: 380099 Sorted by model distance: nonbonded pdb=" OE2 GLU M 129 " pdb="ZN ZN M 602 " model vdw 1.869 2.230 nonbonded pdb=" OE2 GLU E 129 " pdb="ZN ZN E 602 " model vdw 1.877 2.230 nonbonded pdb=" OE2 GLU G 129 " pdb="ZN ZN G 602 " model vdw 1.883 2.230 nonbonded pdb=" OE2 GLU X 129 " pdb="ZN ZN X 602 " model vdw 1.889 2.230 nonbonded pdb=" OE2 GLU O 129 " pdb="ZN ZN O 602 " model vdw 1.889 2.230 ... (remaining 380094 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 3 through 270 or resid 272 through 314 or resid 317 throug \ h 378 or resid 380 through 469 or resid 1005)) selection = (chain 'C' and (resid 3 through 270 or resid 272 through 314 or resid 317 throug \ h 378 or resid 380 through 469 or resid 605)) selection = (chain 'E' and (resid 3 through 270 or resid 272 through 314 or resid 317 throug \ h 378 or resid 380 through 469 or resid 605)) selection = (chain 'G' and (resid 3 through 270 or resid 272 through 314 or resid 317 throug \ h 378 or resid 380 through 469 or resid 605)) selection = (chain 'I' and (resid 3 through 270 or resid 272 through 314 or resid 317 throug \ h 378 or resid 380 through 469 or resid 605)) selection = (chain 'K' and (resid 3 through 270 or resid 272 through 314 or resid 317 throug \ h 378 or resid 380 through 469 or resid 605)) selection = (chain 'M' and (resid 3 through 270 or resid 272 through 314 or resid 317 throug \ h 378 or resid 380 through 469 or resid 605)) selection = (chain 'O' and (resid 3 through 270 or resid 272 through 314 or resid 317 throug \ h 378 or resid 380 through 469 or resid 605)) selection = (chain 'Q' and (resid 3 through 270 or resid 272 through 314 or resid 317 throug \ h 378 or resid 380 through 469 or resid 605)) selection = (chain 'S' and (resid 3 through 270 or resid 272 through 314 or resid 317 throug \ h 378 or resid 380 through 469 or resid 605)) selection = (chain 'V' and (resid 3 through 270 or resid 272 through 314 or resid 317 throug \ h 378 or resid 380 through 469 or resid 605)) selection = (chain 'X' and (resid 3 through 270 or resid 272 through 314 or resid 317 throug \ h 378 or resid 380 through 469 or resid 605)) } 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=0.00 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.430 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: 0.050 Extract box with map and model: 0.820 Check model and map are aligned: 0.140 Set scattering table: 0.110 Process input model: 53.810 Find NCS groups from input model: 1.320 Set up NCS constraints: 0.140 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:6.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 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 : 0.012 0.831 44280 Z= 0.521 Angle : 0.978 50.129 60084 Z= 0.471 Chirality : 0.051 0.415 6792 Planarity : 0.007 0.143 7536 Dihedral : 17.191 108.865 16728 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.60 % Allowed : 21.70 % Favored : 76.71 % Cbeta Deviations : 0.02 % 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: -0.28 (0.10), residues: 5412 helix: 1.24 (0.13), residues: 1668 sheet: 0.44 (0.15), residues: 864 loop : -1.29 (0.10), residues: 2880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG X 399 TYR 0.024 0.002 TYR Q 248 PHE 0.021 0.002 PHE Q 264 TRP 0.028 0.002 TRP S 421 HIS 0.005 0.001 HIS E 164 Details of bonding type rmsd/Z covalent geometry : bond 0.01164 / 0.52 (44244) covalent geometry : angle 0.97809 / 0.47 (60084) hydrogen bonds : bond 0.13497 / 9.06 ( 1892) hydrogen bonds : angle 5.78514 / 4.06 ( 5328) metal coordination : bond 0.00641 / 0.39 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10824 Ramachandran restraints generated. 5412 Oldfield, 0 Emsley, 5412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10824 Ramachandran restraints generated. 5412 Oldfield, 0 Emsley, 5412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 707 residues out of total 4620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 635 time to evaluate : 1.653 Fit side-chains REVERT: A 60 THR cc_start: 0.8345 (t) cc_final: 0.8096 (m) REVERT: C 56 ASP cc_start: 0.7018 (t70) cc_final: 0.6646 (t0) REVERT: C 348 THR cc_start: 0.7971 (p) cc_final: 0.7760 (t) REVERT: E 60 THR cc_start: 0.8266 (t) cc_final: 0.8039 (m) REVERT: E 348 THR cc_start: 0.7851 (p) cc_final: 0.7625 (t) REVERT: E 404 ASP cc_start: 0.7851 (t70) cc_final: 0.7121 (t0) REVERT: G 11 ASP cc_start: 0.7249 (m-30) cc_final: 0.7035 (m-30) REVERT: G 56 ASP cc_start: 0.7162 (t0) cc_final: 0.6947 (t70) REVERT: G 60 THR cc_start: 0.8135 (t) cc_final: 0.7850 (m) REVERT: G 75 ASP cc_start: 0.7551 (p0) cc_final: 0.7006 (p0) REVERT: G 132 THR cc_start: 0.8638 (p) cc_final: 0.8416 (t) REVERT: I 232 LYS cc_start: 0.7514 (pmtt) cc_final: 0.6636 (ptmm) REVERT: I 378 THR cc_start: 0.8035 (m) cc_final: 0.7829 (m) REVERT: K 73 MET cc_start: 0.8024 (mmm) cc_final: 0.7820 (mmm) REVERT: K 75 ASP cc_start: 0.7419 (OUTLIER) cc_final: 0.6933 (p0) REVERT: K 232 LYS cc_start: 0.7393 (pmtt) cc_final: 0.6688 (ptmm) REVERT: K 427 LYS cc_start: 0.7300 (ptpt) cc_final: 0.6413 (pptt) REVERT: M 73 MET cc_start: 0.8103 (mmm) cc_final: 0.7797 (mmm) REVERT: M 378 THR cc_start: 0.8077 (m) cc_final: 0.7869 (m) REVERT: M 427 LYS cc_start: 0.7459 (ptpt) cc_final: 0.6596 (pptt) REVERT: O 73 MET cc_start: 0.8008 (mmm) cc_final: 0.7773 (mmm) REVERT: O 75 ASP cc_start: 0.7463 (OUTLIER) cc_final: 0.7123 (p0) REVERT: O 232 LYS cc_start: 0.7691 (pmtt) cc_final: 0.7074 (mmtm) REVERT: O 378 THR cc_start: 0.7645 (m) cc_final: 0.7407 (m) REVERT: Q 5 TYR cc_start: 0.7650 (m-80) cc_final: 0.7416 (m-80) REVERT: Q 73 MET cc_start: 0.7946 (mmm) cc_final: 0.7610 (tpp) REVERT: S 232 LYS cc_start: 0.7846 (pttm) cc_final: 0.7319 (mmtm) REVERT: S 299 LYS cc_start: 0.7860 (tttm) cc_final: 0.7635 (tttm) REVERT: V 322 ASP cc_start: 0.7619 (t0) cc_final: 0.7354 (t0) REVERT: V 400 LYS cc_start: 0.6867 (mtmt) cc_final: 0.6605 (mptm) REVERT: V 469 LYS cc_start: 0.6056 (mttp) cc_final: 0.5705 (mttt) REVERT: X 299 LYS cc_start: 0.8157 (tttm) cc_final: 0.7880 (tttm) outliers start: 72 outliers final: 32 residues processed: 693 average time/residue: 0.6320 time to fit residues: 555.3357 Evaluate side-chains 515 residues out of total 4620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 481 time to evaluate : 1.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain E residue 120 GLN Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain G residue 317 THR Chi-restraints excluded: chain G residue 376 THR Chi-restraints excluded: chain G residue 400 LYS Chi-restraints excluded: chain G residue 451 VAL Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain I residue 317 THR Chi-restraints excluded: chain I residue 451 VAL Chi-restraints excluded: chain K residue 75 ASP Chi-restraints excluded: chain K residue 317 THR Chi-restraints excluded: chain K residue 376 THR Chi-restraints excluded: chain K residue 451 VAL Chi-restraints excluded: chain M residue 109 ASP Chi-restraints excluded: chain M residue 317 THR Chi-restraints excluded: chain M residue 451 VAL Chi-restraints excluded: chain O residue 75 ASP Chi-restraints excluded: chain O residue 285 TYR Chi-restraints excluded: chain O residue 317 THR Chi-restraints excluded: chain O residue 451 VAL Chi-restraints excluded: chain Q residue 285 TYR Chi-restraints excluded: chain Q residue 317 THR Chi-restraints excluded: chain Q residue 451 VAL Chi-restraints excluded: chain S residue 214 SER Chi-restraints excluded: chain S residue 317 THR Chi-restraints excluded: chain V residue 214 SER Chi-restraints excluded: chain V residue 317 THR Chi-restraints excluded: chain X residue 317 THR Chi-restraints excluded: chain X residue 451 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 394 optimal weight: 5.9990 chunk 430 optimal weight: 0.9980 chunk 41 optimal weight: 10.0000 chunk 265 optimal weight: 0.3980 chunk 523 optimal weight: 0.7980 chunk 497 optimal weight: 2.9990 chunk 414 optimal weight: 0.8980 chunk 310 optimal weight: 0.0980 chunk 488 optimal weight: 5.9990 chunk 366 optimal weight: 2.9990 chunk 223 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 165 GLN A 307 HIS A 389 GLN C 165 GLN C 307 HIS C 389 GLN G 165 GLN G 307 HIS G 389 GLN I 307 HIS I 389 GLN K 389 GLN M 389 GLN Q 209 ASN ** S 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 165 GLN V 143 GLN V 209 ASN X 143 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.139600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.104120 restraints weight = 177512.285| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 3.53 r_work: 0.2806 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2792 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2792 r_free = 0.2792 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 48 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2791 r_free = 0.2791 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 9 (15 function evaluations) r_final: 0.2791 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 44280 Z= 0.119 Angle : 0.568 16.533 60084 Z= 0.289 Chirality : 0.044 0.191 6792 Planarity : 0.005 0.080 7536 Dihedral : 6.304 49.099 6525 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 1.62 % Allowed : 20.67 % Favored : 77.71 % 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: 0.29 (0.11), residues: 5412 helix: 2.17 (0.13), residues: 1692 sheet: 0.53 (0.16), residues: 888 loop : -1.22 (0.10), residues: 2832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG V 76 TYR 0.016 0.001 TYR Q 297 PHE 0.017 0.001 PHE Q 264 TRP 0.017 0.001 TRP S 421 HIS 0.005 0.001 HIS S 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (44244) covalent geometry : angle 0.56777 / 0.29 (60084) hydrogen bonds : bond 0.03107 / 2.10 ( 1892) hydrogen bonds : angle 4.25342 / 2.98 ( 5328) metal coordination : bond 0.00182 / 0.11 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10824 Ramachandran restraints generated. 5412 Oldfield, 0 Emsley, 5412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10824 Ramachandran restraints generated. 5412 Oldfield, 0 Emsley, 5412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 616 residues out of total 4620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 542 time to evaluate : 1.657 Fit side-chains revert: symmetry clash REVERT: A 292 MET cc_start: 0.8618 (OUTLIER) cc_final: 0.7663 (mpp) REVERT: A 389 GLN cc_start: 0.7733 (tt0) cc_final: 0.7279 (tp-100) REVERT: A 399 ARG cc_start: 0.7897 (mtp180) cc_final: 0.7681 (mtp180) REVERT: A 400 LYS cc_start: 0.7404 (mptt) cc_final: 0.6688 (mtmp) REVERT: C 56 ASP cc_start: 0.7122 (t70) cc_final: 0.6834 (t0) REVERT: C 75 ASP cc_start: 0.7377 (p0) cc_final: 0.6807 (p0) REVERT: C 463 PRO cc_start: 0.6288 (OUTLIER) cc_final: 0.5780 (Cg_exo) REVERT: E 36 ASP cc_start: 0.7531 (p0) cc_final: 0.7303 (p0) REVERT: E 56 ASP cc_start: 0.7569 (t0) cc_final: 0.7245 (t0) REVERT: E 400 LYS cc_start: 0.7733 (OUTLIER) cc_final: 0.7012 (mtpt) REVERT: E 404 ASP cc_start: 0.8008 (t70) cc_final: 0.7245 (t0) REVERT: G 75 ASP cc_start: 0.7508 (p0) cc_final: 0.7138 (p0) REVERT: G 132 THR cc_start: 0.8529 (p) cc_final: 0.8290 (t) REVERT: G 399 ARG cc_start: 0.8176 (mmm-85) cc_final: 0.7905 (mmt90) REVERT: I 123 MET cc_start: 0.7009 (mmp) cc_final: 0.6808 (mmp) REVERT: I 289 ARG cc_start: 0.8383 (tmt90) cc_final: 0.8135 (ttt-90) REVERT: K 73 MET cc_start: 0.8250 (mmm) cc_final: 0.8002 (mmm) REVERT: K 353 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7523 (tt0) REVERT: K 427 LYS cc_start: 0.7400 (ptpt) cc_final: 0.6530 (pptt) REVERT: M 73 MET cc_start: 0.8287 (mmm) cc_final: 0.8012 (mmm) REVERT: M 127 ASP cc_start: 0.7715 (t0) cc_final: 0.7141 (t0) REVERT: O 60 THR cc_start: 0.7872 (OUTLIER) cc_final: 0.7650 (m) REVERT: O 120 GLN cc_start: 0.7789 (OUTLIER) cc_final: 0.7477 (mt0) REVERT: O 127 ASP cc_start: 0.7725 (t0) cc_final: 0.7072 (t0) REVERT: O 232 LYS cc_start: 0.7567 (OUTLIER) cc_final: 0.6838 (mmtm) REVERT: O 378 THR cc_start: 0.7943 (m) cc_final: 0.7723 (m) REVERT: Q 60 THR cc_start: 0.8049 (OUTLIER) cc_final: 0.7766 (m) REVERT: Q 109 ASP cc_start: 0.6384 (p0) cc_final: 0.6092 (p0) REVERT: Q 127 ASP cc_start: 0.7682 (t0) cc_final: 0.7197 (t0) REVERT: Q 353 GLU cc_start: 0.7798 (mp0) cc_final: 0.7563 (tt0) REVERT: S 120 GLN cc_start: 0.7417 (OUTLIER) cc_final: 0.6928 (mt0) REVERT: S 299 LYS cc_start: 0.8305 (tttm) cc_final: 0.8031 (ptmm) REVERT: V 120 GLN cc_start: 0.7195 (OUTLIER) cc_final: 0.6636 (mt0) REVERT: V 322 ASP cc_start: 0.7786 (t0) cc_final: 0.7548 (t0) REVERT: V 400 LYS cc_start: 0.7120 (mtmt) cc_final: 0.6779 (ttmm) REVERT: V 469 LYS cc_start: 0.5595 (mttp) cc_final: 0.5365 (mttt) REVERT: X 400 LYS cc_start: 0.6876 (mptm) cc_final: 0.5945 (mtpt) outliers start: 74 outliers final: 21 residues processed: 591 average time/residue: 0.6644 time to fit residues: 499.4731 Evaluate side-chains 509 residues out of total 4620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 478 time to evaluate : 1.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain C residue 463 PRO Chi-restraints excluded: chain E residue 400 LYS Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 451 VAL Chi-restraints excluded: chain K residue 353 GLU Chi-restraints excluded: chain K residue 451 VAL Chi-restraints excluded: chain M residue 109 ASP Chi-restraints excluded: chain O residue 60 THR Chi-restraints excluded: chain O residue 120 GLN Chi-restraints excluded: chain O residue 232 LYS Chi-restraints excluded: chain O residue 420 LEU Chi-restraints excluded: chain Q residue 60 THR Chi-restraints excluded: chain Q residue 420 LEU Chi-restraints excluded: chain Q residue 451 VAL Chi-restraints excluded: chain S residue 120 GLN Chi-restraints excluded: chain V residue 86 SER Chi-restraints excluded: chain V residue 120 GLN Chi-restraints excluded: chain V residue 285 TYR Chi-restraints excluded: chain V residue 451 VAL Chi-restraints excluded: chain X residue 132 THR Chi-restraints excluded: chain X residue 214 SER Chi-restraints excluded: chain X residue 285 TYR Chi-restraints excluded: chain X residue 317 THR Chi-restraints excluded: chain X residue 451 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 81 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 404 optimal weight: 0.5980 chunk 467 optimal weight: 8.9990 chunk 401 optimal weight: 10.0000 chunk 355 optimal weight: 2.9990 chunk 449 optimal weight: 0.5980 chunk 195 optimal weight: 5.9990 chunk 468 optimal weight: 4.9990 chunk 420 optimal weight: 5.9990 chunk 407 optimal weight: 0.0370 overall best weight: 1.6462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 389 GLN C 429 HIS E 389 GLN G 389 GLN I 389 GLN K 381 ASN K 389 GLN M 389 GLN V 165 GLN X 35 ASN X 389 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.135840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.100133 restraints weight = 167229.523| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 3.30 r_work: 0.2742 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2728 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2728 r_free = 0.2728 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2728 r_free = 0.2728 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.2728 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8926 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 44280 Z= 0.162 Angle : 0.598 15.257 60084 Z= 0.305 Chirality : 0.046 0.246 6792 Planarity : 0.005 0.058 7536 Dihedral : 6.408 52.131 6490 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.85 % Allowed : 20.76 % Favored : 77.39 % 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: 0.21 (0.11), residues: 5412 helix: 2.00 (0.13), residues: 1764 sheet: 0.68 (0.16), residues: 852 loop : -1.34 (0.10), residues: 2796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG V 76 TYR 0.017 0.002 TYR C 382 PHE 0.017 0.002 PHE O 183 TRP 0.023 0.002 TRP S 421 HIS 0.007 0.001 HIS C 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 (44244) covalent geometry : angle 0.59789 / 0.30 (60084) hydrogen bonds : bond 0.04103 / 2.76 ( 1892) hydrogen bonds : angle 4.20021 / 2.95 ( 5328) metal coordination : bond 0.00676 / 0.43 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10824 Ramachandran restraints generated. 5412 Oldfield, 0 Emsley, 5412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10824 Ramachandran restraints generated. 5412 Oldfield, 0 Emsley, 5412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 4620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 530 time to evaluate : 1.774 Fit side-chains revert: symmetry clash REVERT: A 127 ASP cc_start: 0.7729 (t0) cc_final: 0.7522 (t0) REVERT: A 400 LYS cc_start: 0.7731 (mptt) cc_final: 0.6950 (mtmp) REVERT: A 404 ASP cc_start: 0.7308 (t0) cc_final: 0.6977 (t0) REVERT: C 30 ARG cc_start: 0.8070 (OUTLIER) cc_final: 0.7667 (ttm-80) REVERT: C 75 ASP cc_start: 0.7722 (p0) cc_final: 0.7224 (p0) REVERT: C 106 LYS cc_start: 0.7122 (mtpp) cc_final: 0.6670 (mttp) REVERT: C 400 LYS cc_start: 0.7765 (mmpt) cc_final: 0.7491 (mmpt) REVERT: C 404 ASP cc_start: 0.7379 (t0) cc_final: 0.7054 (t0) REVERT: C 406 LYS cc_start: 0.8035 (mmmt) cc_final: 0.7706 (mmmt) REVERT: C 463 PRO cc_start: 0.6576 (OUTLIER) cc_final: 0.6330 (Cg_exo) REVERT: E 127 ASP cc_start: 0.7744 (m-30) cc_final: 0.7182 (t0) REVERT: E 299 LYS cc_start: 0.8473 (OUTLIER) cc_final: 0.8008 (pttt) REVERT: E 314 MET cc_start: 0.9152 (ttt) cc_final: 0.8809 (ttp) REVERT: E 400 LYS cc_start: 0.7892 (mppt) cc_final: 0.7160 (mttt) REVERT: E 404 ASP cc_start: 0.8220 (t70) cc_final: 0.7416 (t0) REVERT: G 75 ASP cc_start: 0.7610 (p0) cc_final: 0.7237 (p0) REVERT: G 127 ASP cc_start: 0.7774 (m-30) cc_final: 0.7265 (t0) REVERT: G 232 LYS cc_start: 0.7217 (ptmm) cc_final: 0.6864 (pttm) REVERT: G 389 GLN cc_start: 0.8275 (OUTLIER) cc_final: 0.8055 (tt0) REVERT: G 399 ARG cc_start: 0.8257 (mmm-85) cc_final: 0.7776 (mmt90) REVERT: G 400 LYS cc_start: 0.7998 (mptm) cc_final: 0.7429 (mtpt) REVERT: I 127 ASP cc_start: 0.7819 (m-30) cc_final: 0.7444 (t0) REVERT: K 73 MET cc_start: 0.8352 (mmm) cc_final: 0.8114 (mmm) REVERT: K 427 LYS cc_start: 0.7893 (ptpt) cc_final: 0.6873 (pptt) REVERT: M 127 ASP cc_start: 0.7970 (t0) cc_final: 0.7414 (t0) REVERT: O 26 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7754 (mm-30) REVERT: O 106 LYS cc_start: 0.7356 (mtpp) cc_final: 0.7084 (mttp) REVERT: O 127 ASP cc_start: 0.7767 (t0) cc_final: 0.7226 (t0) REVERT: Q 85 ARG cc_start: 0.8254 (OUTLIER) cc_final: 0.7137 (mtm180) REVERT: Q 106 LYS cc_start: 0.7490 (ptpt) cc_final: 0.7280 (ptpt) REVERT: Q 127 ASP cc_start: 0.7804 (t0) cc_final: 0.7281 (t0) REVERT: Q 299 LYS cc_start: 0.8129 (OUTLIER) cc_final: 0.7908 (mtmm) REVERT: Q 393 LYS cc_start: 0.8447 (OUTLIER) cc_final: 0.8175 (mptm) REVERT: Q 467 ARG cc_start: 0.7209 (OUTLIER) cc_final: 0.6993 (ttt180) REVERT: S 120 GLN cc_start: 0.7508 (OUTLIER) cc_final: 0.7052 (mt0) REVERT: S 400 LYS cc_start: 0.7877 (OUTLIER) cc_final: 0.7196 (mtpt) REVERT: V 120 GLN cc_start: 0.7348 (OUTLIER) cc_final: 0.6977 (mt0) REVERT: V 127 ASP cc_start: 0.7837 (t0) cc_final: 0.7310 (t0) REVERT: V 289 ARG cc_start: 0.8619 (ttt-90) cc_final: 0.8202 (ttm110) REVERT: X 127 ASP cc_start: 0.7524 (t0) cc_final: 0.7235 (t0) REVERT: X 400 LYS cc_start: 0.7648 (mptm) cc_final: 0.6910 (mtpt) REVERT: X 404 ASP cc_start: 0.7714 (t0) cc_final: 0.7009 (t0) outliers start: 85 outliers final: 25 residues processed: 594 average time/residue: 0.6716 time to fit residues: 503.9050 Evaluate side-chains 534 residues out of total 4620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 497 time to evaluate : 1.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain C residue 30 ARG Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 463 PRO Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 299 LYS Chi-restraints excluded: chain G residue 60 THR Chi-restraints excluded: chain G residue 86 SER Chi-restraints excluded: chain G residue 277 ASP Chi-restraints excluded: chain G residue 389 GLN Chi-restraints excluded: chain G residue 451 VAL Chi-restraints excluded: chain I residue 60 THR Chi-restraints excluded: chain I residue 420 LEU Chi-restraints excluded: chain K residue 299 LYS Chi-restraints excluded: chain K residue 451 VAL Chi-restraints excluded: chain M residue 109 ASP Chi-restraints excluded: chain M residue 410 VAL Chi-restraints excluded: chain O residue 26 GLU Chi-restraints excluded: chain O residue 410 VAL Chi-restraints excluded: chain Q residue 85 ARG Chi-restraints excluded: chain Q residue 214 SER Chi-restraints excluded: chain Q residue 299 LYS Chi-restraints excluded: chain Q residue 393 LYS Chi-restraints excluded: chain Q residue 410 VAL Chi-restraints excluded: chain Q residue 451 VAL Chi-restraints excluded: chain Q residue 467 ARG Chi-restraints excluded: chain S residue 120 GLN Chi-restraints excluded: chain S residue 400 LYS Chi-restraints excluded: chain V residue 120 GLN Chi-restraints excluded: chain V residue 132 THR Chi-restraints excluded: chain V residue 299 LYS Chi-restraints excluded: chain V residue 420 LEU Chi-restraints excluded: chain V residue 451 VAL Chi-restraints excluded: chain X residue 132 THR Chi-restraints excluded: chain X residue 451 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 275 optimal weight: 0.8980 chunk 7 optimal weight: 4.9990 chunk 176 optimal weight: 6.9990 chunk 253 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 373 optimal weight: 0.8980 chunk 539 optimal weight: 8.9990 chunk 353 optimal weight: 3.9990 chunk 312 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 265 optimal weight: 1.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 381 ASN C 389 GLN E 165 GLN E 389 GLN I 389 GLN K 307 HIS K 389 GLN O 307 HIS O 389 GLN Q 389 GLN X 389 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.135629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.093909 restraints weight = 188895.183| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 3.40 r_work: 0.2749 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2737 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2737 r_free = 0.2737 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2737 r_free = 0.2737 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2737 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8921 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 44280 Z= 0.142 Angle : 0.554 15.689 60084 Z= 0.283 Chirality : 0.044 0.163 6792 Planarity : 0.005 0.054 7536 Dihedral : 6.110 41.054 6487 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.62 % Allowed : 20.72 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.11), residues: 5412 helix: 2.42 (0.13), residues: 1680 sheet: 0.28 (0.15), residues: 972 loop : -1.23 (0.10), residues: 2760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG V 76 TYR 0.014 0.001 TYR Q 297 PHE 0.017 0.002 PHE O 183 TRP 0.013 0.001 TRP S 421 HIS 0.005 0.001 HIS Q 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 (44244) covalent geometry : angle 0.55444 / 0.28 (60084) hydrogen bonds : bond 0.03509 / 2.36 ( 1892) hydrogen bonds : angle 4.08249 / 2.87 ( 5328) metal coordination : bond 0.00402 / 0.26 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10824 Ramachandran restraints generated. 5412 Oldfield, 0 Emsley, 5412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10824 Ramachandran restraints generated. 5412 Oldfield, 0 Emsley, 5412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 579 residues out of total 4620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 505 time to evaluate : 1.801 Fit side-chains revert: symmetry clash REVERT: A 292 MET cc_start: 0.8847 (OUTLIER) cc_final: 0.8595 (mpp) REVERT: A 354 ASP cc_start: 0.8455 (m-30) cc_final: 0.8216 (m-30) REVERT: A 400 LYS cc_start: 0.7744 (mptt) cc_final: 0.6946 (mtmp) REVERT: A 404 ASP cc_start: 0.7308 (t0) cc_final: 0.6943 (t0) REVERT: C 75 ASP cc_start: 0.7698 (p0) cc_final: 0.7276 (p0) REVERT: C 106 LYS cc_start: 0.7266 (mtpp) cc_final: 0.6865 (mttp) REVERT: C 292 MET cc_start: 0.8996 (mtm) cc_final: 0.8757 (mpp) REVERT: C 399 ARG cc_start: 0.7914 (mtp180) cc_final: 0.7680 (mmt90) REVERT: C 400 LYS cc_start: 0.7743 (mmpt) cc_final: 0.7522 (mmpt) REVERT: C 404 ASP cc_start: 0.7408 (t0) cc_final: 0.7000 (t0) REVERT: C 406 LYS cc_start: 0.7989 (mmmt) cc_final: 0.7752 (mmmt) REVERT: C 463 PRO cc_start: 0.6596 (OUTLIER) cc_final: 0.6366 (Cg_exo) REVERT: E 127 ASP cc_start: 0.7782 (m-30) cc_final: 0.7310 (t0) REVERT: E 314 MET cc_start: 0.9142 (ttt) cc_final: 0.8785 (ttp) REVERT: E 400 LYS cc_start: 0.7796 (OUTLIER) cc_final: 0.7126 (mtpt) REVERT: E 404 ASP cc_start: 0.8149 (t70) cc_final: 0.7356 (t0) REVERT: G 75 ASP cc_start: 0.7532 (p0) cc_final: 0.7267 (p0) REVERT: G 98 ARG cc_start: 0.7357 (ttp-110) cc_final: 0.6757 (mtp180) REVERT: G 127 ASP cc_start: 0.7740 (m-30) cc_final: 0.7203 (t0) REVERT: G 399 ARG cc_start: 0.8231 (mmm-85) cc_final: 0.7770 (mmt90) REVERT: G 400 LYS cc_start: 0.7971 (mptm) cc_final: 0.7386 (mtpt) REVERT: I 127 ASP cc_start: 0.7816 (m-30) cc_final: 0.7549 (t0) REVERT: K 73 MET cc_start: 0.8286 (mmm) cc_final: 0.8059 (mmm) REVERT: K 127 ASP cc_start: 0.7789 (t0) cc_final: 0.7296 (t0) REVERT: K 353 GLU cc_start: 0.8020 (tt0) cc_final: 0.7570 (mp0) REVERT: K 427 LYS cc_start: 0.7910 (ptpt) cc_final: 0.6902 (pptt) REVERT: M 36 ASP cc_start: 0.8318 (p0) cc_final: 0.8014 (p0) REVERT: M 127 ASP cc_start: 0.7921 (t0) cc_final: 0.7446 (t0) REVERT: O 26 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7713 (mm-30) REVERT: O 73 MET cc_start: 0.8522 (mmm) cc_final: 0.8226 (mmm) REVERT: O 106 LYS cc_start: 0.7460 (mtpp) cc_final: 0.7160 (mttp) REVERT: O 120 GLN cc_start: 0.7823 (OUTLIER) cc_final: 0.7592 (mt0) REVERT: O 127 ASP cc_start: 0.7868 (t0) cc_final: 0.7389 (t0) REVERT: Q 85 ARG cc_start: 0.8270 (OUTLIER) cc_final: 0.7110 (mtm180) REVERT: Q 127 ASP cc_start: 0.7872 (t0) cc_final: 0.7385 (t0) REVERT: Q 299 LYS cc_start: 0.8142 (OUTLIER) cc_final: 0.7916 (mtmm) REVERT: Q 353 GLU cc_start: 0.8098 (tt0) cc_final: 0.7628 (mp0) REVERT: Q 393 LYS cc_start: 0.8452 (OUTLIER) cc_final: 0.8143 (mptm) REVERT: Q 400 LYS cc_start: 0.7849 (mptp) cc_final: 0.7262 (mtmt) REVERT: S 120 GLN cc_start: 0.7397 (OUTLIER) cc_final: 0.7027 (mt0) REVERT: V 73 MET cc_start: 0.8519 (mmm) cc_final: 0.8233 (mmm) REVERT: V 120 GLN cc_start: 0.7282 (OUTLIER) cc_final: 0.6991 (mt0) REVERT: V 127 ASP cc_start: 0.7948 (t0) cc_final: 0.7383 (t0) REVERT: V 399 ARG cc_start: 0.8005 (mtp180) cc_final: 0.7566 (mmt90) REVERT: X 127 ASP cc_start: 0.7798 (t0) cc_final: 0.7499 (t0) REVERT: X 292 MET cc_start: 0.8783 (OUTLIER) cc_final: 0.7908 (mtp) REVERT: X 400 LYS cc_start: 0.7647 (mptm) cc_final: 0.6982 (mtpt) REVERT: X 404 ASP cc_start: 0.7741 (t0) cc_final: 0.7008 (t0) outliers start: 74 outliers final: 29 residues processed: 561 average time/residue: 0.7046 time to fit residues: 495.9652 Evaluate side-chains 538 residues out of total 4620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 498 time to evaluate : 1.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain C residue 463 PRO Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 400 LYS Chi-restraints excluded: chain G residue 86 SER Chi-restraints excluded: chain G residue 109 ASP Chi-restraints excluded: chain G residue 120 GLN Chi-restraints excluded: chain G residue 348 THR Chi-restraints excluded: chain G residue 451 VAL Chi-restraints excluded: chain I residue 109 ASP Chi-restraints excluded: chain K residue 86 SER Chi-restraints excluded: chain K residue 299 LYS Chi-restraints excluded: chain K residue 451 VAL Chi-restraints excluded: chain M residue 109 ASP Chi-restraints excluded: chain M residue 410 VAL Chi-restraints excluded: chain O residue 26 GLU Chi-restraints excluded: chain O residue 120 GLN Chi-restraints excluded: chain O residue 410 VAL Chi-restraints excluded: chain O residue 420 LEU Chi-restraints excluded: chain Q residue 85 ARG Chi-restraints excluded: chain Q residue 86 SER Chi-restraints excluded: chain Q residue 214 SER Chi-restraints excluded: chain Q residue 299 LYS Chi-restraints excluded: chain Q residue 393 LYS Chi-restraints excluded: chain Q residue 410 VAL Chi-restraints excluded: chain Q residue 451 VAL Chi-restraints excluded: chain S residue 120 GLN Chi-restraints excluded: chain S residue 451 VAL Chi-restraints excluded: chain V residue 120 GLN Chi-restraints excluded: chain V residue 132 THR Chi-restraints excluded: chain V residue 299 LYS Chi-restraints excluded: chain V residue 451 VAL Chi-restraints excluded: chain X residue 132 THR Chi-restraints excluded: chain X residue 292 MET Chi-restraints excluded: chain X residue 317 THR Chi-restraints excluded: chain X residue 451 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 35 optimal weight: 1.9990 chunk 309 optimal weight: 8.9990 chunk 126 optimal weight: 0.9990 chunk 400 optimal weight: 0.7980 chunk 150 optimal weight: 0.3980 chunk 170 optimal weight: 0.5980 chunk 58 optimal weight: 0.7980 chunk 119 optimal weight: 0.0000 chunk 102 optimal weight: 7.9990 chunk 128 optimal weight: 0.8980 chunk 238 optimal weight: 0.7980 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 389 GLN E 389 GLN G 389 GLN I 389 GLN K 389 GLN O 389 GLN Q 307 HIS Q 381 ASN V 307 HIS V 381 ASN X 389 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.139726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.104060 restraints weight = 183803.699| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 3.77 r_work: 0.2800 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2768 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2768 r_free = 0.2768 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2768 r_free = 0.2768 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (8 function evaluations) r_final: 0.2768 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8916 moved from start: 0.3446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 44280 Z= 0.095 Angle : 0.500 15.769 60084 Z= 0.255 Chirality : 0.042 0.136 6792 Planarity : 0.004 0.047 7536 Dihedral : 5.731 37.274 6487 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 1.56 % Allowed : 20.52 % Favored : 77.92 % 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: 0.53 (0.11), residues: 5412 helix: 2.61 (0.13), residues: 1680 sheet: 0.38 (0.15), residues: 972 loop : -1.16 (0.10), residues: 2760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG V 76 TYR 0.011 0.001 TYR Q 297 PHE 0.012 0.001 PHE C 264 TRP 0.009 0.001 TRP S 421 HIS 0.003 0.001 HIS Q 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.09 (44244) covalent geometry : angle 0.50022 / 0.26 (60084) hydrogen bonds : bond 0.02729 / 1.84 ( 1892) hydrogen bonds : angle 3.94527 / 2.77 ( 5328) metal coordination : bond 0.00109 / 0.07 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10824 Ramachandran restraints generated. 5412 Oldfield, 0 Emsley, 5412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10824 Ramachandran restraints generated. 5412 Oldfield, 0 Emsley, 5412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 595 residues out of total 4620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 524 time to evaluate : 1.758 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 109 ASP cc_start: 0.6586 (p0) cc_final: 0.6378 (OUTLIER) REVERT: A 269 LYS cc_start: 0.7728 (OUTLIER) cc_final: 0.7496 (pttt) REVERT: A 354 ASP cc_start: 0.8462 (m-30) cc_final: 0.8243 (m-30) REVERT: A 400 LYS cc_start: 0.7716 (mptt) cc_final: 0.6926 (mtmp) REVERT: C 30 ARG cc_start: 0.8059 (OUTLIER) cc_final: 0.7660 (ttm-80) REVERT: C 75 ASP cc_start: 0.7688 (p0) cc_final: 0.7318 (p0) REVERT: C 106 LYS cc_start: 0.7332 (mtpp) cc_final: 0.6982 (mttp) REVERT: C 292 MET cc_start: 0.8910 (mtm) cc_final: 0.8662 (mpp) REVERT: C 404 ASP cc_start: 0.7556 (t0) cc_final: 0.7202 (t0) REVERT: C 427 LYS cc_start: 0.7328 (OUTLIER) cc_final: 0.6964 (pmtt) REVERT: E 127 ASP cc_start: 0.7787 (m-30) cc_final: 0.7356 (t0) REVERT: E 314 MET cc_start: 0.9142 (ttt) cc_final: 0.8812 (ttp) REVERT: E 400 LYS cc_start: 0.7789 (OUTLIER) cc_final: 0.7114 (mttt) REVERT: E 404 ASP cc_start: 0.8138 (t70) cc_final: 0.7434 (t0) REVERT: G 75 ASP cc_start: 0.7499 (p0) cc_final: 0.7256 (p0) REVERT: G 98 ARG cc_start: 0.7409 (ttp-110) cc_final: 0.6830 (mtp180) REVERT: G 127 ASP cc_start: 0.7793 (m-30) cc_final: 0.7339 (t0) REVERT: G 146 ASP cc_start: 0.8397 (m-30) cc_final: 0.8078 (m-30) REVERT: G 399 ARG cc_start: 0.8204 (mmm-85) cc_final: 0.7917 (mtp180) REVERT: G 400 LYS cc_start: 0.7926 (mptm) cc_final: 0.7393 (mtpt) REVERT: I 127 ASP cc_start: 0.7868 (m-30) cc_final: 0.7580 (t0) REVERT: K 73 MET cc_start: 0.8259 (mmm) cc_final: 0.8038 (mmm) REVERT: K 127 ASP cc_start: 0.7883 (t0) cc_final: 0.7434 (t0) REVERT: K 353 GLU cc_start: 0.8090 (tt0) cc_final: 0.7602 (mp0) REVERT: M 127 ASP cc_start: 0.8034 (t0) cc_final: 0.7556 (t0) REVERT: M 400 LYS cc_start: 0.7939 (mptp) cc_final: 0.7307 (mtpt) REVERT: O 26 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7843 (mm-30) REVERT: O 73 MET cc_start: 0.8567 (mmm) cc_final: 0.8274 (mmm) REVERT: O 106 LYS cc_start: 0.7432 (mtpp) cc_final: 0.7161 (mttp) REVERT: O 127 ASP cc_start: 0.8002 (t0) cc_final: 0.7507 (t0) REVERT: O 319 ASP cc_start: 0.8642 (OUTLIER) cc_final: 0.8435 (t70) REVERT: O 400 LYS cc_start: 0.7929 (mptp) cc_final: 0.7367 (mtpt) REVERT: Q 85 ARG cc_start: 0.8199 (OUTLIER) cc_final: 0.7042 (mtm180) REVERT: Q 109 ASP cc_start: 0.6373 (p0) cc_final: 0.6146 (p0) REVERT: Q 127 ASP cc_start: 0.7970 (t0) cc_final: 0.7492 (t0) REVERT: Q 269 LYS cc_start: 0.7495 (OUTLIER) cc_final: 0.7295 (pttt) REVERT: Q 299 LYS cc_start: 0.8307 (OUTLIER) cc_final: 0.7946 (tttm) REVERT: Q 353 GLU cc_start: 0.8114 (tt0) cc_final: 0.7580 (mp0) REVERT: Q 393 LYS cc_start: 0.8470 (OUTLIER) cc_final: 0.8146 (mptm) REVERT: Q 400 LYS cc_start: 0.7855 (mptp) cc_final: 0.7298 (mtmt) REVERT: Q 427 LYS cc_start: 0.7830 (ptpp) cc_final: 0.7629 (ptpt) REVERT: S 16 LYS cc_start: 0.8643 (mttt) cc_final: 0.8401 (mptm) REVERT: S 20 ARG cc_start: 0.8218 (mmp-170) cc_final: 0.7749 (mmp80) REVERT: S 299 LYS cc_start: 0.8505 (tttm) cc_final: 0.8257 (pptt) REVERT: V 73 MET cc_start: 0.8487 (mmm) cc_final: 0.8185 (mmm) REVERT: V 127 ASP cc_start: 0.8043 (t0) cc_final: 0.7469 (t0) REVERT: V 299 LYS cc_start: 0.8687 (OUTLIER) cc_final: 0.8203 (pptt) REVERT: V 399 ARG cc_start: 0.8042 (mtp180) cc_final: 0.7666 (mmt90) REVERT: X 127 ASP cc_start: 0.7814 (t0) cc_final: 0.7481 (t0) REVERT: X 292 MET cc_start: 0.8795 (OUTLIER) cc_final: 0.7851 (mtp) REVERT: X 400 LYS cc_start: 0.7591 (mptm) cc_final: 0.6983 (mtpt) REVERT: X 404 ASP cc_start: 0.7831 (t0) cc_final: 0.7171 (t0) outliers start: 71 outliers final: 27 residues processed: 576 average time/residue: 0.6782 time to fit residues: 491.3787 Evaluate side-chains 540 residues out of total 4620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 502 time to evaluate : 1.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 269 LYS Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain C residue 30 ARG Chi-restraints excluded: chain C residue 427 LYS Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 400 LYS Chi-restraints excluded: chain E residue 451 VAL Chi-restraints excluded: chain G residue 86 SER Chi-restraints excluded: chain G residue 109 ASP Chi-restraints excluded: chain G residue 451 VAL Chi-restraints excluded: chain I residue 109 ASP Chi-restraints excluded: chain I residue 420 LEU Chi-restraints excluded: chain K residue 86 SER Chi-restraints excluded: chain K residue 451 VAL Chi-restraints excluded: chain M residue 410 VAL Chi-restraints excluded: chain O residue 26 GLU Chi-restraints excluded: chain O residue 319 ASP Chi-restraints excluded: chain O residue 410 VAL Chi-restraints excluded: chain O residue 420 LEU Chi-restraints excluded: chain Q residue 16 LYS Chi-restraints excluded: chain Q residue 85 ARG Chi-restraints excluded: chain Q residue 86 SER Chi-restraints excluded: chain Q residue 269 LYS Chi-restraints excluded: chain Q residue 299 LYS Chi-restraints excluded: chain Q residue 393 LYS Chi-restraints excluded: chain Q residue 410 VAL Chi-restraints excluded: chain Q residue 451 VAL Chi-restraints excluded: chain S residue 274 CYS Chi-restraints excluded: chain S residue 451 VAL Chi-restraints excluded: chain V residue 132 THR Chi-restraints excluded: chain V residue 299 LYS Chi-restraints excluded: chain V residue 451 VAL Chi-restraints excluded: chain X residue 132 THR Chi-restraints excluded: chain X residue 292 MET Chi-restraints excluded: chain X residue 317 THR Chi-restraints excluded: chain X residue 451 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 454 optimal weight: 1.9990 chunk 451 optimal weight: 0.5980 chunk 480 optimal weight: 10.0000 chunk 294 optimal weight: 0.3980 chunk 505 optimal weight: 9.9990 chunk 383 optimal weight: 0.8980 chunk 147 optimal weight: 10.0000 chunk 397 optimal weight: 3.9990 chunk 313 optimal weight: 2.9990 chunk 378 optimal weight: 3.9990 chunk 312 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 389 GLN E 389 GLN G 203 GLN I 389 GLN K 389 GLN V 389 GLN X 389 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.136856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.099533 restraints weight = 169698.904| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 3.61 r_work: 0.2779 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2748 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2748 r_free = 0.2748 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2748 r_free = 0.2748 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2748 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8917 moved from start: 0.3513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 44280 Z= 0.132 Angle : 0.531 9.659 60084 Z= 0.270 Chirality : 0.044 0.136 6792 Planarity : 0.004 0.048 7536 Dihedral : 5.896 38.753 6485 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.36 % Allowed : 21.14 % Favored : 77.49 % 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: 0.33 (0.11), residues: 5412 helix: 2.20 (0.13), residues: 1752 sheet: 0.40 (0.15), residues: 972 loop : -1.26 (0.10), residues: 2688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 399 TYR 0.013 0.001 TYR X 195 PHE 0.016 0.002 PHE O 183 TRP 0.009 0.001 TRP S 421 HIS 0.004 0.001 HIS V 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 (44244) covalent geometry : angle 0.53079 / 0.27 (60084) hydrogen bonds : bond 0.03324 / 2.23 ( 1892) hydrogen bonds : angle 3.96925 / 2.79 ( 5328) metal coordination : bond 0.00412 / 0.26 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10824 Ramachandran restraints generated. 5412 Oldfield, 0 Emsley, 5412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10824 Ramachandran restraints generated. 5412 Oldfield, 0 Emsley, 5412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 4620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 506 time to evaluate : 1.632 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 ASP cc_start: 0.8199 (p0) cc_final: 0.7997 (p0) REVERT: A 354 ASP cc_start: 0.8394 (m-30) cc_final: 0.8134 (m-30) REVERT: A 399 ARG cc_start: 0.8001 (mtp180) cc_final: 0.7710 (mtp180) REVERT: A 400 LYS cc_start: 0.7621 (mptt) cc_final: 0.6796 (mtmp) REVERT: A 404 ASP cc_start: 0.7197 (t0) cc_final: 0.6803 (t0) REVERT: C 30 ARG cc_start: 0.8142 (OUTLIER) cc_final: 0.7696 (ttm-80) REVERT: C 75 ASP cc_start: 0.7724 (p0) cc_final: 0.7415 (p0) REVERT: C 106 LYS cc_start: 0.7398 (mtpp) cc_final: 0.7073 (mttp) REVERT: C 292 MET cc_start: 0.9033 (mtm) cc_final: 0.8710 (mpp) REVERT: C 400 LYS cc_start: 0.7819 (mmpt) cc_final: 0.7546 (mmpt) REVERT: C 404 ASP cc_start: 0.7536 (t0) cc_final: 0.7116 (t0) REVERT: C 429 HIS cc_start: 0.8872 (m-70) cc_final: 0.8655 (m170) REVERT: E 127 ASP cc_start: 0.7887 (m-30) cc_final: 0.7527 (t0) REVERT: E 314 MET cc_start: 0.9188 (ttt) cc_final: 0.8815 (ttp) REVERT: E 353 GLU cc_start: 0.7848 (tt0) cc_final: 0.7594 (mp0) REVERT: E 400 LYS cc_start: 0.7746 (OUTLIER) cc_final: 0.7023 (mttt) REVERT: E 404 ASP cc_start: 0.8111 (t70) cc_final: 0.7389 (t0) REVERT: G 75 ASP cc_start: 0.7492 (p0) cc_final: 0.7275 (p0) REVERT: G 98 ARG cc_start: 0.7429 (ttp-110) cc_final: 0.6810 (mtp180) REVERT: G 127 ASP cc_start: 0.7804 (m-30) cc_final: 0.7440 (t0) REVERT: G 146 ASP cc_start: 0.8348 (m-30) cc_final: 0.8010 (m-30) REVERT: G 399 ARG cc_start: 0.8209 (mmm-85) cc_final: 0.7745 (mmt90) REVERT: G 400 LYS cc_start: 0.7855 (mptm) cc_final: 0.7291 (mtpt) REVERT: I 127 ASP cc_start: 0.7875 (m-30) cc_final: 0.7649 (t0) REVERT: K 127 ASP cc_start: 0.7931 (t0) cc_final: 0.7482 (t0) REVERT: K 319 ASP cc_start: 0.8586 (OUTLIER) cc_final: 0.8217 (t0) REVERT: K 353 GLU cc_start: 0.8115 (tt0) cc_final: 0.7624 (mp0) REVERT: M 127 ASP cc_start: 0.8029 (t0) cc_final: 0.7576 (t0) REVERT: O 26 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7773 (mm-30) REVERT: O 106 LYS cc_start: 0.7434 (mtpp) cc_final: 0.7221 (mttp) REVERT: O 127 ASP cc_start: 0.8056 (t0) cc_final: 0.7511 (t0) REVERT: O 400 LYS cc_start: 0.7912 (mptp) cc_final: 0.7320 (mtpt) REVERT: Q 85 ARG cc_start: 0.8248 (OUTLIER) cc_final: 0.7003 (mtm180) REVERT: Q 109 ASP cc_start: 0.6422 (p0) cc_final: 0.6197 (p0) REVERT: Q 127 ASP cc_start: 0.8026 (t0) cc_final: 0.7701 (t0) REVERT: Q 299 LYS cc_start: 0.8281 (OUTLIER) cc_final: 0.7919 (tttt) REVERT: Q 353 GLU cc_start: 0.8116 (tt0) cc_final: 0.7580 (mp0) REVERT: Q 393 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.8149 (mptm) REVERT: Q 400 LYS cc_start: 0.7816 (mptp) cc_final: 0.7253 (mtmt) REVERT: Q 427 LYS cc_start: 0.7794 (ptpp) cc_final: 0.7567 (ptpt) REVERT: V 127 ASP cc_start: 0.8120 (t0) cc_final: 0.7713 (t0) REVERT: V 399 ARG cc_start: 0.8019 (mtp180) cc_final: 0.7700 (mtp180) REVERT: X 127 ASP cc_start: 0.7922 (t0) cc_final: 0.7599 (t0) REVERT: X 400 LYS cc_start: 0.7501 (mptm) cc_final: 0.6934 (mtpt) REVERT: X 404 ASP cc_start: 0.7755 (t0) cc_final: 0.7075 (t0) outliers start: 62 outliers final: 34 residues processed: 559 average time/residue: 0.6705 time to fit residues: 473.4813 Evaluate side-chains 539 residues out of total 4620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 498 time to evaluate : 1.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain C residue 30 ARG Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 120 GLN Chi-restraints excluded: chain E residue 400 LYS Chi-restraints excluded: chain E residue 451 VAL Chi-restraints excluded: chain G residue 86 SER Chi-restraints excluded: chain G residue 109 ASP Chi-restraints excluded: chain G residue 120 GLN Chi-restraints excluded: chain G residue 451 VAL Chi-restraints excluded: chain I residue 420 LEU Chi-restraints excluded: chain K residue 44 SER Chi-restraints excluded: chain K residue 86 SER Chi-restraints excluded: chain K residue 319 ASP Chi-restraints excluded: chain K residue 451 VAL Chi-restraints excluded: chain M residue 86 SER Chi-restraints excluded: chain M residue 109 ASP Chi-restraints excluded: chain M residue 120 GLN Chi-restraints excluded: chain M residue 410 VAL Chi-restraints excluded: chain O residue 26 GLU Chi-restraints excluded: chain O residue 410 VAL Chi-restraints excluded: chain O residue 420 LEU Chi-restraints excluded: chain Q residue 16 LYS Chi-restraints excluded: chain Q residue 85 ARG Chi-restraints excluded: chain Q residue 86 SER Chi-restraints excluded: chain Q residue 299 LYS Chi-restraints excluded: chain Q residue 393 LYS Chi-restraints excluded: chain Q residue 410 VAL Chi-restraints excluded: chain Q residue 451 VAL Chi-restraints excluded: chain S residue 132 THR Chi-restraints excluded: chain S residue 274 CYS Chi-restraints excluded: chain S residue 451 VAL Chi-restraints excluded: chain V residue 132 THR Chi-restraints excluded: chain V residue 299 LYS Chi-restraints excluded: chain V residue 451 VAL Chi-restraints excluded: chain X residue 132 THR Chi-restraints excluded: chain X residue 317 THR Chi-restraints excluded: chain X residue 451 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 116 optimal weight: 4.9990 chunk 469 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 chunk 177 optimal weight: 3.9990 chunk 176 optimal weight: 6.9990 chunk 93 optimal weight: 3.9990 chunk 499 optimal weight: 0.9990 chunk 261 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 chunk 163 optimal weight: 3.9990 chunk 308 optimal weight: 4.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 389 GLN E 389 GLN I 389 GLN K 389 GLN X 389 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.136123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.098802 restraints weight = 168345.793| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 3.42 r_work: 0.2753 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2723 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2723 r_free = 0.2723 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2722 r_free = 0.2722 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2722 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8945 moved from start: 0.3634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 44280 Z= 0.180 Angle : 0.581 9.899 60084 Z= 0.295 Chirality : 0.046 0.152 6792 Planarity : 0.005 0.048 7536 Dihedral : 6.175 40.282 6485 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.49 % Allowed : 20.97 % Favored : 77.54 % 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: 0.19 (0.11), residues: 5412 helix: 2.03 (0.13), residues: 1752 sheet: 0.29 (0.15), residues: 972 loop : -1.29 (0.10), residues: 2688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 434 TYR 0.017 0.002 TYR X 195 PHE 0.019 0.002 PHE O 183 TRP 0.010 0.002 TRP X 421 HIS 0.005 0.001 HIS C 307 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.18 (44244) covalent geometry : angle 0.58056 / 0.29 (60084) hydrogen bonds : bond 0.03921 / 2.63 ( 1892) hydrogen bonds : angle 4.09464 / 2.88 ( 5328) metal coordination : bond 0.00626 / 0.40 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10824 Ramachandran restraints generated. 5412 Oldfield, 0 Emsley, 5412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10824 Ramachandran restraints generated. 5412 Oldfield, 0 Emsley, 5412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 4620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 499 time to evaluate : 2.036 Fit side-chains revert: symmetry clash REVERT: A 400 LYS cc_start: 0.7666 (mptt) cc_final: 0.6864 (mtmp) REVERT: A 404 ASP cc_start: 0.7267 (t0) cc_final: 0.6794 (t0) REVERT: C 30 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.7671 (ttm-80) REVERT: C 75 ASP cc_start: 0.7690 (p0) cc_final: 0.7411 (p0) REVERT: C 106 LYS cc_start: 0.7515 (mtpp) cc_final: 0.7203 (mttp) REVERT: C 404 ASP cc_start: 0.7565 (t0) cc_final: 0.7064 (t0) REVERT: E 127 ASP cc_start: 0.7812 (m-30) cc_final: 0.7565 (t0) REVERT: E 314 MET cc_start: 0.9180 (ttt) cc_final: 0.8825 (ttp) REVERT: E 353 GLU cc_start: 0.7984 (tt0) cc_final: 0.7603 (mp0) REVERT: E 400 LYS cc_start: 0.7765 (OUTLIER) cc_final: 0.7100 (mtpt) REVERT: E 404 ASP cc_start: 0.8147 (t70) cc_final: 0.7390 (t0) REVERT: G 127 ASP cc_start: 0.7784 (m-30) cc_final: 0.7488 (t0) REVERT: G 146 ASP cc_start: 0.8355 (m-30) cc_final: 0.8068 (m-30) REVERT: G 399 ARG cc_start: 0.8257 (mmm-85) cc_final: 0.7944 (mmt90) REVERT: G 400 LYS cc_start: 0.7915 (mptm) cc_final: 0.7320 (mtpt) REVERT: I 98 ARG cc_start: 0.6853 (mmp80) cc_final: 0.5754 (mtp180) REVERT: I 467 ARG cc_start: 0.7268 (OUTLIER) cc_final: 0.6295 (ttt180) REVERT: K 127 ASP cc_start: 0.8020 (t0) cc_final: 0.7583 (t0) REVERT: K 319 ASP cc_start: 0.8595 (OUTLIER) cc_final: 0.8353 (t0) REVERT: K 353 GLU cc_start: 0.8196 (tt0) cc_final: 0.7669 (mp0) REVERT: K 427 LYS cc_start: 0.7924 (ptpt) cc_final: 0.6842 (pptt) REVERT: M 127 ASP cc_start: 0.8100 (t0) cc_final: 0.7658 (t0) REVERT: O 26 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7715 (mm-30) REVERT: O 98 ARG cc_start: 0.6941 (mmp80) cc_final: 0.5766 (mtp180) REVERT: O 106 LYS cc_start: 0.7515 (mtpp) cc_final: 0.7298 (mttp) REVERT: O 127 ASP cc_start: 0.8083 (t0) cc_final: 0.7546 (t0) REVERT: Q 85 ARG cc_start: 0.8284 (OUTLIER) cc_final: 0.6987 (mtm180) REVERT: Q 109 ASP cc_start: 0.6542 (p0) cc_final: 0.6339 (p0) REVERT: Q 127 ASP cc_start: 0.8116 (t0) cc_final: 0.7812 (t0) REVERT: Q 299 LYS cc_start: 0.8253 (OUTLIER) cc_final: 0.8038 (mtmm) REVERT: Q 353 GLU cc_start: 0.8187 (tt0) cc_final: 0.7615 (mp0) REVERT: Q 393 LYS cc_start: 0.8492 (OUTLIER) cc_final: 0.8178 (mptm) REVERT: Q 427 LYS cc_start: 0.7845 (ptpp) cc_final: 0.7643 (ptpt) REVERT: S 299 LYS cc_start: 0.8487 (tmtt) cc_final: 0.8162 (pptt) REVERT: V 106 LYS cc_start: 0.7303 (mtpp) cc_final: 0.7030 (mttp) REVERT: V 127 ASP cc_start: 0.8164 (t0) cc_final: 0.7780 (t0) REVERT: V 399 ARG cc_start: 0.8118 (mtp180) cc_final: 0.7847 (mmt90) REVERT: X 106 LYS cc_start: 0.7071 (ttmm) cc_final: 0.6842 (mtpp) REVERT: X 127 ASP cc_start: 0.8041 (t0) cc_final: 0.7722 (t0) REVERT: X 393 LYS cc_start: 0.8430 (OUTLIER) cc_final: 0.8195 (mttt) REVERT: X 400 LYS cc_start: 0.7529 (mptm) cc_final: 0.6969 (mtpt) REVERT: X 404 ASP cc_start: 0.7739 (t0) cc_final: 0.7039 (t0) outliers start: 68 outliers final: 36 residues processed: 552 average time/residue: 0.6794 time to fit residues: 471.4005 Evaluate side-chains 529 residues out of total 4620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 484 time to evaluate : 2.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain C residue 30 ARG Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 400 LYS Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain E residue 451 VAL Chi-restraints excluded: chain G residue 86 SER Chi-restraints excluded: chain G residue 109 ASP Chi-restraints excluded: chain G residue 120 GLN Chi-restraints excluded: chain G residue 451 VAL Chi-restraints excluded: chain I residue 420 LEU Chi-restraints excluded: chain I residue 467 ARG Chi-restraints excluded: chain K residue 44 SER Chi-restraints excluded: chain K residue 86 SER Chi-restraints excluded: chain K residue 319 ASP Chi-restraints excluded: chain K residue 451 VAL Chi-restraints excluded: chain M residue 86 SER Chi-restraints excluded: chain M residue 109 ASP Chi-restraints excluded: chain M residue 120 GLN Chi-restraints excluded: chain M residue 410 VAL Chi-restraints excluded: chain O residue 26 GLU Chi-restraints excluded: chain O residue 410 VAL Chi-restraints excluded: chain Q residue 16 LYS Chi-restraints excluded: chain Q residue 61 ILE Chi-restraints excluded: chain Q residue 85 ARG Chi-restraints excluded: chain Q residue 86 SER Chi-restraints excluded: chain Q residue 120 GLN Chi-restraints excluded: chain Q residue 299 LYS Chi-restraints excluded: chain Q residue 393 LYS Chi-restraints excluded: chain Q residue 410 VAL Chi-restraints excluded: chain Q residue 451 VAL Chi-restraints excluded: chain S residue 132 THR Chi-restraints excluded: chain S residue 274 CYS Chi-restraints excluded: chain S residue 451 VAL Chi-restraints excluded: chain V residue 132 THR Chi-restraints excluded: chain V residue 299 LYS Chi-restraints excluded: chain V residue 451 VAL Chi-restraints excluded: chain X residue 120 GLN Chi-restraints excluded: chain X residue 132 THR Chi-restraints excluded: chain X residue 317 THR Chi-restraints excluded: chain X residue 393 LYS Chi-restraints excluded: chain X residue 451 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 121 optimal weight: 3.9990 chunk 306 optimal weight: 2.9990 chunk 177 optimal weight: 2.9990 chunk 281 optimal weight: 0.9980 chunk 250 optimal weight: 7.9990 chunk 401 optimal weight: 0.9990 chunk 509 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 526 optimal weight: 1.9990 chunk 184 optimal weight: 0.7980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 389 GLN E 389 GLN I 381 ASN I 389 GLN K 389 GLN X 389 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.136868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.099830 restraints weight = 170244.585| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 3.53 r_work: 0.2746 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2743 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2743 r_free = 0.2743 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2743 r_free = 0.2743 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2743 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8941 moved from start: 0.3698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 44280 Z= 0.142 Angle : 0.544 9.191 60084 Z= 0.277 Chirality : 0.044 0.131 6792 Planarity : 0.004 0.047 7536 Dihedral : 6.047 39.077 6485 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.24 % Allowed : 21.10 % Favored : 77.66 % 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: 0.19 (0.11), residues: 5412 helix: 2.04 (0.13), residues: 1752 sheet: 0.25 (0.15), residues: 972 loop : -1.28 (0.10), residues: 2688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 399 TYR 0.014 0.001 TYR X 195 PHE 0.017 0.002 PHE O 183 TRP 0.010 0.001 TRP S 421 HIS 0.004 0.001 HIS Q 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 (44244) covalent geometry : angle 0.54405 / 0.28 (60084) hydrogen bonds : bond 0.03487 / 2.35 ( 1892) hydrogen bonds : angle 4.04194 / 2.84 ( 5328) metal coordination : bond 0.00440 / 0.28 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10824 Ramachandran restraints generated. 5412 Oldfield, 0 Emsley, 5412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10824 Ramachandran restraints generated. 5412 Oldfield, 0 Emsley, 5412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 4620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 492 time to evaluate : 1.827 Fit side-chains revert: symmetry clash REVERT: A 399 ARG cc_start: 0.7999 (mtp180) cc_final: 0.7768 (mtp180) REVERT: A 400 LYS cc_start: 0.7667 (mptt) cc_final: 0.6839 (mtmp) REVERT: A 404 ASP cc_start: 0.7273 (t0) cc_final: 0.6783 (t0) REVERT: C 30 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.7716 (ttm-80) REVERT: C 75 ASP cc_start: 0.7674 (p0) cc_final: 0.7414 (p0) REVERT: C 106 LYS cc_start: 0.7488 (mtpp) cc_final: 0.7226 (mttp) REVERT: C 400 LYS cc_start: 0.7887 (mmpt) cc_final: 0.7682 (mmpt) REVERT: C 404 ASP cc_start: 0.7557 (t0) cc_final: 0.7090 (t0) REVERT: E 314 MET cc_start: 0.9185 (ttt) cc_final: 0.8873 (ttp) REVERT: E 353 GLU cc_start: 0.7980 (tt0) cc_final: 0.7609 (mp0) REVERT: E 400 LYS cc_start: 0.7746 (OUTLIER) cc_final: 0.6999 (mttt) REVERT: E 404 ASP cc_start: 0.8108 (t70) cc_final: 0.7406 (t0) REVERT: G 127 ASP cc_start: 0.7772 (m-30) cc_final: 0.7543 (t0) REVERT: G 146 ASP cc_start: 0.8379 (m-30) cc_final: 0.8099 (m-30) REVERT: G 399 ARG cc_start: 0.8269 (mmm-85) cc_final: 0.7764 (mmt90) REVERT: G 400 LYS cc_start: 0.7907 (mptm) cc_final: 0.7312 (mtpt) REVERT: I 98 ARG cc_start: 0.6858 (mmp80) cc_final: 0.6028 (ttt180) REVERT: K 127 ASP cc_start: 0.8056 (t0) cc_final: 0.7609 (t0) REVERT: K 319 ASP cc_start: 0.8597 (OUTLIER) cc_final: 0.8335 (t70) REVERT: K 353 GLU cc_start: 0.8202 (tt0) cc_final: 0.7670 (mp0) REVERT: K 427 LYS cc_start: 0.7943 (ptpt) cc_final: 0.6864 (pptt) REVERT: M 127 ASP cc_start: 0.8134 (t0) cc_final: 0.7694 (t0) REVERT: O 26 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7722 (mm-30) REVERT: O 98 ARG cc_start: 0.6885 (mmp80) cc_final: 0.5977 (ttt180) REVERT: O 106 LYS cc_start: 0.7526 (mtpp) cc_final: 0.7314 (mttp) REVERT: O 120 GLN cc_start: 0.7935 (OUTLIER) cc_final: 0.7709 (mt0) REVERT: O 127 ASP cc_start: 0.8111 (t0) cc_final: 0.7577 (t0) REVERT: Q 85 ARG cc_start: 0.8241 (OUTLIER) cc_final: 0.6909 (mtm180) REVERT: Q 127 ASP cc_start: 0.8126 (t0) cc_final: 0.7775 (t0) REVERT: Q 299 LYS cc_start: 0.8312 (OUTLIER) cc_final: 0.7944 (tttt) REVERT: Q 353 GLU cc_start: 0.8195 (tt0) cc_final: 0.7621 (mp0) REVERT: Q 393 LYS cc_start: 0.8475 (OUTLIER) cc_final: 0.8163 (mptm) REVERT: Q 427 LYS cc_start: 0.7848 (ptpp) cc_final: 0.7640 (ptpt) REVERT: S 299 LYS cc_start: 0.8479 (tmtt) cc_final: 0.8161 (pptt) REVERT: V 106 LYS cc_start: 0.7352 (mtpp) cc_final: 0.7077 (mttp) REVERT: V 127 ASP cc_start: 0.8158 (t0) cc_final: 0.7761 (t0) REVERT: V 399 ARG cc_start: 0.8122 (mtp180) cc_final: 0.7900 (mmt90) REVERT: X 127 ASP cc_start: 0.8073 (t0) cc_final: 0.7792 (t0) REVERT: X 393 LYS cc_start: 0.8438 (OUTLIER) cc_final: 0.8221 (mttt) REVERT: X 400 LYS cc_start: 0.7506 (mptm) cc_final: 0.6944 (mtpt) REVERT: X 404 ASP cc_start: 0.7745 (t0) cc_final: 0.7097 (t0) outliers start: 56 outliers final: 36 residues processed: 539 average time/residue: 0.6666 time to fit residues: 452.3458 Evaluate side-chains 534 residues out of total 4620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 489 time to evaluate : 1.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain C residue 30 ARG Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 400 LYS Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain E residue 451 VAL Chi-restraints excluded: chain G residue 86 SER Chi-restraints excluded: chain G residue 109 ASP Chi-restraints excluded: chain G residue 120 GLN Chi-restraints excluded: chain G residue 386 VAL Chi-restraints excluded: chain G residue 451 VAL Chi-restraints excluded: chain I residue 420 LEU Chi-restraints excluded: chain K residue 86 SER Chi-restraints excluded: chain K residue 319 ASP Chi-restraints excluded: chain K residue 451 VAL Chi-restraints excluded: chain M residue 86 SER Chi-restraints excluded: chain M residue 120 GLN Chi-restraints excluded: chain M residue 274 CYS Chi-restraints excluded: chain M residue 386 VAL Chi-restraints excluded: chain M residue 410 VAL Chi-restraints excluded: chain O residue 26 GLU Chi-restraints excluded: chain O residue 120 GLN Chi-restraints excluded: chain O residue 410 VAL Chi-restraints excluded: chain Q residue 16 LYS Chi-restraints excluded: chain Q residue 61 ILE Chi-restraints excluded: chain Q residue 85 ARG Chi-restraints excluded: chain Q residue 86 SER Chi-restraints excluded: chain Q residue 120 GLN Chi-restraints excluded: chain Q residue 299 LYS Chi-restraints excluded: chain Q residue 393 LYS Chi-restraints excluded: chain Q residue 410 VAL Chi-restraints excluded: chain Q residue 451 VAL Chi-restraints excluded: chain S residue 132 THR Chi-restraints excluded: chain S residue 274 CYS Chi-restraints excluded: chain S residue 451 VAL Chi-restraints excluded: chain V residue 132 THR Chi-restraints excluded: chain V residue 299 LYS Chi-restraints excluded: chain V residue 451 VAL Chi-restraints excluded: chain X residue 132 THR Chi-restraints excluded: chain X residue 317 THR Chi-restraints excluded: chain X residue 393 LYS Chi-restraints excluded: chain X residue 451 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 227 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 chunk 436 optimal weight: 5.9990 chunk 469 optimal weight: 0.8980 chunk 52 optimal weight: 7.9990 chunk 383 optimal weight: 1.9990 chunk 501 optimal weight: 5.9990 chunk 277 optimal weight: 1.9990 chunk 530 optimal weight: 0.9990 chunk 222 optimal weight: 0.0670 chunk 395 optimal weight: 0.6980 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 389 GLN E 389 GLN I 389 GLN K 389 GLN V 389 GLN X 307 HIS X 389 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.139499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.103112 restraints weight = 171752.889| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 3.45 r_work: 0.2804 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2774 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2774 r_free = 0.2774 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2774 r_free = 0.2774 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2774 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8897 moved from start: 0.3770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 44280 Z= 0.101 Angle : 0.502 8.953 60084 Z= 0.256 Chirality : 0.042 0.128 6792 Planarity : 0.004 0.045 7536 Dihedral : 5.733 35.900 6485 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.11 % Allowed : 21.27 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.11), residues: 5412 helix: 2.51 (0.13), residues: 1680 sheet: 0.29 (0.15), residues: 972 loop : -1.12 (0.10), residues: 2760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 399 TYR 0.011 0.001 TYR Q 297 PHE 0.014 0.001 PHE O 183 TRP 0.007 0.001 TRP X 421 HIS 0.003 0.001 HIS Q 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 (44244) covalent geometry : angle 0.50182 / 0.26 (60084) hydrogen bonds : bond 0.02860 / 1.93 ( 1892) hydrogen bonds : angle 3.94610 / 2.77 ( 5328) metal coordination : bond 0.00207 / 0.13 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10824 Ramachandran restraints generated. 5412 Oldfield, 0 Emsley, 5412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10824 Ramachandran restraints generated. 5412 Oldfield, 0 Emsley, 5412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 4620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 510 time to evaluate : 1.732 Fit side-chains revert: symmetry clash REVERT: A 354 ASP cc_start: 0.8375 (m-30) cc_final: 0.8154 (m-30) REVERT: A 399 ARG cc_start: 0.7954 (mtp180) cc_final: 0.7704 (mtp180) REVERT: A 400 LYS cc_start: 0.7630 (mptt) cc_final: 0.6810 (mtmp) REVERT: A 404 ASP cc_start: 0.7211 (t0) cc_final: 0.6756 (t0) REVERT: C 30 ARG cc_start: 0.8089 (OUTLIER) cc_final: 0.7642 (ttm-80) REVERT: C 75 ASP cc_start: 0.7709 (p0) cc_final: 0.7467 (p0) REVERT: C 106 LYS cc_start: 0.7452 (mtpp) cc_final: 0.7223 (mttp) REVERT: C 292 MET cc_start: 0.8991 (mtm) cc_final: 0.8673 (mpp) REVERT: C 400 LYS cc_start: 0.7844 (mmpt) cc_final: 0.7615 (mmpt) REVERT: C 404 ASP cc_start: 0.7536 (t0) cc_final: 0.7078 (t0) REVERT: E 314 MET cc_start: 0.9161 (ttt) cc_final: 0.8857 (ttp) REVERT: E 353 GLU cc_start: 0.7917 (tt0) cc_final: 0.7578 (mp0) REVERT: E 400 LYS cc_start: 0.7702 (OUTLIER) cc_final: 0.7099 (mtpt) REVERT: E 404 ASP cc_start: 0.8054 (t70) cc_final: 0.7388 (t0) REVERT: G 98 ARG cc_start: 0.7446 (ttp-110) cc_final: 0.6302 (ttt180) REVERT: G 127 ASP cc_start: 0.7774 (m-30) cc_final: 0.7505 (t0) REVERT: G 146 ASP cc_start: 0.8353 (m-30) cc_final: 0.8070 (m-30) REVERT: G 399 ARG cc_start: 0.8185 (mmm-85) cc_final: 0.7693 (mmt90) REVERT: G 400 LYS cc_start: 0.7880 (mptm) cc_final: 0.7296 (mtpt) REVERT: I 98 ARG cc_start: 0.6848 (mmp80) cc_final: 0.6019 (ttt180) REVERT: I 467 ARG cc_start: 0.7246 (OUTLIER) cc_final: 0.6237 (ttt180) REVERT: K 127 ASP cc_start: 0.8044 (t0) cc_final: 0.7616 (t0) REVERT: K 353 GLU cc_start: 0.8151 (tt0) cc_final: 0.7618 (mp0) REVERT: M 127 ASP cc_start: 0.8167 (t0) cc_final: 0.7754 (t0) REVERT: O 98 ARG cc_start: 0.6820 (mmp80) cc_final: 0.5689 (mtp180) REVERT: O 106 LYS cc_start: 0.7520 (mtpp) cc_final: 0.7302 (mttp) REVERT: O 120 GLN cc_start: 0.7835 (OUTLIER) cc_final: 0.7616 (mt0) REVERT: O 127 ASP cc_start: 0.8126 (t0) cc_final: 0.7606 (t0) REVERT: O 400 LYS cc_start: 0.7892 (mptp) cc_final: 0.7319 (mtpt) REVERT: Q 85 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.6916 (mtm180) REVERT: Q 127 ASP cc_start: 0.8149 (t0) cc_final: 0.7820 (t0) REVERT: Q 299 LYS cc_start: 0.8255 (OUTLIER) cc_final: 0.7933 (tttt) REVERT: Q 353 GLU cc_start: 0.8139 (tt0) cc_final: 0.7594 (mp0) REVERT: Q 393 LYS cc_start: 0.8429 (OUTLIER) cc_final: 0.8088 (mptm) REVERT: Q 400 LYS cc_start: 0.7811 (mptp) cc_final: 0.7251 (mtmt) REVERT: Q 427 LYS cc_start: 0.7767 (ptpp) cc_final: 0.7436 (ptpt) REVERT: S 20 ARG cc_start: 0.8122 (mmp-170) cc_final: 0.7636 (mmp80) REVERT: S 299 LYS cc_start: 0.8364 (tmtt) cc_final: 0.8095 (pptt) REVERT: S 400 LYS cc_start: 0.7900 (mptp) cc_final: 0.7311 (mtpt) REVERT: V 106 LYS cc_start: 0.7324 (mtpp) cc_final: 0.7088 (mttp) REVERT: V 127 ASP cc_start: 0.8205 (t0) cc_final: 0.7818 (t0) REVERT: V 399 ARG cc_start: 0.7929 (mtp180) cc_final: 0.7715 (mmt90) REVERT: X 127 ASP cc_start: 0.8120 (t0) cc_final: 0.7826 (t0) REVERT: X 393 LYS cc_start: 0.8408 (OUTLIER) cc_final: 0.8176 (mttt) REVERT: X 400 LYS cc_start: 0.7474 (mptm) cc_final: 0.6904 (mtpt) REVERT: X 404 ASP cc_start: 0.7748 (t0) cc_final: 0.7110 (t0) outliers start: 50 outliers final: 29 residues processed: 549 average time/residue: 0.6830 time to fit residues: 470.1219 Evaluate side-chains 541 residues out of total 4620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 504 time to evaluate : 1.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain C residue 30 ARG Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 400 LYS Chi-restraints excluded: chain E residue 451 VAL Chi-restraints excluded: chain G residue 86 SER Chi-restraints excluded: chain G residue 120 GLN Chi-restraints excluded: chain G residue 386 VAL Chi-restraints excluded: chain G residue 451 VAL Chi-restraints excluded: chain I residue 420 LEU Chi-restraints excluded: chain I residue 467 ARG Chi-restraints excluded: chain K residue 86 SER Chi-restraints excluded: chain K residue 451 VAL Chi-restraints excluded: chain M residue 274 CYS Chi-restraints excluded: chain O residue 120 GLN Chi-restraints excluded: chain O residue 410 VAL Chi-restraints excluded: chain Q residue 16 LYS Chi-restraints excluded: chain Q residue 85 ARG Chi-restraints excluded: chain Q residue 120 GLN Chi-restraints excluded: chain Q residue 299 LYS Chi-restraints excluded: chain Q residue 393 LYS Chi-restraints excluded: chain Q residue 410 VAL Chi-restraints excluded: chain Q residue 451 VAL Chi-restraints excluded: chain Q residue 460 LEU Chi-restraints excluded: chain S residue 132 THR Chi-restraints excluded: chain S residue 274 CYS Chi-restraints excluded: chain S residue 451 VAL Chi-restraints excluded: chain V residue 132 THR Chi-restraints excluded: chain V residue 451 VAL Chi-restraints excluded: chain X residue 120 GLN Chi-restraints excluded: chain X residue 132 THR Chi-restraints excluded: chain X residue 317 THR Chi-restraints excluded: chain X residue 393 LYS Chi-restraints excluded: chain X residue 451 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 502 optimal weight: 7.9990 chunk 136 optimal weight: 0.5980 chunk 428 optimal weight: 0.5980 chunk 295 optimal weight: 3.9990 chunk 268 optimal weight: 0.1980 chunk 30 optimal weight: 0.8980 chunk 348 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 131 optimal weight: 10.0000 chunk 368 optimal weight: 0.9990 chunk 105 optimal weight: 0.0050 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 389 GLN E 389 GLN I 389 GLN K 389 GLN S 307 HIS V 389 GLN X 389 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.138961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.103920 restraints weight = 171817.059| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 3.32 r_work: 0.2818 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2794 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2794 r_free = 0.2794 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2794 r_free = 0.2794 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2794 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8883 moved from start: 0.3792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 44280 Z= 0.091 Angle : 0.491 8.878 60084 Z= 0.251 Chirality : 0.042 0.153 6792 Planarity : 0.004 0.044 7536 Dihedral : 5.614 34.631 6485 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.87 % Allowed : 21.70 % Favored : 77.43 % 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: 0.55 (0.11), residues: 5412 helix: 2.57 (0.13), residues: 1680 sheet: 0.33 (0.16), residues: 972 loop : -1.08 (0.10), residues: 2760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 110 TYR 0.010 0.001 TYR M 150 PHE 0.012 0.001 PHE O 183 TRP 0.007 0.001 TRP X 421 HIS 0.003 0.001 HIS Q 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00202 / 0.09 (44244) covalent geometry : angle 0.49142 / 0.25 (60084) hydrogen bonds : bond 0.02704 / 1.83 ( 1892) hydrogen bonds : angle 3.92394 / 2.75 ( 5328) metal coordination : bond 0.00150 / 0.09 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10824 Ramachandran restraints generated. 5412 Oldfield, 0 Emsley, 5412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10824 Ramachandran restraints generated. 5412 Oldfield, 0 Emsley, 5412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 4620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 503 time to evaluate : 1.737 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 269 LYS cc_start: 0.7715 (OUTLIER) cc_final: 0.7497 (pttt) REVERT: A 354 ASP cc_start: 0.8369 (m-30) cc_final: 0.8149 (m-30) REVERT: A 399 ARG cc_start: 0.7948 (mtp180) cc_final: 0.7684 (mtp180) REVERT: A 400 LYS cc_start: 0.7622 (mptt) cc_final: 0.6802 (mtmp) REVERT: A 404 ASP cc_start: 0.7213 (t0) cc_final: 0.6769 (t0) REVERT: C 30 ARG cc_start: 0.8047 (OUTLIER) cc_final: 0.7600 (ttm-80) REVERT: C 75 ASP cc_start: 0.7671 (p0) cc_final: 0.7440 (p0) REVERT: C 106 LYS cc_start: 0.7464 (mtpp) cc_final: 0.7244 (mttp) REVERT: C 292 MET cc_start: 0.8922 (mtm) cc_final: 0.8599 (mpp) REVERT: C 400 LYS cc_start: 0.7807 (mmpt) cc_final: 0.7588 (mmpt) REVERT: C 404 ASP cc_start: 0.7536 (t0) cc_final: 0.7088 (t0) REVERT: E 314 MET cc_start: 0.9158 (ttt) cc_final: 0.8846 (ttp) REVERT: E 353 GLU cc_start: 0.7872 (tt0) cc_final: 0.7543 (mp0) REVERT: E 400 LYS cc_start: 0.7680 (OUTLIER) cc_final: 0.7099 (mtpt) REVERT: E 404 ASP cc_start: 0.8046 (t70) cc_final: 0.7393 (t0) REVERT: G 98 ARG cc_start: 0.7413 (ttp-110) cc_final: 0.6293 (ttt180) REVERT: G 146 ASP cc_start: 0.8333 (m-30) cc_final: 0.8043 (m-30) REVERT: G 399 ARG cc_start: 0.8174 (mmm-85) cc_final: 0.7692 (mmt90) REVERT: G 400 LYS cc_start: 0.7858 (mptm) cc_final: 0.7288 (mtpt) REVERT: I 98 ARG cc_start: 0.6794 (mmp80) cc_final: 0.5732 (mtp180) REVERT: I 467 ARG cc_start: 0.7235 (OUTLIER) cc_final: 0.6219 (ttt180) REVERT: K 109 ASP cc_start: 0.6576 (p0) cc_final: 0.6341 (p0) REVERT: K 127 ASP cc_start: 0.8041 (t0) cc_final: 0.7607 (t0) REVERT: K 353 GLU cc_start: 0.8145 (tt0) cc_final: 0.7615 (mp0) REVERT: M 127 ASP cc_start: 0.8172 (t0) cc_final: 0.7753 (t0) REVERT: O 98 ARG cc_start: 0.6837 (mmp80) cc_final: 0.5733 (mtp180) REVERT: O 120 GLN cc_start: 0.7790 (OUTLIER) cc_final: 0.7583 (mt0) REVERT: O 127 ASP cc_start: 0.8119 (t0) cc_final: 0.7626 (t0) REVERT: O 400 LYS cc_start: 0.7916 (mptp) cc_final: 0.7323 (mtpt) REVERT: Q 127 ASP cc_start: 0.8149 (t0) cc_final: 0.7819 (t0) REVERT: Q 299 LYS cc_start: 0.8244 (OUTLIER) cc_final: 0.7933 (tttt) REVERT: Q 353 GLU cc_start: 0.8111 (tt0) cc_final: 0.7571 (mp0) REVERT: Q 393 LYS cc_start: 0.8413 (OUTLIER) cc_final: 0.8080 (mptm) REVERT: Q 400 LYS cc_start: 0.7821 (mptp) cc_final: 0.7252 (mtmt) REVERT: Q 427 LYS cc_start: 0.7782 (ptpp) cc_final: 0.7461 (ptpt) REVERT: S 20 ARG cc_start: 0.8120 (mmp-170) cc_final: 0.7710 (mmp80) REVERT: S 299 LYS cc_start: 0.8388 (tmtt) cc_final: 0.8109 (pptt) REVERT: S 400 LYS cc_start: 0.7889 (mptp) cc_final: 0.7313 (mtpt) REVERT: V 106 LYS cc_start: 0.7314 (mtpp) cc_final: 0.7091 (mttp) REVERT: V 127 ASP cc_start: 0.8208 (t0) cc_final: 0.7819 (t0) REVERT: X 73 MET cc_start: 0.8387 (mmm) cc_final: 0.8126 (mmm) REVERT: X 127 ASP cc_start: 0.8129 (t0) cc_final: 0.7839 (t0) REVERT: X 400 LYS cc_start: 0.7529 (mptm) cc_final: 0.6946 (mtpt) REVERT: X 404 ASP cc_start: 0.7730 (t0) cc_final: 0.7103 (t0) outliers start: 39 outliers final: 21 residues processed: 534 average time/residue: 0.6750 time to fit residues: 451.0570 Evaluate side-chains 522 residues out of total 4620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 494 time to evaluate : 1.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 269 LYS Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain C residue 30 ARG Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 400 LYS Chi-restraints excluded: chain E residue 451 VAL Chi-restraints excluded: chain G residue 120 GLN Chi-restraints excluded: chain G residue 451 VAL Chi-restraints excluded: chain I residue 420 LEU Chi-restraints excluded: chain I residue 467 ARG Chi-restraints excluded: chain K residue 86 SER Chi-restraints excluded: chain M residue 274 CYS Chi-restraints excluded: chain O residue 120 GLN Chi-restraints excluded: chain Q residue 120 GLN Chi-restraints excluded: chain Q residue 299 LYS Chi-restraints excluded: chain Q residue 393 LYS Chi-restraints excluded: chain Q residue 410 VAL Chi-restraints excluded: chain Q residue 451 VAL Chi-restraints excluded: chain Q residue 460 LEU Chi-restraints excluded: chain S residue 274 CYS Chi-restraints excluded: chain S residue 451 VAL Chi-restraints excluded: chain V residue 132 THR Chi-restraints excluded: chain V residue 451 VAL Chi-restraints excluded: chain X residue 132 THR Chi-restraints excluded: chain X residue 393 LYS Chi-restraints excluded: chain X residue 451 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 382 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 chunk 33 optimal weight: 0.0060 chunk 277 optimal weight: 0.4980 chunk 7 optimal weight: 3.9990 chunk 203 optimal weight: 0.0980 chunk 107 optimal weight: 3.9990 chunk 314 optimal weight: 1.9990 chunk 292 optimal weight: 4.9990 chunk 147 optimal weight: 10.0000 chunk 49 optimal weight: 1.9990 overall best weight: 0.9200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 389 GLN E 389 GLN I 389 GLN K 389 GLN V 389 GLN X 381 ASN X 389 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.138520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.101650 restraints weight = 171139.590| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 3.52 r_work: 0.2801 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2762 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2762 r_free = 0.2762 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2762 r_free = 0.2762 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2762 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8907 moved from start: 0.3813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 44280 Z= 0.108 Angle : 0.507 8.882 60084 Z= 0.258 Chirality : 0.043 0.149 6792 Planarity : 0.004 0.044 7536 Dihedral : 5.638 35.390 6484 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 0.87 % Allowed : 21.76 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.11), residues: 5412 helix: 2.55 (0.13), residues: 1680 sheet: 0.36 (0.16), residues: 972 loop : -1.06 (0.10), residues: 2760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG V 76 TYR 0.011 0.001 TYR M 150 PHE 0.014 0.001 PHE C 183 TRP 0.007 0.001 TRP X 421 HIS 0.003 0.001 HIS Q 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (44244) covalent geometry : angle 0.50674 / 0.26 (60084) hydrogen bonds : bond 0.02955 / 1.99 ( 1892) hydrogen bonds : angle 3.92900 / 2.76 ( 5328) metal coordination : bond 0.00272 / 0.17 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15254.62 seconds wall clock time: 262 minutes 5.43 seconds (15725.43 seconds total)