Starting phenix.real_space_refine on Mon Mar 25 15:43:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ijo_9680/03_2024/6ijo_9680_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ijo_9680/03_2024/6ijo_9680.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ijo_9680/03_2024/6ijo_9680_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ijo_9680/03_2024/6ijo_9680_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ijo_9680/03_2024/6ijo_9680_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ijo_9680/03_2024/6ijo_9680.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ijo_9680/03_2024/6ijo_9680.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ijo_9680/03_2024/6ijo_9680_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ijo_9680/03_2024/6ijo_9680_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.022 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 Fe 12 7.16 5 P 16 5.49 5 Mg 243 5.21 5 S 138 5.16 5 C 35289 2.51 5 N 6621 2.21 5 O 7366 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 97": "NH1" <-> "NH2" Residue "A ARG 558": "NH1" <-> "NH2" Residue "A ARG 561": "NH1" <-> "NH2" Residue "A ARG 690": "NH1" <-> "NH2" Residue "B PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 397": "NH1" <-> "NH2" Residue "B ARG 411": "NH1" <-> "NH2" Residue "C ARG 19": "NH1" <-> "NH2" Residue "D ARG 158": "NH1" <-> "NH2" Residue "D ARG 216": "NH1" <-> "NH2" Residue "E ARG 85": "NH1" <-> "NH2" Residue "F ARG 212": "NH1" <-> "NH2" Residue "K ARG 97": "NH1" <-> "NH2" Residue "L ARG 138": "NH1" <-> "NH2" Residue "L ARG 169": "NH1" <-> "NH2" Residue "3 PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 162": "NH1" <-> "NH2" Residue "4 ARG 131": "NH1" <-> "NH2" Residue "4 TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 189": "NH1" <-> "NH2" Residue "5 ARG 96": "NH1" <-> "NH2" Residue "5 ARG 152": "NH1" <-> "NH2" Residue "5 ARG 208": "NH1" <-> "NH2" Residue "6 ARG 90": "NH1" <-> "NH2" Residue "6 ARG 137": "NH1" <-> "NH2" Residue "6 ARG 188": "NH1" <-> "NH2" Residue "7 ARG 135": "NH1" <-> "NH2" Residue "7 ARG 195": "NH1" <-> "NH2" Residue "8 ARG 107": "NH1" <-> "NH2" Residue "2 PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 106": "NH1" <-> "NH2" Residue "2 ARG 143": "NH1" <-> "NH2" Residue "9 ARG 62": "NH1" <-> "NH2" Residue "9 ARG 75": "NH1" <-> "NH2" Residue "9 PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 49685 Number of models: 1 Model: "" Number of chains: 41 Chain: "A" Number of atoms: 5819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 741, 5819 Classifications: {'peptide': 741} Link IDs: {'PTRANS': 29, 'TRANS': 711} Chain: "B" Number of atoms: 5812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 731, 5812 Classifications: {'peptide': 731} Link IDs: {'PTRANS': 30, 'TRANS': 700} Chain: "C" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 600 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 4, 'TRANS': 75} Chain: "D" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1129 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 12, 'TRANS': 131} Chain: "E" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 505 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 3, 'TRANS': 60} Chain: "F" Number of atoms: 1254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1254 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 9, 'TRANS': 154} Chain: "G" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 514 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 357 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 48} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 242 Classifications: {'peptide': 32} Link IDs: {'PTRANS': 4, 'TRANS': 27} Chain: "J" Number of atoms: 337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 337 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 3, 'TRANS': 37} Chain: "K" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 578 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 2, 'TRANS': 82} Chain: "L" Number of atoms: 768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 768 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 6, 'TRANS': 99} Chain breaks: 1 Chain: "1" Number of atoms: 1433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1433 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 13, 'TRANS': 179} Chain: "a" Number of atoms: 1444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1444 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 13, 'TRANS': 180} Chain: "3" Number of atoms: 1683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1683 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 14, 'TRANS': 206} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "4" Number of atoms: 1631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1631 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 17, 'TRANS': 192} Chain: "5" Number of atoms: 1765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1765 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 18, 'TRANS': 207} Chain: "6" Number of atoms: 1771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1771 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 25, 'TRANS': 204} Chain: "7" Number of atoms: 1649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1649 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 15, 'TRANS': 197} Chain: "8" Number of atoms: 1630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1630 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 16, 'TRANS': 198} Chain: "2" Number of atoms: 1346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1346 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 163} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "9" Number of atoms: 1302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1302 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 10, 'TRANS': 161} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "X" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 130 Classifications: {'peptide': 26} Link IDs: {'TRANS': 25} Chain: "A" Number of atoms: 3128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 3128 Unusual residues: {'BCR': 6, 'CLA': 45, 'LHG': 2, 'LMG': 1, 'LMU': 3, 'PQN': 1, 'SF4': 1} Classifications: {'undetermined': 59} Link IDs: {None: 58} Unresolved non-hydrogen bonds: 336 Unresolved non-hydrogen angles: 405 Unresolved non-hydrogen dihedrals: 200 Unresolved non-hydrogen chiralities: 38 Planarities with less than four sites: {'CLA:plan-3': 1, 'CLA:plan-4': 3, 'CLA:plan-5': 6} Unresolved non-hydrogen planarities: 39 Chain: "B" Number of atoms: 2683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 2683 Unusual residues: {'BCR': 7, 'CLA': 40, 'DGD': 1, 'LHG': 1, 'PQN': 1} Classifications: {'undetermined': 50} Link IDs: {None: 49} Unresolved non-hydrogen bonds: 345 Unresolved non-hydrogen angles: 419 Unresolved non-hydrogen dihedrals: 197 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'CLA:plan-2': 1, 'CLA:plan-4': 8, 'CLA:plan-5': 10} Unresolved non-hydrogen planarities: 66 Chain: "C" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 180 Unusual residues: {'BCR': 1, 'CLA': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'CLA:plan-4': 2, 'CLA:plan-5': 2} Unresolved non-hydrogen planarities: 17 Chain: "G" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 127 Unusual residues: {'BCR': 1, 'CLA': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'CLA:plan-4': 1, 'CLA:plan-5': 2} Unresolved non-hydrogen planarities: 13 Chain: "J" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 180 Unusual residues: {'BCR': 1, 'CLA': 1, 'DGD': 1, 'LMG': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CLA:plan-4': 1, 'CLA:plan-5': 1} Unresolved non-hydrogen planarities: 8 Chain: "K" Number of atoms: 316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 316 Unusual residues: {'BCR': 2, 'CLA': 4, 'LMU': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'CLA:plan-5': 3} Unresolved non-hydrogen planarities: 14 Chain: "L" Number of atoms: 215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 215 Unusual residues: {'BCR': 2, 'CLA': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'CLA:plan-5': 3} Unresolved non-hydrogen planarities: 15 Chain: "1" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 849 Unusual residues: {'BCR': 1, 'CLA': 14, 'LHG': 1, 'LUT': 1, 'XAT': 1} Classifications: {'undetermined': 18} Link IDs: {None: 17} Unresolved non-hydrogen bonds: 236 Unresolved non-hydrogen angles: 287 Unresolved non-hydrogen dihedrals: 126 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'CLA:plan-2': 3, 'CLA:plan-3': 1, 'CLA:plan-4': 6, 'CLA:plan-5': 8} Unresolved non-hydrogen planarities: 66 Chain: "a" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 884 Unusual residues: {'BCR': 1, 'CLA': 14, 'LHG': 1, 'LUT': 1, 'XAT': 1} Classifications: {'undetermined': 18} Link IDs: {None: 17} Unresolved non-hydrogen bonds: 201 Unresolved non-hydrogen angles: 243 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'CLA:plan-2': 1, 'CLA:plan-3': 1, 'CLA:plan-4': 2, 'CLA:plan-5': 7} Unresolved non-hydrogen planarities: 45 Chain: "3" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 1024 Unusual residues: {'BCR': 3, 'CLA': 14, 'LHG': 2, 'LUT': 1, 'XAT': 1} Classifications: {'undetermined': 21} Link IDs: {None: 20} Unresolved non-hydrogen bonds: 190 Unresolved non-hydrogen angles: 228 Unresolved non-hydrogen dihedrals: 103 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'CLA:plan-2': 2, 'CLA:plan-4': 6, 'CLA:plan-5': 5} Unresolved non-hydrogen planarities: 45 Chain: "4" Number of atoms: 1037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 1037 Unusual residues: {'BCR': 1, 'CLA': 15, 'LHG': 1, 'LMG': 2, 'LUT': 1, 'XAT': 1} Classifications: {'undetermined': 21} Link IDs: {None: 20} Unresolved non-hydrogen bonds: 223 Unresolved non-hydrogen angles: 262 Unresolved non-hydrogen dihedrals: 141 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'CLA:plan-2': 4, 'CLA:plan-4': 4, 'CLA:plan-5': 7} Unresolved non-hydrogen planarities: 51 Chain: "5" Number of atoms: 1259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 1259 Unusual residues: {'BCR': 1, 'CLA': 17, 'LHG': 2, 'LMG': 2, 'LMU': 1, 'LUT': 1, 'NEX': 1, 'XAT': 1} Classifications: {'undetermined': 26} Link IDs: {None: 25} Unresolved non-hydrogen bonds: 259 Unresolved non-hydrogen angles: 307 Unresolved non-hydrogen dihedrals: 158 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'CLA:plan-2': 5, 'CLA:plan-3': 1, 'CLA:plan-4': 5, 'CLA:plan-5': 7} Unresolved non-hydrogen planarities: 54 Chain: "6" Number of atoms: 1130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 1130 Unusual residues: {'BCR': 1, 'CLA': 17, 'LHG': 1, 'LUT': 1, 'NEX': 1, 'XAT': 1} Classifications: {'undetermined': 22} Link IDs: {None: 21} Unresolved non-hydrogen bonds: 194 Unresolved non-hydrogen angles: 234 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'CLA:plan-2': 3, 'CLA:plan-4': 5, 'CLA:plan-5': 7} Unresolved non-hydrogen planarities: 54 Chain: "7" Number of atoms: 1007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 1007 Unusual residues: {'BCR': 2, 'CLA': 15, 'LHG': 1, 'LMG': 1, 'LUT': 1, 'XAT': 1} Classifications: {'undetermined': 21} Link IDs: {None: 20} Unresolved non-hydrogen bonds: 238 Unresolved non-hydrogen angles: 283 Unresolved non-hydrogen dihedrals: 144 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'CLA:plan-2': 2, 'CLA:plan-3': 2, 'CLA:plan-4': 3, 'CLA:plan-5': 8} Unresolved non-hydrogen planarities: 54 Chain: "8" Number of atoms: 1019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 1019 Unusual residues: {'BCR': 1, 'CLA': 14, 'LHG': 2, 'LMU': 2, 'LUT': 1, 'XAT': 1} Classifications: {'undetermined': 21} Link IDs: {None: 20} Unresolved non-hydrogen bonds: 185 Unresolved non-hydrogen angles: 222 Unresolved non-hydrogen dihedrals: 105 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'CLA:plan-2': 3, 'CLA:plan-4': 3, 'CLA:plan-5': 6} Unresolved non-hydrogen planarities: 42 Chain: "2" Number of atoms: 473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 473 Unusual residues: {'CLA': 13, 'LHG': 1, 'LUT': 1, 'XAT': 1} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 508 Unresolved non-hydrogen angles: 705 Unresolved non-hydrogen dihedrals: 415 Unresolved non-hydrogen chiralities: 65 Planarities with less than four sites: {'CLA:plan-2': 13, 'CLA:plan-3': 13, 'CLA:plan-4': 13, 'CLA:plan-5': 13, 'CLA:plan-6': 13} Unresolved non-hydrogen planarities: 261 Chain: "9" Number of atoms: 459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 459 Unusual residues: {'CLA': 12, 'LHG': 1, 'LUT': 1, 'XAT': 1} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 456 Unresolved non-hydrogen angles: 636 Unresolved non-hydrogen dihedrals: 372 Unresolved non-hydrogen chiralities: 60 Planarities with less than four sites: {'CLA:plan-2': 12, 'CLA:plan-3': 12, 'CLA:plan-4': 12, 'CLA:plan-5': 12, 'CLA:plan-6': 12} Unresolved non-hydrogen planarities: 240 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 10193 SG CYS B 560 85.051 69.337 88.599 1.00 22.79 S ATOM 4443 SG CYS A 575 84.876 71.344 95.692 1.00 19.31 S ATOM 11751 SG CYS C 17 100.537 61.263 93.872 1.00 33.08 S ATOM 11711 SG CYS C 11 106.430 62.048 89.642 1.00 42.89 S Time building chain proxies: 25.32, per 1000 atoms: 0.51 Number of scatterers: 49685 At special positions: 0 Unit cell: (152.88, 196.56, 186.16, 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) Fe 12 26.01 S 138 16.00 P 16 15.00 Mg 243 11.99 O 7366 8.00 N 6621 7.00 C 35289 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS F 70 " - pdb=" SG CYS F 125 " distance=2.03 Simple disulfide: pdb=" SG CYS 5 251 " - pdb=" SG CYS 5 268 " distance=2.03 Simple disulfide: pdb=" SG CYS 6 294 " - pdb=" SG CYS 6 311 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM42273 O6 LHG a 620 .*. O " rejected from bonding due to valence issues. Atom "HETATM41389 O6 LHG 1 620 .*. O " rejected from bonding due to valence issues. Atom "HETATM44254 O6 LHG 4 622 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=182, symmetry=0 Number of additional bonds: simple=182, symmetry=0 Coordination: Other bonds: Time building additional restraints: 21.67 Conformation dependent library (CDL) restraints added in 6.2 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 A 853 " pdb="FE4 SF4 A 853 " - pdb=" SG CYS A 575 " pdb="FE1 SF4 A 853 " - pdb=" SG CYS B 560 " pdb="FE3 SF4 A 853 " - pdb=" SG CYS B 569 " pdb="FE2 SF4 A 853 " - pdb=" SG CYS A 584 " pdb=" SF4 C 101 " pdb="FE3 SF4 C 101 " - pdb=" SG CYS C 21 " pdb="FE1 SF4 C 101 " - pdb=" SG CYS C 54 " pdb="FE4 SF4 C 101 " - pdb=" SG CYS C 48 " pdb=" SF4 C 102 " pdb="FE2 SF4 C 102 " - pdb=" SG CYS C 17 " pdb="FE4 SF4 C 102 " - pdb=" SG CYS C 11 " pdb="FE1 SF4 C 102 " - pdb=" SG CYS C 58 " Number of angles added : 30 8660 Ramachandran restraints generated. 4330 Oldfield, 0 Emsley, 4330 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7822 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 158 helices and 9 sheets defined 49.5% alpha, 1.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.41 Creating SS restraints... Processing helix chain 'A' and resid 26 through 28 No H-bonds generated for 'chain 'A' and resid 26 through 28' Processing helix chain 'A' and resid 47 through 54 removed outlier: 3.808A pdb=" N HIS A 53 " --> pdb=" O ILE A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 62 No H-bonds generated for 'chain 'A' and resid 59 through 62' Processing helix chain 'A' and resid 66 through 96 removed outlier: 3.602A pdb=" N PHE A 78 " --> pdb=" O PHE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 106 removed outlier: 3.640A pdb=" N LEU A 105 " --> pdb=" O TYR A 101 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N SER A 106 " --> pdb=" O GLU A 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 101 through 106' Processing helix chain 'A' and resid 124 through 127 Processing helix chain 'A' and resid 144 through 151 Processing helix chain 'A' and resid 156 through 182 Processing helix chain 'A' and resid 188 through 191 No H-bonds generated for 'chain 'A' and resid 188 through 191' Processing helix chain 'A' and resid 194 through 203 Processing helix chain 'A' and resid 206 through 219 Processing helix chain 'A' and resid 221 through 230 Processing helix chain 'A' and resid 242 through 245 No H-bonds generated for 'chain 'A' and resid 242 through 245' Processing helix chain 'A' and resid 247 through 253 removed outlier: 3.604A pdb=" N ASP A 252 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU A 253 " --> pdb=" O ILE A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 259 No H-bonds generated for 'chain 'A' and resid 257 through 259' Processing helix chain 'A' and resid 262 through 265 No H-bonds generated for 'chain 'A' and resid 262 through 265' Processing helix chain 'A' and resid 269 through 272 Processing helix chain 'A' and resid 291 through 310 removed outlier: 3.765A pdb=" N HIS A 310 " --> pdb=" O LEU A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 328 Processing helix chain 'A' and resid 341 through 344 No H-bonds generated for 'chain 'A' and resid 341 through 344' Processing helix chain 'A' and resid 349 through 372 removed outlier: 3.654A pdb=" N ILE A 355 " --> pdb=" O ALA A 351 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE A 365 " --> pdb=" O GLY A 361 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N TYR A 372 " --> pdb=" O ALA A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 414 removed outlier: 3.671A pdb=" N HIS A 394 " --> pdb=" O LEU A 390 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY A 398 " --> pdb=" O HIS A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 464 removed outlier: 3.639A pdb=" N ILE A 431 " --> pdb=" O LEU A 427 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N ASP A 435 " --> pdb=" O ILE A 431 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ALA A 436 " --> pdb=" O ARG A 432 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N LEU A 455 " --> pdb=" O HIS A 451 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TYR A 456 " --> pdb=" O SER A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 470 No H-bonds generated for 'chain 'A' and resid 468 through 470' Processing helix chain 'A' and resid 482 through 491 Processing helix chain 'A' and resid 494 through 497 No H-bonds generated for 'chain 'A' and resid 494 through 497' Processing helix chain 'A' and resid 530 through 555 Processing helix chain 'A' and resid 566 through 569 No H-bonds generated for 'chain 'A' and resid 566 through 569' Processing helix chain 'A' and resid 588 through 617 removed outlier: 3.655A pdb=" N VAL A 592 " --> pdb=" O ALA A 588 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU A 596 " --> pdb=" O VAL A 592 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N PHE A 597 " --> pdb=" O PHE A 593 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TRP A 598 " --> pdb=" O LEU A 594 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE A 605 " --> pdb=" O ASN A 601 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLN A 615 " --> pdb=" O SER A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 647 Processing helix chain 'A' and resid 653 through 656 removed outlier: 3.855A pdb=" N GLN A 656 " --> pdb=" O GLN A 653 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 653 through 656' Processing helix chain 'A' and resid 664 through 687 removed outlier: 4.059A pdb=" N ALA A 667 " --> pdb=" O ALA A 664 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE A 671 " --> pdb=" O TYR A 668 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE A 672 " --> pdb=" O GLY A 669 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ALA A 675 " --> pdb=" O PHE A 672 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N HIS A 676 " --> pdb=" O LEU A 673 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N TRP A 679 " --> pdb=" O HIS A 676 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU A 686 " --> pdb=" O LEU A 683 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N PHE A 687 " --> pdb=" O MET A 684 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 706 removed outlier: 3.930A pdb=" N GLU A 695 " --> pdb=" O GLY A 691 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA A 703 " --> pdb=" O SER A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 750 removed outlier: 3.660A pdb=" N THR A 738 " --> pdb=" O GLY A 734 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR A 739 " --> pdb=" O GLY A 735 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N SER A 749 " --> pdb=" O ALA A 745 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 14 No H-bonds generated for 'chain 'B' and resid 11 through 14' Processing helix chain 'B' and resid 20 through 27 Processing helix chain 'B' and resid 32 through 34 No H-bonds generated for 'chain 'B' and resid 32 through 34' Processing helix chain 'B' and resid 40 through 72 removed outlier: 3.538A pdb=" N GLN B 45 " --> pdb=" O GLU B 41 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS B 46 " --> pdb=" O ASN B 42 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE B 52 " --> pdb=" O PHE B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 80 removed outlier: 4.298A pdb=" N THR B 80 " --> pdb=" O GLU B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 103 Processing helix chain 'B' and resid 121 through 127 Processing helix chain 'B' and resid 133 through 158 removed outlier: 3.609A pdb=" N VAL B 138 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY B 139 " --> pdb=" O ASP B 135 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU B 158 " --> pdb=" O GLY B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 169 No H-bonds generated for 'chain 'B' and resid 166 through 169' Processing helix chain 'B' and resid 172 through 181 removed outlier: 3.570A pdb=" N LEU B 180 " --> pdb=" O LEU B 176 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER B 181 " --> pdb=" O ASN B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 197 Processing helix chain 'B' and resid 199 through 203 removed outlier: 3.845A pdb=" N SER B 203 " --> pdb=" O ALA B 199 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 199 through 203' Processing helix chain 'B' and resid 224 through 228 Processing helix chain 'B' and resid 231 through 235 Processing helix chain 'B' and resid 271 through 290 removed outlier: 3.535A pdb=" N ALA B 282 " --> pdb=" O HIS B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 304 No H-bonds generated for 'chain 'B' and resid 302 through 304' Processing helix chain 'B' and resid 324 through 328 Processing helix chain 'B' and resid 331 through 354 removed outlier: 3.653A pdb=" N SER B 347 " --> pdb=" O GLY B 343 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL B 349 " --> pdb=" O ILE B 345 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N TYR B 354 " --> pdb=" O ALA B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 397 removed outlier: 3.646A pdb=" N HIS B 376 " --> pdb=" O LEU B 372 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE B 388 " --> pdb=" O MET B 384 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N PHE B 395 " --> pdb=" O GLY B 391 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE B 396 " --> pdb=" O ALA B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 414 removed outlier: 3.558A pdb=" N LEU B 413 " --> pdb=" O LEU B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 446 removed outlier: 4.215A pdb=" N LEU B 437 " --> pdb=" O HIS B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 452 No H-bonds generated for 'chain 'B' and resid 450 through 452' Processing helix chain 'B' and resid 459 through 468 removed outlier: 3.997A pdb=" N ILE B 464 " --> pdb=" O PHE B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 488 No H-bonds generated for 'chain 'B' and resid 485 through 488' Processing helix chain 'B' and resid 495 through 503 removed outlier: 3.641A pdb=" N ASN B 503 " --> pdb=" O LEU B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 542 removed outlier: 3.509A pdb=" N VAL B 520 " --> pdb=" O GLY B 516 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA B 542 " --> pdb=" O GLY B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 554 No H-bonds generated for 'chain 'B' and resid 551 through 554' Processing helix chain 'B' and resid 573 through 604 removed outlier: 3.946A pdb=" N LEU B 579 " --> pdb=" O ASP B 575 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ALA B 580 " --> pdb=" O ALA B 576 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL B 581 " --> pdb=" O PHE B 577 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N PHE B 582 " --> pdb=" O TYR B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 613 removed outlier: 3.891A pdb=" N ASP B 611 " --> pdb=" O VAL B 607 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER B 613 " --> pdb=" O GLN B 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 617 through 622 Processing helix chain 'B' and resid 625 through 628 No H-bonds generated for 'chain 'B' and resid 625 through 628' Processing helix chain 'B' and resid 630 through 635 removed outlier: 3.656A pdb=" N ASN B 634 " --> pdb=" O SER B 630 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLY B 635 " --> pdb=" O GLN B 631 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 630 through 635' Processing helix chain 'B' and resid 645 through 663 removed outlier: 3.535A pdb=" N HIS B 655 " --> pdb=" O PHE B 651 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N MET B 663 " --> pdb=" O ALA B 659 " (cutoff:3.500A) Processing helix chain 'B' and resid 671 through 684 Processing helix chain 'B' and resid 703 through 733 removed outlier: 3.943A pdb=" N ARG B 733 " --> pdb=" O SER B 729 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 20 Processing helix chain 'D' and resid 128 through 131 No H-bonds generated for 'chain 'D' and resid 128 through 131' Processing helix chain 'D' and resid 170 through 180 removed outlier: 3.667A pdb=" N LEU D 175 " --> pdb=" O GLN D 171 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLN D 178 " --> pdb=" O ALA D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 228 No H-bonds generated for 'chain 'D' and resid 226 through 228' Processing helix chain 'F' and resid 74 through 93 removed outlier: 5.076A pdb=" N GLN F 93 " --> pdb=" O LYS F 89 " (cutoff:3.500A) Processing helix chain 'F' and resid 99 through 120 removed outlier: 3.988A pdb=" N LEU F 104 " --> pdb=" O PRO F 100 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA F 113 " --> pdb=" O GLU F 109 " (cutoff:3.500A) Processing helix chain 'F' and resid 152 through 174 removed outlier: 3.883A pdb=" N LEU F 157 " --> pdb=" O THR F 153 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL F 159 " --> pdb=" O GLY F 155 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY F 161 " --> pdb=" O LEU F 157 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL F 174 " --> pdb=" O TYR F 170 " (cutoff:3.500A) Processing helix chain 'F' and resid 182 through 185 No H-bonds generated for 'chain 'F' and resid 182 through 185' Processing helix chain 'F' and resid 189 through 198 removed outlier: 3.698A pdb=" N LYS F 194 " --> pdb=" O PRO F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 202 through 212 removed outlier: 4.094A pdb=" N GLN F 208 " --> pdb=" O LEU F 204 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG F 212 " --> pdb=" O GLN F 208 " (cutoff:3.500A) Processing helix chain 'G' and resid 70 through 78 Processing helix chain 'G' and resid 81 through 84 No H-bonds generated for 'chain 'G' and resid 81 through 84' Processing helix chain 'G' and resid 87 through 90 No H-bonds generated for 'chain 'G' and resid 87 through 90' Processing helix chain 'G' and resid 130 through 152 removed outlier: 3.880A pdb=" N SER G 152 " --> pdb=" O LEU G 148 " (cutoff:3.500A) Processing helix chain 'H' and resid 105 through 123 removed outlier: 4.130A pdb=" N THR H 122 " --> pdb=" O ALA H 118 " (cutoff:3.500A) Processing helix chain 'I' and resid 75 through 77 No H-bonds generated for 'chain 'I' and resid 75 through 77' Processing helix chain 'I' and resid 79 through 85 removed outlier: 3.605A pdb=" N GLY I 84 " --> pdb=" O VAL I 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 87 through 97 removed outlier: 3.555A pdb=" N LEU I 95 " --> pdb=" O ALA I 91 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE I 96 " --> pdb=" O MET I 92 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 8 Processing helix chain 'J' and resid 11 through 32 removed outlier: 3.815A pdb=" N THR J 20 " --> pdb=" O THR J 16 " (cutoff:3.500A) Processing helix chain 'K' and resid 80 through 97 removed outlier: 4.084A pdb=" N ALA K 91 " --> pdb=" O ALA K 87 " (cutoff:3.500A) Processing helix chain 'K' and resid 133 through 157 removed outlier: 3.823A pdb=" N GLY K 149 " --> pdb=" O GLY K 145 " (cutoff:3.500A) Processing helix chain 'L' and resid 130 through 132 No H-bonds generated for 'chain 'L' and resid 130 through 132' Processing helix chain 'L' and resid 143 through 153 Processing helix chain 'L' and resid 155 through 165 removed outlier: 4.190A pdb=" N ALA L 159 " --> pdb=" O GLY L 155 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N GLY L 160 " --> pdb=" O PHE L 156 " (cutoff:3.500A) Proline residue: L 161 - end of helix Processing helix chain 'L' and resid 178 through 201 removed outlier: 3.516A pdb=" N TYR L 197 " --> pdb=" O CYS L 193 " (cutoff:3.500A) Processing helix chain 'L' and resid 228 through 249 Processing helix chain '1' and resid 88 through 118 removed outlier: 3.804A pdb=" N VAL 1 99 " --> pdb=" O THR 1 95 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL 1 115 " --> pdb=" O GLY 1 111 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLU 1 116 " --> pdb=" O SER 1 112 " (cutoff:3.500A) Processing helix chain '1' and resid 147 through 165 removed outlier: 3.978A pdb=" N ALA 1 152 " --> pdb=" O ASN 1 148 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N MET 1 158 " --> pdb=" O GLU 1 154 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLN 1 164 " --> pdb=" O ALA 1 160 " (cutoff:3.500A) Processing helix chain '1' and resid 190 through 217 removed outlier: 3.912A pdb=" N GLN 1 214 " --> pdb=" O GLY 1 210 " (cutoff:3.500A) Processing helix chain '1' and resid 222 through 231 removed outlier: 4.215A pdb=" N GLU 1 228 " --> pdb=" O ALA 1 224 " (cutoff:3.500A) Processing helix chain 'a' and resid 88 through 118 removed outlier: 3.805A pdb=" N VAL a 99 " --> pdb=" O THR a 95 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL a 115 " --> pdb=" O GLY a 111 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLU a 116 " --> pdb=" O SER a 112 " (cutoff:3.500A) Processing helix chain 'a' and resid 147 through 165 removed outlier: 3.979A pdb=" N ALA a 152 " --> pdb=" O ASN a 148 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N MET a 158 " --> pdb=" O GLU a 154 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLN a 164 " --> pdb=" O ALA a 160 " (cutoff:3.500A) Processing helix chain 'a' and resid 190 through 217 removed outlier: 3.913A pdb=" N GLN a 214 " --> pdb=" O GLY a 210 " (cutoff:3.500A) Processing helix chain 'a' and resid 222 through 231 removed outlier: 4.214A pdb=" N GLU a 228 " --> pdb=" O ALA a 224 " (cutoff:3.500A) Processing helix chain '3' and resid 52 through 54 No H-bonds generated for 'chain '3' and resid 52 through 54' Processing helix chain '3' and resid 80 through 82 No H-bonds generated for 'chain '3' and resid 80 through 82' Processing helix chain '3' and resid 84 through 102 removed outlier: 3.674A pdb=" N GLN 3 88 " --> pdb=" O PRO 3 84 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LEU 3 100 " --> pdb=" O ARG 3 96 " (cutoff:3.500A) Processing helix chain '3' and resid 107 through 113 Processing helix chain '3' and resid 119 through 121 No H-bonds generated for 'chain '3' and resid 119 through 121' Processing helix chain '3' and resid 125 through 127 No H-bonds generated for 'chain '3' and resid 125 through 127' Processing helix chain '3' and resid 146 through 167 removed outlier: 4.195A pdb=" N ARG 3 161 " --> pdb=" O PHE 3 157 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASP 3 165 " --> pdb=" O ARG 3 161 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N PHE 3 166 " --> pdb=" O ARG 3 162 " (cutoff:3.500A) Processing helix chain '3' and resid 180 through 182 No H-bonds generated for 'chain '3' and resid 180 through 182' Processing helix chain '3' and resid 207 through 238 removed outlier: 3.906A pdb=" N GLU 3 212 " --> pdb=" O ALA 3 208 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU 3 213 " --> pdb=" O ALA 3 209 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE 3 218 " --> pdb=" O LYS 3 214 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ALA 3 224 " --> pdb=" O ASN 3 220 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU 3 226 " --> pdb=" O ARG 3 222 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N GLN 3 234 " --> pdb=" O GLY 3 230 " (cutoff:3.500A) Processing helix chain '3' and resid 242 through 251 Processing helix chain '3' and resid 259 through 261 No H-bonds generated for 'chain '3' and resid 259 through 261' Processing helix chain '4' and resid 116 through 148 removed outlier: 3.813A pdb=" N TRP 4 121 " --> pdb=" O VAL 4 117 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLN 4 124 " --> pdb=" O LYS 4 120 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL 4 142 " --> pdb=" O ALA 4 138 " (cutoff:3.500A) Proline residue: 4 143 - end of helix removed outlier: 3.720A pdb=" N SER 4 147 " --> pdb=" O PRO 4 143 " (cutoff:3.500A) Processing helix chain '4' and resid 172 through 195 removed outlier: 3.672A pdb=" N LEU 4 181 " --> pdb=" O GLY 4 177 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ALA 4 184 " --> pdb=" O MET 4 180 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ILE 4 188 " --> pdb=" O ALA 4 184 " (cutoff:3.500A) Processing helix chain '4' and resid 222 through 224 No H-bonds generated for 'chain '4' and resid 222 through 224' Processing helix chain '4' and resid 234 through 261 removed outlier: 3.754A pdb=" N ALA 4 248 " --> pdb=" O ASN 4 244 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLY 4 257 " --> pdb=" O ALA 4 253 " (cutoff:3.500A) Processing helix chain '4' and resid 269 through 275 Processing helix chain '4' and resid 282 through 289 Processing helix chain '5' and resid 81 through 111 removed outlier: 3.585A pdb=" N LYS 5 85 " --> pdb=" O PRO 5 81 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N TRP 5 86 " --> pdb=" O THR 5 82 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA 5 98 " --> pdb=" O HIS 5 94 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N VAL 5 107 " --> pdb=" O ALA 5 103 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU 5 109 " --> pdb=" O VAL 5 105 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ILE 5 110 " --> pdb=" O LEU 5 106 " (cutoff:3.500A) Processing helix chain '5' and resid 123 through 125 No H-bonds generated for 'chain '5' and resid 123 through 125' Processing helix chain '5' and resid 135 through 158 removed outlier: 3.698A pdb=" N ILE 5 144 " --> pdb=" O ALA 5 140 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL 5 149 " --> pdb=" O LEU 5 145 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL 5 151 " --> pdb=" O HIS 5 147 " (cutoff:3.500A) Processing helix chain '5' and resid 196 through 222 removed outlier: 3.709A pdb=" N ILE 5 204 " --> pdb=" O GLN 5 200 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA 5 221 " --> pdb=" O PHE 5 217 " (cutoff:3.500A) Processing helix chain '5' and resid 228 through 237 Processing helix chain '6' and resid 122 through 152 removed outlier: 3.752A pdb=" N LYS 6 126 " --> pdb=" O ALA 6 122 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N TRP 6 127 " --> pdb=" O GLU 6 123 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU 6 133 " --> pdb=" O LYS 6 129 " (cutoff:3.500A) Processing helix chain '6' and resid 171 through 194 removed outlier: 4.027A pdb=" N LEU 6 175 " --> pdb=" O PRO 6 171 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL 6 185 " --> pdb=" O LEU 6 181 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N VAL 6 187 " --> pdb=" O HIS 6 183 " (cutoff:3.500A) Processing helix chain '6' and resid 230 through 255 removed outlier: 3.822A pdb=" N ILE 6 238 " --> pdb=" O LYS 6 234 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL 6 249 " --> pdb=" O MET 6 245 " (cutoff:3.500A) Processing helix chain '6' and resid 264 through 271 Processing helix chain '6' and resid 278 through 281 No H-bonds generated for 'chain '6' and resid 278 through 281' Processing helix chain '7' and resid 64 through 92 removed outlier: 3.555A pdb=" N GLN 7 70 " --> pdb=" O LYS 7 66 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY 7 92 " --> pdb=" O LEU 7 88 " (cutoff:3.500A) Processing helix chain '7' and resid 105 through 109 removed outlier: 3.659A pdb=" N VAL 7 109 " --> pdb=" O ALA 7 105 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 105 through 109' Processing helix chain '7' and resid 117 through 139 removed outlier: 3.984A pdb=" N ILE 7 123 " --> pdb=" O THR 7 119 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR 7 133 " --> pdb=" O GLY 7 129 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS 7 134 " --> pdb=" O TRP 7 130 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ARG 7 135 " --> pdb=" O ALA 7 131 " (cutoff:3.500A) Processing helix chain '7' and resid 167 through 170 No H-bonds generated for 'chain '7' and resid 167 through 170' Processing helix chain '7' and resid 181 through 210 removed outlier: 3.612A pdb=" N GLU 7 185 " --> pdb=" O ALA 7 181 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ALA 7 205 " --> pdb=" O CYS 7 201 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA 7 206 " --> pdb=" O LEU 7 202 " (cutoff:3.500A) Processing helix chain '7' and resid 215 through 224 Processing helix chain '7' and resid 231 through 233 No H-bonds generated for 'chain '7' and resid 231 through 233' Processing helix chain '8' and resid 67 through 69 No H-bonds generated for 'chain '8' and resid 67 through 69' Processing helix chain '8' and resid 92 through 115 removed outlier: 3.572A pdb=" N ILE 8 104 " --> pdb=" O GLN 8 100 " (cutoff:3.500A) Processing helix chain '8' and resid 118 through 124 removed outlier: 3.746A pdb=" N THR 8 123 " --> pdb=" O PRO 8 119 " (cutoff:3.500A) Processing helix chain '8' and resid 148 through 171 removed outlier: 4.264A pdb=" N VAL 8 154 " --> pdb=" O SER 8 150 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL 8 162 " --> pdb=" O LEU 8 158 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS 8 165 " --> pdb=" O PHE 8 161 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN 8 168 " --> pdb=" O ALA 8 164 " (cutoff:3.500A) Processing helix chain '8' and resid 185 through 189 removed outlier: 3.550A pdb=" N SER 8 188 " --> pdb=" O PHE 8 185 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU 8 189 " --> pdb=" O GLU 8 186 " (cutoff:3.500A) No H-bonds generated for 'chain '8' and resid 185 through 189' Processing helix chain '8' and resid 200 through 202 No H-bonds generated for 'chain '8' and resid 200 through 202' Processing helix chain '8' and resid 214 through 240 Processing helix chain '8' and resid 246 through 255 Processing helix chain '2' and resid 41 through 66 removed outlier: 4.018A pdb=" N TRP 2 46 " --> pdb=" O ASP 2 42 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLU 2 49 " --> pdb=" O LYS 2 45 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN 2 54 " --> pdb=" O ALA 2 50 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLY 2 55 " --> pdb=" O GLU 2 51 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N TRP 2 57 " --> pdb=" O THR 2 53 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ALA 2 58 " --> pdb=" O ASN 2 54 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ALA 2 60 " --> pdb=" O ARG 2 56 " (cutoff:3.500A) Processing helix chain '2' and resid 76 through 79 No H-bonds generated for 'chain '2' and resid 76 through 79' Processing helix chain '2' and resid 88 through 110 removed outlier: 3.672A pdb=" N ALA 2 97 " --> pdb=" O LEU 2 93 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N PHE 2 99 " --> pdb=" O GLU 2 95 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL 2 101 " --> pdb=" O ALA 2 97 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU 2 102 " --> pdb=" O VAL 2 98 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N GLU 2 108 " --> pdb=" O GLY 2 104 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ILE 2 109 " --> pdb=" O LYS 2 105 " (cutoff:3.500A) Processing helix chain '2' and resid 135 through 158 removed outlier: 3.536A pdb=" N ASN 2 141 " --> pdb=" O LYS 2 137 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY 2 142 " --> pdb=" O GLU 2 138 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG 2 143 " --> pdb=" O LEU 2 139 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEU 2 144 " --> pdb=" O LYS 2 140 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA 2 145 " --> pdb=" O ASN 2 141 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU 2 150 " --> pdb=" O MET 2 146 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N SER 2 154 " --> pdb=" O LEU 2 150 " (cutoff:3.500A) Processing helix chain '2' and resid 165 through 172 Processing helix chain '9' and resid 63 through 83 removed outlier: 4.314A pdb=" N GLU 9 68 " --> pdb=" O LYS 9 64 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA 9 77 " --> pdb=" O ASN 9 73 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N MET 9 79 " --> pdb=" O ARG 9 75 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA 9 80 " --> pdb=" O TRP 9 76 " (cutoff:3.500A) Processing helix chain '9' and resid 86 through 89 No H-bonds generated for 'chain '9' and resid 86 through 89' Processing helix chain '9' and resid 112 through 130 removed outlier: 3.501A pdb=" N MET 9 119 " --> pdb=" O GLU 9 115 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLY 9 120 " --> pdb=" O PHE 9 116 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU 9 122 " --> pdb=" O VAL 9 118 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS 9 125 " --> pdb=" O PHE 9 121 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N GLY 9 129 " --> pdb=" O LYS 9 125 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N PHE 9 130 " --> pdb=" O ARG 9 126 " (cutoff:3.500A) Processing helix chain '9' and resid 154 through 172 removed outlier: 4.129A pdb=" N VAL 9 167 " --> pdb=" O ARG 9 163 " (cutoff:3.500A) Processing helix chain '9' and resid 186 through 192 removed outlier: 3.563A pdb=" N ALA 9 192 " --> pdb=" O THR 9 188 " (cutoff:3.500A) Processing helix chain '9' and resid 199 through 201 No H-bonds generated for 'chain '9' and resid 199 through 201' Processing helix chain 'X' and resid 2 through 24 removed outlier: 3.829A pdb=" N ALA X 13 " --> pdb=" O ALA X 9 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA X 23 " --> pdb=" O ALA X 19 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 17 through 19 Processing sheet with id= B, first strand: chain 'A' and resid 515 through 517 removed outlier: 3.972A pdb=" N MET A 523 " --> pdb=" O VAL A 515 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N VAL A 517 " --> pdb=" O VAL A 521 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N VAL A 521 " --> pdb=" O VAL A 517 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 27 through 30 Processing sheet with id= D, first strand: chain 'D' and resid 135 through 141 Processing sheet with id= E, first strand: chain 'D' and resid 145 through 147 Processing sheet with id= F, first strand: chain 'D' and resid 190 through 192 Processing sheet with id= G, first strand: chain 'E' and resid 139 through 141 removed outlier: 7.101A pdb=" N VAL E 118 " --> pdb=" O VAL E 106 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'K' and resid 106 through 108 Processing sheet with id= I, first strand: chain '6' and resid 283 through 285 1392 hydrogen bonds defined for protein. 4098 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: 13.60 Time building geometry restraints manager: 23.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.39: 18736 1.39 - 1.57: 32726 1.57 - 1.75: 42 1.75 - 1.94: 219 1.94 - 2.12: 1008 Bond restraints: 52731 Sorted by residual: bond pdb=" C33 NEX 5 624 " pdb=" C34 NEX 5 624 " ideal model delta sigma weight residual 2.765 1.339 1.426 2.00e-02 2.50e+03 5.08e+03 bond pdb=" C33 NEX 6 624 " pdb=" C34 NEX 6 624 " ideal model delta sigma weight residual 2.765 1.341 1.424 2.00e-02 2.50e+03 5.07e+03 bond pdb=" C29 NEX 5 624 " pdb=" C39 NEX 5 624 " ideal model delta sigma weight residual 2.347 1.492 0.855 2.00e-02 2.50e+03 1.83e+03 bond pdb=" C29 NEX 6 624 " pdb=" C39 NEX 6 624 " ideal model delta sigma weight residual 2.347 1.497 0.850 2.00e-02 2.50e+03 1.81e+03 bond pdb=" C10 NEX 5 624 " pdb=" C11 NEX 5 624 " ideal model delta sigma weight residual 2.048 1.453 0.595 2.00e-02 2.50e+03 8.84e+02 ... (remaining 52726 not shown) Histogram of bond angle deviations from ideal: 57.05 - 81.46: 66 81.46 - 105.87: 3194 105.87 - 130.29: 69971 130.29 - 154.70: 1634 154.70 - 179.12: 488 Bond angle restraints: 75353 Sorted by residual: angle pdb=" C11 LUT 9 619 " pdb=" C12 LUT 9 619 " pdb=" C13 LUT 9 619 " ideal model delta sigma weight residual 85.87 128.10 -42.23 3.00e+00 1.11e-01 1.98e+02 angle pdb=" C29 LUT 5 620 " pdb=" C30 LUT 5 620 " pdb=" C31 LUT 5 620 " ideal model delta sigma weight residual 85.90 126.81 -40.91 3.00e+00 1.11e-01 1.86e+02 angle pdb=" C11 LUT 6 619 " pdb=" C10 LUT 6 619 " pdb=" C9 LUT 6 619 " ideal model delta sigma weight residual 85.87 126.65 -40.78 3.00e+00 1.11e-01 1.85e+02 angle pdb=" C11 LUT 5 620 " pdb=" C12 LUT 5 620 " pdb=" C13 LUT 5 620 " ideal model delta sigma weight residual 85.87 126.49 -40.62 3.00e+00 1.11e-01 1.83e+02 angle pdb=" C11 LUT 7 619 " pdb=" C10 LUT 7 619 " pdb=" C9 LUT 7 619 " ideal model delta sigma weight residual 85.87 125.72 -39.85 3.00e+00 1.11e-01 1.76e+02 ... (remaining 75348 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.98: 22063 25.98 - 51.96: 1686 51.96 - 77.93: 505 77.93 - 103.91: 155 103.91 - 129.89: 96 Dihedral angle restraints: 24505 sinusoidal: 12189 harmonic: 12316 Sorted by residual: dihedral pdb=" CB CYS 6 294 " pdb=" SG CYS 6 294 " pdb=" SG CYS 6 311 " pdb=" CB CYS 6 311 " ideal model delta sinusoidal sigma weight residual 93.00 163.74 -70.74 1 1.00e+01 1.00e-02 6.43e+01 dihedral pdb=" CA CYS 6 311 " pdb=" C CYS 6 311 " pdb=" N PHE 6 312 " pdb=" CA PHE 6 312 " ideal model delta harmonic sigma weight residual -180.00 -150.29 -29.71 0 5.00e+00 4.00e-02 3.53e+01 dihedral pdb=" CA THR D 105 " pdb=" C THR D 105 " pdb=" N VAL D 106 " pdb=" CA VAL D 106 " ideal model delta harmonic sigma weight residual 180.00 150.62 29.38 0 5.00e+00 4.00e-02 3.45e+01 ... (remaining 24502 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.109: 6166 1.109 - 2.218: 12 2.218 - 3.327: 2 3.327 - 4.436: 0 4.436 - 5.545: 12 Chirality restraints: 6192 Sorted by residual: chirality pdb=" C5 NEX 6 624 " pdb=" C18 NEX 6 624 " pdb=" C4 NEX 6 624 " pdb=" C6 NEX 6 624 " both_signs ideal model delta sigma weight residual False 2.95 -2.59 5.54 2.00e-01 2.50e+01 7.69e+02 chirality pdb=" C5 NEX 5 624 " pdb=" C18 NEX 5 624 " pdb=" C4 NEX 5 624 " pdb=" C6 NEX 5 624 " both_signs ideal model delta sigma weight residual False 2.95 -2.56 5.51 2.00e-01 2.50e+01 7.59e+02 chirality pdb=" C26 LUT 9 619 " pdb=" C21 LUT 9 619 " pdb=" C25 LUT 9 619 " pdb=" C27 LUT 9 619 " both_signs ideal model delta sigma weight residual False -2.77 2.57 -5.34 2.00e-01 2.50e+01 7.14e+02 ... (remaining 6189 not shown) Planarity restraints: 9997 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 NEX 6 624 " -0.224 2.00e-02 2.50e+03 3.04e-01 1.38e+03 pdb=" C5 NEX 6 624 " -0.008 2.00e-02 2.50e+03 pdb=" C6 NEX 6 624 " -0.001 2.00e-02 2.50e+03 pdb=" C7 NEX 6 624 " 0.233 2.00e-02 2.50e+03 pdb=" C8 NEX 6 624 " 0.473 2.00e-02 2.50e+03 pdb=" C9 NEX 6 624 " -0.474 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 NEX 5 624 " -0.035 2.00e-02 2.50e+03 2.15e-01 6.91e+02 pdb=" C5 NEX 5 624 " 0.176 2.00e-02 2.50e+03 pdb=" C6 NEX 5 624 " 0.011 2.00e-02 2.50e+03 pdb=" C7 NEX 5 624 " -0.125 2.00e-02 2.50e+03 pdb=" C8 NEX 5 624 " -0.352 2.00e-02 2.50e+03 pdb=" C9 NEX 5 624 " 0.324 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C11 PQN B 842 " 0.092 2.00e-02 2.50e+03 2.21e-01 6.09e+02 pdb=" C12 PQN B 842 " 0.008 2.00e-02 2.50e+03 pdb=" C13 PQN B 842 " -0.422 2.00e-02 2.50e+03 pdb=" C14 PQN B 842 " 0.112 2.00e-02 2.50e+03 pdb=" C15 PQN B 842 " 0.211 2.00e-02 2.50e+03 ... (remaining 9994 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 759 2.64 - 3.20: 38881 3.20 - 3.77: 85915 3.77 - 4.33: 117736 4.33 - 4.90: 188173 Nonbonded interactions: 431464 Sorted by model distance: nonbonded pdb=" CE1 HIS 8 105 " pdb="MG CLA 8 603 " model vdw 2.074 3.130 nonbonded pdb=" NB CLA 9 611 " pdb=" O4 LHG 9 622 " model vdw 2.199 3.120 nonbonded pdb=" OH TYR F 162 " pdb=" O ALA F 196 " model vdw 2.211 2.440 nonbonded pdb=" OD1 ASP K 127 " pdb=" NA CLA K 201 " model vdw 2.216 3.120 nonbonded pdb=" CE1 HIS 3 94 " pdb="MG CLA 3 603 " model vdw 2.221 3.130 ... (remaining 431459 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain '1' and (resid 55 through 247 or resid 601 through 602 or (resid 603 and \ (name NB or name ND or name C1A or name C1B or name C1C or name C1D or name C2A \ or name C2B or name C2C or name C2D or name C3A or name C3B or name C3C or name \ C3D or name C4A or name C4B or name C4C or name C4D or name CAA or name CAB or n \ ame CAC or name CAD or name CBA or name CBB or name CBC or name CBD or name CGD \ or name CHA or name CHB or name CHC or name CHD or name CMA or name CMB or name \ CMC or name CMD or name NA or name NC or name O1D or name O2D or name OBD or nam \ e MG )) or resid 604 through 608 or (resid 609 and (name NB or name ND or name C \ 1A or name C1B or name C1C or name C1D or name C2A or name C2B or name C2C or na \ me C2D or name C3A or name C3B or name C3C or name C3D or name C4A or name C4B o \ r name C4C or name C4D or name CAA or name CAB or name CAC or name CAD or name C \ BC or name CBD or name CGD or name CHA or name CHB or name CHC or name CHD or na \ me CMA or name CMB or name CMC or name CMD or name NA or name NC or name O1D or \ name O2D or name OBD or name MG )) or resid 610 or (resid 611 and (name NB or na \ me ND or name C1A or name C1B or name C1C or name C1D or name C2A or name C2B or \ name C2C or name C2D or name C3A or name C3B or name C3C or name C3D or name C4 \ A or name C4B or name C4C or name C4D or name CAA or name CAB or name CAC or nam \ e CAD or name CBD or name CGD or name CHA or name CHB or name CHC or name CHD or \ name CMA or name CMB or name CMC or name CMD or name NA or name NC or name O1D \ or name O2D or name OBD or name MG )) or resid 612 through 620)) selection = (chain 'a' and (resid 55 through 247 or resid 601 through 602 or (resid 603 and \ (name NB or name ND or name C1A or name C1B or name C1C or name C1D or name C2A \ or name C2B or name C2C or name C2D or name C3A or name C3B or name C3C or name \ C3D or name C4A or name C4B or name C4C or name C4D or name CAA or name CAB or n \ ame CAC or name CAD or name CBA or name CBB or name CBC or name CBD or name CGD \ or name CHA or name CHB or name CHC or name CHD or name CMA or name CMB or name \ CMC or name CMD or name NA or name NC or name O1D or name O2D or name OBD or nam \ e MG )) or resid 604 or (resid 606 and (name NB or name ND or name C1A or name C \ 1B or name C1C or name C1D or name C2A or name C2B or name C2C or name C2D or na \ me C3A or name C3B or name C3C or name C3D or name C4A or name C4B or name C4C o \ r name C4D or name CAB or name CAC or name CAD or name CBB or name CBC or name C \ BD or name CED or name CGD or name CHA or name CHB or name CHC or name CHD or na \ me CMA or name CMB or name CMC or name CMD or name NA or name NC or name O2D or \ name OBD or name MG )) or (resid 607 and (name NB or name ND or name C1A or name \ C1B or name C1C or name C1D or name C2A or name C2B or name C2C or name C2D or \ name C3A or name C3B or name C3C or name C3D or name C4A or name C4B or name C4C \ or name C4D or name CAA or name CAB or name CAC or name CAD or name CBB or name \ CBC or name CBD or name CGD or name CHA or name CHB or name CHC or name CHD or \ name CMA or name CMB or name CMC or name CMD or name NA or name NC or name O1D o \ r name O2D or name OBD or name MG )) or resid 608 or (resid 609 and (name NB or \ name ND or name C1A or name C1B or name C1C or name C1D or name C2A or name C2B \ or name C2C or name C2D or name C3A or name C3B or name C3C or name C3D or name \ C4A or name C4B or name C4C or name C4D or name CAA or name CAB or name CAC or n \ ame CAD or name CBC or name CBD or name CGD or name CHA or name CHB or name CHC \ or name CHD or name CMA or name CMB or name CMC or name CMD or name NA or name N \ C or name O1D or name O2D or name OBD or name MG )) or (resid 610 and (name NB o \ r name ND or name C1A or name C1B or name C1C or name C1D or name C2A or name C2 \ B or name C2C or name C2D or name C3A or name C3B or name C3C or name C3D or nam \ e C4A or name C4B or name C4C or name C4D or name CAB or name CAC or name CAD or \ name CBB or name CBD or name CED or name CGD or name CHA or name CHB or name CH \ C or name CHD or name CMA or name CMB or name CMC or name CMD or name NA or name \ NC or name O1D or name O2D or name OBD or name MG )) or resid 611 through 613 o \ r (resid 614 and (name NB or name ND or name C1A or name C1B or name C1C or name \ C1D or name C2A or name C2B or name C2C or name C2D or name C3A or name C3B or \ name C3C or name C3D or name C4A or name C4B or name C4C or name C4D or name CAA \ or name CAB or name CAC or name CAD or name CBD or name CGD or name CHA or name \ CHB or name CHC or name CHD or name CMB or name CMC or name CMD or name NA or n \ ame NC or name O1D or name O2D or name OBD or name MG )) or (resid 616 and (name \ NB or name ND or name C1A or name C1B or name C1C or name C1D or name C2A or na \ me C2B or name C2C or name C2D or name C3A or name C3B or name C3C or name C3D o \ r name C4A or name C4B or name C4C or name C4D or name CAA or name CAB or name C \ AC or name CAD or name CBA or name CBD or name CED or name CGA or name CGD or na \ me CHA or name CHB or name CHC or name CHD or name CMA or name CMB or name CMC o \ r name CMD or name NA or name NC or name O1A or name O1D or name O2A or name O2D \ or name OBD or name MG )) or resid 617 through 620)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.310 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: 0.040 Extract box with map and model: 4.880 Check model and map are aligned: 0.750 Set scattering table: 0.430 Process input model: 129.790 Find NCS groups from input model: 1.600 Set up NCS constraints: 0.180 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:3.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 141.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 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 : 0.021 1.426 52731 Z= 1.078 Angle : 2.103 42.233 75353 Z= 0.820 Chirality : 0.264 5.545 6192 Planarity : 0.010 0.304 9997 Dihedral : 21.974 129.890 16674 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.60 % Favored : 92.36 % Rotamer: Outliers : 0.41 % Allowed : 4.40 % Favored : 95.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.92 (0.09), residues: 4330 helix: -3.64 (0.06), residues: 2261 sheet: -2.46 (0.50), residues: 85 loop : -2.70 (0.12), residues: 1984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.004 TRP A 612 HIS 0.023 0.003 HIS A 539 PHE 0.043 0.004 PHE 6 225 TYR 0.043 0.004 TYR 3 89 ARG 0.023 0.002 ARG 5 208 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8660 Ramachandran restraints generated. 4330 Oldfield, 0 Emsley, 4330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8660 Ramachandran restraints generated. 4330 Oldfield, 0 Emsley, 4330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1096 residues out of total 3413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 1082 time to evaluate : 4.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 VAL cc_start: 0.9161 (t) cc_final: 0.8934 (t) REVERT: A 475 THR cc_start: 0.7393 (p) cc_final: 0.7168 (p) REVERT: A 684 MET cc_start: 0.8673 (ttp) cc_final: 0.8167 (ttp) REVERT: B 57 ILE cc_start: 0.8728 (mt) cc_final: 0.8352 (mt) REVERT: B 561 ASP cc_start: 0.8428 (t0) cc_final: 0.8167 (t70) REVERT: B 575 ASP cc_start: 0.6823 (m-30) cc_final: 0.6412 (m-30) REVERT: B 663 MET cc_start: 0.8526 (ttp) cc_final: 0.8286 (ttm) REVERT: B 684 GLU cc_start: 0.7028 (mt-10) cc_final: 0.6715 (mt-10) REVERT: G 86 PHE cc_start: 0.7455 (m-10) cc_final: 0.7204 (m-80) REVERT: J 14 ILE cc_start: 0.8763 (mt) cc_final: 0.8456 (mt) REVERT: K 132 THR cc_start: 0.7822 (p) cc_final: 0.7455 (p) REVERT: L 141 VAL cc_start: 0.7536 (p) cc_final: 0.7257 (t) REVERT: L 197 TYR cc_start: 0.8336 (t80) cc_final: 0.7937 (t80) REVERT: 1 97 SER cc_start: 0.6597 (p) cc_final: 0.6355 (t) REVERT: 1 101 HIS cc_start: 0.7179 (m90) cc_final: 0.6856 (m90) REVERT: a 92 LYS cc_start: 0.8363 (ttpt) cc_final: 0.8144 (tptt) REVERT: a 162 GLU cc_start: 0.7433 (mm-30) cc_final: 0.7113 (mm-30) REVERT: 3 214 LYS cc_start: 0.9064 (mttt) cc_final: 0.8746 (mtpt) REVERT: 4 126 GLU cc_start: 0.8222 (tt0) cc_final: 0.7768 (tt0) REVERT: 4 178 VAL cc_start: 0.8121 (t) cc_final: 0.7788 (p) REVERT: 4 279 SER cc_start: 0.8101 (m) cc_final: 0.7758 (p) REVERT: 5 99 MET cc_start: 0.8740 (mtm) cc_final: 0.8454 (mtt) REVERT: 8 97 TRP cc_start: 0.7978 (t-100) cc_final: 0.7686 (t-100) REVERT: 8 98 TYR cc_start: 0.8212 (m-10) cc_final: 0.7938 (m-80) outliers start: 14 outliers final: 4 residues processed: 1091 average time/residue: 0.6662 time to fit residues: 1185.1675 Evaluate side-chains 578 residues out of total 3413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 574 time to evaluate : 3.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 578 TYR Chi-restraints excluded: chain 4 residue 203 ASP Chi-restraints excluded: chain 2 residue 155 GLN Chi-restraints excluded: chain 9 residue 131 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 364 optimal weight: 6.9990 chunk 327 optimal weight: 7.9990 chunk 181 optimal weight: 40.0000 chunk 111 optimal weight: 5.9990 chunk 220 optimal weight: 20.0000 chunk 174 optimal weight: 7.9990 chunk 338 optimal weight: 5.9990 chunk 131 optimal weight: 5.9990 chunk 205 optimal weight: 2.9990 chunk 252 optimal weight: 7.9990 chunk 392 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 GLN A 241 HIS A 350 HIS ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 609 HIS ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 15 GLN B 35 HIS B 42 ASN B 115 ASN B 163 GLN B 236 GLN B 295 ASN B 332 HIS ** B 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 604 GLN B 606 ASN C 16 GLN D 159 GLN F 132 HIS J 30 ASN K 126 ASN 1 58 ASN a 164 GLN ** 3 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 124 GLN ** 4 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 260 GLN 6 288 GLN 7 70 GLN 7 114 ASN 7 184 GLN 8 75 GLN 8 100 GLN 8 105 HIS 8 238 GLN 2 176 HIS 2 178 ASN 9 49 ASN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 52731 Z= 0.273 Angle : 1.052 28.140 75353 Z= 0.410 Chirality : 0.057 1.614 6192 Planarity : 0.006 0.065 9997 Dihedral : 22.751 114.749 9278 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 17.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 3.46 % Allowed : 10.92 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.77 (0.11), residues: 4330 helix: -1.51 (0.09), residues: 2254 sheet: -2.44 (0.50), residues: 85 loop : -2.14 (0.13), residues: 1991 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 443 HIS 0.014 0.002 HIS B 415 PHE 0.029 0.002 PHE 7 170 TYR 0.025 0.002 TYR E 97 ARG 0.008 0.001 ARG 8 166 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8660 Ramachandran restraints generated. 4330 Oldfield, 0 Emsley, 4330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8660 Ramachandran restraints generated. 4330 Oldfield, 0 Emsley, 4330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 769 residues out of total 3413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 651 time to evaluate : 4.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ASP cc_start: 0.7267 (m-30) cc_final: 0.7039 (m-30) REVERT: B 57 ILE cc_start: 0.8812 (mt) cc_final: 0.8514 (mt) REVERT: B 281 ILE cc_start: 0.8741 (tp) cc_final: 0.8508 (mt) REVERT: B 609 GLN cc_start: 0.8315 (tm130) cc_final: 0.8100 (tp40) REVERT: F 208 GLN cc_start: 0.6334 (tp-100) cc_final: 0.6124 (tp-100) REVERT: H 151 VAL cc_start: 0.7753 (p) cc_final: 0.7526 (t) REVERT: L 141 VAL cc_start: 0.7697 (p) cc_final: 0.7457 (t) REVERT: L 197 TYR cc_start: 0.8229 (t80) cc_final: 0.7616 (t80) REVERT: 1 158 MET cc_start: 0.6529 (mmm) cc_final: 0.6303 (mmm) REVERT: a 92 LYS cc_start: 0.8283 (ttpt) cc_final: 0.8032 (tptt) REVERT: a 98 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7732 (tt0) REVERT: 3 214 LYS cc_start: 0.9087 (mttt) cc_final: 0.8733 (mtpt) REVERT: 4 101 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8683 (mp) REVERT: 4 144 GLU cc_start: 0.6671 (mm-30) cc_final: 0.6276 (mm-30) REVERT: 4 210 LYS cc_start: 0.8156 (ttpp) cc_final: 0.7855 (tttm) REVERT: 5 72 TRP cc_start: 0.8048 (OUTLIER) cc_final: 0.7547 (t60) REVERT: 5 99 MET cc_start: 0.8611 (mtm) cc_final: 0.8402 (mtt) REVERT: 5 139 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.7942 (tm) REVERT: 5 144 ILE cc_start: 0.9225 (mt) cc_final: 0.8853 (mp) REVERT: 6 302 TYR cc_start: 0.7247 (t80) cc_final: 0.6928 (t80) REVERT: 7 240 ILE cc_start: 0.7405 (mt) cc_final: 0.7203 (mt) REVERT: 8 98 TYR cc_start: 0.8207 (m-10) cc_final: 0.7815 (m-80) REVERT: 8 238 GLN cc_start: 0.8116 (mt0) cc_final: 0.7789 (pt0) REVERT: 2 30 TYR cc_start: 0.4726 (m-80) cc_final: 0.4291 (m-80) REVERT: 2 94 ILE cc_start: 0.2571 (OUTLIER) cc_final: 0.2309 (mt) REVERT: 2 130 LYS cc_start: 0.5488 (ptmm) cc_final: 0.4303 (mptt) REVERT: 9 116 PHE cc_start: 0.5928 (m-80) cc_final: 0.5637 (m-80) REVERT: 9 131 LYS cc_start: 0.0950 (OUTLIER) cc_final: 0.0595 (ptmt) outliers start: 118 outliers final: 68 residues processed: 729 average time/residue: 0.5781 time to fit residues: 714.1176 Evaluate side-chains 625 residues out of total 3413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 551 time to evaluate : 5.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 657 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 97 PHE Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 578 TYR Chi-restraints excluded: chain B residue 667 SER Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 211 LYS Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain J residue 10 THR Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain K residue 88 SER Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain L residue 150 ILE Chi-restraints excluded: chain L residue 174 THR Chi-restraints excluded: chain L residue 182 SER Chi-restraints excluded: chain 1 residue 63 SER Chi-restraints excluded: chain 1 residue 83 SER Chi-restraints excluded: chain 1 residue 99 VAL Chi-restraints excluded: chain a residue 98 GLU Chi-restraints excluded: chain a residue 172 VAL Chi-restraints excluded: chain a residue 212 VAL Chi-restraints excluded: chain 3 residue 138 ASN Chi-restraints excluded: chain 3 residue 238 THR Chi-restraints excluded: chain 4 residue 101 LEU Chi-restraints excluded: chain 4 residue 264 THR Chi-restraints excluded: chain 5 residue 72 TRP Chi-restraints excluded: chain 5 residue 131 THR Chi-restraints excluded: chain 5 residue 139 LEU Chi-restraints excluded: chain 5 residue 187 ASP Chi-restraints excluded: chain 5 residue 199 LEU Chi-restraints excluded: chain 5 residue 212 ILE Chi-restraints excluded: chain 6 residue 98 THR Chi-restraints excluded: chain 6 residue 135 HIS Chi-restraints excluded: chain 6 residue 155 ASP Chi-restraints excluded: chain 6 residue 167 SER Chi-restraints excluded: chain 6 residue 221 VAL Chi-restraints excluded: chain 6 residue 229 ASP Chi-restraints excluded: chain 6 residue 235 VAL Chi-restraints excluded: chain 7 residue 88 LEU Chi-restraints excluded: chain 7 residue 141 ASN Chi-restraints excluded: chain 7 residue 207 GLN Chi-restraints excluded: chain 8 residue 118 ILE Chi-restraints excluded: chain 8 residue 247 VAL Chi-restraints excluded: chain 8 residue 264 THR Chi-restraints excluded: chain 8 residue 267 VAL Chi-restraints excluded: chain 2 residue 63 VAL Chi-restraints excluded: chain 2 residue 66 LEU Chi-restraints excluded: chain 2 residue 94 ILE Chi-restraints excluded: chain 2 residue 116 THR Chi-restraints excluded: chain 2 residue 144 LEU Chi-restraints excluded: chain 2 residue 155 GLN Chi-restraints excluded: chain 9 residue 54 LEU Chi-restraints excluded: chain 9 residue 81 VAL Chi-restraints excluded: chain 9 residue 127 TYR Chi-restraints excluded: chain 9 residue 131 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 218 optimal weight: 0.9980 chunk 121 optimal weight: 20.0000 chunk 326 optimal weight: 10.0000 chunk 267 optimal weight: 8.9990 chunk 108 optimal weight: 10.0000 chunk 393 optimal weight: 5.9990 chunk 424 optimal weight: 30.0000 chunk 350 optimal weight: 9.9990 chunk 389 optimal weight: 9.9990 chunk 133 optimal weight: 0.9980 chunk 315 optimal weight: 30.0000 overall best weight: 5.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 442 ASN A 615 GLN ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 362 GLN B 369 GLN F 117 ASN 1 58 ASN ** 3 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 192 GLN 6 288 GLN 8 105 HIS 8 129 ASN ** 2 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 178 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 52731 Z= 0.268 Angle : 0.993 26.510 75353 Z= 0.385 Chirality : 0.057 1.708 6192 Planarity : 0.005 0.055 9997 Dihedral : 21.386 112.192 9276 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 18.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 3.55 % Allowed : 12.94 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.12), residues: 4330 helix: -0.65 (0.10), residues: 2274 sheet: -2.09 (0.52), residues: 85 loop : -1.87 (0.14), residues: 1971 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP 1 138 HIS 0.012 0.002 HIS B 415 PHE 0.038 0.002 PHE 2 47 TYR 0.022 0.002 TYR E 97 ARG 0.006 0.001 ARG 8 166 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8660 Ramachandran restraints generated. 4330 Oldfield, 0 Emsley, 4330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8660 Ramachandran restraints generated. 4330 Oldfield, 0 Emsley, 4330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 709 residues out of total 3413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 588 time to evaluate : 4.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ASP cc_start: 0.7265 (m-30) cc_final: 0.7021 (m-30) REVERT: A 272 TYR cc_start: 0.8430 (m-80) cc_final: 0.8189 (m-10) REVERT: B 57 ILE cc_start: 0.8847 (mt) cc_final: 0.8557 (mt) REVERT: B 281 ILE cc_start: 0.8699 (tp) cc_final: 0.8489 (mt) REVERT: B 493 LEU cc_start: 0.5773 (mp) cc_final: 0.5304 (mp) REVERT: B 695 LYS cc_start: 0.8467 (mmmt) cc_final: 0.8022 (tmtt) REVERT: H 151 VAL cc_start: 0.7726 (p) cc_final: 0.7518 (t) REVERT: a 91 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.7937 (tp) REVERT: a 92 LYS cc_start: 0.8348 (ttpt) cc_final: 0.8006 (tptt) REVERT: a 98 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7644 (tt0) REVERT: a 226 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8727 (tp) REVERT: 3 152 ILE cc_start: 0.9300 (mm) cc_final: 0.8980 (tt) REVERT: 3 165 ASP cc_start: 0.8073 (t0) cc_final: 0.7674 (t0) REVERT: 4 101 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8680 (mp) REVERT: 5 72 TRP cc_start: 0.8291 (OUTLIER) cc_final: 0.7912 (t60) REVERT: 5 99 MET cc_start: 0.8609 (mtm) cc_final: 0.8389 (mtt) REVERT: 5 118 TYR cc_start: 0.8053 (t80) cc_final: 0.7788 (t80) REVERT: 5 139 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.8065 (tm) REVERT: 5 144 ILE cc_start: 0.9299 (mt) cc_final: 0.8866 (mp) REVERT: 7 240 ILE cc_start: 0.7444 (mt) cc_final: 0.7163 (mt) REVERT: 8 98 TYR cc_start: 0.8228 (m-10) cc_final: 0.7837 (m-80) REVERT: 2 130 LYS cc_start: 0.5272 (ptmm) cc_final: 0.4292 (mptt) REVERT: 9 131 LYS cc_start: 0.1053 (OUTLIER) cc_final: 0.0588 (ptmt) outliers start: 121 outliers final: 74 residues processed: 665 average time/residue: 0.5802 time to fit residues: 653.9964 Evaluate side-chains 610 residues out of total 3413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 529 time to evaluate : 4.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 657 VAL Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 97 PHE Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 578 TYR Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 211 LYS Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 234 LYS Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain I residue 87 LEU Chi-restraints excluded: chain J residue 10 THR Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain K residue 88 SER Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain K residue 133 ILE Chi-restraints excluded: chain L residue 174 THR Chi-restraints excluded: chain L residue 181 LEU Chi-restraints excluded: chain L residue 196 ILE Chi-restraints excluded: chain 1 residue 83 SER Chi-restraints excluded: chain 1 residue 99 VAL Chi-restraints excluded: chain 1 residue 115 VAL Chi-restraints excluded: chain 1 residue 209 LEU Chi-restraints excluded: chain a residue 91 LEU Chi-restraints excluded: chain a residue 98 GLU Chi-restraints excluded: chain a residue 151 LEU Chi-restraints excluded: chain a residue 172 VAL Chi-restraints excluded: chain a residue 226 LEU Chi-restraints excluded: chain 3 residue 130 VAL Chi-restraints excluded: chain 3 residue 138 ASN Chi-restraints excluded: chain 3 residue 178 LEU Chi-restraints excluded: chain 3 residue 238 THR Chi-restraints excluded: chain 3 residue 260 THR Chi-restraints excluded: chain 4 residue 101 LEU Chi-restraints excluded: chain 4 residue 264 THR Chi-restraints excluded: chain 4 residue 279 SER Chi-restraints excluded: chain 5 residue 72 TRP Chi-restraints excluded: chain 5 residue 139 LEU Chi-restraints excluded: chain 5 residue 187 ASP Chi-restraints excluded: chain 5 residue 199 LEU Chi-restraints excluded: chain 5 residue 212 ILE Chi-restraints excluded: chain 5 residue 253 VAL Chi-restraints excluded: chain 6 residue 98 THR Chi-restraints excluded: chain 6 residue 135 HIS Chi-restraints excluded: chain 6 residue 155 ASP Chi-restraints excluded: chain 6 residue 167 SER Chi-restraints excluded: chain 6 residue 221 VAL Chi-restraints excluded: chain 6 residue 229 ASP Chi-restraints excluded: chain 6 residue 288 GLN Chi-restraints excluded: chain 7 residue 88 LEU Chi-restraints excluded: chain 7 residue 125 PHE Chi-restraints excluded: chain 7 residue 207 GLN Chi-restraints excluded: chain 8 residue 264 THR Chi-restraints excluded: chain 8 residue 267 VAL Chi-restraints excluded: chain 2 residue 63 VAL Chi-restraints excluded: chain 2 residue 66 LEU Chi-restraints excluded: chain 2 residue 144 LEU Chi-restraints excluded: chain 2 residue 169 LEU Chi-restraints excluded: chain 9 residue 54 LEU Chi-restraints excluded: chain 9 residue 127 TYR Chi-restraints excluded: chain 9 residue 131 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 388 optimal weight: 20.0000 chunk 295 optimal weight: 10.0000 chunk 203 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 187 optimal weight: 4.9990 chunk 263 optimal weight: 20.0000 chunk 394 optimal weight: 5.9990 chunk 417 optimal weight: 40.0000 chunk 206 optimal weight: 10.0000 chunk 373 optimal weight: 9.9990 chunk 112 optimal weight: 7.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 615 GLN ** B 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 604 GLN B 606 ASN F 117 ASN F 221 ASN 1 58 ASN ** 3 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 192 GLN 5 164 ASN ** 6 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 129 ASN 2 43 ASN ** 2 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 178 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 52731 Z= 0.226 Angle : 0.960 26.328 75353 Z= 0.370 Chirality : 0.055 1.695 6192 Planarity : 0.005 0.066 9997 Dihedral : 20.445 110.227 9273 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 17.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 4.23 % Allowed : 13.41 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.13), residues: 4330 helix: -0.17 (0.11), residues: 2273 sheet: -2.04 (0.49), residues: 91 loop : -1.70 (0.14), residues: 1966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP a 129 HIS 0.010 0.002 HIS B 415 PHE 0.019 0.002 PHE I 96 TYR 0.019 0.002 TYR F 118 ARG 0.004 0.000 ARG F 212 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8660 Ramachandran restraints generated. 4330 Oldfield, 0 Emsley, 4330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8660 Ramachandran restraints generated. 4330 Oldfield, 0 Emsley, 4330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 722 residues out of total 3413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 578 time to evaluate : 4.170 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 ASP cc_start: 0.7290 (m-30) cc_final: 0.7008 (m-30) REVERT: A 272 TYR cc_start: 0.8422 (m-80) cc_final: 0.8207 (m-10) REVERT: B 57 ILE cc_start: 0.8855 (mt) cc_final: 0.8560 (mt) REVERT: B 493 LEU cc_start: 0.6128 (mp) cc_final: 0.5699 (mp) REVERT: B 695 LYS cc_start: 0.8461 (mmmt) cc_final: 0.8013 (tmtt) REVERT: G 129 ASN cc_start: 0.5753 (p0) cc_final: 0.4073 (t0) REVERT: a 91 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.7981 (tp) REVERT: a 92 LYS cc_start: 0.8263 (ttpt) cc_final: 0.7873 (tptt) REVERT: a 98 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7581 (tt0) REVERT: 3 152 ILE cc_start: 0.9243 (mm) cc_final: 0.8964 (tt) REVERT: 4 101 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8673 (mp) REVERT: 5 72 TRP cc_start: 0.8305 (OUTLIER) cc_final: 0.7903 (t60) REVERT: 5 99 MET cc_start: 0.8586 (mtm) cc_final: 0.8369 (mtt) REVERT: 5 130 PHE cc_start: 0.8185 (m-80) cc_final: 0.7947 (m-80) REVERT: 5 144 ILE cc_start: 0.9273 (mt) cc_final: 0.8851 (mp) REVERT: 5 195 ASN cc_start: 0.5738 (t0) cc_final: 0.5217 (p0) REVERT: 5 269 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8353 (mm) REVERT: 7 240 ILE cc_start: 0.7538 (mt) cc_final: 0.7138 (mt) REVERT: 8 98 TYR cc_start: 0.8235 (m-10) cc_final: 0.7860 (m-80) REVERT: 2 11 MET cc_start: 0.3594 (mmt) cc_final: 0.3390 (mmt) REVERT: 2 30 TYR cc_start: 0.4667 (m-80) cc_final: 0.4275 (m-80) REVERT: 2 130 LYS cc_start: 0.5095 (ptmm) cc_final: 0.4178 (mptt) REVERT: 9 131 LYS cc_start: 0.1166 (OUTLIER) cc_final: 0.0611 (ptmt) outliers start: 144 outliers final: 88 residues processed: 678 average time/residue: 0.5821 time to fit residues: 668.3416 Evaluate side-chains 623 residues out of total 3413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 529 time to evaluate : 4.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 415 ARG Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 657 VAL Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 676 HIS Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 97 PHE Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 412 MET Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 578 TYR Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 211 LYS Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 234 LYS Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain I residue 87 LEU Chi-restraints excluded: chain J residue 10 THR Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain K residue 88 SER Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain K residue 132 THR Chi-restraints excluded: chain K residue 133 ILE Chi-restraints excluded: chain K residue 160 LEU Chi-restraints excluded: chain L residue 132 SER Chi-restraints excluded: chain L residue 174 THR Chi-restraints excluded: chain L residue 180 SER Chi-restraints excluded: chain L residue 181 LEU Chi-restraints excluded: chain L residue 182 SER Chi-restraints excluded: chain L residue 196 ILE Chi-restraints excluded: chain 1 residue 63 SER Chi-restraints excluded: chain 1 residue 83 SER Chi-restraints excluded: chain 1 residue 99 VAL Chi-restraints excluded: chain 1 residue 115 VAL Chi-restraints excluded: chain 1 residue 209 LEU Chi-restraints excluded: chain a residue 91 LEU Chi-restraints excluded: chain a residue 98 GLU Chi-restraints excluded: chain a residue 151 LEU Chi-restraints excluded: chain 3 residue 138 ASN Chi-restraints excluded: chain 3 residue 178 LEU Chi-restraints excluded: chain 3 residue 218 ILE Chi-restraints excluded: chain 3 residue 238 THR Chi-restraints excluded: chain 3 residue 260 THR Chi-restraints excluded: chain 4 residue 86 SER Chi-restraints excluded: chain 4 residue 101 LEU Chi-restraints excluded: chain 4 residue 264 THR Chi-restraints excluded: chain 4 residue 265 THR Chi-restraints excluded: chain 5 residue 72 TRP Chi-restraints excluded: chain 5 residue 131 THR Chi-restraints excluded: chain 5 residue 199 LEU Chi-restraints excluded: chain 5 residue 212 ILE Chi-restraints excluded: chain 5 residue 269 LEU Chi-restraints excluded: chain 6 residue 98 THR Chi-restraints excluded: chain 6 residue 135 HIS Chi-restraints excluded: chain 6 residue 155 ASP Chi-restraints excluded: chain 6 residue 167 SER Chi-restraints excluded: chain 6 residue 221 VAL Chi-restraints excluded: chain 6 residue 229 ASP Chi-restraints excluded: chain 7 residue 32 VAL Chi-restraints excluded: chain 7 residue 88 LEU Chi-restraints excluded: chain 7 residue 125 PHE Chi-restraints excluded: chain 7 residue 207 GLN Chi-restraints excluded: chain 8 residue 264 THR Chi-restraints excluded: chain 8 residue 267 VAL Chi-restraints excluded: chain 2 residue 63 VAL Chi-restraints excluded: chain 2 residue 66 LEU Chi-restraints excluded: chain 2 residue 91 LEU Chi-restraints excluded: chain 2 residue 93 LEU Chi-restraints excluded: chain 2 residue 116 THR Chi-restraints excluded: chain 2 residue 144 LEU Chi-restraints excluded: chain 2 residue 169 LEU Chi-restraints excluded: chain 9 residue 54 LEU Chi-restraints excluded: chain 9 residue 127 TYR Chi-restraints excluded: chain 9 residue 131 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 347 optimal weight: 10.0000 chunk 237 optimal weight: 6.9990 chunk 6 optimal weight: 0.9980 chunk 310 optimal weight: 0.0980 chunk 172 optimal weight: 4.9990 chunk 356 optimal weight: 10.0000 chunk 288 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 213 optimal weight: 1.9990 chunk 374 optimal weight: 5.9990 chunk 105 optimal weight: 50.0000 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 501 ASN ** B 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 117 ASN 1 58 ASN ** 3 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 114 GLN 4 192 GLN 6 288 GLN 7 114 ASN 2 155 GLN 2 178 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 52731 Z= 0.167 Angle : 0.923 25.960 75353 Z= 0.353 Chirality : 0.054 1.705 6192 Planarity : 0.005 0.062 9997 Dihedral : 19.614 109.062 9273 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 17.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 3.38 % Allowed : 14.35 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.13), residues: 4330 helix: 0.17 (0.11), residues: 2269 sheet: -1.85 (0.51), residues: 91 loop : -1.58 (0.14), residues: 1970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP 1 138 HIS 0.010 0.001 HIS 6 135 PHE 0.031 0.001 PHE 2 47 TYR 0.023 0.002 TYR B 359 ARG 0.006 0.000 ARG K 97 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8660 Ramachandran restraints generated. 4330 Oldfield, 0 Emsley, 4330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8660 Ramachandran restraints generated. 4330 Oldfield, 0 Emsley, 4330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 694 residues out of total 3413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 579 time to evaluate : 3.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ASP cc_start: 0.7281 (m-30) cc_final: 0.6999 (m-30) REVERT: B 57 ILE cc_start: 0.8826 (mt) cc_final: 0.8516 (mt) REVERT: B 477 PHE cc_start: 0.6663 (t80) cc_final: 0.6315 (t80) REVERT: B 695 LYS cc_start: 0.8473 (mmmt) cc_final: 0.8005 (tmtt) REVERT: C 39 MET cc_start: 0.7688 (ttm) cc_final: 0.7389 (ttm) REVERT: G 129 ASN cc_start: 0.5876 (p0) cc_final: 0.4199 (t0) REVERT: a 91 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7867 (tp) REVERT: a 92 LYS cc_start: 0.8190 (ttpt) cc_final: 0.7849 (tptt) REVERT: a 98 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7461 (tt0) REVERT: a 154 GLU cc_start: 0.5620 (mt-10) cc_final: 0.5389 (tp30) REVERT: a 164 GLN cc_start: 0.6616 (mm110) cc_final: 0.6368 (mm110) REVERT: 3 152 ILE cc_start: 0.9170 (mm) cc_final: 0.8919 (tt) REVERT: 4 101 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8579 (mp) REVERT: 5 72 TRP cc_start: 0.8278 (OUTLIER) cc_final: 0.7791 (t60) REVERT: 5 130 PHE cc_start: 0.8072 (m-80) cc_final: 0.7706 (m-80) REVERT: 5 144 ILE cc_start: 0.9216 (mt) cc_final: 0.8805 (mp) REVERT: 5 269 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.7999 (mm) REVERT: 8 98 TYR cc_start: 0.8239 (m-10) cc_final: 0.7867 (m-80) REVERT: 2 130 LYS cc_start: 0.4866 (ptmm) cc_final: 0.3828 (mptt) REVERT: 2 176 HIS cc_start: 0.3856 (m-70) cc_final: 0.3253 (m-70) REVERT: 9 131 LYS cc_start: 0.1239 (OUTLIER) cc_final: 0.0649 (ptmt) REVERT: 9 173 CYS cc_start: 0.6891 (m) cc_final: 0.6671 (m) outliers start: 115 outliers final: 82 residues processed: 659 average time/residue: 0.5857 time to fit residues: 657.2670 Evaluate side-chains 614 residues out of total 3413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 526 time to evaluate : 4.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 415 ARG Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 604 SER Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 97 PHE Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 412 MET Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 521 HIS Chi-restraints excluded: chain B residue 578 TYR Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain D residue 211 LYS Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 234 LYS Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain I residue 87 LEU Chi-restraints excluded: chain J residue 10 THR Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain K residue 132 THR Chi-restraints excluded: chain K residue 133 ILE Chi-restraints excluded: chain K residue 160 LEU Chi-restraints excluded: chain L residue 174 THR Chi-restraints excluded: chain L residue 180 SER Chi-restraints excluded: chain L residue 181 LEU Chi-restraints excluded: chain L residue 182 SER Chi-restraints excluded: chain L residue 196 ILE Chi-restraints excluded: chain 1 residue 58 ASN Chi-restraints excluded: chain 1 residue 209 LEU Chi-restraints excluded: chain a residue 91 LEU Chi-restraints excluded: chain a residue 98 GLU Chi-restraints excluded: chain a residue 151 LEU Chi-restraints excluded: chain 3 residue 138 ASN Chi-restraints excluded: chain 3 residue 178 LEU Chi-restraints excluded: chain 3 residue 218 ILE Chi-restraints excluded: chain 3 residue 238 THR Chi-restraints excluded: chain 3 residue 252 ASP Chi-restraints excluded: chain 3 residue 260 THR Chi-restraints excluded: chain 4 residue 93 LEU Chi-restraints excluded: chain 4 residue 101 LEU Chi-restraints excluded: chain 4 residue 265 THR Chi-restraints excluded: chain 4 residue 279 SER Chi-restraints excluded: chain 5 residue 72 TRP Chi-restraints excluded: chain 5 residue 131 THR Chi-restraints excluded: chain 5 residue 269 LEU Chi-restraints excluded: chain 6 residue 98 THR Chi-restraints excluded: chain 6 residue 135 HIS Chi-restraints excluded: chain 6 residue 150 GLU Chi-restraints excluded: chain 6 residue 155 ASP Chi-restraints excluded: chain 6 residue 167 SER Chi-restraints excluded: chain 6 residue 221 VAL Chi-restraints excluded: chain 6 residue 229 ASP Chi-restraints excluded: chain 6 residue 288 GLN Chi-restraints excluded: chain 7 residue 32 VAL Chi-restraints excluded: chain 7 residue 88 LEU Chi-restraints excluded: chain 7 residue 125 PHE Chi-restraints excluded: chain 7 residue 207 GLN Chi-restraints excluded: chain 8 residue 189 LEU Chi-restraints excluded: chain 8 residue 247 VAL Chi-restraints excluded: chain 8 residue 264 THR Chi-restraints excluded: chain 8 residue 267 VAL Chi-restraints excluded: chain 2 residue 63 VAL Chi-restraints excluded: chain 2 residue 66 LEU Chi-restraints excluded: chain 2 residue 93 LEU Chi-restraints excluded: chain 2 residue 116 THR Chi-restraints excluded: chain 2 residue 144 LEU Chi-restraints excluded: chain 2 residue 169 LEU Chi-restraints excluded: chain 9 residue 54 LEU Chi-restraints excluded: chain 9 residue 127 TYR Chi-restraints excluded: chain 9 residue 131 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 140 optimal weight: 0.9990 chunk 376 optimal weight: 20.0000 chunk 82 optimal weight: 7.9990 chunk 245 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 417 optimal weight: 30.0000 chunk 346 optimal weight: 30.0000 chunk 193 optimal weight: 40.0000 chunk 34 optimal weight: 20.0000 chunk 138 optimal weight: 10.0000 chunk 219 optimal weight: 0.0070 overall best weight: 2.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 615 GLN ** B 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 117 ASN ** 1 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 214 GLN ** 3 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 179 GLN 4 192 GLN 5 134 ASN 8 129 ASN ** 2 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 52731 Z= 0.176 Angle : 0.914 26.159 75353 Z= 0.350 Chirality : 0.053 1.700 6192 Planarity : 0.005 0.067 9997 Dihedral : 19.094 110.574 9273 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 16.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 3.46 % Allowed : 15.56 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.39 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.13), residues: 4330 helix: 0.35 (0.11), residues: 2277 sheet: -1.88 (0.51), residues: 93 loop : -1.50 (0.14), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP a 129 HIS 0.010 0.001 HIS 6 135 PHE 0.033 0.001 PHE K 76 TYR 0.022 0.002 TYR 5 118 ARG 0.005 0.000 ARG K 97 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8660 Ramachandran restraints generated. 4330 Oldfield, 0 Emsley, 4330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8660 Ramachandran restraints generated. 4330 Oldfield, 0 Emsley, 4330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 675 residues out of total 3413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 557 time to evaluate : 4.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ASP cc_start: 0.7304 (m-30) cc_final: 0.7076 (m-30) REVERT: B 57 ILE cc_start: 0.8833 (mt) cc_final: 0.8508 (mt) REVERT: B 301 ARG cc_start: 0.6966 (ptt180) cc_final: 0.6214 (ptp-170) REVERT: B 477 PHE cc_start: 0.6730 (t80) cc_final: 0.6353 (t80) REVERT: B 695 LYS cc_start: 0.8459 (mmmt) cc_final: 0.8031 (tmtt) REVERT: 1 93 ARG cc_start: 0.7171 (tmt170) cc_final: 0.6861 (tmt170) REVERT: 1 139 PHE cc_start: 0.7261 (OUTLIER) cc_final: 0.6777 (m-80) REVERT: a 91 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7756 (tp) REVERT: a 98 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7537 (tt0) REVERT: a 164 GLN cc_start: 0.6585 (mm110) cc_final: 0.6335 (mm110) REVERT: 4 101 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8610 (mp) REVERT: 5 72 TRP cc_start: 0.8273 (OUTLIER) cc_final: 0.7773 (t60) REVERT: 5 144 ILE cc_start: 0.9226 (mt) cc_final: 0.8798 (mp) REVERT: 8 98 TYR cc_start: 0.8249 (m-10) cc_final: 0.7876 (m-80) REVERT: 2 130 LYS cc_start: 0.4955 (ptmm) cc_final: 0.3889 (mptt) REVERT: 9 131 LYS cc_start: 0.1203 (OUTLIER) cc_final: 0.0557 (ptmt) REVERT: 9 173 CYS cc_start: 0.6945 (m) cc_final: 0.6744 (m) outliers start: 118 outliers final: 89 residues processed: 631 average time/residue: 0.5995 time to fit residues: 644.4878 Evaluate side-chains 629 residues out of total 3413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 534 time to evaluate : 3.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain A residue 415 ARG Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 604 SER Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 676 HIS Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 97 PHE Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 412 MET Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 521 HIS Chi-restraints excluded: chain B residue 578 TYR Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain D residue 211 LYS Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 234 LYS Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain I residue 77 SER Chi-restraints excluded: chain I residue 87 LEU Chi-restraints excluded: chain J residue 10 THR Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain K residue 88 SER Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain K residue 132 THR Chi-restraints excluded: chain K residue 133 ILE Chi-restraints excluded: chain K residue 160 LEU Chi-restraints excluded: chain L residue 132 SER Chi-restraints excluded: chain L residue 174 THR Chi-restraints excluded: chain L residue 180 SER Chi-restraints excluded: chain L residue 181 LEU Chi-restraints excluded: chain L residue 182 SER Chi-restraints excluded: chain L residue 196 ILE Chi-restraints excluded: chain 1 residue 115 VAL Chi-restraints excluded: chain 1 residue 139 PHE Chi-restraints excluded: chain 1 residue 209 LEU Chi-restraints excluded: chain a residue 91 LEU Chi-restraints excluded: chain a residue 98 GLU Chi-restraints excluded: chain a residue 151 LEU Chi-restraints excluded: chain 3 residue 138 ASN Chi-restraints excluded: chain 3 residue 178 LEU Chi-restraints excluded: chain 3 residue 218 ILE Chi-restraints excluded: chain 3 residue 237 MET Chi-restraints excluded: chain 3 residue 260 THR Chi-restraints excluded: chain 4 residue 86 SER Chi-restraints excluded: chain 4 residue 93 LEU Chi-restraints excluded: chain 4 residue 101 LEU Chi-restraints excluded: chain 4 residue 265 THR Chi-restraints excluded: chain 5 residue 72 TRP Chi-restraints excluded: chain 5 residue 131 THR Chi-restraints excluded: chain 5 residue 168 ILE Chi-restraints excluded: chain 5 residue 199 LEU Chi-restraints excluded: chain 6 residue 98 THR Chi-restraints excluded: chain 6 residue 135 HIS Chi-restraints excluded: chain 6 residue 150 GLU Chi-restraints excluded: chain 6 residue 155 ASP Chi-restraints excluded: chain 6 residue 167 SER Chi-restraints excluded: chain 6 residue 182 MET Chi-restraints excluded: chain 6 residue 221 VAL Chi-restraints excluded: chain 6 residue 229 ASP Chi-restraints excluded: chain 7 residue 32 VAL Chi-restraints excluded: chain 7 residue 88 LEU Chi-restraints excluded: chain 7 residue 125 PHE Chi-restraints excluded: chain 7 residue 207 GLN Chi-restraints excluded: chain 8 residue 182 PHE Chi-restraints excluded: chain 8 residue 189 LEU Chi-restraints excluded: chain 8 residue 247 VAL Chi-restraints excluded: chain 8 residue 264 THR Chi-restraints excluded: chain 8 residue 267 VAL Chi-restraints excluded: chain 2 residue 63 VAL Chi-restraints excluded: chain 2 residue 116 THR Chi-restraints excluded: chain 2 residue 144 LEU Chi-restraints excluded: chain 2 residue 169 LEU Chi-restraints excluded: chain 9 residue 54 LEU Chi-restraints excluded: chain 9 residue 127 TYR Chi-restraints excluded: chain 9 residue 131 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 402 optimal weight: 30.0000 chunk 47 optimal weight: 5.9990 chunk 238 optimal weight: 50.0000 chunk 305 optimal weight: 9.9990 chunk 236 optimal weight: 4.9990 chunk 351 optimal weight: 30.0000 chunk 233 optimal weight: 6.9990 chunk 416 optimal weight: 20.0000 chunk 260 optimal weight: 50.0000 chunk 253 optimal weight: 0.0870 chunk 192 optimal weight: 40.0000 overall best weight: 5.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 615 GLN ** B 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 117 ASN ** G 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 58 ASN ** 1 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 256 ASN ** 4 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 192 GLN ** 6 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 129 ASN 2 155 GLN ** 2 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 52731 Z= 0.270 Angle : 0.960 26.299 75353 Z= 0.372 Chirality : 0.056 1.685 6192 Planarity : 0.005 0.070 9997 Dihedral : 19.170 112.071 9273 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 18.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 3.64 % Allowed : 16.17 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.39 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.13), residues: 4330 helix: 0.38 (0.11), residues: 2282 sheet: -1.86 (0.52), residues: 85 loop : -1.42 (0.15), residues: 1963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP a 129 HIS 0.011 0.002 HIS 6 135 PHE 0.019 0.002 PHE B 714 TYR 0.023 0.002 TYR F 118 ARG 0.007 0.001 ARG K 97 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8660 Ramachandran restraints generated. 4330 Oldfield, 0 Emsley, 4330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8660 Ramachandran restraints generated. 4330 Oldfield, 0 Emsley, 4330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 677 residues out of total 3413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 553 time to evaluate : 3.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ASP cc_start: 0.7248 (m-30) cc_final: 0.6984 (m-30) REVERT: A 415 ARG cc_start: 0.7677 (OUTLIER) cc_final: 0.7323 (mtt180) REVERT: A 536 HIS cc_start: 0.8637 (OUTLIER) cc_final: 0.7925 (m90) REVERT: B 57 ILE cc_start: 0.8880 (mt) cc_final: 0.8662 (mt) REVERT: B 301 ARG cc_start: 0.7043 (ptt180) cc_final: 0.6264 (ptp-170) REVERT: B 477 PHE cc_start: 0.6786 (t80) cc_final: 0.6442 (t80) REVERT: G 129 ASN cc_start: 0.5716 (p0) cc_final: 0.4091 (t0) REVERT: K 76 PHE cc_start: 0.7587 (t80) cc_final: 0.7374 (t80) REVERT: 1 93 ARG cc_start: 0.7222 (tmt170) cc_final: 0.6922 (tmt170) REVERT: a 91 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7797 (tp) REVERT: a 98 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7783 (tt0) REVERT: a 164 GLN cc_start: 0.6692 (mm110) cc_final: 0.6438 (mm110) REVERT: 4 101 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8647 (mp) REVERT: 5 72 TRP cc_start: 0.8446 (OUTLIER) cc_final: 0.8028 (t60) REVERT: 5 130 PHE cc_start: 0.7904 (m-80) cc_final: 0.7658 (m-80) REVERT: 5 144 ILE cc_start: 0.9293 (mt) cc_final: 0.8836 (mp) REVERT: 7 240 ILE cc_start: 0.7575 (mt) cc_final: 0.7185 (mt) REVERT: 8 98 TYR cc_start: 0.8324 (m-10) cc_final: 0.7935 (m-80) REVERT: 2 130 LYS cc_start: 0.5132 (ptmm) cc_final: 0.4058 (mptt) REVERT: 9 131 LYS cc_start: 0.1206 (OUTLIER) cc_final: 0.0546 (ptmt) outliers start: 124 outliers final: 93 residues processed: 631 average time/residue: 0.6019 time to fit residues: 644.3062 Evaluate side-chains 624 residues out of total 3413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 524 time to evaluate : 4.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ASP Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 415 ARG Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 536 HIS Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 604 SER Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 676 HIS Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 97 PHE Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 578 TYR Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 234 LYS Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 210 LEU Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain I residue 77 SER Chi-restraints excluded: chain I residue 87 LEU Chi-restraints excluded: chain J residue 10 THR Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain K residue 88 SER Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain K residue 133 ILE Chi-restraints excluded: chain K residue 160 LEU Chi-restraints excluded: chain L residue 132 SER Chi-restraints excluded: chain L residue 174 THR Chi-restraints excluded: chain L residue 180 SER Chi-restraints excluded: chain L residue 181 LEU Chi-restraints excluded: chain L residue 182 SER Chi-restraints excluded: chain L residue 196 ILE Chi-restraints excluded: chain 1 residue 63 SER Chi-restraints excluded: chain 1 residue 83 SER Chi-restraints excluded: chain 1 residue 115 VAL Chi-restraints excluded: chain 1 residue 209 LEU Chi-restraints excluded: chain a residue 91 LEU Chi-restraints excluded: chain a residue 98 GLU Chi-restraints excluded: chain a residue 151 LEU Chi-restraints excluded: chain 3 residue 138 ASN Chi-restraints excluded: chain 3 residue 178 LEU Chi-restraints excluded: chain 3 residue 218 ILE Chi-restraints excluded: chain 3 residue 237 MET Chi-restraints excluded: chain 3 residue 260 THR Chi-restraints excluded: chain 4 residue 86 SER Chi-restraints excluded: chain 4 residue 92 ASP Chi-restraints excluded: chain 4 residue 93 LEU Chi-restraints excluded: chain 4 residue 101 LEU Chi-restraints excluded: chain 4 residue 264 THR Chi-restraints excluded: chain 4 residue 265 THR Chi-restraints excluded: chain 4 residue 279 SER Chi-restraints excluded: chain 5 residue 72 TRP Chi-restraints excluded: chain 5 residue 131 THR Chi-restraints excluded: chain 5 residue 168 ILE Chi-restraints excluded: chain 5 residue 199 LEU Chi-restraints excluded: chain 5 residue 243 ASN Chi-restraints excluded: chain 6 residue 98 THR Chi-restraints excluded: chain 6 residue 135 HIS Chi-restraints excluded: chain 6 residue 150 GLU Chi-restraints excluded: chain 6 residue 155 ASP Chi-restraints excluded: chain 6 residue 167 SER Chi-restraints excluded: chain 6 residue 182 MET Chi-restraints excluded: chain 6 residue 221 VAL Chi-restraints excluded: chain 6 residue 229 ASP Chi-restraints excluded: chain 7 residue 32 VAL Chi-restraints excluded: chain 7 residue 88 LEU Chi-restraints excluded: chain 7 residue 125 PHE Chi-restraints excluded: chain 7 residue 207 GLN Chi-restraints excluded: chain 8 residue 118 ILE Chi-restraints excluded: chain 8 residue 182 PHE Chi-restraints excluded: chain 8 residue 264 THR Chi-restraints excluded: chain 8 residue 267 VAL Chi-restraints excluded: chain 2 residue 63 VAL Chi-restraints excluded: chain 2 residue 116 THR Chi-restraints excluded: chain 2 residue 144 LEU Chi-restraints excluded: chain 2 residue 169 LEU Chi-restraints excluded: chain 9 residue 54 LEU Chi-restraints excluded: chain 9 residue 127 TYR Chi-restraints excluded: chain 9 residue 131 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 257 optimal weight: 50.0000 chunk 166 optimal weight: 10.0000 chunk 248 optimal weight: 10.0000 chunk 125 optimal weight: 10.0000 chunk 81 optimal weight: 9.9990 chunk 80 optimal weight: 8.9990 chunk 264 optimal weight: 5.9990 chunk 283 optimal weight: 9.9990 chunk 205 optimal weight: 9.9990 chunk 38 optimal weight: 10.0000 chunk 327 optimal weight: 8.9990 overall best weight: 8.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 GLN B 161 ASN ** B 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 491 GLN D 159 GLN F 117 ASN ** G 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 58 ASN ** 1 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 288 GLN 7 218 ASN 8 64 GLN 8 129 ASN ** 2 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.3461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 52731 Z= 0.375 Angle : 1.033 26.537 75353 Z= 0.406 Chirality : 0.059 1.676 6192 Planarity : 0.006 0.076 9997 Dihedral : 19.676 113.899 9273 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 20.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 3.70 % Allowed : 16.64 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.13), residues: 4330 helix: 0.17 (0.11), residues: 2288 sheet: -1.90 (0.51), residues: 85 loop : -1.52 (0.14), residues: 1957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP a 129 HIS 0.012 0.002 HIS 6 135 PHE 0.032 0.002 PHE 7 170 TYR 0.033 0.002 TYR B 359 ARG 0.008 0.001 ARG K 97 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8660 Ramachandran restraints generated. 4330 Oldfield, 0 Emsley, 4330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8660 Ramachandran restraints generated. 4330 Oldfield, 0 Emsley, 4330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 655 residues out of total 3413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 529 time to evaluate : 4.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ASP cc_start: 0.7218 (m-30) cc_final: 0.6994 (m-30) REVERT: A 415 ARG cc_start: 0.7725 (OUTLIER) cc_final: 0.7353 (mtt180) REVERT: A 536 HIS cc_start: 0.8725 (OUTLIER) cc_final: 0.8006 (m90) REVERT: B 57 ILE cc_start: 0.8918 (mt) cc_final: 0.8715 (mt) REVERT: B 301 ARG cc_start: 0.7082 (ptt180) cc_final: 0.6315 (ptp-170) REVERT: B 477 PHE cc_start: 0.6746 (t80) cc_final: 0.6400 (t80) REVERT: B 695 LYS cc_start: 0.8465 (mmmt) cc_final: 0.8046 (tmtt) REVERT: D 205 ASP cc_start: 0.8044 (p0) cc_final: 0.7751 (p0) REVERT: 1 93 ARG cc_start: 0.7261 (tmt170) cc_final: 0.6993 (tmt170) REVERT: a 55 LYS cc_start: 0.7770 (tttm) cc_final: 0.7568 (tmtt) REVERT: a 98 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7806 (tt0) REVERT: a 164 GLN cc_start: 0.6839 (mm110) cc_final: 0.6462 (mm110) REVERT: 3 122 ASN cc_start: 0.7989 (t0) cc_final: 0.7681 (t0) REVERT: 4 101 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8700 (mp) REVERT: 5 72 TRP cc_start: 0.8588 (OUTLIER) cc_final: 0.8240 (t60) REVERT: 5 144 ILE cc_start: 0.9361 (OUTLIER) cc_final: 0.8885 (mp) REVERT: 6 314 GLN cc_start: 0.7212 (tp40) cc_final: 0.6959 (tp40) REVERT: 7 240 ILE cc_start: 0.7702 (mt) cc_final: 0.7343 (mt) REVERT: 8 260 VAL cc_start: 0.8351 (t) cc_final: 0.8129 (p) REVERT: 9 131 LYS cc_start: 0.1321 (OUTLIER) cc_final: 0.0635 (ptmt) REVERT: 9 201 TYR cc_start: 0.2494 (m-80) cc_final: 0.2200 (m-80) outliers start: 126 outliers final: 100 residues processed: 612 average time/residue: 0.5809 time to fit residues: 603.3955 Evaluate side-chains 613 residues out of total 3413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 506 time to evaluate : 4.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ASP Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 415 ARG Chi-restraints excluded: chain A residue 463 SER Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 536 HIS Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 604 SER Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 676 HIS Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 97 PHE Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 578 TYR Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 234 LYS Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 101 GLN Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 210 LEU Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain I residue 77 SER Chi-restraints excluded: chain I residue 87 LEU Chi-restraints excluded: chain J residue 10 THR Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain K residue 88 SER Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain K residue 133 ILE Chi-restraints excluded: chain K residue 160 LEU Chi-restraints excluded: chain L residue 132 SER Chi-restraints excluded: chain L residue 174 THR Chi-restraints excluded: chain L residue 180 SER Chi-restraints excluded: chain L residue 181 LEU Chi-restraints excluded: chain L residue 182 SER Chi-restraints excluded: chain L residue 196 ILE Chi-restraints excluded: chain 1 residue 63 SER Chi-restraints excluded: chain 1 residue 83 SER Chi-restraints excluded: chain 1 residue 99 VAL Chi-restraints excluded: chain 1 residue 115 VAL Chi-restraints excluded: chain a residue 98 GLU Chi-restraints excluded: chain a residue 151 LEU Chi-restraints excluded: chain 3 residue 138 ASN Chi-restraints excluded: chain 3 residue 178 LEU Chi-restraints excluded: chain 3 residue 237 MET Chi-restraints excluded: chain 3 residue 260 THR Chi-restraints excluded: chain 4 residue 86 SER Chi-restraints excluded: chain 4 residue 92 ASP Chi-restraints excluded: chain 4 residue 101 LEU Chi-restraints excluded: chain 4 residue 264 THR Chi-restraints excluded: chain 4 residue 279 SER Chi-restraints excluded: chain 4 residue 285 ASN Chi-restraints excluded: chain 5 residue 72 TRP Chi-restraints excluded: chain 5 residue 106 LEU Chi-restraints excluded: chain 5 residue 131 THR Chi-restraints excluded: chain 5 residue 144 ILE Chi-restraints excluded: chain 5 residue 168 ILE Chi-restraints excluded: chain 5 residue 243 ASN Chi-restraints excluded: chain 5 residue 248 ILE Chi-restraints excluded: chain 6 residue 98 THR Chi-restraints excluded: chain 6 residue 135 HIS Chi-restraints excluded: chain 6 residue 150 GLU Chi-restraints excluded: chain 6 residue 155 ASP Chi-restraints excluded: chain 6 residue 167 SER Chi-restraints excluded: chain 6 residue 182 MET Chi-restraints excluded: chain 6 residue 221 VAL Chi-restraints excluded: chain 6 residue 229 ASP Chi-restraints excluded: chain 6 residue 272 ASP Chi-restraints excluded: chain 6 residue 281 LYS Chi-restraints excluded: chain 7 residue 32 VAL Chi-restraints excluded: chain 7 residue 88 LEU Chi-restraints excluded: chain 7 residue 125 PHE Chi-restraints excluded: chain 7 residue 207 GLN Chi-restraints excluded: chain 8 residue 118 ILE Chi-restraints excluded: chain 8 residue 139 VAL Chi-restraints excluded: chain 8 residue 182 PHE Chi-restraints excluded: chain 8 residue 212 ASP Chi-restraints excluded: chain 8 residue 247 VAL Chi-restraints excluded: chain 8 residue 264 THR Chi-restraints excluded: chain 8 residue 267 VAL Chi-restraints excluded: chain 2 residue 63 VAL Chi-restraints excluded: chain 2 residue 116 THR Chi-restraints excluded: chain 2 residue 144 LEU Chi-restraints excluded: chain 2 residue 169 LEU Chi-restraints excluded: chain 9 residue 54 LEU Chi-restraints excluded: chain 9 residue 127 TYR Chi-restraints excluded: chain 9 residue 131 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 378 optimal weight: 20.0000 chunk 398 optimal weight: 20.0000 chunk 363 optimal weight: 9.9990 chunk 388 optimal weight: 0.8980 chunk 233 optimal weight: 5.9990 chunk 169 optimal weight: 20.0000 chunk 304 optimal weight: 6.9990 chunk 119 optimal weight: 2.9990 chunk 350 optimal weight: 9.9990 chunk 366 optimal weight: 0.6980 chunk 386 optimal weight: 5.9990 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 615 GLN B 161 ASN ** B 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 159 GLN F 117 ASN ** G 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 58 ASN ** 1 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 244 GLN 4 179 GLN 8 129 ASN 2 177 ASN ** 9 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.3533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 52731 Z= 0.201 Angle : 0.933 25.947 75353 Z= 0.361 Chirality : 0.055 1.686 6192 Planarity : 0.005 0.073 9997 Dihedral : 18.901 111.666 9273 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 18.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 3.08 % Allowed : 17.73 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.13), residues: 4330 helix: 0.41 (0.11), residues: 2286 sheet: -1.93 (0.52), residues: 85 loop : -1.45 (0.15), residues: 1959 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP 1 138 HIS 0.010 0.001 HIS 6 135 PHE 0.028 0.001 PHE 7 170 TYR 0.021 0.002 TYR B 359 ARG 0.006 0.000 ARG K 97 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8660 Ramachandran restraints generated. 4330 Oldfield, 0 Emsley, 4330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8660 Ramachandran restraints generated. 4330 Oldfield, 0 Emsley, 4330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 653 residues out of total 3413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 548 time to evaluate : 3.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ASP cc_start: 0.7269 (m-30) cc_final: 0.6979 (m-30) REVERT: A 536 HIS cc_start: 0.8460 (OUTLIER) cc_final: 0.7624 (m90) REVERT: B 57 ILE cc_start: 0.8849 (mt) cc_final: 0.8561 (mt) REVERT: B 301 ARG cc_start: 0.7032 (ptt180) cc_final: 0.6319 (ptp-170) REVERT: B 477 PHE cc_start: 0.6681 (t80) cc_final: 0.6322 (t80) REVERT: B 695 LYS cc_start: 0.8504 (mmmt) cc_final: 0.8096 (tmtt) REVERT: D 205 ASP cc_start: 0.7877 (p0) cc_final: 0.7552 (p0) REVERT: G 129 ASN cc_start: 0.5920 (p0) cc_final: 0.4208 (t0) REVERT: K 76 PHE cc_start: 0.7607 (t80) cc_final: 0.7254 (t80) REVERT: 1 93 ARG cc_start: 0.7063 (tmt170) cc_final: 0.6774 (tmt170) REVERT: a 98 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7736 (tt0) REVERT: a 164 GLN cc_start: 0.6705 (mm110) cc_final: 0.6312 (mm-40) REVERT: 3 122 ASN cc_start: 0.7927 (t0) cc_final: 0.7712 (t0) REVERT: 4 101 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8693 (mp) REVERT: 5 72 TRP cc_start: 0.8441 (OUTLIER) cc_final: 0.8019 (t60) REVERT: 5 144 ILE cc_start: 0.9281 (OUTLIER) cc_final: 0.8836 (mp) REVERT: 7 117 PHE cc_start: 0.8782 (t80) cc_final: 0.8508 (t80) REVERT: 7 240 ILE cc_start: 0.7426 (mt) cc_final: 0.7111 (mt) REVERT: 8 260 VAL cc_start: 0.8373 (t) cc_final: 0.8156 (p) REVERT: 2 130 LYS cc_start: 0.5188 (ptmm) cc_final: 0.4070 (mptt) REVERT: 9 131 LYS cc_start: 0.1255 (OUTLIER) cc_final: 0.0646 (ptmt) outliers start: 105 outliers final: 86 residues processed: 614 average time/residue: 0.5913 time to fit residues: 614.6626 Evaluate side-chains 606 residues out of total 3413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 514 time to evaluate : 4.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ASP Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 415 ARG Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 536 HIS Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 604 SER Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 97 PHE Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 578 TYR Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 234 LYS Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain I residue 77 SER Chi-restraints excluded: chain I residue 87 LEU Chi-restraints excluded: chain J residue 10 THR Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain K residue 88 SER Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain K residue 133 ILE Chi-restraints excluded: chain K residue 160 LEU Chi-restraints excluded: chain L residue 132 SER Chi-restraints excluded: chain L residue 174 THR Chi-restraints excluded: chain L residue 180 SER Chi-restraints excluded: chain L residue 181 LEU Chi-restraints excluded: chain L residue 182 SER Chi-restraints excluded: chain L residue 196 ILE Chi-restraints excluded: chain 1 residue 58 ASN Chi-restraints excluded: chain 1 residue 63 SER Chi-restraints excluded: chain 1 residue 83 SER Chi-restraints excluded: chain 1 residue 115 VAL Chi-restraints excluded: chain 1 residue 209 LEU Chi-restraints excluded: chain a residue 98 GLU Chi-restraints excluded: chain a residue 151 LEU Chi-restraints excluded: chain 3 residue 138 ASN Chi-restraints excluded: chain 3 residue 178 LEU Chi-restraints excluded: chain 3 residue 200 LEU Chi-restraints excluded: chain 3 residue 237 MET Chi-restraints excluded: chain 3 residue 260 THR Chi-restraints excluded: chain 4 residue 86 SER Chi-restraints excluded: chain 4 residue 92 ASP Chi-restraints excluded: chain 4 residue 101 LEU Chi-restraints excluded: chain 4 residue 264 THR Chi-restraints excluded: chain 4 residue 279 SER Chi-restraints excluded: chain 5 residue 72 TRP Chi-restraints excluded: chain 5 residue 131 THR Chi-restraints excluded: chain 5 residue 144 ILE Chi-restraints excluded: chain 5 residue 168 ILE Chi-restraints excluded: chain 5 residue 243 ASN Chi-restraints excluded: chain 6 residue 98 THR Chi-restraints excluded: chain 6 residue 135 HIS Chi-restraints excluded: chain 6 residue 150 GLU Chi-restraints excluded: chain 6 residue 155 ASP Chi-restraints excluded: chain 6 residue 182 MET Chi-restraints excluded: chain 6 residue 221 VAL Chi-restraints excluded: chain 6 residue 229 ASP Chi-restraints excluded: chain 6 residue 272 ASP Chi-restraints excluded: chain 7 residue 32 VAL Chi-restraints excluded: chain 7 residue 88 LEU Chi-restraints excluded: chain 7 residue 125 PHE Chi-restraints excluded: chain 7 residue 207 GLN Chi-restraints excluded: chain 8 residue 118 ILE Chi-restraints excluded: chain 8 residue 182 PHE Chi-restraints excluded: chain 8 residue 247 VAL Chi-restraints excluded: chain 8 residue 264 THR Chi-restraints excluded: chain 8 residue 267 VAL Chi-restraints excluded: chain 2 residue 63 VAL Chi-restraints excluded: chain 2 residue 116 THR Chi-restraints excluded: chain 2 residue 144 LEU Chi-restraints excluded: chain 2 residue 169 LEU Chi-restraints excluded: chain 2 residue 177 ASN Chi-restraints excluded: chain 9 residue 127 TYR Chi-restraints excluded: chain 9 residue 131 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 254 optimal weight: 20.0000 chunk 410 optimal weight: 6.9990 chunk 250 optimal weight: 5.9990 chunk 194 optimal weight: 20.0000 chunk 285 optimal weight: 20.0000 chunk 430 optimal weight: 50.0000 chunk 396 optimal weight: 9.9990 chunk 342 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 264 optimal weight: 8.9990 chunk 210 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 615 GLN ** B 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 159 GLN F 117 ASN 1 58 ASN ** 1 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.183 52731 Z= 0.259 Angle : 1.019 59.199 75353 Z= 0.440 Chirality : 0.055 1.683 6192 Planarity : 0.005 0.077 9997 Dihedral : 18.901 111.667 9273 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 19.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 2.64 % Allowed : 18.32 % Favored : 79.04 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.13), residues: 4330 helix: 0.42 (0.11), residues: 2286 sheet: -1.92 (0.52), residues: 85 loop : -1.44 (0.15), residues: 1959 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP 1 138 HIS 0.011 0.001 HIS 1 101 PHE 0.130 0.002 PHE 7 170 TYR 0.024 0.002 TYR L 130 ARG 0.009 0.000 ARG 1 103 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8660 Ramachandran restraints generated. 4330 Oldfield, 0 Emsley, 4330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8660 Ramachandran restraints generated. 4330 Oldfield, 0 Emsley, 4330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 603 residues out of total 3413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 513 time to evaluate : 4.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ASP cc_start: 0.7273 (m-30) cc_final: 0.6982 (m-30) REVERT: A 536 HIS cc_start: 0.8466 (OUTLIER) cc_final: 0.7638 (m90) REVERT: B 57 ILE cc_start: 0.8851 (mt) cc_final: 0.8565 (mt) REVERT: B 301 ARG cc_start: 0.7090 (ptt180) cc_final: 0.6322 (ptp-170) REVERT: B 477 PHE cc_start: 0.6681 (t80) cc_final: 0.6324 (t80) REVERT: B 695 LYS cc_start: 0.8503 (mmmt) cc_final: 0.8099 (tmtt) REVERT: D 205 ASP cc_start: 0.7878 (p0) cc_final: 0.7555 (p0) REVERT: G 129 ASN cc_start: 0.5921 (p0) cc_final: 0.4210 (t0) REVERT: K 76 PHE cc_start: 0.7612 (t80) cc_final: 0.7261 (t80) REVERT: 1 93 ARG cc_start: 0.7072 (tmt170) cc_final: 0.6782 (tmt170) REVERT: a 98 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7740 (tt0) REVERT: a 164 GLN cc_start: 0.6706 (mm110) cc_final: 0.6313 (mm-40) REVERT: 3 122 ASN cc_start: 0.7931 (t0) cc_final: 0.7714 (t0) REVERT: 4 101 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8696 (mp) REVERT: 5 72 TRP cc_start: 0.8452 (OUTLIER) cc_final: 0.8040 (t60) REVERT: 5 144 ILE cc_start: 0.9279 (OUTLIER) cc_final: 0.8838 (mp) REVERT: 7 117 PHE cc_start: 0.8783 (t80) cc_final: 0.8510 (t80) REVERT: 7 240 ILE cc_start: 0.7430 (mt) cc_final: 0.7116 (mt) REVERT: 8 260 VAL cc_start: 0.8384 (t) cc_final: 0.8159 (p) REVERT: 2 130 LYS cc_start: 0.5191 (ptmm) cc_final: 0.4070 (mptt) REVERT: 9 131 LYS cc_start: 0.1257 (OUTLIER) cc_final: 0.0647 (ptmt) outliers start: 90 outliers final: 81 residues processed: 567 average time/residue: 0.5930 time to fit residues: 569.3278 Evaluate side-chains 597 residues out of total 3413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 510 time to evaluate : 4.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ASP Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain A residue 415 ARG Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 536 HIS Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 604 SER Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 97 PHE Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 578 TYR Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 234 LYS Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain I residue 77 SER Chi-restraints excluded: chain I residue 87 LEU Chi-restraints excluded: chain J residue 10 THR Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain K residue 88 SER Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain K residue 133 ILE Chi-restraints excluded: chain K residue 160 LEU Chi-restraints excluded: chain L residue 132 SER Chi-restraints excluded: chain L residue 174 THR Chi-restraints excluded: chain L residue 180 SER Chi-restraints excluded: chain L residue 181 LEU Chi-restraints excluded: chain L residue 182 SER Chi-restraints excluded: chain L residue 196 ILE Chi-restraints excluded: chain 1 residue 63 SER Chi-restraints excluded: chain 1 residue 83 SER Chi-restraints excluded: chain 1 residue 115 VAL Chi-restraints excluded: chain 1 residue 209 LEU Chi-restraints excluded: chain a residue 98 GLU Chi-restraints excluded: chain a residue 151 LEU Chi-restraints excluded: chain 3 residue 138 ASN Chi-restraints excluded: chain 3 residue 178 LEU Chi-restraints excluded: chain 3 residue 200 LEU Chi-restraints excluded: chain 3 residue 237 MET Chi-restraints excluded: chain 3 residue 260 THR Chi-restraints excluded: chain 4 residue 86 SER Chi-restraints excluded: chain 4 residue 92 ASP Chi-restraints excluded: chain 4 residue 101 LEU Chi-restraints excluded: chain 4 residue 264 THR Chi-restraints excluded: chain 5 residue 72 TRP Chi-restraints excluded: chain 5 residue 131 THR Chi-restraints excluded: chain 5 residue 144 ILE Chi-restraints excluded: chain 5 residue 168 ILE Chi-restraints excluded: chain 5 residue 243 ASN Chi-restraints excluded: chain 6 residue 98 THR Chi-restraints excluded: chain 6 residue 135 HIS Chi-restraints excluded: chain 6 residue 150 GLU Chi-restraints excluded: chain 6 residue 155 ASP Chi-restraints excluded: chain 6 residue 182 MET Chi-restraints excluded: chain 6 residue 221 VAL Chi-restraints excluded: chain 6 residue 229 ASP Chi-restraints excluded: chain 6 residue 272 ASP Chi-restraints excluded: chain 7 residue 32 VAL Chi-restraints excluded: chain 7 residue 88 LEU Chi-restraints excluded: chain 7 residue 125 PHE Chi-restraints excluded: chain 7 residue 207 GLN Chi-restraints excluded: chain 8 residue 118 ILE Chi-restraints excluded: chain 8 residue 182 PHE Chi-restraints excluded: chain 8 residue 247 VAL Chi-restraints excluded: chain 8 residue 264 THR Chi-restraints excluded: chain 8 residue 267 VAL Chi-restraints excluded: chain 2 residue 63 VAL Chi-restraints excluded: chain 2 residue 116 THR Chi-restraints excluded: chain 2 residue 144 LEU Chi-restraints excluded: chain 2 residue 169 LEU Chi-restraints excluded: chain 9 residue 127 TYR Chi-restraints excluded: chain 9 residue 131 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 272 optimal weight: 0.6980 chunk 365 optimal weight: 8.9990 chunk 104 optimal weight: 6.9990 chunk 316 optimal weight: 8.9990 chunk 50 optimal weight: 20.0000 chunk 95 optimal weight: 6.9990 chunk 343 optimal weight: 7.9990 chunk 143 optimal weight: 20.0000 chunk 352 optimal weight: 4.9990 chunk 43 optimal weight: 0.7980 chunk 63 optimal weight: 5.9990 overall best weight: 3.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 161 ASN ** B 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 159 GLN F 117 ASN ** 1 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.130881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.111054 restraints weight = 99253.063| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 1.57 r_work: 0.3272 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.3557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.183 52731 Z= 0.259 Angle : 1.019 59.199 75353 Z= 0.440 Chirality : 0.055 1.683 6192 Planarity : 0.005 0.081 9997 Dihedral : 18.901 111.667 9273 Min Nonbonded Distance : 1.724 Molprobity Statistics. All-atom Clashscore : 19.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 2.58 % Allowed : 18.43 % Favored : 78.98 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.13), residues: 4330 helix: 0.42 (0.11), residues: 2286 sheet: -1.92 (0.52), residues: 85 loop : -1.44 (0.15), residues: 1959 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP 1 138 HIS 0.011 0.001 HIS 1 101 PHE 0.130 0.002 PHE 7 170 TYR 0.024 0.002 TYR L 130 ARG 0.009 0.000 ARG 1 103 =============================================================================== Job complete usr+sys time: 11970.51 seconds wall clock time: 215 minutes 48.27 seconds (12948.27 seconds total)