Starting phenix.real_space_refine on Sat Jul 4 07:01:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nr6_49723/07_2026/9nr6_49723.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nr6_49723/07_2026/9nr6_49723.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9nr6_49723/07_2026/9nr6_49723.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nr6_49723/07_2026/9nr6_49723.map" model { file = "/net/cci-nas-00/data/ceres_data/9nr6_49723/07_2026/9nr6_49723.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nr6_49723/07_2026/9nr6_49723.cif" } resolution = 3.26 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.035 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: 5 Type Number sf(0) Gaussians Ca 2 9.91 5 S 72 5.16 5 C 12121 2.51 5 N 3353 2.21 5 O 3691 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19239 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 2992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2992 Classifications: {'peptide': 371} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 357} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ASN:plan1': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 16 Chain: "B" Number of atoms: 3032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 3032 Classifications: {'peptide': 378} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 363} 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: "C" Number of atoms: 2999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2999 Classifications: {'peptide': 373} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 13, 'TRANS': 359} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'ASN:plan1': 2, 'PHE:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "D" Number of atoms: 3032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 3032 Classifications: {'peptide': 378} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 363} 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: "E" Number of atoms: 1124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1124 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 193} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 216} Chain breaks: 1 Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 683 Unresolved non-hydrogen angles: 881 Unresolved non-hydrogen dihedrals: 584 Unresolved non-hydrogen chiralities: 59 Planarities with less than four sites: {'GLU:plan': 11, 'GLN:plan1': 11, 'PHE:plan': 7, 'ASP:plan': 13, 'TYR:plan': 12, 'TRP:plan': 5, 'ARG:plan': 10, 'ASN:plan1': 5, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 368 Chain: "F" Number of atoms: 1124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1124 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 193} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 216} Chain breaks: 1 Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 683 Unresolved non-hydrogen angles: 881 Unresolved non-hydrogen dihedrals: 584 Unresolved non-hydrogen chiralities: 59 Planarities with less than four sites: {'GLU:plan': 11, 'GLN:plan1': 11, 'PHE:plan': 7, 'ASP:plan': 13, 'TYR:plan': 12, 'TRP:plan': 5, 'ARG:plan': 10, 'ASN:plan1': 5, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 368 Chain: "G" Number of atoms: 2232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2232 Classifications: {'peptide': 277} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 9, 'TRANS': 267} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "H" Number of atoms: 2232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2232 Classifications: {'peptide': 277} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 9, 'TRANS': 267} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 14 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 14 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.00, per 1000 atoms: 0.21 Number of scatterers: 19239 At special positions: 0 Unit cell: (234.06, 115.62, 136.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 2 19.99 S 72 16.00 O 3691 8.00 N 3353 7.00 C 12121 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 57 " - pdb=" SG CYS A 305 " distance=2.03 Simple disulfide: pdb=" SG CYS B 64 " - pdb=" SG CYS B 311 " distance=2.03 Simple disulfide: pdb=" SG CYS C 57 " - pdb=" SG CYS C 305 " distance=2.03 Simple disulfide: pdb=" SG CYS D 64 " - pdb=" SG CYS D 311 " distance=2.03 Simple disulfide: pdb=" SG CYS G 221 " - pdb=" SG CYS H 221 " distance=2.03 Simple disulfide: pdb=" SG CYS G 227 " - pdb=" SG CYS G 409 " distance=2.03 Simple disulfide: pdb=" SG CYS H 227 " - pdb=" SG CYS H 409 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " NAG-ASN " NAG A 401 " - " ASN A 239 " " NAG B 401 " - " ASN B 238 " " NAG B 402 " - " ASN B 36 " " NAG C 401 " - " ASN C 239 " " NAG D 401 " - " ASN D 238 " " NAG D 402 " - " ASN D 36 " " NAG H 501 " - " ASN H 473 " " NAG I 1 " - " ASN A 45 " " NAG J 1 " - " ASN C 45 " " NAG K 1 " - " ASN H 394 " " NAG L 1 " - " ASN G 307 " " NAG M 1 " - " ASN G 394 " " NAG N 1 " - " ASN H 307 " " NAG O 1 " - " ASN D 351 " " NAG P 1 " - " ASN B 351 " " NAG Q 1 " - " ASN A 345 " " NAG R 1 " - " ASN A 231 " " NAG S 1 " - " ASN C 231 " " NAG T 1 " - " ASN C 345 " Time building additional restraints: 1.80 Conformation dependent library (CDL) restraints added in 884.2 milliseconds 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4664 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 30 sheets defined 26.6% alpha, 22.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 18 through 31 Processing helix chain 'A' and resid 48 through 63 Processing helix chain 'A' and resid 75 through 87 Processing helix chain 'A' and resid 111 through 123 Processing helix chain 'A' and resid 137 through 151 Processing helix chain 'A' and resid 163 through 175 Processing helix chain 'A' and resid 190 through 200 Processing helix chain 'A' and resid 222 through 228 Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 269 through 292 removed outlier: 3.769A pdb=" N ALA A 273 " --> pdb=" O LYS A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 325 removed outlier: 4.336A pdb=" N ASP A 318 " --> pdb=" O GLY A 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 33 removed outlier: 3.688A pdb=" N TYR B 21 " --> pdb=" O THR B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 69 Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'B' and resid 119 through 129 removed outlier: 3.621A pdb=" N HIS B 128 " --> pdb=" O SER B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 158 Processing helix chain 'B' and resid 170 through 184 Processing helix chain 'B' and resid 194 through 209 Processing helix chain 'B' and resid 229 through 236 Processing helix chain 'B' and resid 249 through 261 removed outlier: 3.578A pdb=" N LYS B 261 " --> pdb=" O ASP B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 298 Processing helix chain 'B' and resid 321 through 331 Processing helix chain 'C' and resid 18 through 31 removed outlier: 3.540A pdb=" N ALA C 22 " --> pdb=" O SER C 18 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU C 31 " --> pdb=" O ALA C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 63 Processing helix chain 'C' and resid 75 through 87 Processing helix chain 'C' and resid 113 through 122 Processing helix chain 'C' and resid 133 through 136 removed outlier: 3.914A pdb=" N GLY C 136 " --> pdb=" O ALA C 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 133 through 136' Processing helix chain 'C' and resid 137 through 151 Processing helix chain 'C' and resid 163 through 177 removed outlier: 4.012A pdb=" N LYS C 177 " --> pdb=" O ASP C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 201 removed outlier: 4.654A pdb=" N ALA C 193 " --> pdb=" O GLU C 189 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU C 201 " --> pdb=" O GLN C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 254 Processing helix chain 'C' and resid 269 through 292 removed outlier: 3.903A pdb=" N ALA C 273 " --> pdb=" O LYS C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 325 removed outlier: 4.420A pdb=" N ASP C 318 " --> pdb=" O GLY C 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 33 Processing helix chain 'D' and resid 55 through 69 removed outlier: 3.613A pdb=" N ARG D 69 " --> pdb=" O SER D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 93 Processing helix chain 'D' and resid 118 through 129 Processing helix chain 'D' and resid 144 through 158 Processing helix chain 'D' and resid 170 through 184 Processing helix chain 'D' and resid 194 through 209 Processing helix chain 'D' and resid 230 through 236 removed outlier: 3.562A pdb=" N HIS D 234 " --> pdb=" O GLU D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 261 removed outlier: 3.657A pdb=" N ARG D 258 " --> pdb=" O LYS D 254 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS D 261 " --> pdb=" O ASP D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 298 Processing helix chain 'D' and resid 321 through 331 Processing helix chain 'G' and resid 205 through 225 Processing helix chain 'G' and resid 280 through 285 removed outlier: 3.781A pdb=" N ASN G 285 " --> pdb=" O VAL G 281 " (cutoff:3.500A) Processing helix chain 'H' and resid 205 through 225 Processing helix chain 'H' and resid 280 through 285 removed outlier: 3.676A pdb=" N ASN H 285 " --> pdb=" O VAL H 281 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 43 removed outlier: 4.303A pdb=" N ALA A 66 " --> pdb=" O GLN A 8 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ILE A 67 " --> pdb=" O ILE A 91 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 153 through 158 removed outlier: 7.128A pdb=" N PHE A 127 " --> pdb=" O THR A 155 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N VAL A 157 " --> pdb=" O PHE A 127 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N TYR A 129 " --> pdb=" O VAL A 157 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N THR A 126 " --> pdb=" O LEU A 181 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N VAL A 183 " --> pdb=" O THR A 126 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N VAL A 128 " --> pdb=" O VAL A 183 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N ASP A 185 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ILE A 130 " --> pdb=" O ASP A 185 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N PHE A 235 " --> pdb=" O LEU A 212 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N LEU A 348 " --> pdb=" O TYR A 363 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N TYR A 363 " --> pdb=" O LEU A 348 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL A 350 " --> pdb=" O ILE A 361 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 327 through 330 Processing sheet with id=AA4, first strand: chain 'B' and resid 43 through 50 removed outlier: 10.689A pdb=" N ALA B 73 " --> pdb=" O SER B 6 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N GLN B 8 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 8.685A pdb=" N PHE B 75 " --> pdb=" O GLN B 8 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N GLY B 10 " --> pdb=" O PHE B 75 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N LEU B 97 " --> pdb=" O LEU B 112 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 160 through 165 removed outlier: 7.443A pdb=" N CYS B 133 " --> pdb=" O LYS B 188 " (cutoff:3.500A) removed outlier: 8.808A pdb=" N VAL B 190 " --> pdb=" O CYS B 133 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N VAL B 135 " --> pdb=" O VAL B 190 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ASP B 192 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU B 137 " --> pdb=" O ASP B 192 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N PHE B 242 " --> pdb=" O ILE B 219 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N VAL B 239 " --> pdb=" O LEU B 359 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY B 368 " --> pdb=" O VAL B 356 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N GLU B 358 " --> pdb=" O LYS B 366 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N LYS B 366 " --> pdb=" O GLU B 358 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 333 through 336 Processing sheet with id=AA7, first strand: chain 'C' and resid 36 through 43 removed outlier: 4.131A pdb=" N ALA C 66 " --> pdb=" O GLN C 8 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ILE C 67 " --> pdb=" O ILE C 91 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 153 through 158 removed outlier: 7.109A pdb=" N PHE C 127 " --> pdb=" O THR C 155 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N VAL C 157 " --> pdb=" O PHE C 127 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N TYR C 129 " --> pdb=" O VAL C 157 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N THR C 126 " --> pdb=" O LEU C 181 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N VAL C 183 " --> pdb=" O THR C 126 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N VAL C 128 " --> pdb=" O VAL C 183 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N ASP C 185 " --> pdb=" O VAL C 128 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ILE C 130 " --> pdb=" O ASP C 185 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL C 182 " --> pdb=" O ILE C 211 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N TYR C 210 " --> pdb=" O THR C 233 " (cutoff:3.500A) removed outlier: 8.815A pdb=" N PHE C 235 " --> pdb=" O TYR C 210 " (cutoff:3.500A) removed outlier: 8.413A pdb=" N LEU C 212 " --> pdb=" O PHE C 235 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LEU C 348 " --> pdb=" O TYR C 363 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N TYR C 363 " --> pdb=" O LEU C 348 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N VAL C 350 " --> pdb=" O ILE C 361 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 327 through 329 Processing sheet with id=AB1, first strand: chain 'D' and resid 43 through 50 removed outlier: 6.485A pdb=" N VAL D 7 " --> pdb=" O VAL D 45 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N HIS D 47 " --> pdb=" O VAL D 7 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ILE D 9 " --> pdb=" O HIS D 47 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N ASP D 49 " --> pdb=" O ILE D 9 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N GLY D 11 " --> pdb=" O ASP D 49 " (cutoff:3.500A) removed outlier: 10.575A pdb=" N ALA D 73 " --> pdb=" O SER D 6 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N GLN D 8 " --> pdb=" O ALA D 73 " (cutoff:3.500A) removed outlier: 8.477A pdb=" N PHE D 75 " --> pdb=" O GLN D 8 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N GLY D 10 " --> pdb=" O PHE D 75 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N LEU D 97 " --> pdb=" O LEU D 112 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 160 through 165 removed outlier: 7.067A pdb=" N PHE D 134 " --> pdb=" O SER D 162 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N ILE D 164 " --> pdb=" O PHE D 134 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N PHE D 136 " --> pdb=" O ILE D 164 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N CYS D 133 " --> pdb=" O LYS D 188 " (cutoff:3.500A) removed outlier: 8.614A pdb=" N VAL D 190 " --> pdb=" O CYS D 133 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N VAL D 135 " --> pdb=" O VAL D 190 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N ASP D 192 " --> pdb=" O VAL D 135 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU D 137 " --> pdb=" O ASP D 192 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N PHE D 242 " --> pdb=" O ILE D 219 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N VAL D 239 " --> pdb=" O LEU D 359 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N MET D 354 " --> pdb=" O TYR D 369 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N TYR D 369 " --> pdb=" O MET D 354 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL D 356 " --> pdb=" O VAL D 367 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 333 through 336 Processing sheet with id=AB4, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.817A pdb=" N SER E 7 " --> pdb=" O SER E 21 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N SER E 21 " --> pdb=" O SER E 7 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N CYS E 22 " --> pdb=" O LEU E 79 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 45 through 50 removed outlier: 6.504A pdb=" N TRP E 36 " --> pdb=" O ILE E 48 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 138 through 141 Processing sheet with id=AB7, first strand: chain 'E' and resid 144 through 147 removed outlier: 3.549A pdb=" N GLU E 243 " --> pdb=" O LEU E 145 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N VAL E 147 " --> pdb=" O GLU E 243 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL E 171 " --> pdb=" O PHE E 187 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N PHE E 187 " --> pdb=" O VAL E 171 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N TRP E 173 " --> pdb=" O LEU E 185 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N LYS E 177 " --> pdb=" O PRO E 181 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 3 through 7 removed outlier: 3.849A pdb=" N SER F 7 " --> pdb=" O SER F 21 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N SER F 21 " --> pdb=" O SER F 7 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N CYS F 22 " --> pdb=" O LEU F 79 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 45 through 50 removed outlier: 6.487A pdb=" N TRP F 36 " --> pdb=" O ILE F 48 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 138 through 141 Processing sheet with id=AC2, first strand: chain 'F' and resid 144 through 147 removed outlier: 3.565A pdb=" N GLU F 243 " --> pdb=" O LEU F 145 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N VAL F 147 " --> pdb=" O GLU F 243 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL F 171 " --> pdb=" O PHE F 187 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N PHE F 187 " --> pdb=" O VAL F 171 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N TRP F 173 " --> pdb=" O LEU F 185 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 229 through 233 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 229 through 233 current: chain 'G' and resid 460 through 465 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 468 through 479 current: chain 'H' and resid 460 through 465 Processing sheet with id=AC4, first strand: chain 'G' and resid 247 through 251 removed outlier: 4.889A pdb=" N ASP G 266 " --> pdb=" O PHE G 273 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N PHE G 273 " --> pdb=" O ASP G 266 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 304 through 306 removed outlier: 4.119A pdb=" N LYS G 332 " --> pdb=" O ARG G 322 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ASP G 324 " --> pdb=" O ILE G 330 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ILE G 330 " --> pdb=" O ASP G 324 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 356 through 360 removed outlier: 4.396A pdb=" N LEU G 364 " --> pdb=" O LEU G 382 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N ILE G 377 " --> pdb=" O THR G 395 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLN G 391 " --> pdb=" O LYS G 381 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 405 through 408 Processing sheet with id=AC8, first strand: chain 'H' and resid 247 through 250 Processing sheet with id=AC9, first strand: chain 'H' and resid 273 through 275 Processing sheet with id=AD1, first strand: chain 'H' and resid 304 through 306 removed outlier: 4.161A pdb=" N LYS H 332 " --> pdb=" O ARG H 322 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N ASP H 324 " --> pdb=" O ILE H 330 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ILE H 330 " --> pdb=" O ASP H 324 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 356 through 360 removed outlier: 4.411A pdb=" N LEU H 364 " --> pdb=" O LEU H 382 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N ILE H 377 " --> pdb=" O ASN H 394 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N ASN H 394 " --> pdb=" O ILE H 377 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ILE H 379 " --> pdb=" O THR H 392 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N THR H 392 " --> pdb=" O ILE H 379 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LYS H 381 " --> pdb=" O LEU H 390 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 405 through 407 removed outlier: 4.806A pdb=" N LYS H 423 " --> pdb=" O ILE H 440 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N ILE H 440 " --> pdb=" O LYS H 423 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N HIS H 425 " --> pdb=" O ILE H 438 " (cutoff:3.500A) 764 hydrogen bonds defined for protein. 2157 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: 3.45 Time building geometry restraints manager: 2.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6407 1.34 - 1.46: 4778 1.46 - 1.58: 8333 1.58 - 1.70: 0 1.70 - 1.82: 116 Bond restraints: 19634 Sorted by residual: bond pdb=" N ASN G 455 " pdb=" CA ASN G 455 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.25e-02 6.40e+03 7.81e+00 bond pdb=" N ASP G 439 " pdb=" CA ASP G 439 " ideal model delta sigma weight residual 1.459 1.483 -0.024 9.10e-03 1.21e+04 6.99e+00 bond pdb=" N LYS G 457 " pdb=" CA LYS G 457 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.23e-02 6.61e+03 6.35e+00 bond pdb=" N PRO G 456 " pdb=" CD PRO G 456 " ideal model delta sigma weight residual 1.473 1.439 0.034 1.40e-02 5.10e+03 5.77e+00 bond pdb=" C1 NAG L 1 " pdb=" O5 NAG L 1 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.91e+00 ... (remaining 19629 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 26219 1.88 - 3.77: 387 3.77 - 5.65: 61 5.65 - 7.53: 23 7.53 - 9.42: 5 Bond angle restraints: 26695 Sorted by residual: angle pdb=" CA PHE G 442 " pdb=" CB PHE G 442 " pdb=" CG PHE G 442 " ideal model delta sigma weight residual 113.80 119.34 -5.54 1.00e+00 1.00e+00 3.07e+01 angle pdb=" N PRO G 441 " pdb=" CA PRO G 441 " pdb=" CB PRO G 441 " ideal model delta sigma weight residual 103.25 97.45 5.80 1.05e+00 9.07e-01 3.05e+01 angle pdb=" C ASP G 458 " pdb=" N ARG G 459 " pdb=" CA ARG G 459 " ideal model delta sigma weight residual 122.19 115.25 6.94 1.41e+00 5.03e-01 2.42e+01 angle pdb=" CA ASP G 458 " pdb=" CB ASP G 458 " pdb=" CG ASP G 458 " ideal model delta sigma weight residual 112.60 117.16 -4.56 1.00e+00 1.00e+00 2.08e+01 angle pdb=" C PRO G 441 " pdb=" CA PRO G 441 " pdb=" CB PRO G 441 " ideal model delta sigma weight residual 111.56 119.08 -7.52 1.65e+00 3.67e-01 2.08e+01 ... (remaining 26690 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.64: 10894 21.64 - 43.28: 881 43.28 - 64.91: 159 64.91 - 86.55: 27 86.55 - 108.19: 26 Dihedral angle restraints: 11987 sinusoidal: 4721 harmonic: 7266 Sorted by residual: dihedral pdb=" CB CYS D 64 " pdb=" SG CYS D 64 " pdb=" SG CYS D 311 " pdb=" CB CYS D 311 " ideal model delta sinusoidal sigma weight residual 93.00 -179.78 -87.22 1 1.00e+01 1.00e-02 9.13e+01 dihedral pdb=" CB CYS A 57 " pdb=" SG CYS A 57 " pdb=" SG CYS A 305 " pdb=" CB CYS A 305 " ideal model delta sinusoidal sigma weight residual -86.00 -149.30 63.30 1 1.00e+01 1.00e-02 5.29e+01 dihedral pdb=" CA GLU D 52 " pdb=" C GLU D 52 " pdb=" N THR D 53 " pdb=" CA THR D 53 " ideal model delta harmonic sigma weight residual -180.00 -154.97 -25.03 0 5.00e+00 4.00e-02 2.51e+01 ... (remaining 11984 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.213: 3055 0.213 - 0.426: 6 0.426 - 0.639: 1 0.639 - 0.852: 0 0.852 - 1.064: 1 Chirality restraints: 3063 Sorted by residual: chirality pdb=" C1 NAG P 1 " pdb=" ND2 ASN B 351 " pdb=" C2 NAG P 1 " pdb=" O5 NAG P 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.34 -1.06 2.00e-01 2.50e+01 2.83e+01 chirality pdb=" C1 NAG M 1 " pdb=" ND2 ASN G 394 " pdb=" C2 NAG M 1 " pdb=" O5 NAG M 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.80 -0.60 2.00e-01 2.50e+01 9.06e+00 chirality pdb=" C5 BMA I 3 " pdb=" C4 BMA I 3 " pdb=" C6 BMA I 3 " pdb=" O5 BMA I 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.88e+00 ... (remaining 3060 not shown) Planarity restraints: 3481 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 351 " -0.007 2.00e-02 2.50e+03 4.37e-02 2.38e+01 pdb=" CG ASN B 351 " 0.050 2.00e-02 2.50e+03 pdb=" OD1 ASN B 351 " -0.050 2.00e-02 2.50e+03 pdb=" ND2 ASN B 351 " 0.051 2.00e-02 2.50e+03 pdb=" C1 NAG P 1 " -0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE H 440 " 0.059 5.00e-02 4.00e+02 8.97e-02 1.29e+01 pdb=" N PRO H 441 " -0.155 5.00e-02 4.00e+02 pdb=" CA PRO H 441 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO H 441 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 351 " -0.012 2.00e-02 2.50e+03 2.33e-02 5.43e+00 pdb=" CG ASN B 351 " 0.040 2.00e-02 2.50e+03 pdb=" OD1 ASN B 351 " -0.015 2.00e-02 2.50e+03 pdb=" ND2 ASN B 351 " -0.014 2.00e-02 2.50e+03 ... (remaining 3478 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 5005 2.81 - 3.33: 15877 3.33 - 3.85: 31904 3.85 - 4.38: 35468 4.38 - 4.90: 63733 Nonbonded interactions: 151987 Sorted by model distance: nonbonded pdb=" OG1 THR B 140 " pdb=" OE2 GLU B 167 " model vdw 2.281 3.040 nonbonded pdb=" OH TYR A 122 " pdb=" OE1 GLU A 352 " model vdw 2.288 3.040 nonbonded pdb=" OG1 THR D 22 " pdb=" O PRO D 268 " model vdw 2.304 3.040 nonbonded pdb=" OG1 THR B 22 " pdb=" O PRO B 268 " model vdw 2.325 3.040 nonbonded pdb=" O SER C 47 " pdb=" O6 NAG J 1 " model vdw 2.334 3.040 ... (remaining 151982 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 3 and (name N or name CA or name C or name O or name CB ) \ ) or resid 4 through 401)) selection = (chain 'C' and (resid 3 through 203 or (resid 204 and (name N or name CA or name \ C or name O or name CB )) or resid 205 through 401)) } ncs_group { reference = (chain 'B' and (resid 2 through 38 or (resid 39 through 40 and (name N or name C \ A or name C or name O or name CB )) or resid 41 through 402)) selection = (chain 'D' and (resid 2 through 106 or (resid 107 and (name N or name CA or name \ C or name O or name CB )) or resid 108 through 402)) } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.800 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: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 18.000 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 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 : 0.003 0.044 19674 Z= 0.164 Angle : 0.622 16.330 26808 Z= 0.314 Chirality : 0.050 1.064 3063 Planarity : 0.004 0.090 3462 Dihedral : 16.708 108.190 7302 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.11 % Allowed : 19.55 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.16), residues: 2492 helix: 0.69 (0.19), residues: 685 sheet: 0.05 (0.21), residues: 610 loop : -1.43 (0.17), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 15 TYR 0.015 0.001 TYR A 346 PHE 0.029 0.001 PHE D 29 TRP 0.008 0.001 TRP B 259 HIS 0.003 0.001 HIS B 345 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.16 (19634) covalent geometry : angle 0.58942 / 0.31 (26695) SS BOND : bond 0.00207 / 0.12 ( 7) SS BOND : angle 1.37249 / 0.70 ( 14) hydrogen bonds : bond 0.12248 / 7.92 ( 764) hydrogen bonds : angle 5.56360 / 3.90 ( 2157) link_BETA1-4 : bond 0.00576 / 0.30 ( 14) link_BETA1-4 : angle 1.36546 / 0.92 ( 42) link_NAG-ASN : bond 0.00636 / 0.34 ( 19) link_NAG-ASN : angle 4.15897 / 2.63 ( 57) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 184 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 15 ARG cc_start: 0.7610 (ttp-110) cc_final: 0.7216 (ttp80) outliers start: 2 outliers final: 1 residues processed: 186 average time/residue: 0.1252 time to fit residues: 36.8086 Evaluate side-chains 179 residues out of total 2185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 178 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 438 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 216 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 4.9990 chunk 227 optimal weight: 9.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.2980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.0170 chunk 235 optimal weight: 3.9990 overall best weight: 0.8422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 8 GLN C 40 GLN C 308 ASN ** D 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 269 HIS G 455 ASN H 443 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.173628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.137275 restraints weight = 22105.733| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 1.80 r_work: 0.3254 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.0952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19674 Z= 0.140 Angle : 0.541 14.081 26808 Z= 0.269 Chirality : 0.044 0.504 3063 Planarity : 0.004 0.068 3462 Dihedral : 8.061 65.987 3430 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.80 % Allowed : 17.98 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.17), residues: 2492 helix: 1.30 (0.19), residues: 685 sheet: -0.04 (0.21), residues: 638 loop : -1.31 (0.18), residues: 1169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 190 TYR 0.019 0.001 TYR G 426 PHE 0.015 0.002 PHE A 24 TRP 0.008 0.001 TRP G 365 HIS 0.003 0.001 HIS H 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (19634) covalent geometry : angle 0.50866 / 0.26 (26695) SS BOND : bond 0.00235 / 0.12 ( 7) SS BOND : angle 1.15155 / 0.59 ( 14) hydrogen bonds : bond 0.03611 / 2.31 ( 764) hydrogen bonds : angle 4.38372 / 3.02 ( 2157) link_BETA1-4 : bond 0.00590 / 0.30 ( 14) link_BETA1-4 : angle 1.56750 / 1.06 ( 42) link_NAG-ASN : bond 0.00500 / 0.30 ( 19) link_NAG-ASN : angle 3.80139 / 2.46 ( 57) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 190 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 ASP cc_start: 0.8200 (t70) cc_final: 0.7929 (t0) REVERT: G 444 ASN cc_start: 0.7577 (t0) cc_final: 0.7308 (t0) outliers start: 32 outliers final: 21 residues processed: 215 average time/residue: 0.1276 time to fit residues: 43.3401 Evaluate side-chains 199 residues out of total 2185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 178 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 361 SER Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 256 ASP Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 282 MET Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 302 ILE Chi-restraints excluded: chain D residue 361 SER Chi-restraints excluded: chain G residue 331 LEU Chi-restraints excluded: chain G residue 415 THR Chi-restraints excluded: chain G residue 479 VAL Chi-restraints excluded: chain H residue 239 VAL Chi-restraints excluded: chain H residue 331 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 128 optimal weight: 2.9990 chunk 158 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 chunk 185 optimal weight: 40.0000 chunk 103 optimal weight: 0.0770 chunk 136 optimal weight: 1.9990 chunk 31 optimal weight: 0.3980 chunk 181 optimal weight: 9.9990 chunk 95 optimal weight: 1.9990 chunk 163 optimal weight: 20.0000 chunk 36 optimal weight: 1.9990 overall best weight: 1.2944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 221 ASN C 308 ASN G 352 HIS G 478 HIS H 443 GLN ** H 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.165917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.129482 restraints weight = 22581.030| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 1.91 r_work: 0.3132 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 19674 Z= 0.192 Angle : 0.597 15.588 26808 Z= 0.296 Chirality : 0.046 0.552 3063 Planarity : 0.004 0.077 3462 Dihedral : 6.212 59.280 3428 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.75 % Allowed : 18.26 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.17), residues: 2492 helix: 1.16 (0.19), residues: 693 sheet: -0.03 (0.21), residues: 622 loop : -1.49 (0.17), residues: 1177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 265 TYR 0.025 0.002 TYR H 426 PHE 0.018 0.002 PHE G 246 TRP 0.009 0.001 TRP G 464 HIS 0.005 0.001 HIS H 425 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.19 (19634) covalent geometry : angle 0.56152 / 0.29 (26695) SS BOND : bond 0.00431 / 0.22 ( 7) SS BOND : angle 1.80664 / 1.00 ( 14) hydrogen bonds : bond 0.04088 / 2.62 ( 764) hydrogen bonds : angle 4.43941 / 3.06 ( 2157) link_BETA1-4 : bond 0.00626 / 0.35 ( 14) link_BETA1-4 : angle 1.61224 / 1.11 ( 42) link_NAG-ASN : bond 0.00566 / 0.36 ( 19) link_NAG-ASN : angle 4.11895 / 2.73 ( 57) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 194 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 345 ASN cc_start: 0.8819 (t0) cc_final: 0.8438 (t0) REVERT: D 98 ILE cc_start: 0.9043 (OUTLIER) cc_final: 0.8688 (mm) REVERT: G 464 TRP cc_start: 0.8555 (t-100) cc_final: 0.8217 (t60) outliers start: 49 outliers final: 33 residues processed: 232 average time/residue: 0.1202 time to fit residues: 45.0202 Evaluate side-chains 212 residues out of total 2185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 178 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 361 SER Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 186 CYS Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 256 ASP Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain D residue 302 ILE Chi-restraints excluded: chain D residue 361 SER Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain G residue 303 GLN Chi-restraints excluded: chain G residue 331 LEU Chi-restraints excluded: chain G residue 395 THR Chi-restraints excluded: chain G residue 415 THR Chi-restraints excluded: chain G residue 479 VAL Chi-restraints excluded: chain H residue 218 LEU Chi-restraints excluded: chain H residue 239 VAL Chi-restraints excluded: chain H residue 395 THR Chi-restraints excluded: chain H residue 415 THR Chi-restraints excluded: chain H residue 480 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 13 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 138 optimal weight: 0.0020 chunk 112 optimal weight: 0.9990 chunk 125 optimal weight: 2.9990 chunk 59 optimal weight: 0.4980 chunk 53 optimal weight: 3.9990 chunk 116 optimal weight: 0.3980 chunk 7 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 205 optimal weight: 3.9990 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 308 ASN ** D 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 316 GLN ** H 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 469 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.167729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.130681 restraints weight = 22430.551| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 1.87 r_work: 0.3168 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 19674 Z= 0.108 Angle : 0.518 14.327 26808 Z= 0.257 Chirality : 0.043 0.520 3063 Planarity : 0.003 0.075 3462 Dihedral : 5.240 58.658 3428 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.08 % Allowed : 18.82 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.17), residues: 2492 helix: 1.57 (0.20), residues: 687 sheet: -0.06 (0.21), residues: 630 loop : -1.36 (0.17), residues: 1175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 15 TYR 0.018 0.001 TYR G 426 PHE 0.012 0.001 PHE C 171 TRP 0.007 0.001 TRP B 259 HIS 0.003 0.001 HIS C 260 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (19634) covalent geometry : angle 0.48149 / 0.25 (26695) SS BOND : bond 0.00198 / 0.10 ( 7) SS BOND : angle 1.02444 / 0.59 ( 14) hydrogen bonds : bond 0.03250 / 2.09 ( 764) hydrogen bonds : angle 4.16163 / 2.88 ( 2157) link_BETA1-4 : bond 0.00517 / 0.28 ( 14) link_BETA1-4 : angle 1.45399 / 1.01 ( 42) link_NAG-ASN : bond 0.00465 / 0.27 ( 19) link_NAG-ASN : angle 3.99501 / 2.75 ( 57) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 188 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 345 ASN cc_start: 0.8853 (t0) cc_final: 0.8438 (t0) REVERT: G 443 GLN cc_start: 0.8191 (tt0) cc_final: 0.7926 (tp40) REVERT: G 464 TRP cc_start: 0.8479 (t-100) cc_final: 0.8126 (t60) outliers start: 37 outliers final: 29 residues processed: 214 average time/residue: 0.1237 time to fit residues: 42.6776 Evaluate side-chains 205 residues out of total 2185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 176 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 361 SER Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 186 CYS Chi-restraints excluded: chain C residue 256 ASP Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 251 MET Chi-restraints excluded: chain D residue 302 ILE Chi-restraints excluded: chain D residue 311 CYS Chi-restraints excluded: chain D residue 361 SER Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain G residue 303 GLN Chi-restraints excluded: chain G residue 415 THR Chi-restraints excluded: chain G residue 479 VAL Chi-restraints excluded: chain G residue 480 ILE Chi-restraints excluded: chain H residue 218 LEU Chi-restraints excluded: chain H residue 239 VAL Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 395 THR Chi-restraints excluded: chain H residue 479 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 16 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 157 optimal weight: 8.9990 chunk 187 optimal weight: 30.0000 chunk 1 optimal weight: 0.0270 chunk 71 optimal weight: 0.8980 chunk 176 optimal weight: 40.0000 chunk 203 optimal weight: 4.9990 chunk 243 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 overall best weight: 0.9842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 308 ASN ** D 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 316 GLN H 373 ASN ** H 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 466 ASN H 469 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.165285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.128558 restraints weight = 22373.621| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 1.88 r_work: 0.3144 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 19674 Z= 0.157 Angle : 0.550 14.911 26808 Z= 0.274 Chirality : 0.044 0.538 3063 Planarity : 0.004 0.072 3462 Dihedral : 5.062 56.319 3428 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.70 % Allowed : 19.10 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.17), residues: 2492 helix: 1.51 (0.19), residues: 690 sheet: -0.10 (0.21), residues: 632 loop : -1.42 (0.17), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 15 TYR 0.022 0.002 TYR H 426 PHE 0.014 0.002 PHE A 26 TRP 0.016 0.001 TRP H 464 HIS 0.003 0.001 HIS H 425 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.16 (19634) covalent geometry : angle 0.51605 / 0.27 (26695) SS BOND : bond 0.00332 / 0.17 ( 7) SS BOND : angle 1.28307 / 0.70 ( 14) hydrogen bonds : bond 0.03564 / 2.29 ( 764) hydrogen bonds : angle 4.20723 / 2.90 ( 2157) link_BETA1-4 : bond 0.00542 / 0.31 ( 14) link_BETA1-4 : angle 1.34871 / 0.95 ( 42) link_NAG-ASN : bond 0.00513 / 0.30 ( 19) link_NAG-ASN : angle 4.00038 / 2.72 ( 57) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 189 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 345 ASN cc_start: 0.8850 (t0) cc_final: 0.8458 (t0) REVERT: G 464 TRP cc_start: 0.8566 (t-100) cc_final: 0.8204 (t60) REVERT: H 279 SER cc_start: 0.8457 (m) cc_final: 0.8183 (p) outliers start: 48 outliers final: 42 residues processed: 228 average time/residue: 0.1278 time to fit residues: 47.3396 Evaluate side-chains 214 residues out of total 2185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 172 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 TYR Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 361 SER Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 186 CYS Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain D residue 36 ASN Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 251 MET Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain D residue 302 ILE Chi-restraints excluded: chain D residue 311 CYS Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 361 SER Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain G residue 303 GLN Chi-restraints excluded: chain G residue 395 THR Chi-restraints excluded: chain G residue 415 THR Chi-restraints excluded: chain G residue 479 VAL Chi-restraints excluded: chain G residue 480 ILE Chi-restraints excluded: chain H residue 218 LEU Chi-restraints excluded: chain H residue 239 VAL Chi-restraints excluded: chain H residue 315 PHE Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 395 THR Chi-restraints excluded: chain H residue 415 THR Chi-restraints excluded: chain H residue 479 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 70 optimal weight: 0.7980 chunk 203 optimal weight: 3.9990 chunk 105 optimal weight: 0.5980 chunk 154 optimal weight: 40.0000 chunk 130 optimal weight: 1.9990 chunk 150 optimal weight: 30.0000 chunk 131 optimal weight: 0.9980 chunk 73 optimal weight: 0.6980 chunk 167 optimal weight: 50.0000 chunk 47 optimal weight: 1.9990 chunk 214 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 308 ASN ** D 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 316 GLN H 373 ASN ** H 443 GLN ** 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 = 0.3852 r_free = 0.3852 target = 0.165830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.129178 restraints weight = 22407.234| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 1.85 r_work: 0.3144 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 19674 Z= 0.134 Angle : 0.523 14.591 26808 Z= 0.261 Chirality : 0.044 0.530 3063 Planarity : 0.003 0.073 3462 Dihedral : 4.874 56.590 3428 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 3.03 % Allowed : 18.65 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.17), residues: 2492 helix: 1.61 (0.19), residues: 690 sheet: -0.08 (0.21), residues: 632 loop : -1.41 (0.17), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 334 TYR 0.019 0.001 TYR H 426 PHE 0.013 0.002 PHE G 246 TRP 0.007 0.001 TRP H 263 HIS 0.003 0.001 HIS H 468 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.13 (19634) covalent geometry : angle 0.48731 / 0.25 (26695) SS BOND : bond 0.00269 / 0.14 ( 7) SS BOND : angle 1.04287 / 0.58 ( 14) hydrogen bonds : bond 0.03329 / 2.14 ( 764) hydrogen bonds : angle 4.11461 / 2.84 ( 2157) link_BETA1-4 : bond 0.00475 / 0.25 ( 14) link_BETA1-4 : angle 1.29762 / 0.90 ( 42) link_NAG-ASN : bond 0.00520 / 0.28 ( 19) link_NAG-ASN : angle 3.96640 / 2.75 ( 57) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 182 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 GLN cc_start: 0.7715 (OUTLIER) cc_final: 0.7485 (pm20) REVERT: A 110 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7410 (mp0) REVERT: A 345 ASN cc_start: 0.8838 (t0) cc_final: 0.8448 (t0) REVERT: D 98 ILE cc_start: 0.9019 (OUTLIER) cc_final: 0.8732 (mm) REVERT: D 127 ASP cc_start: 0.8205 (OUTLIER) cc_final: 0.7998 (m-30) REVERT: G 332 LYS cc_start: 0.8242 (mmmm) cc_final: 0.8037 (mmmm) REVERT: G 464 TRP cc_start: 0.8565 (t-100) cc_final: 0.8181 (t60) REVERT: H 279 SER cc_start: 0.8433 (m) cc_final: 0.8166 (p) REVERT: H 464 TRP cc_start: 0.8520 (t-100) cc_final: 0.8247 (t60) outliers start: 54 outliers final: 42 residues processed: 226 average time/residue: 0.1323 time to fit residues: 48.1391 Evaluate side-chains 224 residues out of total 2185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 178 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLN Chi-restraints excluded: chain A residue 71 TYR Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 361 SER Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 186 CYS Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain D residue 36 ASN Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 127 ASP Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 251 MET Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain D residue 302 ILE Chi-restraints excluded: chain D residue 311 CYS Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 361 SER Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain G residue 303 GLN Chi-restraints excluded: chain G residue 415 THR Chi-restraints excluded: chain G residue 479 VAL Chi-restraints excluded: chain G residue 480 ILE Chi-restraints excluded: chain H residue 218 LEU Chi-restraints excluded: chain H residue 239 VAL Chi-restraints excluded: chain H residue 315 PHE Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 395 THR Chi-restraints excluded: chain H residue 415 THR Chi-restraints excluded: chain H residue 479 VAL Chi-restraints excluded: chain H residue 480 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 31 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 chunk 207 optimal weight: 2.9990 chunk 175 optimal weight: 0.0870 chunk 58 optimal weight: 0.8980 chunk 171 optimal weight: 2.9990 chunk 146 optimal weight: 1.9990 chunk 131 optimal weight: 0.9980 chunk 206 optimal weight: 0.5980 chunk 169 optimal weight: 4.9990 chunk 195 optimal weight: 0.8980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 308 ASN ** D 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 316 GLN G 478 HIS ** H 443 GLN ** 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 = 0.3857 r_free = 0.3857 target = 0.166307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.128813 restraints weight = 22297.608| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.87 r_work: 0.3155 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 19674 Z= 0.114 Angle : 0.504 14.095 26808 Z= 0.252 Chirality : 0.043 0.511 3063 Planarity : 0.003 0.070 3462 Dihedral : 4.623 57.109 3428 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.75 % Allowed : 19.38 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.17), residues: 2492 helix: 1.75 (0.20), residues: 688 sheet: -0.01 (0.21), residues: 622 loop : -1.35 (0.17), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 15 TYR 0.018 0.001 TYR H 426 PHE 0.011 0.001 PHE A 24 TRP 0.007 0.001 TRP B 259 HIS 0.003 0.001 HIS D 345 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.11 (19634) covalent geometry : angle 0.47104 / 0.24 (26695) SS BOND : bond 0.00207 / 0.11 ( 7) SS BOND : angle 0.87718 / 0.49 ( 14) hydrogen bonds : bond 0.03135 / 2.01 ( 764) hydrogen bonds : angle 4.02900 / 2.78 ( 2157) link_BETA1-4 : bond 0.00492 / 0.26 ( 14) link_BETA1-4 : angle 1.27032 / 0.88 ( 42) link_NAG-ASN : bond 0.00520 / 0.28 ( 19) link_NAG-ASN : angle 3.78514 / 2.61 ( 57) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 186 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 345 ASN cc_start: 0.8851 (t0) cc_final: 0.8491 (t0) REVERT: D 98 ILE cc_start: 0.8954 (OUTLIER) cc_final: 0.8678 (mm) REVERT: D 127 ASP cc_start: 0.8250 (OUTLIER) cc_final: 0.8042 (m-30) REVERT: G 464 TRP cc_start: 0.8523 (t-100) cc_final: 0.8197 (t60) REVERT: H 279 SER cc_start: 0.8491 (m) cc_final: 0.8238 (p) outliers start: 49 outliers final: 42 residues processed: 226 average time/residue: 0.1293 time to fit residues: 47.0696 Evaluate side-chains 222 residues out of total 2185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 178 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 361 SER Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 186 CYS Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain D residue 36 ASN Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 127 ASP Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 251 MET Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain D residue 302 ILE Chi-restraints excluded: chain D residue 311 CYS Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 361 SER Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain G residue 303 GLN Chi-restraints excluded: chain G residue 309 SER Chi-restraints excluded: chain G residue 415 THR Chi-restraints excluded: chain H residue 218 LEU Chi-restraints excluded: chain H residue 239 VAL Chi-restraints excluded: chain H residue 315 PHE Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 395 THR Chi-restraints excluded: chain H residue 415 THR Chi-restraints excluded: chain H residue 479 VAL Chi-restraints excluded: chain H residue 480 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 196 optimal weight: 0.6980 chunk 28 optimal weight: 4.9990 chunk 148 optimal weight: 30.0000 chunk 147 optimal weight: 0.5980 chunk 152 optimal weight: 9.9990 chunk 158 optimal weight: 6.9990 chunk 9 optimal weight: 0.6980 chunk 224 optimal weight: 0.0020 chunk 31 optimal weight: 0.9990 chunk 191 optimal weight: 5.9990 chunk 165 optimal weight: 20.0000 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 148 GLN C 308 ASN ** D 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 316 GLN G 478 HIS H 373 ASN ** H 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.167126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.130910 restraints weight = 22216.930| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 1.75 r_work: 0.3176 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 19674 Z= 0.110 Angle : 0.497 13.862 26808 Z= 0.249 Chirality : 0.043 0.504 3063 Planarity : 0.003 0.070 3462 Dihedral : 4.440 57.122 3428 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.64 % Allowed : 19.55 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.17), residues: 2492 helix: 1.81 (0.20), residues: 688 sheet: -0.01 (0.21), residues: 624 loop : -1.34 (0.17), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 334 TYR 0.018 0.001 TYR H 426 PHE 0.011 0.001 PHE A 24 TRP 0.007 0.001 TRP B 259 HIS 0.003 0.001 HIS D 345 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 (19634) covalent geometry : angle 0.46569 / 0.24 (26695) SS BOND : bond 0.00216 / 0.11 ( 7) SS BOND : angle 0.85924 / 0.48 ( 14) hydrogen bonds : bond 0.03082 / 1.98 ( 764) hydrogen bonds : angle 3.99970 / 2.76 ( 2157) link_BETA1-4 : bond 0.00473 / 0.25 ( 14) link_BETA1-4 : angle 1.20017 / 0.85 ( 42) link_NAG-ASN : bond 0.00478 / 0.26 ( 19) link_NAG-ASN : angle 3.67955 / 2.52 ( 57) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 182 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 GLN cc_start: 0.7735 (OUTLIER) cc_final: 0.7534 (pm20) REVERT: A 345 ASN cc_start: 0.8849 (t0) cc_final: 0.8500 (t0) REVERT: D 98 ILE cc_start: 0.8951 (OUTLIER) cc_final: 0.8683 (mm) REVERT: G 464 TRP cc_start: 0.8497 (t-100) cc_final: 0.8193 (t60) REVERT: H 279 SER cc_start: 0.8484 (m) cc_final: 0.8239 (p) REVERT: H 464 TRP cc_start: 0.8487 (t-100) cc_final: 0.8248 (t60) outliers start: 47 outliers final: 41 residues processed: 222 average time/residue: 0.1295 time to fit residues: 46.3950 Evaluate side-chains 220 residues out of total 2185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 177 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLN Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 361 SER Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 36 ASN Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 251 MET Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain D residue 302 ILE Chi-restraints excluded: chain D residue 311 CYS Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 361 SER Chi-restraints excluded: chain G residue 303 GLN Chi-restraints excluded: chain G residue 309 SER Chi-restraints excluded: chain G residue 415 THR Chi-restraints excluded: chain H residue 218 LEU Chi-restraints excluded: chain H residue 239 VAL Chi-restraints excluded: chain H residue 315 PHE Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 395 THR Chi-restraints excluded: chain H residue 415 THR Chi-restraints excluded: chain H residue 479 VAL Chi-restraints excluded: chain H residue 480 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 56 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 167 optimal weight: 0.5980 chunk 82 optimal weight: 1.9990 chunk 189 optimal weight: 40.0000 chunk 195 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 71 optimal weight: 0.4980 chunk 28 optimal weight: 4.9990 chunk 103 optimal weight: 0.4980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 308 ASN ** D 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 316 GLN G 478 HIS ** H 443 GLN ** 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 = 0.3860 r_free = 0.3860 target = 0.166365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.130079 restraints weight = 22092.174| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 1.76 r_work: 0.3159 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 19674 Z= 0.123 Angle : 0.508 14.041 26808 Z= 0.255 Chirality : 0.043 0.508 3063 Planarity : 0.003 0.068 3462 Dihedral : 4.411 56.504 3428 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.58 % Allowed : 19.83 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.17), residues: 2492 helix: 1.75 (0.20), residues: 690 sheet: -0.07 (0.21), residues: 644 loop : -1.34 (0.17), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 15 TYR 0.019 0.001 TYR H 426 PHE 0.012 0.001 PHE A 24 TRP 0.009 0.001 TRP A 252 HIS 0.003 0.001 HIS D 345 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.12 (19634) covalent geometry : angle 0.47679 / 0.25 (26695) SS BOND : bond 0.00254 / 0.13 ( 7) SS BOND : angle 0.92314 / 0.51 ( 14) hydrogen bonds : bond 0.03197 / 2.05 ( 764) hydrogen bonds : angle 4.01835 / 2.78 ( 2157) link_BETA1-4 : bond 0.00477 / 0.25 ( 14) link_BETA1-4 : angle 1.29342 / 0.90 ( 42) link_NAG-ASN : bond 0.00517 / 0.28 ( 19) link_NAG-ASN : angle 3.69952 / 2.52 ( 57) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 185 time to evaluate : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 345 ASN cc_start: 0.8845 (t0) cc_final: 0.8494 (t0) REVERT: B 180 GLU cc_start: 0.7961 (tp30) cc_final: 0.7749 (tp30) REVERT: D 15 ARG cc_start: 0.8407 (ttp-110) cc_final: 0.8096 (ttp80) REVERT: D 98 ILE cc_start: 0.8976 (OUTLIER) cc_final: 0.8706 (mm) REVERT: G 464 TRP cc_start: 0.8524 (t-100) cc_final: 0.8229 (t60) REVERT: H 279 SER cc_start: 0.8459 (m) cc_final: 0.8227 (p) REVERT: H 464 TRP cc_start: 0.8506 (t-100) cc_final: 0.8302 (t60) outliers start: 46 outliers final: 41 residues processed: 223 average time/residue: 0.1348 time to fit residues: 48.3187 Evaluate side-chains 221 residues out of total 2185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 179 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 361 SER Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain D residue 36 ASN Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain D residue 302 ILE Chi-restraints excluded: chain D residue 311 CYS Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 361 SER Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain G residue 303 GLN Chi-restraints excluded: chain G residue 309 SER Chi-restraints excluded: chain G residue 415 THR Chi-restraints excluded: chain H residue 218 LEU Chi-restraints excluded: chain H residue 239 VAL Chi-restraints excluded: chain H residue 315 PHE Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 395 THR Chi-restraints excluded: chain H residue 415 THR Chi-restraints excluded: chain H residue 479 VAL Chi-restraints excluded: chain H residue 480 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 74 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 188 optimal weight: 30.0000 chunk 238 optimal weight: 0.8980 chunk 171 optimal weight: 0.0470 chunk 154 optimal weight: 0.0050 chunk 242 optimal weight: 0.6980 chunk 182 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 overall best weight: 0.4692 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 308 ASN ** D 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 316 GLN G 478 HIS ** H 443 GLN ** 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 = 0.3863 r_free = 0.3863 target = 0.166985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.130938 restraints weight = 22131.088| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 1.79 r_work: 0.3177 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 19674 Z= 0.102 Angle : 0.516 14.982 26808 Z= 0.254 Chirality : 0.043 0.492 3063 Planarity : 0.003 0.066 3462 Dihedral : 4.529 57.420 3428 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.36 % Allowed : 20.00 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.17), residues: 2492 helix: 1.79 (0.20), residues: 702 sheet: -0.03 (0.21), residues: 646 loop : -1.29 (0.17), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 15 TYR 0.016 0.001 TYR H 426 PHE 0.011 0.001 PHE A 24 TRP 0.009 0.001 TRP A 252 HIS 0.003 0.001 HIS D 345 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.10 (19634) covalent geometry : angle 0.47404 / 0.25 (26695) SS BOND : bond 0.00178 / 0.09 ( 7) SS BOND : angle 0.77569 / 0.43 ( 14) hydrogen bonds : bond 0.02967 / 1.91 ( 764) hydrogen bonds : angle 3.94421 / 2.73 ( 2157) link_BETA1-4 : bond 0.00455 / 0.24 ( 14) link_BETA1-4 : angle 1.17602 / 0.82 ( 42) link_NAG-ASN : bond 0.00492 / 0.27 ( 19) link_NAG-ASN : angle 4.31854 / 3.13 ( 57) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 182 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 345 ASN cc_start: 0.8849 (t0) cc_final: 0.8500 (t0) REVERT: D 98 ILE cc_start: 0.8972 (OUTLIER) cc_final: 0.8715 (mm) REVERT: G 464 TRP cc_start: 0.8489 (t-100) cc_final: 0.8208 (t60) REVERT: H 279 SER cc_start: 0.8425 (m) cc_final: 0.8187 (p) REVERT: H 464 TRP cc_start: 0.8485 (t-100) cc_final: 0.8277 (t60) outliers start: 42 outliers final: 40 residues processed: 217 average time/residue: 0.1329 time to fit residues: 46.2895 Evaluate side-chains 217 residues out of total 2185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 176 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 361 SER Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 36 ASN Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain D residue 302 ILE Chi-restraints excluded: chain D residue 311 CYS Chi-restraints excluded: chain D residue 361 SER Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain G residue 303 GLN Chi-restraints excluded: chain G residue 309 SER Chi-restraints excluded: chain G residue 415 THR Chi-restraints excluded: chain H residue 218 LEU Chi-restraints excluded: chain H residue 239 VAL Chi-restraints excluded: chain H residue 315 PHE Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 395 THR Chi-restraints excluded: chain H residue 415 THR Chi-restraints excluded: chain H residue 479 VAL Chi-restraints excluded: chain H residue 480 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 96 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 66 optimal weight: 0.5980 chunk 215 optimal weight: 1.9990 chunk 155 optimal weight: 9.9990 chunk 227 optimal weight: 9.9990 chunk 216 optimal weight: 0.9980 chunk 142 optimal weight: 0.0770 chunk 125 optimal weight: 1.9990 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 308 ASN ** D 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 176 GLN G 316 GLN G 478 HIS ** H 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.165795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.129484 restraints weight = 22191.634| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 1.77 r_work: 0.3159 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19674 Z= 0.120 Angle : 0.513 13.914 26808 Z= 0.256 Chirality : 0.043 0.502 3063 Planarity : 0.003 0.064 3462 Dihedral : 4.448 56.115 3428 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.42 % Allowed : 20.06 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.17), residues: 2492 helix: 1.76 (0.19), residues: 702 sheet: -0.05 (0.21), residues: 646 loop : -1.30 (0.17), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 15 TYR 0.019 0.001 TYR H 426 PHE 0.012 0.001 PHE A 24 TRP 0.008 0.001 TRP A 252 HIS 0.003 0.001 HIS D 345 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 (19634) covalent geometry : angle 0.47800 / 0.25 (26695) SS BOND : bond 0.00245 / 0.12 ( 7) SS BOND : angle 0.88963 / 0.50 ( 14) hydrogen bonds : bond 0.03161 / 2.03 ( 764) hydrogen bonds : angle 3.98705 / 2.76 ( 2157) link_BETA1-4 : bond 0.00472 / 0.25 ( 14) link_BETA1-4 : angle 1.19740 / 0.85 ( 42) link_NAG-ASN : bond 0.00604 / 0.38 ( 19) link_NAG-ASN : angle 3.91844 / 2.75 ( 57) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5445.30 seconds wall clock time: 93 minutes 48.15 seconds (5628.15 seconds total)