Starting phenix.real_space_refine on Thu Sep 18 18:33:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nr6_49723/09_2025/9nr6_49723.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nr6_49723/09_2025/9nr6_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 { model { file = "/net/cci-nas-00/data/ceres_data/9nr6_49723/09_2025/9nr6_49723.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nr6_49723/09_2025/9nr6_49723.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9nr6_49723/09_2025/9nr6_49723.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nr6_49723/09_2025/9nr6_49723.map" } 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-2.0-5805/lib/python3.9/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, 15 Unusual residues: {' CA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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, 15 Unusual residues: {' CA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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: 5.41, per 1000 atoms: 0.28 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: 1.87 Conformation dependent library (CDL) restraints added in 958.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.81 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: 3.55 Time building geometry restraints manager: 2.46 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.380 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 20.070 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 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 aren 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 covalent geometry : bond 0.00320 (19634) covalent geometry : angle 0.58942 (26695) SS BOND : bond 0.00207 ( 7) SS BOND : angle 1.37249 ( 14) hydrogen bonds : bond 0.12248 ( 764) hydrogen bonds : angle 5.56360 ( 2157) link_BETA1-4 : bond 0.00576 ( 14) link_BETA1-4 : angle 1.36546 ( 42) link_NAG-ASN : bond 0.00636 ( 19) link_NAG-ASN : angle 4.15897 ( 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 : 0.745 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: 0.1421 time to fit residues: 41.9429 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 : 0.732 ------------------------------------------------------------------------------- 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: 0.7980 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: 0.6020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3999 r_free = 0.3999 target = 0.177970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.142322 restraints weight = 21960.829| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 1.76 r_work: 0.3264 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.0857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 19674 Z= 0.115 Angle : 0.518 13.656 26808 Z= 0.256 Chirality : 0.044 0.496 3063 Planarity : 0.004 0.070 3462 Dihedral : 7.797 63.469 3430 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.69 % Allowed : 17.70 % Favored : 80.62 % 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 aren not related in a simple way. whole: -0.28 (0.17), residues: 2492 helix: 1.42 (0.20), residues: 685 sheet: 0.04 (0.21), residues: 628 loop : -1.29 (0.17), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 304 TYR 0.017 0.001 TYR G 426 PHE 0.014 0.001 PHE B 29 TRP 0.007 0.001 TRP G 365 HIS 0.003 0.001 HIS H 352 Details of bonding type rmsd covalent geometry : bond 0.00261 (19634) covalent geometry : angle 0.48528 (26695) SS BOND : bond 0.00147 ( 7) SS BOND : angle 1.05195 ( 14) hydrogen bonds : bond 0.03318 ( 764) hydrogen bonds : angle 4.29773 ( 2157) link_BETA1-4 : bond 0.00699 ( 14) link_BETA1-4 : angle 1.59134 ( 42) link_NAG-ASN : bond 0.00523 ( 19) link_NAG-ASN : angle 3.67919 ( 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: 30 poor density : 192 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 ASP cc_start: 0.8151 (t70) cc_final: 0.7844 (t0) REVERT: G 444 ASN cc_start: 0.7448 (t0) cc_final: 0.7197 (t0) outliers start: 30 outliers final: 20 residues processed: 214 average time/residue: 0.1273 time to fit residues: 43.8026 Evaluate side-chains 200 residues out of total 2185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 180 time to evaluate : 0.600 ------------------------------------------------------------------------------- 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 282 MET Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 302 ILE Chi-restraints excluded: chain D residue 361 SER Chi-restraints excluded: chain G residue 231 THR 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 239 VAL 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: 10.0000 chunk 10 optimal weight: 2.9990 chunk 185 optimal weight: 30.0000 chunk 103 optimal weight: 0.6980 chunk 136 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 181 optimal weight: 6.9990 chunk 95 optimal weight: 1.9990 chunk 163 optimal weight: 20.0000 chunk 36 optimal weight: 0.0040 overall best weight: 1.0796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 308 ASN ** D 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 443 GLN ** H 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.167152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.130548 restraints weight = 22530.408| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 1.95 r_work: 0.3157 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 19674 Z= 0.168 Angle : 0.573 15.147 26808 Z= 0.284 Chirality : 0.046 0.528 3063 Planarity : 0.004 0.103 3462 Dihedral : 5.911 57.314 3428 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.36 % Allowed : 18.15 % Favored : 79.49 % 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 aren not related in a simple way. whole: -0.30 (0.17), residues: 2492 helix: 1.44 (0.20), residues: 679 sheet: 0.04 (0.21), residues: 616 loop : -1.32 (0.17), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 245 TYR 0.021 0.002 TYR C 71 PHE 0.023 0.002 PHE H 246 TRP 0.008 0.001 TRP G 464 HIS 0.004 0.001 HIS H 425 Details of bonding type rmsd covalent geometry : bond 0.00402 (19634) covalent geometry : angle 0.53980 (26695) SS BOND : bond 0.00388 ( 7) SS BOND : angle 1.46060 ( 14) hydrogen bonds : bond 0.03927 ( 764) hydrogen bonds : angle 4.34407 ( 2157) link_BETA1-4 : bond 0.00587 ( 14) link_BETA1-4 : angle 1.63784 ( 42) link_NAG-ASN : bond 0.00613 ( 19) link_NAG-ASN : angle 3.94787 ( 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 242 residues out of total 2185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 200 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 345 ASN cc_start: 0.8812 (t0) cc_final: 0.8424 (t0) REVERT: B 264 GLN cc_start: 0.8114 (tt0) cc_final: 0.7909 (mp10) REVERT: G 454 TYR cc_start: 0.8372 (t80) cc_final: 0.8165 (t80) REVERT: G 464 TRP cc_start: 0.8528 (t-100) cc_final: 0.8184 (t60) outliers start: 42 outliers final: 28 residues processed: 234 average time/residue: 0.1181 time to fit residues: 43.9093 Evaluate side-chains 209 residues out of total 2185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 181 time to evaluate : 0.716 ------------------------------------------------------------------------------- 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 83 VAL Chi-restraints excluded: chain B residue 150 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 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 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 361 SER 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 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: 3.9990 chunk 71 optimal weight: 0.9980 chunk 138 optimal weight: 0.9980 chunk 112 optimal weight: 0.8980 chunk 125 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 116 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 205 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 221 ASN C 308 ASN ** D 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 316 GLN G 352 HIS G 478 HIS H 373 ASN H 443 GLN ** H 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.166211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.129706 restraints weight = 22561.341| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.87 r_work: 0.3152 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 19674 Z= 0.151 Angle : 0.546 14.752 26808 Z= 0.271 Chirality : 0.044 0.540 3063 Planarity : 0.004 0.074 3462 Dihedral : 5.126 57.894 3428 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.47 % Allowed : 18.37 % Favored : 79.16 % 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 aren not related in a simple way. whole: -0.34 (0.17), residues: 2492 helix: 1.50 (0.19), residues: 687 sheet: -0.09 (0.21), residues: 630 loop : -1.36 (0.17), residues: 1175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 265 TYR 0.020 0.001 TYR H 426 PHE 0.013 0.002 PHE C 171 TRP 0.007 0.001 TRP G 464 HIS 0.003 0.001 HIS A 349 Details of bonding type rmsd covalent geometry : bond 0.00360 (19634) covalent geometry : angle 0.50902 (26695) SS BOND : bond 0.00287 ( 7) SS BOND : angle 1.24202 ( 14) hydrogen bonds : bond 0.03498 ( 764) hydrogen bonds : angle 4.21877 ( 2157) link_BETA1-4 : bond 0.00511 ( 14) link_BETA1-4 : angle 1.46113 ( 42) link_NAG-ASN : bond 0.00470 ( 19) link_NAG-ASN : angle 4.11954 ( 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 232 residues out of total 2185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 188 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 345 ASN cc_start: 0.8869 (t0) cc_final: 0.8443 (t0) REVERT: D 98 ILE cc_start: 0.9030 (OUTLIER) cc_final: 0.8711 (mm) REVERT: G 242 SER cc_start: 0.7678 (p) cc_final: 0.7465 (p) REVERT: G 443 GLN cc_start: 0.8230 (tt0) cc_final: 0.7949 (tp40) REVERT: G 464 TRP cc_start: 0.8546 (t-100) cc_final: 0.8189 (t60) outliers start: 44 outliers final: 35 residues processed: 221 average time/residue: 0.1232 time to fit residues: 43.2766 Evaluate side-chains 210 residues out of total 2185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 174 time to evaluate : 0.537 ------------------------------------------------------------------------------- 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 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 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 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 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 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 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 415 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: 0.0770 chunk 36 optimal weight: 1.9990 chunk 157 optimal weight: 7.9990 chunk 187 optimal weight: 20.0000 chunk 1 optimal weight: 0.0770 chunk 71 optimal weight: 0.4980 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: 0.7980 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 308 ASN ** D 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 316 GLN H 373 ASN H 443 GLN H 469 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.172282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.137026 restraints weight = 21916.565| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 1.72 r_work: 0.3177 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.1886 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= 0.121 Angle : 0.516 14.443 26808 Z= 0.257 Chirality : 0.044 0.520 3063 Planarity : 0.003 0.071 3462 Dihedral : 4.889 57.136 3428 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.70 % Allowed : 18.82 % Favored : 78.48 % 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 aren not related in a simple way. whole: -0.25 (0.17), residues: 2492 helix: 1.66 (0.20), residues: 688 sheet: -0.08 (0.21), residues: 634 loop : -1.34 (0.17), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 265 TYR 0.019 0.001 TYR H 426 PHE 0.011 0.001 PHE A 24 TRP 0.006 0.001 TRP B 259 HIS 0.003 0.001 HIS D 345 Details of bonding type rmsd covalent geometry : bond 0.00283 (19634) covalent geometry : angle 0.48144 (26695) SS BOND : bond 0.00253 ( 7) SS BOND : angle 1.05323 ( 14) hydrogen bonds : bond 0.03245 ( 764) hydrogen bonds : angle 4.10879 ( 2157) link_BETA1-4 : bond 0.00487 ( 14) link_BETA1-4 : angle 1.32554 ( 42) link_NAG-ASN : bond 0.00743 ( 19) link_NAG-ASN : angle 3.91634 ( 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 239 residues out of total 2185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 191 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 GLU cc_start: 0.7302 (tm-30) cc_final: 0.7018 (tm-30) REVERT: A 345 ASN cc_start: 0.8840 (t0) cc_final: 0.8421 (t0) REVERT: D 98 ILE cc_start: 0.8994 (OUTLIER) cc_final: 0.8696 (mm) REVERT: G 242 SER cc_start: 0.7680 (p) cc_final: 0.7479 (p) REVERT: G 464 TRP cc_start: 0.8557 (t-100) cc_final: 0.8166 (t60) REVERT: H 279 SER cc_start: 0.8424 (m) cc_final: 0.8113 (p) outliers start: 48 outliers final: 38 residues processed: 230 average time/residue: 0.1171 time to fit residues: 43.2113 Evaluate side-chains 217 residues out of total 2185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 178 time to evaluate : 0.863 ------------------------------------------------------------------------------- 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 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 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 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 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 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: 0.5980 chunk 203 optimal weight: 4.9990 chunk 105 optimal weight: 0.6980 chunk 154 optimal weight: 40.0000 chunk 130 optimal weight: 1.9990 chunk 150 optimal weight: 30.0000 chunk 131 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 chunk 167 optimal weight: 50.0000 chunk 47 optimal weight: 1.9990 chunk 214 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 308 ASN ** D 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 316 GLN G 478 HIS H 373 ASN H 443 GLN H 466 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.163132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.125921 restraints weight = 22557.598| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.89 r_work: 0.3117 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 19674 Z= 0.186 Angle : 0.576 15.429 26808 Z= 0.288 Chirality : 0.045 0.559 3063 Planarity : 0.004 0.073 3462 Dihedral : 4.939 54.234 3428 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 3.15 % Allowed : 18.54 % 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 aren not related in a simple way. whole: -0.42 (0.17), residues: 2492 helix: 1.46 (0.19), residues: 690 sheet: -0.14 (0.21), residues: 632 loop : -1.44 (0.17), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 15 TYR 0.024 0.002 TYR H 426 PHE 0.016 0.002 PHE A 26 TRP 0.015 0.001 TRP H 464 HIS 0.004 0.001 HIS H 425 Details of bonding type rmsd covalent geometry : bond 0.00452 (19634) covalent geometry : angle 0.54102 (26695) SS BOND : bond 0.00377 ( 7) SS BOND : angle 1.31782 ( 14) hydrogen bonds : bond 0.03773 ( 764) hydrogen bonds : angle 4.26855 ( 2157) link_BETA1-4 : bond 0.00504 ( 14) link_BETA1-4 : angle 1.42489 ( 42) link_NAG-ASN : bond 0.00524 ( 19) link_NAG-ASN : angle 4.09841 ( 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 239 residues out of total 2185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 183 time to evaluate : 0.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 GLN cc_start: 0.7740 (OUTLIER) cc_final: 0.7512 (pm20) REVERT: A 110 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7381 (mp0) REVERT: A 189 GLU cc_start: 0.7430 (tm-30) cc_final: 0.7189 (tm-30) REVERT: A 345 ASN cc_start: 0.8858 (t0) cc_final: 0.8446 (t0) REVERT: B 15 ARG cc_start: 0.8182 (ptm-80) cc_final: 0.7938 (ptm160) REVERT: D 98 ILE cc_start: 0.9084 (OUTLIER) cc_final: 0.8789 (mm) REVERT: D 127 ASP cc_start: 0.8283 (OUTLIER) cc_final: 0.8029 (m-30) REVERT: G 464 TRP cc_start: 0.8690 (t-100) cc_final: 0.8334 (t60) REVERT: H 279 SER cc_start: 0.8475 (m) cc_final: 0.8221 (p) outliers start: 56 outliers final: 44 residues processed: 230 average time/residue: 0.1196 time to fit residues: 44.6733 Evaluate side-chains 224 residues out of total 2185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 176 time to evaluate : 0.616 ------------------------------------------------------------------------------- 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 81 SER 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 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 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 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: 0.9980 chunk 47 optimal weight: 0.7980 chunk 207 optimal weight: 0.6980 chunk 175 optimal weight: 0.7980 chunk 58 optimal weight: 0.7980 chunk 171 optimal weight: 5.9990 chunk 146 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 206 optimal weight: 0.6980 chunk 169 optimal weight: 4.9990 chunk 195 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 308 ASN ** D 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 316 GLN H 443 GLN H 478 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.164993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.125229 restraints weight = 22648.329| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.16 r_work: 0.3137 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.2247 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= 0.131 Angle : 0.538 14.754 26808 Z= 0.267 Chirality : 0.044 0.538 3063 Planarity : 0.003 0.073 3462 Dihedral : 4.863 54.608 3428 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.58 % Allowed : 19.27 % Favored : 78.15 % 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 aren not related in a simple way. whole: -0.33 (0.17), residues: 2492 helix: 1.53 (0.19), residues: 702 sheet: -0.14 (0.21), residues: 654 loop : -1.40 (0.17), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 334 TYR 0.020 0.001 TYR H 426 PHE 0.042 0.002 PHE G 246 TRP 0.008 0.001 TRP H 464 HIS 0.005 0.001 HIS H 478 Details of bonding type rmsd covalent geometry : bond 0.00309 (19634) covalent geometry : angle 0.49753 (26695) SS BOND : bond 0.00257 ( 7) SS BOND : angle 1.03481 ( 14) hydrogen bonds : bond 0.03359 ( 764) hydrogen bonds : angle 4.15027 ( 2157) link_BETA1-4 : bond 0.00487 ( 14) link_BETA1-4 : angle 1.24141 ( 42) link_NAG-ASN : bond 0.00597 ( 19) link_NAG-ASN : angle 4.36145 ( 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 232 residues out of total 2185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 186 time to evaluate : 0.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 GLN cc_start: 0.7766 (OUTLIER) cc_final: 0.7534 (pm20) REVERT: A 189 GLU cc_start: 0.7471 (tm-30) cc_final: 0.7266 (tm-30) REVERT: A 345 ASN cc_start: 0.8869 (t0) cc_final: 0.8444 (t0) REVERT: D 98 ILE cc_start: 0.9022 (OUTLIER) cc_final: 0.8744 (mm) REVERT: D 127 ASP cc_start: 0.8270 (OUTLIER) cc_final: 0.7991 (m-30) REVERT: G 464 TRP cc_start: 0.8746 (t-100) cc_final: 0.8297 (t60) REVERT: H 279 SER cc_start: 0.8443 (m) cc_final: 0.8151 (p) REVERT: H 464 TRP cc_start: 0.8588 (t-100) cc_final: 0.8216 (t60) outliers start: 46 outliers final: 41 residues processed: 223 average time/residue: 0.1270 time to fit residues: 45.6081 Evaluate side-chains 220 residues out of total 2185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 176 time to evaluate : 0.744 ------------------------------------------------------------------------------- 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 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 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 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 196 optimal weight: 6.9990 chunk 28 optimal weight: 0.9980 chunk 148 optimal weight: 20.0000 chunk 147 optimal weight: 3.9990 chunk 152 optimal weight: 20.0000 chunk 158 optimal weight: 8.9990 chunk 9 optimal weight: 2.9990 chunk 224 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 191 optimal weight: 7.9990 chunk 165 optimal weight: 0.1980 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 19 GLN C 30 GLN C 308 ASN G 316 GLN G 478 HIS H 443 GLN H 478 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.161725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.127103 restraints weight = 22496.884| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.74 r_work: 0.3117 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 19674 Z= 0.213 Angle : 0.615 16.301 26808 Z= 0.307 Chirality : 0.047 0.592 3063 Planarity : 0.004 0.071 3462 Dihedral : 5.079 51.604 3428 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.81 % Allowed : 19.55 % Favored : 77.64 % 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 aren not related in a simple way. whole: -0.59 (0.17), residues: 2492 helix: 1.25 (0.19), residues: 698 sheet: -0.28 (0.21), residues: 660 loop : -1.52 (0.17), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 15 TYR 0.027 0.002 TYR H 426 PHE 0.028 0.002 PHE G 246 TRP 0.017 0.002 TRP H 263 HIS 0.004 0.001 HIS D 345 Details of bonding type rmsd covalent geometry : bond 0.00521 (19634) covalent geometry : angle 0.57785 (26695) SS BOND : bond 0.00447 ( 7) SS BOND : angle 1.45212 ( 14) hydrogen bonds : bond 0.04063 ( 764) hydrogen bonds : angle 4.40481 ( 2157) link_BETA1-4 : bond 0.00575 ( 14) link_BETA1-4 : angle 1.48121 ( 42) link_NAG-ASN : bond 0.00800 ( 19) link_NAG-ASN : angle 4.41653 ( 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 239 residues out of total 2185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 189 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 GLU cc_start: 0.7379 (tm-30) cc_final: 0.7176 (tm-30) REVERT: A 345 ASN cc_start: 0.8858 (t0) cc_final: 0.8499 (t0) REVERT: B 15 ARG cc_start: 0.8138 (ptm-80) cc_final: 0.7917 (ptm160) REVERT: D 15 ARG cc_start: 0.8502 (ttp-110) cc_final: 0.8300 (ttp80) REVERT: D 98 ILE cc_start: 0.9060 (OUTLIER) cc_final: 0.8744 (mm) REVERT: D 127 ASP cc_start: 0.8348 (OUTLIER) cc_final: 0.8076 (m-30) REVERT: G 444 ASN cc_start: 0.7920 (t0) cc_final: 0.7583 (t0) REVERT: G 464 TRP cc_start: 0.8732 (t-100) cc_final: 0.8430 (t60) REVERT: H 279 SER cc_start: 0.8384 (m) cc_final: 0.8160 (p) REVERT: H 464 TRP cc_start: 0.8601 (t-100) cc_final: 0.8340 (t60) outliers start: 50 outliers final: 40 residues processed: 231 average time/residue: 0.1331 time to fit residues: 48.8069 Evaluate side-chains 228 residues out of total 2185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 186 time to evaluate : 0.613 ------------------------------------------------------------------------------- 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 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 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 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 56 optimal weight: 0.9980 chunk 109 optimal weight: 0.0030 chunk 167 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 chunk 189 optimal weight: 0.8980 chunk 195 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 chunk 71 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 308 ASN ** D 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 176 GLN ** H 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.164553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.128129 restraints weight = 22169.648| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 1.78 r_work: 0.3162 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2550 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= 0.120 Angle : 0.536 14.749 26808 Z= 0.267 Chirality : 0.044 0.539 3063 Planarity : 0.003 0.070 3462 Dihedral : 4.759 51.613 3428 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.42 % Allowed : 20.11 % Favored : 77.47 % 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 aren not related in a simple way. whole: -0.33 (0.17), residues: 2492 helix: 1.63 (0.20), residues: 686 sheet: -0.15 (0.21), residues: 652 loop : -1.43 (0.17), residues: 1154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG B 265 TYR 0.019 0.001 TYR H 426 PHE 0.047 0.002 PHE G 246 TRP 0.009 0.001 TRP H 263 HIS 0.003 0.001 HIS B 345 Details of bonding type rmsd covalent geometry : bond 0.00281 (19634) covalent geometry : angle 0.49880 (26695) SS BOND : bond 0.00223 ( 7) SS BOND : angle 0.96482 ( 14) hydrogen bonds : bond 0.03287 ( 764) hydrogen bonds : angle 4.16075 ( 2157) link_BETA1-4 : bond 0.00483 ( 14) link_BETA1-4 : angle 1.23294 ( 42) link_NAG-ASN : bond 0.00507 ( 19) link_NAG-ASN : angle 4.13661 ( 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 233 residues out of total 2185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 190 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 345 ASN cc_start: 0.8846 (t0) cc_final: 0.8502 (t0) REVERT: D 98 ILE cc_start: 0.8992 (OUTLIER) cc_final: 0.8717 (mm) REVERT: D 185 GLN cc_start: 0.8103 (OUTLIER) cc_final: 0.7084 (mp10) REVERT: G 464 TRP cc_start: 0.8630 (t-100) cc_final: 0.8315 (t60) REVERT: H 279 SER cc_start: 0.8344 (m) cc_final: 0.8116 (p) REVERT: H 464 TRP cc_start: 0.8514 (t-100) cc_final: 0.8307 (t60) outliers start: 43 outliers final: 36 residues processed: 224 average time/residue: 0.1238 time to fit residues: 44.4838 Evaluate side-chains 223 residues out of total 2185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 185 time to evaluate : 0.713 ------------------------------------------------------------------------------- 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 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 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 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 185 GLN 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: 0.6980 chunk 73 optimal weight: 0.9990 chunk 97 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 chunk 188 optimal weight: 20.0000 chunk 238 optimal weight: 2.9990 chunk 171 optimal weight: 20.0000 chunk 154 optimal weight: 9.9990 chunk 242 optimal weight: 1.9990 chunk 182 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 308 ASN G 316 GLN H 443 GLN H 448 HIS ** H 468 HIS ** 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 = 0.3808 r_free = 0.3808 target = 0.161536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.124004 restraints weight = 22393.978| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 1.91 r_work: 0.3106 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 19674 Z= 0.222 Angle : 0.628 16.034 26808 Z= 0.311 Chirality : 0.047 0.581 3063 Planarity : 0.004 0.070 3462 Dihedral : 5.116 49.158 3428 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 2.47 % Allowed : 20.00 % 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 aren not related in a simple way. whole: -0.56 (0.17), residues: 2492 helix: 1.29 (0.19), residues: 698 sheet: -0.28 (0.21), residues: 662 loop : -1.49 (0.17), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 265 TYR 0.026 0.002 TYR H 426 PHE 0.043 0.002 PHE G 246 TRP 0.020 0.002 TRP H 263 HIS 0.004 0.001 HIS D 345 Details of bonding type rmsd covalent geometry : bond 0.00545 (19634) covalent geometry : angle 0.58692 (26695) SS BOND : bond 0.00462 ( 7) SS BOND : angle 1.36643 ( 14) hydrogen bonds : bond 0.04026 ( 764) hydrogen bonds : angle 4.36427 ( 2157) link_BETA1-4 : bond 0.00501 ( 14) link_BETA1-4 : angle 1.37265 ( 42) link_NAG-ASN : bond 0.00720 ( 19) link_NAG-ASN : angle 4.71481 ( 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 231 residues out of total 2185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 187 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 345 ASN cc_start: 0.8893 (t0) cc_final: 0.8510 (t0) REVERT: B 15 ARG cc_start: 0.8124 (ptm-80) cc_final: 0.7883 (ptm160) REVERT: D 98 ILE cc_start: 0.9084 (OUTLIER) cc_final: 0.8795 (mm) REVERT: D 185 GLN cc_start: 0.8236 (OUTLIER) cc_final: 0.7184 (mp10) REVERT: G 464 TRP cc_start: 0.8788 (t-100) cc_final: 0.8430 (t60) REVERT: H 279 SER cc_start: 0.8336 (m) cc_final: 0.8102 (p) REVERT: H 464 TRP cc_start: 0.8685 (t-100) cc_final: 0.8410 (t60) outliers start: 44 outliers final: 38 residues processed: 224 average time/residue: 0.1352 time to fit residues: 48.0281 Evaluate side-chains 226 residues out of total 2185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 186 time to evaluate : 0.803 ------------------------------------------------------------------------------- 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 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 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 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 185 GLN 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 96 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 66 optimal weight: 0.1980 chunk 215 optimal weight: 1.9990 chunk 155 optimal weight: 10.0000 chunk 227 optimal weight: 2.9990 chunk 216 optimal weight: 0.9980 chunk 142 optimal weight: 0.9990 chunk 125 optimal weight: 1.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 176 GLN G 316 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.163764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.128952 restraints weight = 22288.469| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 1.68 r_work: 0.3150 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.2736 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= 0.137 Angle : 0.546 14.910 26808 Z= 0.272 Chirality : 0.044 0.543 3063 Planarity : 0.003 0.068 3462 Dihedral : 4.836 49.173 3428 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.25 % Allowed : 20.06 % Favored : 77.70 % 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 aren not related in a simple way. whole: -0.39 (0.17), residues: 2492 helix: 1.51 (0.20), residues: 699 sheet: -0.18 (0.21), residues: 650 loop : -1.44 (0.17), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 15 TYR 0.020 0.001 TYR H 426 PHE 0.041 0.002 PHE G 246 TRP 0.011 0.001 TRP H 263 HIS 0.005 0.001 HIS D 345 Details of bonding type rmsd covalent geometry : bond 0.00329 (19634) covalent geometry : angle 0.50966 (26695) SS BOND : bond 0.00239 ( 7) SS BOND : angle 1.03790 ( 14) hydrogen bonds : bond 0.03394 ( 764) hydrogen bonds : angle 4.18038 ( 2157) link_BETA1-4 : bond 0.00470 ( 14) link_BETA1-4 : angle 1.24299 ( 42) link_NAG-ASN : bond 0.00569 ( 19) link_NAG-ASN : angle 4.16717 ( 57) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5520.99 seconds wall clock time: 94 minutes 58.53 seconds (5698.53 seconds total)