Starting phenix.real_space_refine on Fri Jun 5 11:32:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j5j_61143/06_2026/9j5j_61143.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j5j_61143/06_2026/9j5j_61143.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9j5j_61143/06_2026/9j5j_61143.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j5j_61143/06_2026/9j5j_61143.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9j5j_61143/06_2026/9j5j_61143.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j5j_61143/06_2026/9j5j_61143.map" } resolution = 4.05 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= 0.033 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 P 2 5.49 5 S 94 5.16 5 C 12868 2.51 5 N 3460 2.21 5 O 3873 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20297 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 1399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1399 Classifications: {'peptide': 205} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 10, 'TRANS': 192} Unresolved non-hydrogen bonds: 217 Unresolved non-hydrogen angles: 270 Unresolved non-hydrogen dihedrals: 187 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLU:plan': 11, 'HIS:plan': 3, 'TYR:plan': 3, 'PHE:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 137 Chain: "B" Number of atoms: 1725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1725 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 12, 'TRANS': 217} Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 130 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 5, 'GLN:plan1': 1, 'TYR:plan': 1, 'PHE:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 70 Chain: "C" Number of atoms: 2269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2269 Classifications: {'peptide': 304} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 291} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 59 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 1, 'GLN:plan1': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 50 Chain: "D" Number of atoms: 3775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3775 Classifications: {'peptide': 483} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 3, 'PTRANS': 21, 'TRANS': 458} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 4, 'GLN:plan1': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "E" Number of atoms: 3858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3858 Classifications: {'peptide': 493} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PCIS': 3, 'PTRANS': 27, 'TRANS': 462} Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 3, 'TYR:plan': 1, 'ASP:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 57 Chain: "G" Number of atoms: 3781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3781 Classifications: {'peptide': 491} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 30, 'TRANS': 460} Unresolved non-hydrogen bonds: 156 Unresolved non-hydrogen angles: 192 Unresolved non-hydrogen dihedrals: 139 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 8, 'ARG:plan': 7, 'ASN:plan1': 1, 'ASP:plan': 2, 'TYR:plan': 2, 'HIS:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 116 Chain: "H" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1585 Classifications: {'peptide': 205} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 11, 'TRANS': 193} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "I" Number of atoms: 1801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1801 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 12, 'TRANS': 216} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "J" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "K" 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: "D" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'H6P': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.12, per 1000 atoms: 0.25 Number of scatterers: 20297 At special positions: 0 Unit cell: (155.1, 194.7, 297, 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) S 94 16.00 P 2 15.00 O 3873 8.00 N 3460 7.00 C 12868 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 23 " - pdb=" SG CYS A 92 " distance=2.03 Simple disulfide: pdb=" SG CYS A 140 " - pdb=" SG CYS A 191 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 97 " distance=2.03 Simple disulfide: pdb=" SG CYS B 154 " - pdb=" SG CYS B 210 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 97 " distance=2.04 Simple disulfide: pdb=" SG CYS C 137 " - pdb=" SG CYS C 191 " distance=2.04 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 97 " distance=2.04 Simple disulfide: pdb=" SG CYS D 137 " - pdb=" SG CYS D 191 " distance=2.05 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 97 " distance=2.04 Simple disulfide: pdb=" SG CYS E 137 " - pdb=" SG CYS E 191 " distance=2.04 Simple disulfide: pdb=" SG CYS E 219 " - pdb=" SG CYS G 219 " distance=2.03 Simple disulfide: pdb=" SG CYS E 237 " - pdb=" SG CYS G 237 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 97 " distance=2.04 Simple disulfide: pdb=" SG CYS G 137 " - pdb=" SG CYS G 191 " distance=2.04 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS H 140 " - pdb=" SG CYS H 191 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 97 " distance=2.04 Simple disulfide: pdb=" SG CYS I 154 " - pdb=" SG CYS I 210 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-6 " BMA J 3 " - " MAN J 4 " BETA1-4 " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " Time building additional restraints: 1.89 Conformation dependent library (CDL) restraints added in 896.9 milliseconds 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4910 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 46 sheets defined 16.2% alpha, 37.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'A' and resid 29 through 33 removed outlier: 3.641A pdb=" N TYR A 33 " --> pdb=" O ILE A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 189 Processing helix chain 'A' and resid 201 through 206 removed outlier: 3.740A pdb=" N PHE A 205 " --> pdb=" O HIS A 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 92 Processing helix chain 'B' and resid 140 through 148 Processing helix chain 'B' and resid 200 through 204 Processing helix chain 'B' and resid 217 through 221 Processing helix chain 'C' and resid 210 through 214 Processing helix chain 'C' and resid 217 through 303 Proline residue: C 228 - end of helix removed outlier: 4.148A pdb=" N GLY C 294 " --> pdb=" O TYR C 290 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU C 295 " --> pdb=" O LEU C 291 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU C 296 " --> pdb=" O THR C 292 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N THR C 301 " --> pdb=" O SER C 297 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASN C 302 " --> pdb=" O SER C 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 92 Processing helix chain 'D' and resid 209 through 214 removed outlier: 3.815A pdb=" N PHE D 212 " --> pdb=" O ALA D 209 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ARG D 214 " --> pdb=" O PRO D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 290 removed outlier: 4.081A pdb=" N ALA D 222 " --> pdb=" O ARG D 218 " (cutoff:3.500A) Proline residue: D 228 - end of helix removed outlier: 3.660A pdb=" N GLU D 263 " --> pdb=" O GLN D 259 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N MET D 264 " --> pdb=" O GLU D 260 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA D 265 " --> pdb=" O LEU D 261 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N MET D 269 " --> pdb=" O ALA D 265 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N LEU D 280 " --> pdb=" O ARG D 276 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N GLU D 281 " --> pdb=" O VAL D 277 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N GLU D 282 " --> pdb=" O LYS D 278 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU D 283 " --> pdb=" O LEU D 279 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG D 284 " --> pdb=" O LEU D 280 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N ILE D 288 " --> pdb=" O ARG D 284 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLN D 289 " --> pdb=" O TRP D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 307 removed outlier: 3.651A pdb=" N LYS D 305 " --> pdb=" O ASN D 301 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU D 307 " --> pdb=" O TRP D 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 92 removed outlier: 3.602A pdb=" N ASN E 92 " --> pdb=" O ALA E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 221 through 293 Proline residue: E 233 - end of helix removed outlier: 3.871A pdb=" N LYS E 246 " --> pdb=" O ASN E 242 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLU E 263 " --> pdb=" O ARG E 259 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ILE E 264 " --> pdb=" O GLU E 260 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU E 269 " --> pdb=" O ALA E 265 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLN E 287 " --> pdb=" O LYS E 283 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLU E 288 " --> pdb=" O GLU E 284 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLU E 289 " --> pdb=" O LYS E 285 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N LEU E 290 " --> pdb=" O LEU E 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 309 removed outlier: 3.791A pdb=" N THR E 308 " --> pdb=" O ASP E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 388 through 392 Processing helix chain 'G' and resid 75 through 79 removed outlier: 3.854A pdb=" N GLY G 78 " --> pdb=" O ILE G 75 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N SER G 79 " --> pdb=" O SER G 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 75 through 79' Processing helix chain 'G' and resid 88 through 92 Processing helix chain 'G' and resid 218 through 230 removed outlier: 3.670A pdb=" N ALA G 222 " --> pdb=" O PRO G 218 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU G 223 " --> pdb=" O CYS G 219 " (cutoff:3.500A) Proline residue: G 224 - end of helix Processing helix chain 'G' and resid 230 through 293 removed outlier: 3.792A pdb=" N ILE G 234 " --> pdb=" O LEU G 230 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N LEU G 251 " --> pdb=" O GLU G 247 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLU G 256 " --> pdb=" O SER G 252 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLN G 275 " --> pdb=" O LYS G 271 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLN G 281 " --> pdb=" O GLU G 277 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N VAL G 282 " --> pdb=" O GLU G 278 " (cutoff:3.500A) Processing helix chain 'H' and resid 185 through 189 removed outlier: 3.743A pdb=" N SER H 188 " --> pdb=" O ASP H 185 " (cutoff:3.500A) Processing helix chain 'I' and resid 88 through 92 removed outlier: 3.901A pdb=" N ILE I 92 " --> pdb=" O LYS I 89 " (cutoff:3.500A) Processing helix chain 'I' and resid 141 through 146 removed outlier: 3.732A pdb=" N LEU I 146 " --> pdb=" O ALA I 142 " (cutoff:3.500A) Processing helix chain 'I' and resid 201 through 205 removed outlier: 3.713A pdb=" N LEU I 204 " --> pdb=" O GLU I 201 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP I 205 " --> pdb=" O GLU I 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 201 through 205' Processing helix chain 'I' and resid 217 through 221 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 14 removed outlier: 6.740A pdb=" N ARG A 39 " --> pdb=" O PHE A 48 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N PHE A 48 " --> pdb=" O ARG A 39 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 10 through 14 Processing sheet with id=AA4, first strand: chain 'A' and resid 128 through 134 removed outlier: 4.471A pdb=" N ASN A 137 " --> pdb=" O TYR A 183 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N TYR A 183 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N ALA A 139 " --> pdb=" O GLY A 181 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N GLY A 181 " --> pdb=" O ALA A 139 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N LEU A 141 " --> pdb=" O LYS A 179 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N LYS A 179 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N LYS A 143 " --> pdb=" O ALA A 177 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ALA A 177 " --> pdb=" O LYS A 143 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 128 through 134 removed outlier: 4.471A pdb=" N ASN A 137 " --> pdb=" O TYR A 183 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N TYR A 183 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N ALA A 139 " --> pdb=" O GLY A 181 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N GLY A 181 " --> pdb=" O ALA A 139 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N LEU A 141 " --> pdb=" O LYS A 179 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N LYS A 179 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N LYS A 143 " --> pdb=" O ALA A 177 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ALA A 177 " --> pdb=" O LYS A 143 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 151 through 155 Processing sheet with id=AA7, first strand: chain 'B' and resid 3 through 5 Processing sheet with id=AA8, first strand: chain 'B' and resid 10 through 13 removed outlier: 5.640A pdb=" N SER B 11 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA B 93 " --> pdb=" O LEU B 119 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL B 35 " --> pdb=" O SER B 51 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N SER B 51 " --> pdb=" O VAL B 35 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N TRP B 37 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 10 through 13 removed outlier: 5.640A pdb=" N SER B 11 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA B 93 " --> pdb=" O LEU B 119 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 133 through 137 removed outlier: 4.359A pdb=" N PHE B 194 " --> pdb=" O ASN B 183 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N ASN B 183 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N TRP B 196 " --> pdb=" O GLU B 181 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N GLU B 181 " --> pdb=" O TRP B 196 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 165 through 170 Processing sheet with id=AB3, first strand: chain 'C' and resid 3 through 5 removed outlier: 7.127A pdb=" N LYS C 79 " --> pdb=" O ASP C 73 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N ASP C 73 " --> pdb=" O LYS C 79 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 11 through 13 removed outlier: 6.303A pdb=" N SER C 40 " --> pdb=" O VAL C 46 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N VAL C 46 " --> pdb=" O SER C 40 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 161 through 162 removed outlier: 5.772A pdb=" N TYR C 173 " --> pdb=" O GLY C 141 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N GLY C 132 " --> pdb=" O TYR C 128 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N TYR C 128 " --> pdb=" O GLY C 132 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N HIS C 134 " --> pdb=" O LYS C 126 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL C 123 " --> pdb=" O SER D 205 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N SER D 207 " --> pdb=" O VAL C 123 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N VAL C 125 " --> pdb=" O SER D 207 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 147 through 151 removed outlier: 8.903A pdb=" N VAL D 123 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N SER C 205 " --> pdb=" O VAL D 123 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N VAL D 125 " --> pdb=" O SER C 205 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N SER C 207 " --> pdb=" O VAL D 125 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N GLY D 127 " --> pdb=" O SER C 207 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N HIS D 134 " --> pdb=" O LYS D 126 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N TYR D 128 " --> pdb=" O GLY D 132 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N GLY D 132 " --> pdb=" O TYR D 128 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N HIS D 134 " --> pdb=" O MET D 181 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N MET D 181 " --> pdb=" O HIS D 134 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N GLU D 136 " --> pdb=" O VAL D 179 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N VAL D 179 " --> pdb=" O GLU D 136 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N ARG D 138 " --> pdb=" O ALA D 177 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ALA D 177 " --> pdb=" O ARG D 138 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N THR D 140 " --> pdb=" O VAL D 175 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N VAL D 175 " --> pdb=" O THR D 140 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 147 through 151 removed outlier: 8.903A pdb=" N VAL D 123 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N SER C 205 " --> pdb=" O VAL D 123 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N VAL D 125 " --> pdb=" O SER C 205 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N SER C 207 " --> pdb=" O VAL D 125 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N GLY D 127 " --> pdb=" O SER C 207 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N HIS D 134 " --> pdb=" O LYS D 126 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N TYR D 128 " --> pdb=" O GLY D 132 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N GLY D 132 " --> pdb=" O TYR D 128 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N HIS D 134 " --> pdb=" O MET D 181 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N MET D 181 " --> pdb=" O HIS D 134 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N GLU D 136 " --> pdb=" O VAL D 179 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N VAL D 179 " --> pdb=" O GLU D 136 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N ARG D 138 " --> pdb=" O ALA D 177 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ALA D 177 " --> pdb=" O ARG D 138 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N THR D 140 " --> pdb=" O VAL D 175 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N VAL D 175 " --> pdb=" O THR D 140 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL D 166 " --> pdb=" O ALA D 174 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 3 through 5 Processing sheet with id=AB9, first strand: chain 'D' and resid 11 through 13 removed outlier: 6.359A pdb=" N SER D 40 " --> pdb=" O VAL D 46 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N VAL D 46 " --> pdb=" O SER D 40 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 309 through 310 removed outlier: 3.989A pdb=" N LYS D 309 " --> pdb=" O ARG D 365 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N TYR D 367 " --> pdb=" O LYS D 309 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLU D 369 " --> pdb=" O CYS D 482 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR D 480 " --> pdb=" O GLU D 371 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU D 479 " --> pdb=" O VAL D 333 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 309 through 310 removed outlier: 3.989A pdb=" N LYS D 309 " --> pdb=" O ARG D 365 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N TYR D 367 " --> pdb=" O LYS D 309 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N HIS D 454 " --> pdb=" O PHE D 444 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N ASN D 446 " --> pdb=" O HIS D 452 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N HIS D 452 " --> pdb=" O ASN D 446 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 354 through 356 Processing sheet with id=AC4, first strand: chain 'E' and resid 4 through 5 removed outlier: 3.789A pdb=" N ALA E 81 " --> pdb=" O VAL E 71 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 11 through 14 removed outlier: 6.435A pdb=" N ILE E 11 " --> pdb=" O VAL E 113 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N ALA E 115 " --> pdb=" O ILE E 11 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ALA E 13 " --> pdb=" O ALA E 115 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP E 106 " --> pdb=" O PHE E 99 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU E 35 " --> pdb=" O GLN E 100 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 122 through 129 removed outlier: 5.738A pdb=" N ILE E 123 " --> pdb=" O ILE E 138 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ILE E 138 " --> pdb=" O ILE E 123 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N MET E 125 " --> pdb=" O GLU E 136 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N GLU E 136 " --> pdb=" O MET E 125 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N GLY E 127 " --> pdb=" O ARG E 134 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG E 134 " --> pdb=" O GLY E 127 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE E 133 " --> pdb=" O ILE E 181 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ILE E 181 " --> pdb=" O ILE E 133 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL E 179 " --> pdb=" O LEU E 135 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N PHE E 173 " --> pdb=" O GLY E 141 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 157 through 158 removed outlier: 4.787A pdb=" N TRP E 150 " --> pdb=" O ALA E 158 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 297 through 299 removed outlier: 3.757A pdb=" N TYR E 359 " --> pdb=" O HIS E 298 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N PHE E 470 " --> pdb=" O GLU E 363 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 297 through 299 removed outlier: 3.757A pdb=" N TYR E 359 " --> pdb=" O HIS E 298 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N ASN E 437 " --> pdb=" O HIS E 443 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N HIS E 443 " --> pdb=" O ASN E 437 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 346 through 348 removed outlier: 4.020A pdb=" N VAL E 372 " --> pdb=" O LEU E 396 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N HIS E 399 " --> pdb=" O GLN E 402 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 11 through 14 removed outlier: 5.941A pdb=" N ILE G 11 " --> pdb=" O VAL G 113 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N ALA G 115 " --> pdb=" O ILE G 11 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ALA G 13 " --> pdb=" O ALA G 115 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE G 39 " --> pdb=" O ARG G 96 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL G 36 " --> pdb=" O TYR G 50 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 11 through 14 removed outlier: 5.941A pdb=" N ILE G 11 " --> pdb=" O VAL G 113 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N ALA G 115 " --> pdb=" O ILE G 11 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ALA G 13 " --> pdb=" O ALA G 115 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N PHE G 99 " --> pdb=" O ASP G 106 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ASP G 106 " --> pdb=" O PHE G 99 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 19 through 23 Processing sheet with id=AD5, first strand: chain 'G' and resid 122 through 129 removed outlier: 5.965A pdb=" N ILE G 123 " --> pdb=" O ILE G 138 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N ILE G 138 " --> pdb=" O ILE G 123 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N MET G 125 " --> pdb=" O GLU G 136 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N GLU G 136 " --> pdb=" O MET G 125 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N GLY G 127 " --> pdb=" O ARG G 134 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL G 175 " --> pdb=" O SER G 139 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 147 through 151 Processing sheet with id=AD7, first strand: chain 'G' and resid 313 through 314 Processing sheet with id=AD8, first strand: chain 'G' and resid 346 through 347 removed outlier: 4.722A pdb=" N TYR G 403 " --> pdb=" O LEU G 413 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 357 through 363 removed outlier: 6.910A pdb=" N VAL G 433 " --> pdb=" O THR G 446 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N THR G 446 " --> pdb=" O VAL G 433 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N PHE G 435 " --> pdb=" O ILE G 444 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.816A pdb=" N THR H 116 " --> pdb=" O VAL H 11 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N ILE H 35 " --> pdb=" O ARG H 51 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ARG H 51 " --> pdb=" O ILE H 35 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N TRP H 37 " --> pdb=" O ILE H 49 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG H 51 " --> pdb=" O ILE H 55 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ILE H 55 " --> pdb=" O ARG H 51 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.816A pdb=" N THR H 116 " --> pdb=" O VAL H 11 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 21 through 22 removed outlier: 3.618A pdb=" N LEU H 74 " --> pdb=" O ASP H 69 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASP H 69 " --> pdb=" O LEU H 74 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 130 through 133 removed outlier: 5.608A pdb=" N TYR H 175 " --> pdb=" O GLU H 144 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 3 through 5 Processing sheet with id=AE6, first strand: chain 'I' and resid 10 through 14 removed outlier: 6.327A pdb=" N SER I 11 " --> pdb=" O ILE I 120 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N THR I 122 " --> pdb=" O SER I 11 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N LYS I 13 " --> pdb=" O THR I 122 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL I 50 " --> pdb=" O TRP I 37 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ARG I 39 " --> pdb=" O PHE I 48 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N PHE I 48 " --> pdb=" O ARG I 39 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 10 through 14 removed outlier: 6.327A pdb=" N SER I 11 " --> pdb=" O ILE I 120 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N THR I 122 " --> pdb=" O SER I 11 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N LYS I 13 " --> pdb=" O THR I 122 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 133 through 135 removed outlier: 6.155A pdb=" N TYR I 191 " --> pdb=" O LYS I 158 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLN I 180 " --> pdb=" O TRP I 196 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 133 through 135 removed outlier: 6.155A pdb=" N TYR I 191 " --> pdb=" O LYS I 158 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 165 through 170 removed outlier: 3.782A pdb=" N HIS I 208 " --> pdb=" O PHE I 227 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLN I 223 " --> pdb=" O VAL I 212 " (cutoff:3.500A) 901 hydrogen bonds defined for protein. 2289 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: 3.88 Time building geometry restraints manager: 2.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6662 1.34 - 1.46: 4678 1.46 - 1.59: 9257 1.59 - 1.71: 3 1.71 - 1.83: 134 Bond restraints: 20734 Sorted by residual: bond pdb=" C27 H6P D 501 " pdb=" C30 H6P D 501 " ideal model delta sigma weight residual 1.334 1.527 -0.193 2.00e-02 2.50e+03 9.32e+01 bond pdb=" O16 H6P D 501 " pdb=" P17 H6P D 501 " ideal model delta sigma weight residual 1.697 1.645 0.052 2.00e-02 2.50e+03 6.71e+00 bond pdb=" O16 H6P D 501 " pdb=" P13 H6P D 501 " ideal model delta sigma weight residual 1.594 1.645 -0.051 2.00e-02 2.50e+03 6.47e+00 bond pdb=" C GLN C 217 " pdb=" N PRO C 218 " ideal model delta sigma weight residual 1.335 1.365 -0.030 1.30e-02 5.92e+03 5.21e+00 bond pdb=" C28 H6P D 501 " pdb=" O29 H6P D 501 " ideal model delta sigma weight residual 1.442 1.398 0.044 2.00e-02 2.50e+03 4.90e+00 ... (remaining 20729 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.21: 27905 3.21 - 6.42: 248 6.42 - 9.64: 19 9.64 - 12.85: 3 12.85 - 16.06: 3 Bond angle restraints: 28178 Sorted by residual: angle pdb=" N ILE I 141 " pdb=" CA ILE I 141 " pdb=" C ILE I 141 " ideal model delta sigma weight residual 113.71 108.23 5.48 9.50e-01 1.11e+00 3.32e+01 angle pdb=" C21 H6P D 501 " pdb=" C30 H6P D 501 " pdb=" C27 H6P D 501 " ideal model delta sigma weight residual 125.58 109.52 16.06 3.00e+00 1.11e-01 2.87e+01 angle pdb=" C PRO G 7 " pdb=" N THR G 8 " pdb=" CA THR G 8 " ideal model delta sigma weight residual 121.54 131.44 -9.90 1.91e+00 2.74e-01 2.69e+01 angle pdb=" C28 H6P D 501 " pdb=" C27 H6P D 501 " pdb=" C30 H6P D 501 " ideal model delta sigma weight residual 127.23 112.49 14.74 3.00e+00 1.11e-01 2.41e+01 angle pdb=" P13 H6P D 501 " pdb=" O16 H6P D 501 " pdb=" P17 H6P D 501 " ideal model delta sigma weight residual 135.28 121.65 13.63 3.00e+00 1.11e-01 2.06e+01 ... (remaining 28173 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.57: 11968 25.57 - 51.14: 563 51.14 - 76.71: 58 76.71 - 102.27: 25 102.27 - 127.84: 16 Dihedral angle restraints: 12630 sinusoidal: 5006 harmonic: 7624 Sorted by residual: dihedral pdb=" CA TYR H 146 " pdb=" C TYR H 146 " pdb=" N PRO H 147 " pdb=" CA PRO H 147 " ideal model delta harmonic sigma weight residual 180.00 -124.09 -55.91 0 5.00e+00 4.00e-02 1.25e+02 dihedral pdb=" CA GLU H 52 " pdb=" C GLU H 52 " pdb=" N LYS H 53 " pdb=" CA LYS H 53 " ideal model delta harmonic sigma weight residual 180.00 124.60 55.40 0 5.00e+00 4.00e-02 1.23e+02 dihedral pdb=" CA SER G 26 " pdb=" C SER G 26 " pdb=" N PRO G 27 " pdb=" CA PRO G 27 " ideal model delta harmonic sigma weight residual -180.00 -133.77 -46.23 0 5.00e+00 4.00e-02 8.55e+01 ... (remaining 12627 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 2489 0.053 - 0.106: 595 0.106 - 0.160: 121 0.160 - 0.213: 4 0.213 - 0.266: 3 Chirality restraints: 3212 Sorted by residual: chirality pdb=" C5 BMA K 3 " pdb=" C4 BMA K 3 " pdb=" C6 BMA K 3 " pdb=" O5 BMA K 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" C5 BMA J 3 " pdb=" C4 BMA J 3 " pdb=" C6 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" CB ILE H 30 " pdb=" CA ILE H 30 " pdb=" CG1 ILE H 30 " pdb=" CG2 ILE H 30 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 3209 not shown) Planarity restraints: 3632 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C21 H6P D 501 " 0.065 2.00e-02 2.50e+03 2.05e-01 5.26e+02 pdb=" C27 H6P D 501 " 0.223 2.00e-02 2.50e+03 pdb=" C28 H6P D 501 " -0.073 2.00e-02 2.50e+03 pdb=" C30 H6P D 501 " -0.361 2.00e-02 2.50e+03 pdb=" C31 H6P D 501 " 0.145 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR H 146 " -0.077 5.00e-02 4.00e+02 1.17e-01 2.18e+01 pdb=" N PRO H 147 " 0.202 5.00e-02 4.00e+02 pdb=" CA PRO H 147 " -0.064 5.00e-02 4.00e+02 pdb=" CD PRO H 147 " -0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER G 26 " -0.059 5.00e-02 4.00e+02 9.08e-02 1.32e+01 pdb=" N PRO G 27 " 0.157 5.00e-02 4.00e+02 pdb=" CA PRO G 27 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO G 27 " -0.050 5.00e-02 4.00e+02 ... (remaining 3629 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1886 2.74 - 3.28: 20852 3.28 - 3.82: 33259 3.82 - 4.36: 37368 4.36 - 4.90: 63760 Nonbonded interactions: 157125 Sorted by model distance: nonbonded pdb=" OG SER C 207 " pdb=" OD1 ASP D 124 " model vdw 2.199 3.040 nonbonded pdb=" OE2 GLU C 272 " pdb=" NE2 GLN D 273 " model vdw 2.219 3.120 nonbonded pdb=" OG SER I 131 " pdb=" O ASN I 216 " model vdw 2.220 3.040 nonbonded pdb=" NH1 ARG D 413 " pdb=" O20 H6P D 501 " model vdw 2.221 3.120 nonbonded pdb=" OG1 THR A 41 " pdb=" OD1 ASN A 44 " model vdw 2.223 3.040 ... (remaining 157120 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 2 through 150 or (resid 151 through 152 and (name N or nam \ e CA or name C or name O or name CB )) or resid 153 through 159 or (resid 160 th \ rough 162 and (name N or name CA or name C or name O or name CB )) or resid 163 \ through 206)) selection = (chain 'H' and (resid 2 or (resid 3 through 4 and (name N or name CA or name C o \ r name O or name CB )) or resid 5 through 6 or (resid 7 through 8 and (name N or \ name CA or name C or name O or name CB )) or resid 9 or (resid 10 and (name N o \ r name CA or name C or name O or name CB )) or resid 11 through 14 or (resid 15 \ and (name N or name CA or name C or name O or name CB )) or resid 16 through 25 \ or (resid 26 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 7 through 33 or (resid 34 and (name N or name CA or name C or name O or name CB \ )) or resid 35 through 51 or (resid 52 and (name N or name CA or name C or name \ O or name CB )) or resid 53 through 59 or (resid 60 through 61 and (name N or na \ me CA or name C or name O or name CB )) or resid 62 or (resid 63 through 64 and \ (name N or name CA or name C or name O or name CB )) or resid 65 through 68 or ( \ resid 69 and (name N or name CA or name C or name O or name CB )) or resid 70 th \ rough 72 or (resid 73 and (name N or name CA or name C or name O or name CB )) o \ r resid 74 through 79 or (resid 80 through 81 and (name N or name CA or name C o \ r name O or name CB )) or resid 82 through 83 or (resid 84 through 87 and (name \ N or name CA or name C or name O or name CB )) or resid 88 through 95 or (resid \ 96 and (name N or name CA or name C or name O or name CB )) or resid 97 through \ 98 or (resid 99 and (name N or name CA or name C or name O or name CB )) or resi \ d 100 through 101 or (resid 102 and (name N or name CA or name C or name O or na \ me CB )) or resid 103 through 104 or (resid 105 and (name N or name CA or name C \ or name O or name CB )) or resid 106 through 110 or (resid 111 and (name N or n \ ame CA or name C or name O or name CB )) or resid 112 through 113 or (resid 114 \ and (name N or name CA or name C or name O or name CB )) or resid 115 through 11 \ 7 or (resid 118 and (name N or name CA or name C or name O or name CB )) or resi \ d 119 through 129 or (resid 130 and (name N or name CA or name C or name O or na \ me CB )) or resid 131 or (resid 132 through 133 and (name N or name CA or name C \ or name O or name CB )) or resid 134 through 143 or (resid 144 through 145 and \ (name N or name CA or name C or name O or name CB )) or resid 146 through 147 or \ (resid 148 and (name N or name CA or name C or name O or name CB )) or resid 14 \ 9 through 151 or (resid 152 and (name N or name CA or name C or name O or name C \ B )) or resid 153 or (resid 154 and (name N or name CA or name C or name O or na \ me CB )) or resid 155 or (resid 156 and (name N or name CA or name C or name O o \ r name CB )) or resid 157 through 161 or (resid 162 and (name N or name CA or na \ me C or name O or name CB )) or resid 163 through 168 or (resid 169 and (name N \ or name CA or name C or name O or name CB )) or resid 170 through 173 or (resid \ 174 through 175 and (name N or name CA or name C or name O or name CB )) or resi \ d 176 through 178 or (resid 179 through 180 and (name N or name CA or name C or \ name O or name CB )) or resid 181 through 182 or (resid 183 through 186 and (nam \ e N or name CA or name C or name O or name CB )) or resid 187 through 188 or (re \ sid 189 and (name N or name CA or name C or name O or name CB )) or resid 190 th \ rough 194 or (resid 195 and (name N or name CA or name C or name O or name CB )) \ or resid 196 through 200 or (resid 201 and (name N or name CA or name C or name \ O or name CB )) or resid 202 through 205 or (resid 206 and (name N or name CA o \ r name C or name O or name CB )))) } ncs_group { reference = (chain 'B' and (resid 2 through 200 or (resid 201 and (name N or name CA or name \ C or name O or name CB )) or resid 202 through 203 or (resid 204 and (name N or \ name CA or name C or name O or name CB )) or resid 205 through 223 or (resid 22 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 225 through \ 229 or (resid 230 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'I' and (resid 2 through 21 or (resid 22 and (name N or name CA or name C \ or name O or name CB )) or resid 23 through 40 or (resid 41 and (name N or name \ CA or name C or name O or name CB )) or resid 42 through 58 or (resid 59 throug \ h 61 and (name N or name CA or name C or name O or name CB )) or resid 62 throug \ h 72 or (resid 73 and (name N or name CA or name C or name O or name CB )) or re \ sid 74 through 102 or (resid 103 and (name N or name CA or name C or name O or n \ ame CB )) or resid 104 through 107 or (resid 108 and (name N or name CA or name \ C or name O or name CB )) or resid 109 through 123 or (resid 124 and (name N or \ name CA or name C or name O or name CB )) or resid 125 through 132 or (resid 133 \ and (name N or name CA or name C or name O or name CB )) or resid 134 through 1 \ 42 or (resid 143 and (name N or name CA or name C or name O or name CB )) or res \ id 144 through 151 or (resid 152 and (name N or name CA or name C or name O or n \ ame CB )) or resid 153 through 157 or (resid 158 and (name N or name CA or name \ C or name O or name CB )) or resid 159 or (resid 160 and (name N or name CA or n \ ame C or name O or name CB )) or resid 161 through 176 or (resid 177 and (name N \ or name CA or name C or name O or name CB )) or resid 178 or (resid 179 and (na \ me N or name CA or name C or name O or name CB )) or resid 180 or (resid 181 and \ (name N or name CA or name C or name O or name CB )) or resid 182 through 206 o \ r (resid 207 through 209 and (name N or name CA or name C or name O or name CB ) \ ) or resid 210 through 212 or (resid 213 and (name N or name CA or name C or nam \ e O or name CB )) or resid 214 through 216 or (resid 217 and (name N or name CA \ or name C or name O or name CB )) or resid 218 through 230)) } ncs_group { reference = (chain 'E' and ((resid 2 and (name N or name CA or name C or name O or name CB ) \ ) or resid 3 through 16 or (resid 17 and (name N or name CA or name C or name O \ or name CB )) or resid 18 through 21 or (resid 22 and (name N or name CA or name \ C or name O or name CB )) or resid 23 through 24 or (resid 25 and (name N or na \ me CA or name C or name O or name CB )) or resid 26 through 29 or (resid 30 thro \ ugh 33 and (name N or name CA or name C or name O or name CB )) or resid 34 thro \ ugh 49 or (resid 50 and (name N or name CA or name C or name O or name CB )) or \ resid 51 through 54 or (resid 55 through 56 and (name N or name CA or name C or \ name O or name CB )) or resid 57 through 60 or (resid 61 and (name N or name CA \ or name C or name O or name CB )) or resid 62 or (resid 63 and (name N or name C \ A or name C or name O or name CB )) or resid 64 or (resid 65 and (name N or name \ CA or name C or name O or name CB )) or resid 66 or (resid 67 and (name N or na \ me CA or name C or name O or name CB )) or resid 68 through 76 or (resid 77 and \ (name N or name CA or name C or name O or name CB )) or resid 78 through 84 or ( \ resid 85 and (name N or name CA or name C or name O or name CB )) or resid 86 th \ rough 94 or (resid 95 and (name N or name CA or name C or name O or name CB )) o \ r resid 96 through 98 or (resid 99 and (name N or name CA or name C or name O or \ name CB )) or resid 100 or (resid 101 and (name N or name CA or name C or name \ O or name CB )) or resid 102 through 144 or (resid 145 and (name N or name CA or \ name C or name O or name CB )) or resid 146 through 203 or (resid 204 and (name \ N or name CA or name C or name O or name CB )) or resid 205 through 323 or (res \ id 324 and (name N or name CA or name C or name O or name CB )) or resid 325 thr \ ough 396 or (resid 397 and (name N or name CA or name C or name O or name CB )) \ or resid 398 through 492)) selection = (chain 'G' and (resid 2 through 55 or (resid 56 and (name N or name CA or name C \ or name O or name CB )) or resid 57 or (resid 58 through 59 and (name N or name \ CA or name C or name O or name CB )) or resid 60 through 153 or (resid 154 and \ (name N or name CA or name C or name O or name CB )) or resid 155 through 182 or \ (resid 183 through 184 and (name N or name CA or name C or name O or name CB )) \ or resid 185 through 200 or (resid 201 and (name N or name CA or name C or name \ O or name CB )) or resid 202 through 215 or (resid 216 and (name N or name CA o \ r name C or name O or name CB )) or resid 217 through 342 or (resid 343 and (nam \ e N or name CA or name C or name O or name CB )) or resid 344 through 370 or (re \ sid 371 and (name N or name CA or name C or name O or name CB )) or resid 372 th \ rough 492)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.180 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 20.350 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.030 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:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 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 : 0.004 0.193 20757 Z= 0.204 Angle : 0.856 16.059 28229 Z= 0.481 Chirality : 0.048 0.266 3212 Planarity : 0.006 0.205 3632 Dihedral : 15.341 127.842 7666 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 16.16 Ramachandran Plot: Outliers : 0.38 % Allowed : 7.36 % Favored : 92.26 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.34 % Cis-general : 0.04 % Twisted Proline : 2.11 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.16), residues: 2624 helix: 0.34 (0.29), residues: 315 sheet: 0.18 (0.17), residues: 950 loop : -1.54 (0.16), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 286 TYR 0.034 0.002 TYR H 146 PHE 0.021 0.001 PHE C 240 TRP 0.022 0.001 TRP D 242 HIS 0.005 0.001 HIS I 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.20 (20734) covalent geometry : angle 0.85519 / 0.48 (28178) SS BOND : bond 0.00749 / 0.50 ( 18) SS BOND : angle 0.96972 / 0.62 ( 36) hydrogen bonds : bond 0.16067 / 11.28 ( 840) hydrogen bonds : angle 7.14291 / 4.90 ( 2289) link_ALPHA1-6 : bond 0.00228 / 0.12 ( 1) link_ALPHA1-6 : angle 1.92108 / 0.87 ( 3) link_BETA1-4 : bond 0.00336 / 0.17 ( 4) link_BETA1-4 : angle 1.81734 / 0.98 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 192 MET cc_start: 0.9448 (mmp) cc_final: 0.9013 (mmp) REVERT: E 398 MET cc_start: 0.8371 (tpt) cc_final: 0.8016 (tpp) REVERT: H 25 MET cc_start: 0.8602 (ttt) cc_final: 0.8047 (tmm) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.1468 time to fit residues: 20.7323 Evaluate side-chains 61 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 0.3980 chunk 132 optimal weight: 2.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 30.0000 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 8.9990 chunk 111 optimal weight: 4.9990 chunk 258 optimal weight: 8.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 ASN D 45 GLN ** D 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 223 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 = 0.3650 r_free = 0.3650 target = 0.045677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.028734 restraints weight = 263531.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.028760 restraints weight = 222765.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.028620 restraints weight = 170136.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.028803 restraints weight = 143424.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.028836 restraints weight = 133039.901| |-----------------------------------------------------------------------------| r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 20757 Z= 0.158 Angle : 0.687 10.870 28229 Z= 0.354 Chirality : 0.046 0.212 3212 Planarity : 0.006 0.118 3632 Dihedral : 9.509 103.631 2992 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.78 % Favored : 92.91 % Rotamer: Outliers : 0.14 % Allowed : 6.75 % Favored : 93.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.34 % Cis-general : 0.04 % Twisted Proline : 2.11 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.16), residues: 2624 helix: 0.44 (0.27), residues: 330 sheet: 0.09 (0.17), residues: 985 loop : -1.39 (0.17), residues: 1309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 286 TYR 0.020 0.001 TYR G 239 PHE 0.015 0.001 PHE H 145 TRP 0.020 0.001 TRP D 303 HIS 0.005 0.001 HIS I 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.16 (20734) covalent geometry : angle 0.68421 / 0.35 (28178) SS BOND : bond 0.00536 / 0.38 ( 18) SS BOND : angle 0.76215 / 0.52 ( 36) hydrogen bonds : bond 0.04029 / 2.71 ( 840) hydrogen bonds : angle 5.95836 / 4.08 ( 2289) link_ALPHA1-6 : bond 0.00033 / 0.02 ( 1) link_ALPHA1-6 : angle 1.65218 / 0.92 ( 3) link_BETA1-4 : bond 0.00403 / 0.16 ( 4) link_BETA1-4 : angle 2.90108 / 1.48 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 72 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 14 MET cc_start: 0.8782 (tpt) cc_final: 0.8546 (tpp) REVERT: D 29 MET cc_start: 0.8609 (pmm) cc_final: 0.8136 (pmm) REVERT: D 181 MET cc_start: 0.8115 (ppp) cc_final: 0.7892 (ppp) REVERT: E 174 MET cc_start: 0.8822 (ppp) cc_final: 0.8571 (tmm) REVERT: H 25 MET cc_start: 0.9081 (ttt) cc_final: 0.7762 (tmm) REVERT: I 192 MET cc_start: 0.8981 (ppp) cc_final: 0.8758 (ppp) outliers start: 3 outliers final: 2 residues processed: 75 average time/residue: 0.1322 time to fit residues: 16.7765 Evaluate side-chains 64 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 62 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 125 optimal weight: 3.9990 chunk 215 optimal weight: 6.9990 chunk 204 optimal weight: 6.9990 chunk 142 optimal weight: 0.2980 chunk 63 optimal weight: 1.9990 chunk 167 optimal weight: 9.9990 chunk 233 optimal weight: 20.0000 chunk 190 optimal weight: 0.8980 chunk 230 optimal weight: 4.9990 chunk 121 optimal weight: 4.9990 chunk 15 optimal weight: 30.0000 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 245 GLN ** D 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 358 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.041066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.030262 restraints weight = 339216.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.030878 restraints weight = 179486.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.031255 restraints weight = 125662.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.031531 restraints weight = 102620.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.031531 restraints weight = 88975.466| |-----------------------------------------------------------------------------| r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 20757 Z= 0.151 Angle : 0.673 11.128 28229 Z= 0.346 Chirality : 0.046 0.195 3212 Planarity : 0.005 0.115 3632 Dihedral : 8.465 101.604 2992 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.20 % Favored : 92.49 % Rotamer: Outliers : 0.05 % Allowed : 4.33 % Favored : 95.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.34 % Cis-general : 0.04 % Twisted Proline : 2.11 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.16), residues: 2624 helix: 0.47 (0.28), residues: 328 sheet: 0.13 (0.17), residues: 976 loop : -1.36 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 253 TYR 0.017 0.001 TYR G 239 PHE 0.016 0.001 PHE B 159 TRP 0.022 0.001 TRP D 242 HIS 0.005 0.001 HIS I 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (20734) covalent geometry : angle 0.67025 / 0.35 (28178) SS BOND : bond 0.00554 / 0.38 ( 18) SS BOND : angle 0.75745 / 0.49 ( 36) hydrogen bonds : bond 0.03812 / 2.58 ( 840) hydrogen bonds : angle 5.80174 / 3.95 ( 2289) link_ALPHA1-6 : bond 0.00566 / 0.30 ( 1) link_ALPHA1-6 : angle 1.70213 / 0.94 ( 3) link_BETA1-4 : bond 0.00361 / 0.15 ( 4) link_BETA1-4 : angle 2.80622 / 1.40 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 70 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 189 ASP cc_start: 0.7927 (m-30) cc_final: 0.7611 (m-30) REVERT: B 192 MET cc_start: 0.9516 (mmp) cc_final: 0.9289 (mmm) REVERT: D 29 MET cc_start: 0.7973 (pmm) cc_final: 0.7193 (pmm) REVERT: D 269 MET cc_start: 0.6654 (tpt) cc_final: 0.6191 (mtm) REVERT: E 174 MET cc_start: 0.8777 (ppp) cc_final: 0.8475 (ppp) REVERT: H 25 MET cc_start: 0.9142 (ttt) cc_final: 0.7866 (tmm) outliers start: 1 outliers final: 1 residues processed: 71 average time/residue: 0.1212 time to fit residues: 14.9413 Evaluate side-chains 62 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 61 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 28 optimal weight: 30.0000 chunk 206 optimal weight: 8.9990 chunk 63 optimal weight: 9.9990 chunk 141 optimal weight: 7.9990 chunk 21 optimal weight: 9.9990 chunk 211 optimal weight: 6.9990 chunk 135 optimal weight: 4.9990 chunk 27 optimal weight: 10.0000 chunk 68 optimal weight: 5.9990 chunk 121 optimal weight: 1.9990 chunk 82 optimal weight: 6.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 157 ASN D 85 HIS ** D 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 149 GLN D 366 HIS ** D 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 8 HIS H 42 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.039891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.029624 restraints weight = 347533.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.029951 restraints weight = 207344.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.029819 restraints weight = 166035.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.029933 restraints weight = 165872.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.029971 restraints weight = 146598.912| |-----------------------------------------------------------------------------| r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 20757 Z= 0.278 Angle : 0.765 10.638 28229 Z= 0.395 Chirality : 0.047 0.223 3212 Planarity : 0.006 0.113 3632 Dihedral : 8.007 107.031 2992 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 19.33 Ramachandran Plot: Outliers : 0.30 % Allowed : 8.23 % Favored : 91.46 % Rotamer: Outliers : 0.14 % Allowed : 5.36 % Favored : 94.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.34 % Cis-general : 0.04 % Twisted Proline : 2.11 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.16), residues: 2624 helix: 0.28 (0.27), residues: 325 sheet: -0.09 (0.17), residues: 962 loop : -1.43 (0.17), residues: 1337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 262 TYR 0.023 0.002 TYR D 143 PHE 0.022 0.002 PHE E 460 TRP 0.068 0.002 TRP D 266 HIS 0.011 0.002 HIS D 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00608 / 0.28 (20734) covalent geometry : angle 0.76240 / 0.39 (28178) SS BOND : bond 0.00551 / 0.37 ( 18) SS BOND : angle 1.06502 / 0.71 ( 36) hydrogen bonds : bond 0.04198 / 2.81 ( 840) hydrogen bonds : angle 6.01111 / 4.11 ( 2289) link_ALPHA1-6 : bond 0.00084 / 0.04 ( 1) link_ALPHA1-6 : angle 1.53999 / 0.86 ( 3) link_BETA1-4 : bond 0.00554 / 0.26 ( 4) link_BETA1-4 : angle 2.89488 / 1.43 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 68 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 189 ASP cc_start: 0.8146 (m-30) cc_final: 0.7909 (m-30) REVERT: D 14 MET cc_start: 0.8569 (tpt) cc_final: 0.8191 (tpp) REVERT: D 29 MET cc_start: 0.8215 (pmm) cc_final: 0.7436 (pmm) REVERT: D 269 MET cc_start: 0.6745 (tpt) cc_final: 0.6405 (mtm) REVERT: E 174 MET cc_start: 0.8996 (ppp) cc_final: 0.8752 (ppp) outliers start: 3 outliers final: 2 residues processed: 71 average time/residue: 0.1322 time to fit residues: 16.3346 Evaluate side-chains 59 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 57 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 256 optimal weight: 10.0000 chunk 164 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 247 optimal weight: 1.9990 chunk 209 optimal weight: 7.9990 chunk 200 optimal weight: 10.0000 chunk 14 optimal weight: 40.0000 chunk 92 optimal weight: 10.0000 chunk 7 optimal weight: 50.0000 chunk 110 optimal weight: 8.9990 chunk 81 optimal weight: 0.3980 overall best weight: 3.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.039965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.029603 restraints weight = 343649.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.030015 restraints weight = 206492.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.029939 restraints weight = 155717.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.030026 restraints weight = 155440.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.030119 restraints weight = 139510.648| |-----------------------------------------------------------------------------| r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 20757 Z= 0.198 Angle : 0.695 10.800 28229 Z= 0.360 Chirality : 0.047 0.221 3212 Planarity : 0.006 0.111 3632 Dihedral : 7.570 103.624 2992 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 16.43 Ramachandran Plot: Outliers : 0.30 % Allowed : 8.04 % Favored : 91.65 % Rotamer: Outliers : 0.05 % Allowed : 3.87 % Favored : 96.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.34 % Cis-general : 0.04 % Twisted Proline : 2.11 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.16), residues: 2624 helix: 0.36 (0.27), residues: 330 sheet: -0.16 (0.16), residues: 978 loop : -1.42 (0.17), residues: 1316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 253 TYR 0.014 0.002 TYR D 143 PHE 0.022 0.002 PHE G 327 TRP 0.022 0.001 TRP D 303 HIS 0.004 0.001 HIS I 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.20 (20734) covalent geometry : angle 0.69363 / 0.36 (28178) SS BOND : bond 0.00423 / 0.31 ( 18) SS BOND : angle 0.76902 / 0.52 ( 36) hydrogen bonds : bond 0.03792 / 2.52 ( 840) hydrogen bonds : angle 5.88778 / 4.02 ( 2289) link_ALPHA1-6 : bond 0.00230 / 0.12 ( 1) link_ALPHA1-6 : angle 1.74781 / 0.94 ( 3) link_BETA1-4 : bond 0.00258 / 0.12 ( 4) link_BETA1-4 : angle 2.31042 / 1.15 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 69 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 189 ASP cc_start: 0.8124 (m-30) cc_final: 0.7892 (m-30) REVERT: B 192 MET cc_start: 0.9557 (mmp) cc_final: 0.9324 (mmp) REVERT: D 14 MET cc_start: 0.8675 (tpt) cc_final: 0.8408 (tpp) REVERT: D 29 MET cc_start: 0.8291 (pmm) cc_final: 0.7448 (pmm) REVERT: D 269 MET cc_start: 0.6889 (tpt) cc_final: 0.6494 (mtm) REVERT: E 174 MET cc_start: 0.8991 (ppp) cc_final: 0.8711 (ppp) outliers start: 1 outliers final: 1 residues processed: 70 average time/residue: 0.1300 time to fit residues: 16.1037 Evaluate side-chains 60 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 59 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 205 optimal weight: 7.9990 chunk 230 optimal weight: 5.9990 chunk 88 optimal weight: 5.9990 chunk 75 optimal weight: 10.0000 chunk 85 optimal weight: 1.9990 chunk 198 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 178 optimal weight: 5.9990 chunk 247 optimal weight: 4.9990 chunk 219 optimal weight: 4.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.040066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.029260 restraints weight = 341338.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.029885 restraints weight = 185300.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.030237 restraints weight = 129469.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.030237 restraints weight = 105950.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.030237 restraints weight = 105906.466| |-----------------------------------------------------------------------------| r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 20757 Z= 0.162 Angle : 0.683 10.624 28229 Z= 0.353 Chirality : 0.047 0.222 3212 Planarity : 0.005 0.110 3632 Dihedral : 7.157 101.166 2992 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.70 % Favored : 92.00 % Rotamer: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.34 % Cis-general : 0.04 % Twisted Proline : 2.11 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.16), residues: 2624 helix: 0.32 (0.27), residues: 325 sheet: -0.16 (0.17), residues: 975 loop : -1.35 (0.17), residues: 1324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 253 TYR 0.012 0.001 TYR G 239 PHE 0.017 0.001 PHE G 327 TRP 0.022 0.001 TRP D 303 HIS 0.005 0.001 HIS G 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 (20734) covalent geometry : angle 0.68147 / 0.35 (28178) SS BOND : bond 0.00461 / 0.29 ( 18) SS BOND : angle 0.68445 / 0.45 ( 36) hydrogen bonds : bond 0.03651 / 2.44 ( 840) hydrogen bonds : angle 5.84459 / 3.98 ( 2289) link_ALPHA1-6 : bond 0.00352 / 0.19 ( 1) link_ALPHA1-6 : angle 1.61529 / 0.85 ( 3) link_BETA1-4 : bond 0.00262 / 0.12 ( 4) link_BETA1-4 : angle 2.17055 / 1.09 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 189 ASP cc_start: 0.7989 (m-30) cc_final: 0.7694 (m-30) REVERT: D 14 MET cc_start: 0.8692 (tpt) cc_final: 0.8432 (tpp) REVERT: D 29 MET cc_start: 0.8255 (pmm) cc_final: 0.7244 (pmm) REVERT: D 269 MET cc_start: 0.6796 (tpt) cc_final: 0.6385 (mtm) REVERT: E 174 MET cc_start: 0.8987 (ppp) cc_final: 0.8714 (ppp) outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.1387 time to fit residues: 16.6663 Evaluate side-chains 57 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 24 optimal weight: 10.0000 chunk 20 optimal weight: 9.9990 chunk 67 optimal weight: 20.0000 chunk 228 optimal weight: 1.9990 chunk 190 optimal weight: 2.9990 chunk 9 optimal weight: 20.0000 chunk 212 optimal weight: 9.9990 chunk 248 optimal weight: 2.9990 chunk 189 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 197 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 24 HIS ** C 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.039853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.029057 restraints weight = 343967.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.029663 restraints weight = 186247.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.029948 restraints weight = 130146.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.030216 restraints weight = 109487.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.030216 restraints weight = 93965.676| |-----------------------------------------------------------------------------| r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 20757 Z= 0.177 Angle : 0.691 10.386 28229 Z= 0.356 Chirality : 0.046 0.197 3212 Planarity : 0.005 0.123 3632 Dihedral : 6.823 101.296 2992 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.70 % Favored : 91.96 % Rotamer: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.34 % Cis-general : 0.04 % Twisted Proline : 2.11 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.16), residues: 2624 helix: 0.43 (0.27), residues: 325 sheet: -0.20 (0.17), residues: 973 loop : -1.34 (0.17), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 253 TYR 0.037 0.002 TYR H 146 PHE 0.021 0.001 PHE E 48 TRP 0.023 0.001 TRP D 242 HIS 0.004 0.001 HIS G 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.18 (20734) covalent geometry : angle 0.68955 / 0.36 (28178) SS BOND : bond 0.00485 / 0.32 ( 18) SS BOND : angle 0.75655 / 0.49 ( 36) hydrogen bonds : bond 0.03673 / 2.45 ( 840) hydrogen bonds : angle 5.81537 / 3.96 ( 2289) link_ALPHA1-6 : bond 0.00306 / 0.16 ( 1) link_ALPHA1-6 : angle 1.64108 / 0.86 ( 3) link_BETA1-4 : bond 0.00229 / 0.11 ( 4) link_BETA1-4 : angle 2.16994 / 1.11 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 189 ASP cc_start: 0.7942 (m-30) cc_final: 0.7632 (m-30) REVERT: B 192 MET cc_start: 0.9529 (mmp) cc_final: 0.9272 (mmm) REVERT: D 14 MET cc_start: 0.8625 (tpt) cc_final: 0.8363 (tpp) REVERT: D 29 MET cc_start: 0.8165 (pmm) cc_final: 0.7246 (pmm) REVERT: D 269 MET cc_start: 0.6741 (tpt) cc_final: 0.6413 (mtm) REVERT: E 174 MET cc_start: 0.8985 (ppp) cc_final: 0.8712 (ppp) outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.1276 time to fit residues: 15.7390 Evaluate side-chains 59 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 58 optimal weight: 4.9990 chunk 94 optimal weight: 9.9990 chunk 7 optimal weight: 40.0000 chunk 238 optimal weight: 50.0000 chunk 3 optimal weight: 30.0000 chunk 76 optimal weight: 10.0000 chunk 135 optimal weight: 2.9990 chunk 140 optimal weight: 7.9990 chunk 22 optimal weight: 30.0000 chunk 92 optimal weight: 0.3980 chunk 152 optimal weight: 20.0000 overall best weight: 5.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 301 ASN ** I 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.039436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.029138 restraints weight = 347742.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.029497 restraints weight = 212585.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.029357 restraints weight = 164953.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.029488 restraints weight = 151759.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.029607 restraints weight = 132310.339| |-----------------------------------------------------------------------------| r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 20757 Z= 0.264 Angle : 0.767 11.820 28229 Z= 0.397 Chirality : 0.047 0.224 3212 Planarity : 0.006 0.125 3632 Dihedral : 6.879 105.775 2992 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 20.31 Ramachandran Plot: Outliers : 0.30 % Allowed : 8.61 % Favored : 91.08 % Rotamer: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.34 % Cis-general : 0.04 % Twisted Proline : 2.11 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.16), residues: 2624 helix: 0.12 (0.27), residues: 334 sheet: -0.45 (0.17), residues: 968 loop : -1.41 (0.17), residues: 1322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG D 253 TYR 0.027 0.002 TYR H 146 PHE 0.019 0.002 PHE B 48 TRP 0.017 0.002 TRP D 242 HIS 0.016 0.002 HIS C 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00579 / 0.26 (20734) covalent geometry : angle 0.76518 / 0.40 (28178) SS BOND : bond 0.00552 / 0.36 ( 18) SS BOND : angle 1.04594 / 0.66 ( 36) hydrogen bonds : bond 0.04093 / 2.74 ( 840) hydrogen bonds : angle 6.10054 / 4.17 ( 2289) link_ALPHA1-6 : bond 0.00193 / 0.10 ( 1) link_ALPHA1-6 : angle 1.91139 / 1.00 ( 3) link_BETA1-4 : bond 0.00279 / 0.14 ( 4) link_BETA1-4 : angle 2.32997 / 1.20 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.826 Fit side-chains revert: symmetry clash REVERT: B 189 ASP cc_start: 0.8391 (m-30) cc_final: 0.8156 (m-30) REVERT: B 192 MET cc_start: 0.9557 (mmp) cc_final: 0.9312 (mmp) REVERT: D 14 MET cc_start: 0.8571 (tpt) cc_final: 0.8189 (tpp) REVERT: D 29 MET cc_start: 0.8372 (pmm) cc_final: 0.7768 (pmm) REVERT: D 269 MET cc_start: 0.7111 (tpt) cc_final: 0.6626 (mtm) REVERT: E 174 MET cc_start: 0.9039 (ppp) cc_final: 0.8786 (ppp) outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.1222 time to fit residues: 13.9975 Evaluate side-chains 57 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 209 optimal weight: 8.9990 chunk 201 optimal weight: 30.0000 chunk 164 optimal weight: 8.9990 chunk 1 optimal weight: 0.0570 chunk 7 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 235 optimal weight: 10.0000 chunk 118 optimal weight: 10.0000 chunk 86 optimal weight: 0.8980 chunk 124 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 overall best weight: 1.7904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 48 ASN D 134 HIS ** D 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 223 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 = 0.3518 r_free = 0.3518 target = 0.039967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.029861 restraints weight = 343622.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.030215 restraints weight = 204066.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.030081 restraints weight = 162146.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.030207 restraints weight = 150724.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.030293 restraints weight = 135963.234| |-----------------------------------------------------------------------------| r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 20757 Z= 0.137 Angle : 0.706 10.381 28229 Z= 0.364 Chirality : 0.047 0.193 3212 Planarity : 0.006 0.127 3632 Dihedral : 6.495 98.185 2992 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.16 % Favored : 92.53 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.34 % Cis-general : 0.04 % Twisted Proline : 2.11 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.16), residues: 2624 helix: 0.33 (0.28), residues: 331 sheet: -0.26 (0.17), residues: 954 loop : -1.35 (0.17), residues: 1339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 253 TYR 0.033 0.001 TYR H 146 PHE 0.012 0.001 PHE E 48 TRP 0.023 0.001 TRP D 242 HIS 0.004 0.001 HIS I 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 (20734) covalent geometry : angle 0.70468 / 0.36 (28178) SS BOND : bond 0.00536 / 0.38 ( 18) SS BOND : angle 0.70706 / 0.45 ( 36) hydrogen bonds : bond 0.03605 / 2.40 ( 840) hydrogen bonds : angle 5.88667 / 4.02 ( 2289) link_ALPHA1-6 : bond 0.00461 / 0.24 ( 1) link_ALPHA1-6 : angle 1.42409 / 0.74 ( 3) link_BETA1-4 : bond 0.00400 / 0.20 ( 4) link_BETA1-4 : angle 1.92864 / 0.98 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.875 Fit side-chains revert: symmetry clash REVERT: A 197 ASN cc_start: 0.9284 (t0) cc_final: 0.9077 (p0) REVERT: B 189 ASP cc_start: 0.8248 (m-30) cc_final: 0.7985 (m-30) REVERT: B 192 MET cc_start: 0.9541 (mmp) cc_final: 0.9174 (mmp) REVERT: D 14 MET cc_start: 0.8645 (tpt) cc_final: 0.8281 (tpp) REVERT: E 174 MET cc_start: 0.9007 (ppp) cc_final: 0.8730 (ppp) REVERT: E 398 MET cc_start: 0.8853 (tpt) cc_final: 0.8596 (tpp) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.1243 time to fit residues: 15.0374 Evaluate side-chains 59 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 156 optimal weight: 7.9990 chunk 47 optimal weight: 8.9990 chunk 152 optimal weight: 5.9990 chunk 132 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 238 optimal weight: 7.9990 chunk 44 optimal weight: 0.0980 chunk 177 optimal weight: 0.9980 chunk 69 optimal weight: 5.9990 chunk 195 optimal weight: 5.9990 chunk 117 optimal weight: 10.0000 overall best weight: 2.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 GLN ** D 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.039832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.029603 restraints weight = 346349.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.029992 restraints weight = 197801.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.029841 restraints weight = 154373.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.030014 restraints weight = 150085.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.030035 restraints weight = 128950.829| |-----------------------------------------------------------------------------| r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 20757 Z= 0.154 Angle : 0.694 9.846 28229 Z= 0.357 Chirality : 0.047 0.205 3212 Planarity : 0.005 0.126 3632 Dihedral : 6.340 95.108 2992 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.47 % Favored : 92.23 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.34 % Cis-general : 0.04 % Twisted Proline : 2.11 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.16), residues: 2624 helix: 0.31 (0.27), residues: 331 sheet: -0.21 (0.17), residues: 946 loop : -1.34 (0.17), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 253 TYR 0.031 0.001 TYR H 146 PHE 0.010 0.001 PHE B 159 TRP 0.023 0.001 TRP D 242 HIS 0.004 0.001 HIS I 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (20734) covalent geometry : angle 0.69245 / 0.36 (28178) SS BOND : bond 0.00471 / 0.32 ( 18) SS BOND : angle 0.69628 / 0.45 ( 36) hydrogen bonds : bond 0.03595 / 2.39 ( 840) hydrogen bonds : angle 5.85723 / 4.00 ( 2289) link_ALPHA1-6 : bond 0.00366 / 0.19 ( 1) link_ALPHA1-6 : angle 1.51502 / 0.77 ( 3) link_BETA1-4 : bond 0.00228 / 0.11 ( 4) link_BETA1-4 : angle 2.02837 / 1.03 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.751 Fit side-chains revert: symmetry clash REVERT: B 189 ASP cc_start: 0.8412 (m-30) cc_final: 0.8175 (m-30) REVERT: B 192 MET cc_start: 0.9554 (mmp) cc_final: 0.9215 (mmp) REVERT: D 14 MET cc_start: 0.8785 (tpt) cc_final: 0.8395 (tpp) REVERT: D 29 MET cc_start: 0.8141 (pmm) cc_final: 0.7503 (pmm) REVERT: E 174 MET cc_start: 0.9127 (ppp) cc_final: 0.8826 (ppp) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.1207 time to fit residues: 14.0606 Evaluate side-chains 58 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 113 optimal weight: 0.5980 chunk 25 optimal weight: 9.9990 chunk 99 optimal weight: 0.9980 chunk 201 optimal weight: 40.0000 chunk 164 optimal weight: 20.0000 chunk 35 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 82 optimal weight: 9.9990 chunk 127 optimal weight: 3.9990 chunk 62 optimal weight: 9.9990 chunk 207 optimal weight: 20.0000 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 ASN ** D 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 223 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.040191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.029613 restraints weight = 339899.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.030190 restraints weight = 188646.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.030512 restraints weight = 130548.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.030762 restraints weight = 106354.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.030762 restraints weight = 92736.766| |-----------------------------------------------------------------------------| r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 20757 Z= 0.135 Angle : 0.682 11.245 28229 Z= 0.350 Chirality : 0.047 0.297 3212 Planarity : 0.005 0.126 3632 Dihedral : 6.216 93.454 2992 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.47 % Favored : 92.23 % Rotamer: Outliers : 0.09 % Allowed : 0.19 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.34 % Cis-general : 0.04 % Twisted Proline : 2.11 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.16), residues: 2624 helix: 0.37 (0.27), residues: 331 sheet: -0.19 (0.17), residues: 958 loop : -1.28 (0.17), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 253 TYR 0.030 0.001 TYR H 146 PHE 0.009 0.001 PHE B 159 TRP 0.024 0.001 TRP D 242 HIS 0.004 0.001 HIS I 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 (20734) covalent geometry : angle 0.68123 / 0.35 (28178) SS BOND : bond 0.00478 / 0.33 ( 18) SS BOND : angle 0.63856 / 0.42 ( 36) hydrogen bonds : bond 0.03472 / 2.30 ( 840) hydrogen bonds : angle 5.75035 / 3.92 ( 2289) link_ALPHA1-6 : bond 0.00475 / 0.25 ( 1) link_ALPHA1-6 : angle 1.44017 / 0.73 ( 3) link_BETA1-4 : bond 0.00304 / 0.14 ( 4) link_BETA1-4 : angle 1.80637 / 0.92 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4506.15 seconds wall clock time: 78 minutes 46.09 seconds (4726.09 seconds total)