Starting phenix.real_space_refine on Wed Mar 4 05:05:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n9f_49167/03_2026/9n9f_49167_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n9f_49167/03_2026/9n9f_49167.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9n9f_49167/03_2026/9n9f_49167_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n9f_49167/03_2026/9n9f_49167_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9n9f_49167/03_2026/9n9f_49167.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n9f_49167/03_2026/9n9f_49167.map" } resolution = 2.91 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= 0.006 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 8 5.49 5 Mg 3 5.21 5 S 70 5.16 5 C 6735 2.51 5 N 1835 2.21 5 O 2070 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10723 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3372 Classifications: {'peptide': 430} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 409} Chain breaks: 1 Chain: "B" Number of atoms: 3351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3351 Classifications: {'peptide': 426} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Chain: "C" Number of atoms: 3372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3372 Classifications: {'peptide': 430} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 409} Chain breaks: 1 Chain: "S" Number of atoms: 464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 464 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'TRANS': 53} 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: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' ZN': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 92 Unusual residues: {' MG': 2, 'GDP': 1, 'TA1': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {' MG': 1, ' ZN': 1, 'GTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 2.58, per 1000 atoms: 0.24 Number of scatterers: 10723 At special positions: 0 Unit cell: (83.93, 71.94, 153.69, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 70 16.00 P 8 15.00 Mg 3 11.99 O 2070 8.00 N 1835 7.00 C 6735 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.85 Conformation dependent library (CDL) restraints added in 476.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 502 " pdb="ZN ZN A 502 " - pdb=" NE2 HIS A 197 " pdb=" ZN C 503 " pdb="ZN ZN C 503 " - pdb=" NE2 HIS C 197 " pdb="ZN ZN C 503 " - pdb=" NE2 HIS C 192 " 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2494 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 8 sheets defined 56.6% alpha, 13.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 10 through 29 removed outlier: 3.762A pdb=" N ALA A 19 " --> pdb=" O GLN A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 51 removed outlier: 3.750A pdb=" N THR A 51 " --> pdb=" O SER A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 80 removed outlier: 4.664A pdb=" N ILE A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 90 No H-bonds generated for 'chain 'A' and resid 88 through 90' Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 110 through 113 Processing helix chain 'A' and resid 114 through 129 Processing helix chain 'A' and resid 143 through 161 removed outlier: 4.274A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 197 removed outlier: 3.544A pdb=" N ASN A 186 " --> pdb=" O VAL A 182 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N HIS A 192 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N THR A 193 " --> pdb=" O LEU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 216 Processing helix chain 'A' and resid 223 through 244 removed outlier: 3.730A pdb=" N LEU A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N LEU A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 260 Processing helix chain 'A' and resid 277 through 284 removed outlier: 3.884A pdb=" N HIS A 283 " --> pdb=" O GLU A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 296 removed outlier: 3.735A pdb=" N PHE A 296 " --> pdb=" O THR A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 324 through 337 Processing helix chain 'A' and resid 383 through 400 removed outlier: 3.974A pdb=" N ALA A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TRP A 388 " --> pdb=" O ILE A 384 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N HIS A 393 " --> pdb=" O ALA A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 411 removed outlier: 4.123A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 435 removed outlier: 4.296A pdb=" N SER A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 28 Processing helix chain 'B' and resid 41 through 48 removed outlier: 4.486A pdb=" N ARG B 48 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 51 No H-bonds generated for 'chain 'B' and resid 49 through 51' Processing helix chain 'B' and resid 71 through 81 removed outlier: 4.619A pdb=" N MET B 75 " --> pdb=" O GLU B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 90 No H-bonds generated for 'chain 'B' and resid 88 through 90' Processing helix chain 'B' and resid 102 through 108 Processing helix chain 'B' and resid 109 through 129 removed outlier: 4.018A pdb=" N GLU B 113 " --> pdb=" O THR B 109 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU B 114 " --> pdb=" O GLU B 110 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ASP B 116 " --> pdb=" O ALA B 112 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N SER B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 161 Processing helix chain 'B' and resid 174 through 178 removed outlier: 3.547A pdb=" N SER B 178 " --> pdb=" O PRO B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 198 removed outlier: 3.697A pdb=" N ASN B 186 " --> pdb=" O VAL B 182 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N GLU B 196 " --> pdb=" O HIS B 192 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASN B 197 " --> pdb=" O GLN B 193 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N THR B 198 " --> pdb=" O LEU B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 216 Processing helix chain 'B' and resid 223 through 239 removed outlier: 3.594A pdb=" N LEU B 227 " --> pdb=" O THR B 223 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N THR B 239 " --> pdb=" O MET B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 260 Processing helix chain 'B' and resid 277 through 281 removed outlier: 3.925A pdb=" N GLN B 281 " --> pdb=" O ARG B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 296 Processing helix chain 'B' and resid 297 through 301 removed outlier: 3.670A pdb=" N MET B 301 " --> pdb=" O ALA B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 310 Processing helix chain 'B' and resid 324 through 339 removed outlier: 3.553A pdb=" N ASN B 339 " --> pdb=" O VAL B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 343 Processing helix chain 'B' and resid 384 through 400 removed outlier: 3.851A pdb=" N PHE B 388 " --> pdb=" O ILE B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 Processing helix chain 'B' and resid 414 through 435 removed outlier: 3.993A pdb=" N PHE B 418 " --> pdb=" O ASP B 414 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N TYR B 435 " --> pdb=" O GLU B 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 29 removed outlier: 3.780A pdb=" N ALA C 19 " --> pdb=" O GLN C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 51 removed outlier: 3.662A pdb=" N THR C 51 " --> pdb=" O SER C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 80 Processing helix chain 'C' and resid 88 through 90 No H-bonds generated for 'chain 'C' and resid 88 through 90' Processing helix chain 'C' and resid 102 through 108 Processing helix chain 'C' and resid 110 through 129 removed outlier: 4.175A pdb=" N ILE C 114 " --> pdb=" O ILE C 110 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ASP C 116 " --> pdb=" O LYS C 112 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N LEU C 117 " --> pdb=" O GLU C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 161 Processing helix chain 'C' and resid 182 through 190 removed outlier: 3.567A pdb=" N ASN C 186 " --> pdb=" O VAL C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 197 Processing helix chain 'C' and resid 205 through 216 removed outlier: 3.615A pdb=" N ILE C 209 " --> pdb=" O ASP C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 244 removed outlier: 3.738A pdb=" N LEU C 227 " --> pdb=" O THR C 223 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N SER C 241 " --> pdb=" O SER C 237 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N LEU C 242 " --> pdb=" O ILE C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 260 Processing helix chain 'C' and resid 277 through 282 removed outlier: 3.927A pdb=" N TYR C 282 " --> pdb=" O ALA C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 296 removed outlier: 3.791A pdb=" N PHE C 296 " --> pdb=" O THR C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 301 Processing helix chain 'C' and resid 306 through 310 Processing helix chain 'C' and resid 324 through 338 Processing helix chain 'C' and resid 383 through 402 removed outlier: 4.085A pdb=" N ALA C 387 " --> pdb=" O ALA C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 410 removed outlier: 4.035A pdb=" N TYR C 408 " --> pdb=" O PHE C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 437 removed outlier: 4.170A pdb=" N SER C 419 " --> pdb=" O GLU C 415 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL C 437 " --> pdb=" O GLU C 433 " (cutoff:3.500A) Processing helix chain 'S' and resid 534 through 586 removed outlier: 3.860A pdb=" N LEU S 545 " --> pdb=" O ARG S 541 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 92 through 94 removed outlier: 8.231A pdb=" N ILE A 93 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N PHE A 67 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N VAL A 66 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N GLU A 3 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLY A 134 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N SER A 140 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 8.415A pdb=" N LEU A 167 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N PHE A 135 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N PHE A 169 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N VAL A 137 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N ILE A 171 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N HIS A 139 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N CYS A 200 " --> pdb=" O LYS A 166 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA3, first strand: chain 'A' and resid 269 through 273 removed outlier: 6.690A pdb=" N ALA A 374 " --> pdb=" O TYR A 319 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N TYR A 319 " --> pdb=" O ALA A 374 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N CYS A 376 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N LEU A 317 " --> pdb=" O CYS A 376 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU A 378 " --> pdb=" O CYS A 315 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N CYS A 315 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ASN A 380 " --> pdb=" O MET A 313 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 92 through 94 removed outlier: 8.271A pdb=" N VAL B 93 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LEU B 67 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N ILE B 66 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N HIS B 6 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N VAL B 68 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N GLN B 8 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N GLU B 3 " --> pdb=" O LEU B 132 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLY B 134 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL B 5 " --> pdb=" O GLY B 134 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N SER B 140 " --> pdb=" O ALA B 9 " (cutoff:3.500A) removed outlier: 8.579A pdb=" N ASN B 167 " --> pdb=" O GLN B 133 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N PHE B 135 " --> pdb=" O ASN B 167 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N PHE B 169 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N LEU B 137 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N VAL B 171 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N HIS B 139 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N THR B 168 " --> pdb=" O TYR B 202 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N ILE B 204 " --> pdb=" O THR B 168 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N SER B 170 " --> pdb=" O ILE B 204 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N THR B 201 " --> pdb=" O PHE B 268 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N CYS B 203 " --> pdb=" O PRO B 270 " (cutoff:3.500A) removed outlier: 10.746A pdb=" N PHE B 272 " --> pdb=" O CYS B 203 " (cutoff:3.500A) removed outlier: 13.937A pdb=" N ASP B 205 " --> pdb=" O PHE B 272 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N PHE B 267 " --> pdb=" O SER B 381 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N SER B 381 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR B 314 " --> pdb=" O ASN B 380 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 53 through 56 Processing sheet with id=AA6, first strand: chain 'C' and resid 92 through 94 removed outlier: 8.143A pdb=" N ILE C 93 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N PHE C 67 " --> pdb=" O ILE C 93 " (cutoff:3.500A) removed outlier: 8.561A pdb=" N VAL C 66 " --> pdb=" O CYS C 4 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N SER C 6 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N VAL C 68 " --> pdb=" O SER C 6 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N HIS C 8 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N GLU C 3 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLY C 134 " --> pdb=" O GLU C 3 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N SER C 140 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N LEU C 167 " --> pdb=" O GLN C 133 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N PHE C 135 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N PHE C 169 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N VAL C 137 " --> pdb=" O PHE C 169 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N ILE C 171 " --> pdb=" O VAL C 137 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N HIS C 139 " --> pdb=" O ILE C 171 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LYS C 166 " --> pdb=" O CYS C 200 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N PHE C 202 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N GLU C 168 " --> pdb=" O PHE C 202 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N VAL C 204 " --> pdb=" O GLU C 168 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N SER C 170 " --> pdb=" O VAL C 204 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AA8, first strand: chain 'C' and resid 269 through 273 removed outlier: 6.623A pdb=" N ALA C 374 " --> pdb=" O TYR C 319 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N TYR C 319 " --> pdb=" O ALA C 374 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N CYS C 376 " --> pdb=" O LEU C 317 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LEU C 317 " --> pdb=" O CYS C 376 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LEU C 378 " --> pdb=" O CYS C 315 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N CYS C 315 " --> pdb=" O LEU C 378 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ASN C 380 " --> pdb=" O MET C 313 " (cutoff:3.500A) 539 hydrogen bonds defined for protein. 1554 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: 1.80 Time building geometry restraints manager: 1.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1977 1.32 - 1.44: 2790 1.44 - 1.57: 6062 1.57 - 1.69: 17 1.69 - 1.81: 108 Bond restraints: 10954 Sorted by residual: bond pdb=" N VAL A 68 " pdb=" CA VAL A 68 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.19e-02 7.06e+03 1.03e+01 bond pdb=" N VAL B 315 " pdb=" CA VAL B 315 " ideal model delta sigma weight residual 1.459 1.495 -0.037 1.19e-02 7.06e+03 9.51e+00 bond pdb=" N VAL B 318 " pdb=" CA VAL B 318 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.19e-02 7.06e+03 9.30e+00 bond pdb=" N VAL A 74 " pdb=" CA VAL A 74 " ideal model delta sigma weight residual 1.461 1.497 -0.035 1.17e-02 7.31e+03 9.19e+00 bond pdb=" N VAL A 159 " pdb=" CA VAL A 159 " ideal model delta sigma weight residual 1.460 1.496 -0.036 1.19e-02 7.06e+03 8.93e+00 ... (remaining 10949 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 14146 1.84 - 3.68: 651 3.68 - 5.53: 63 5.53 - 7.37: 11 7.37 - 9.21: 5 Bond angle restraints: 14876 Sorted by residual: angle pdb=" N ILE A 114 " pdb=" CA ILE A 114 " pdb=" C ILE A 114 " ideal model delta sigma weight residual 113.71 109.44 4.27 9.50e-01 1.11e+00 2.02e+01 angle pdb=" N ARG S 556 " pdb=" CA ARG S 556 " pdb=" C ARG S 556 " ideal model delta sigma weight residual 110.97 106.34 4.63 1.09e+00 8.42e-01 1.80e+01 angle pdb=" CA ARG C 339 " pdb=" CB ARG C 339 " pdb=" CG ARG C 339 " ideal model delta sigma weight residual 114.10 122.58 -8.48 2.00e+00 2.50e-01 1.80e+01 angle pdb=" CA ARG A 339 " pdb=" CB ARG A 339 " pdb=" CG ARG A 339 " ideal model delta sigma weight residual 114.10 122.36 -8.26 2.00e+00 2.50e-01 1.71e+01 angle pdb=" N ARG S 546 " pdb=" CA ARG S 546 " pdb=" C ARG S 546 " ideal model delta sigma weight residual 111.33 106.43 4.90 1.21e+00 6.83e-01 1.64e+01 ... (remaining 14871 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.22: 6423 34.22 - 68.45: 164 68.45 - 102.67: 20 102.67 - 136.89: 4 136.89 - 171.12: 4 Dihedral angle restraints: 6615 sinusoidal: 2735 harmonic: 3880 Sorted by residual: dihedral pdb=" C5' GTP A 501 " pdb=" O5' GTP A 501 " pdb=" PA GTP A 501 " pdb=" O3A GTP A 501 " ideal model delta sinusoidal sigma weight residual 69.27 -119.61 -171.12 1 2.00e+01 2.50e-03 4.77e+01 dihedral pdb=" C5' GTP C 501 " pdb=" O5' GTP C 501 " pdb=" PA GTP C 501 " pdb=" O3A GTP C 501 " ideal model delta sinusoidal sigma weight residual 69.27 -121.22 -169.51 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" C8 GTP C 501 " pdb=" C1' GTP C 501 " pdb=" N9 GTP C 501 " pdb=" O4' GTP C 501 " ideal model delta sinusoidal sigma weight residual 104.59 -41.43 146.03 1 2.00e+01 2.50e-03 4.39e+01 ... (remaining 6612 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1116 0.048 - 0.097: 357 0.097 - 0.145: 131 0.145 - 0.194: 18 0.194 - 0.242: 4 Chirality restraints: 1626 Sorted by residual: chirality pdb=" C21 TA1 B 504 " pdb=" C20 TA1 B 504 " pdb=" C24 TA1 B 504 " pdb=" O09 TA1 B 504 " both_signs ideal model delta sigma weight residual False -2.30 -2.06 -0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CA GLU S 586 " pdb=" N GLU S 586 " pdb=" C GLU S 586 " pdb=" CB GLU S 586 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA ILE B 378 " pdb=" N ILE B 378 " pdb=" C ILE B 378 " pdb=" CB ILE B 378 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.19e+00 ... (remaining 1623 not shown) Planarity restraints: 1932 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG S 566 " -0.279 9.50e-02 1.11e+02 1.25e-01 9.60e+00 pdb=" NE ARG S 566 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG S 566 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG S 566 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG S 566 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG S 577 " -0.244 9.50e-02 1.11e+02 1.09e-01 7.34e+00 pdb=" NE ARG S 577 " 0.015 2.00e-02 2.50e+03 pdb=" CZ ARG S 577 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG S 577 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG S 577 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN S 540 " 0.011 2.00e-02 2.50e+03 2.33e-02 5.45e+00 pdb=" C GLN S 540 " -0.040 2.00e-02 2.50e+03 pdb=" O GLN S 540 " 0.015 2.00e-02 2.50e+03 pdb=" N ARG S 541 " 0.014 2.00e-02 2.50e+03 ... (remaining 1929 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 34 2.44 - 3.06: 6963 3.06 - 3.67: 15612 3.67 - 4.29: 24350 4.29 - 4.90: 42004 Nonbonded interactions: 88963 Sorted by model distance: nonbonded pdb="MG MG C 502 " pdb=" O HOH C 602 " model vdw 1.829 2.170 nonbonded pdb="MG MG C 502 " pdb=" O HOH C 601 " model vdw 1.837 2.170 nonbonded pdb=" O1G GTP C 501 " pdb="MG MG C 502 " model vdw 1.921 2.170 nonbonded pdb=" O1G GTP A 501 " pdb="MG MG B 501 " model vdw 2.135 2.170 nonbonded pdb=" O GLY C 146 " pdb=" OG1 THR C 150 " model vdw 2.234 3.040 ... (remaining 88958 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 1 through 501) selection = (chain 'C' and resid 1 through 501) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.490 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 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: 0.000 Load rotamer database and sin/cos tables:6.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 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 : 0.006 0.049 10957 Z= 0.371 Angle : 0.818 9.211 14876 Z= 0.529 Chirality : 0.054 0.242 1626 Planarity : 0.008 0.125 1932 Dihedral : 16.310 171.118 4121 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.70 % Allowed : 9.89 % Favored : 89.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.22), residues: 1328 helix: 0.95 (0.21), residues: 629 sheet: 0.97 (0.34), residues: 217 loop : -0.62 (0.26), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 322 TYR 0.020 0.001 TYR C 103 PHE 0.016 0.002 PHE A 255 TRP 0.016 0.002 TRP B 103 HIS 0.005 0.001 HIS A 266 Details of bonding type rmsd covalent geometry : bond 0.00631 (10954) covalent geometry : angle 0.81785 (14876) hydrogen bonds : bond 0.17413 ( 539) hydrogen bonds : angle 6.45174 ( 1554) metal coordination : bond 0.00117 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 213 time to evaluate : 0.432 Fit side-chains REVERT: A 1 MET cc_start: 0.7407 (mmt) cc_final: 0.7092 (mmm) REVERT: B 31 ASP cc_start: 0.7785 (m-30) cc_final: 0.7459 (m-30) REVERT: B 76 ASP cc_start: 0.7868 (m-30) cc_final: 0.7466 (m-30) REVERT: B 110 GLU cc_start: 0.8547 (mm-30) cc_final: 0.8322 (mp0) REVERT: B 166 MET cc_start: 0.8458 (tpp) cc_final: 0.8248 (mtp) REVERT: B 311 ARG cc_start: 0.8040 (mtp180) cc_final: 0.7825 (mtp85) REVERT: B 393 GLU cc_start: 0.8293 (mt-10) cc_final: 0.7807 (mm-30) REVERT: C 120 ASP cc_start: 0.8360 (m-30) cc_final: 0.7973 (m-30) REVERT: C 285 GLN cc_start: 0.7678 (pt0) cc_final: 0.7230 (mm-40) REVERT: C 313 MET cc_start: 0.8652 (mtt) cc_final: 0.8400 (mpp) REVERT: C 401 LYS cc_start: 0.4865 (mttm) cc_final: 0.3682 (mmtm) REVERT: C 420 GLU cc_start: 0.7582 (mt-10) cc_final: 0.7068 (mp0) REVERT: S 566 ARG cc_start: 0.7349 (tpt-90) cc_final: 0.7117 (mmt180) REVERT: S 567 LEU cc_start: 0.8180 (mt) cc_final: 0.7899 (mt) outliers start: 8 outliers final: 2 residues processed: 217 average time/residue: 0.8375 time to fit residues: 191.3811 Evaluate side-chains 110 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 108 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain C residue 130 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 0.0060 chunk 91 optimal weight: 0.6980 chunk 55 optimal weight: 0.0770 overall best weight: 0.3954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 GLN ** A 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 11 GLN C 15 GLN C 107 HIS C 206 ASN S 557 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.120588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.100883 restraints weight = 13756.131| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.02 r_work: 0.3221 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10957 Z= 0.119 Angle : 0.533 6.419 14876 Z= 0.276 Chirality : 0.043 0.234 1626 Planarity : 0.005 0.079 1932 Dihedral : 11.606 179.604 1609 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.10 % Allowed : 14.54 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.23), residues: 1328 helix: 1.87 (0.20), residues: 641 sheet: 1.09 (0.35), residues: 216 loop : -0.32 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 215 TYR 0.012 0.001 TYR B 312 PHE 0.014 0.001 PHE A 255 TRP 0.013 0.002 TRP C 21 HIS 0.004 0.001 HIS A 266 Details of bonding type rmsd covalent geometry : bond 0.00235 (10954) covalent geometry : angle 0.53280 (14876) hydrogen bonds : bond 0.05129 ( 539) hydrogen bonds : angle 4.24823 ( 1554) metal coordination : bond 0.00046 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 137 time to evaluate : 0.409 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.7634 (mmt) cc_final: 0.7310 (mmm) REVERT: A 133 GLN cc_start: 0.7173 (OUTLIER) cc_final: 0.6917 (pm20) REVERT: A 377 MET cc_start: 0.9001 (ttm) cc_final: 0.8216 (ttm) REVERT: A 392 ASP cc_start: 0.7988 (m-30) cc_final: 0.7693 (m-30) REVERT: B 31 ASP cc_start: 0.7660 (m-30) cc_final: 0.7404 (m-30) REVERT: B 76 ASP cc_start: 0.7779 (m-30) cc_final: 0.7399 (m-30) REVERT: B 90 ASP cc_start: 0.7956 (t0) cc_final: 0.7661 (m-30) REVERT: B 110 GLU cc_start: 0.8796 (mm-30) cc_final: 0.8351 (mp0) REVERT: B 166 MET cc_start: 0.8533 (tpp) cc_final: 0.8270 (mtp) REVERT: B 196 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.8111 (mt-10) REVERT: B 311 ARG cc_start: 0.8124 (mtp180) cc_final: 0.7897 (mtp85) REVERT: C 96 LYS cc_start: 0.8829 (mttt) cc_final: 0.7886 (mmmt) REVERT: C 120 ASP cc_start: 0.8039 (m-30) cc_final: 0.7698 (m-30) REVERT: C 154 MET cc_start: 0.8399 (mmm) cc_final: 0.8167 (mmm) REVERT: C 285 GLN cc_start: 0.7728 (OUTLIER) cc_final: 0.6981 (mm-40) REVERT: C 420 GLU cc_start: 0.7301 (mt-10) cc_final: 0.6833 (mp0) REVERT: S 567 LEU cc_start: 0.8150 (mt) cc_final: 0.7628 (mt) REVERT: S 577 ARG cc_start: 0.8633 (ttm-80) cc_final: 0.8233 (mtt180) outliers start: 24 outliers final: 4 residues processed: 150 average time/residue: 0.7309 time to fit residues: 116.6486 Evaluate side-chains 113 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 106 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 133 GLN Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain B residue 196 GLU Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain C residue 255 PHE Chi-restraints excluded: chain C residue 285 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 83 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 92 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 120 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 78 optimal weight: 0.7980 chunk 7 optimal weight: 4.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 GLN ** A 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 11 GLN C 15 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.113375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.093756 restraints weight = 14084.533| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 2.04 r_work: 0.3109 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10957 Z= 0.161 Angle : 0.556 11.972 14876 Z= 0.286 Chirality : 0.045 0.227 1626 Planarity : 0.004 0.074 1932 Dihedral : 11.454 178.020 1607 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.54 % Allowed : 15.59 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.23), residues: 1328 helix: 1.97 (0.20), residues: 647 sheet: 0.97 (0.33), residues: 228 loop : -0.39 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 84 TYR 0.014 0.001 TYR B 312 PHE 0.020 0.001 PHE A 255 TRP 0.012 0.002 TRP A 21 HIS 0.005 0.001 HIS C 266 Details of bonding type rmsd covalent geometry : bond 0.00369 (10954) covalent geometry : angle 0.55598 (14876) hydrogen bonds : bond 0.05731 ( 539) hydrogen bonds : angle 4.20567 ( 1554) metal coordination : bond 0.00086 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 116 time to evaluate : 0.472 Fit side-chains REVERT: A 1 MET cc_start: 0.7455 (mmt) cc_final: 0.7137 (mmm) REVERT: A 130 THR cc_start: 0.6216 (OUTLIER) cc_final: 0.5815 (t) REVERT: A 133 GLN cc_start: 0.7543 (OUTLIER) cc_final: 0.6917 (pm20) REVERT: A 372 GLN cc_start: 0.8113 (mm110) cc_final: 0.7662 (mp10) REVERT: A 392 ASP cc_start: 0.7908 (m-30) cc_final: 0.7679 (m-30) REVERT: B 31 ASP cc_start: 0.7673 (m-30) cc_final: 0.7332 (m-30) REVERT: B 76 ASP cc_start: 0.7755 (m-30) cc_final: 0.7388 (m-30) REVERT: B 90 ASP cc_start: 0.8108 (t0) cc_final: 0.7758 (m-30) REVERT: B 110 GLU cc_start: 0.8721 (mm-30) cc_final: 0.8202 (mp0) REVERT: B 166 MET cc_start: 0.8660 (tpp) cc_final: 0.8336 (mtp) REVERT: B 196 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.8256 (mt-10) REVERT: C 163 LYS cc_start: 0.8340 (mttt) cc_final: 0.8100 (mmtp) REVERT: C 245 ASP cc_start: 0.7537 (t0) cc_final: 0.7104 (p0) REVERT: C 280 LYS cc_start: 0.8013 (ttmt) cc_final: 0.6391 (tptt) REVERT: C 285 GLN cc_start: 0.7692 (OUTLIER) cc_final: 0.6947 (mm-40) REVERT: C 420 GLU cc_start: 0.7072 (mt-10) cc_final: 0.6658 (mp0) REVERT: S 546 ARG cc_start: 0.8168 (OUTLIER) cc_final: 0.7877 (ptm-80) REVERT: S 567 LEU cc_start: 0.7994 (mt) cc_final: 0.7593 (mt) outliers start: 29 outliers final: 9 residues processed: 132 average time/residue: 0.6751 time to fit residues: 95.3154 Evaluate side-chains 126 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 133 GLN Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 196 GLU Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 285 GLN Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain S residue 546 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 84 optimal weight: 0.7980 chunk 102 optimal weight: 4.9990 chunk 33 optimal weight: 0.0040 chunk 90 optimal weight: 7.9990 chunk 111 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 8 optimal weight: 0.4980 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 GLN B 433 GLN C 11 GLN C 15 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.115994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.096703 restraints weight = 14018.996| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.03 r_work: 0.3149 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 10957 Z= 0.110 Angle : 0.502 9.293 14876 Z= 0.255 Chirality : 0.043 0.210 1626 Planarity : 0.004 0.046 1932 Dihedral : 11.235 177.561 1607 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.80 % Allowed : 16.02 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.23), residues: 1328 helix: 2.11 (0.20), residues: 644 sheet: 0.94 (0.34), residues: 216 loop : -0.47 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 84 TYR 0.010 0.001 TYR B 312 PHE 0.020 0.001 PHE A 255 TRP 0.012 0.001 TRP A 21 HIS 0.003 0.001 HIS C 266 Details of bonding type rmsd covalent geometry : bond 0.00228 (10954) covalent geometry : angle 0.50223 (14876) hydrogen bonds : bond 0.04619 ( 539) hydrogen bonds : angle 3.97677 ( 1554) metal coordination : bond 0.00054 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 122 time to evaluate : 0.445 Fit side-chains revert: symmetry clash REVERT: A 35 GLN cc_start: 0.7851 (mt0) cc_final: 0.7299 (mp10) REVERT: A 130 THR cc_start: 0.5927 (OUTLIER) cc_final: 0.5613 (t) REVERT: A 133 GLN cc_start: 0.7431 (OUTLIER) cc_final: 0.7064 (pm20) REVERT: A 372 GLN cc_start: 0.8166 (mm110) cc_final: 0.7667 (mp10) REVERT: A 377 MET cc_start: 0.9154 (OUTLIER) cc_final: 0.8566 (ttm) REVERT: A 392 ASP cc_start: 0.7983 (m-30) cc_final: 0.7600 (m-30) REVERT: B 31 ASP cc_start: 0.7745 (m-30) cc_final: 0.7403 (m-30) REVERT: B 47 GLU cc_start: 0.8650 (tt0) cc_final: 0.8414 (tt0) REVERT: B 76 ASP cc_start: 0.7691 (m-30) cc_final: 0.7333 (m-30) REVERT: B 90 ASP cc_start: 0.8172 (t0) cc_final: 0.7781 (m-30) REVERT: B 110 GLU cc_start: 0.8752 (mm-30) cc_final: 0.8225 (mp0) REVERT: C 96 LYS cc_start: 0.8826 (mttt) cc_final: 0.7846 (mmmt) REVERT: C 154 MET cc_start: 0.8390 (mmm) cc_final: 0.8102 (mmm) REVERT: C 245 ASP cc_start: 0.7453 (t0) cc_final: 0.7157 (p0) REVERT: C 280 LYS cc_start: 0.8049 (ttmt) cc_final: 0.6485 (tptt) REVERT: C 285 GLN cc_start: 0.7736 (OUTLIER) cc_final: 0.6938 (mp10) REVERT: C 420 GLU cc_start: 0.7095 (mt-10) cc_final: 0.6684 (mp0) REVERT: S 556 ARG cc_start: 0.8142 (ttm110) cc_final: 0.7889 (ttp80) REVERT: S 567 LEU cc_start: 0.8049 (mt) cc_final: 0.7643 (mt) outliers start: 32 outliers final: 8 residues processed: 138 average time/residue: 0.6530 time to fit residues: 96.6080 Evaluate side-chains 129 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 117 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 133 GLN Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain C residue 285 GLN Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 435 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 72 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 chunk 119 optimal weight: 0.0570 chunk 28 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 chunk 97 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 chunk 110 optimal weight: 0.4980 chunk 86 optimal weight: 4.9990 chunk 7 optimal weight: 0.5980 chunk 0 optimal weight: 7.9990 overall best weight: 1.0302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 GLN C 18 ASN C 107 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.113523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.094257 restraints weight = 13888.259| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.00 r_work: 0.3118 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10957 Z= 0.137 Angle : 0.522 8.170 14876 Z= 0.266 Chirality : 0.044 0.227 1626 Planarity : 0.004 0.038 1932 Dihedral : 11.187 177.454 1607 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.45 % Allowed : 17.25 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.23), residues: 1328 helix: 2.11 (0.21), residues: 645 sheet: 0.88 (0.34), residues: 216 loop : -0.51 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 84 TYR 0.011 0.001 TYR B 312 PHE 0.023 0.001 PHE A 255 TRP 0.011 0.001 TRP A 21 HIS 0.005 0.001 HIS C 266 Details of bonding type rmsd covalent geometry : bond 0.00310 (10954) covalent geometry : angle 0.52160 (14876) hydrogen bonds : bond 0.04944 ( 539) hydrogen bonds : angle 4.00431 ( 1554) metal coordination : bond 0.00121 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 118 time to evaluate : 0.414 Fit side-chains revert: symmetry clash REVERT: A 35 GLN cc_start: 0.7855 (mt0) cc_final: 0.7294 (mp10) REVERT: A 130 THR cc_start: 0.5922 (OUTLIER) cc_final: 0.5680 (t) REVERT: A 133 GLN cc_start: 0.7596 (OUTLIER) cc_final: 0.7308 (pm20) REVERT: A 248 LEU cc_start: 0.8344 (mt) cc_final: 0.7986 (mp) REVERT: A 313 MET cc_start: 0.8922 (OUTLIER) cc_final: 0.8709 (mtt) REVERT: A 372 GLN cc_start: 0.8228 (mm110) cc_final: 0.7750 (mp10) REVERT: A 377 MET cc_start: 0.9176 (OUTLIER) cc_final: 0.8650 (ttm) REVERT: A 392 ASP cc_start: 0.7980 (m-30) cc_final: 0.7590 (m-30) REVERT: B 31 ASP cc_start: 0.7748 (m-30) cc_final: 0.7379 (m-30) REVERT: B 47 GLU cc_start: 0.8663 (tt0) cc_final: 0.8411 (tt0) REVERT: B 76 ASP cc_start: 0.7672 (m-30) cc_final: 0.7319 (m-30) REVERT: B 90 ASP cc_start: 0.8175 (t0) cc_final: 0.7831 (m-30) REVERT: B 281 GLN cc_start: 0.8030 (pp30) cc_final: 0.7486 (pt0) REVERT: C 96 LYS cc_start: 0.8825 (mttt) cc_final: 0.7845 (mmmt) REVERT: C 154 MET cc_start: 0.8363 (mmm) cc_final: 0.8130 (mmm) REVERT: C 245 ASP cc_start: 0.7490 (t0) cc_final: 0.7231 (p0) REVERT: C 280 LYS cc_start: 0.8092 (ttmt) cc_final: 0.6627 (tptt) REVERT: C 285 GLN cc_start: 0.7683 (OUTLIER) cc_final: 0.6929 (mp10) REVERT: C 420 GLU cc_start: 0.7052 (mt-10) cc_final: 0.6612 (mp0) REVERT: S 567 LEU cc_start: 0.8058 (mt) cc_final: 0.7640 (mt) outliers start: 28 outliers final: 8 residues processed: 131 average time/residue: 0.6687 time to fit residues: 93.7358 Evaluate side-chains 127 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 114 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 133 GLN Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 285 GLN Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 435 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 86 optimal weight: 4.9990 chunk 57 optimal weight: 8.9990 chunk 63 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 25 optimal weight: 0.0030 chunk 58 optimal weight: 0.9990 chunk 131 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 10 optimal weight: 0.1980 chunk 108 optimal weight: 0.8980 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.115180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.095887 restraints weight = 14002.152| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.04 r_work: 0.3139 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10957 Z= 0.109 Angle : 0.508 12.737 14876 Z= 0.256 Chirality : 0.043 0.217 1626 Planarity : 0.004 0.047 1932 Dihedral : 10.983 177.907 1607 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.19 % Allowed : 17.86 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.23), residues: 1328 helix: 2.15 (0.21), residues: 646 sheet: 0.86 (0.34), residues: 216 loop : -0.46 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 84 TYR 0.008 0.001 TYR B 312 PHE 0.020 0.001 PHE A 255 TRP 0.012 0.001 TRP A 21 HIS 0.003 0.001 HIS C 266 Details of bonding type rmsd covalent geometry : bond 0.00231 (10954) covalent geometry : angle 0.50849 (14876) hydrogen bonds : bond 0.04420 ( 539) hydrogen bonds : angle 3.90373 ( 1554) metal coordination : bond 0.00078 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 119 time to evaluate : 0.379 Fit side-chains revert: symmetry clash REVERT: A 35 GLN cc_start: 0.7830 (mt0) cc_final: 0.7271 (mp10) REVERT: A 130 THR cc_start: 0.5798 (OUTLIER) cc_final: 0.5575 (t) REVERT: A 133 GLN cc_start: 0.7545 (OUTLIER) cc_final: 0.7279 (pm20) REVERT: A 248 LEU cc_start: 0.8322 (mt) cc_final: 0.7976 (mp) REVERT: A 313 MET cc_start: 0.8911 (OUTLIER) cc_final: 0.8692 (mtt) REVERT: A 327 ASP cc_start: 0.8475 (m-30) cc_final: 0.8201 (m-30) REVERT: A 372 GLN cc_start: 0.8191 (mm110) cc_final: 0.7685 (mp10) REVERT: A 377 MET cc_start: 0.9154 (OUTLIER) cc_final: 0.8630 (ttm) REVERT: A 392 ASP cc_start: 0.8004 (m-30) cc_final: 0.7675 (m-30) REVERT: B 31 ASP cc_start: 0.7722 (m-30) cc_final: 0.7346 (m-30) REVERT: B 47 GLU cc_start: 0.8656 (tt0) cc_final: 0.8396 (tt0) REVERT: B 76 ASP cc_start: 0.7630 (m-30) cc_final: 0.7292 (m-30) REVERT: B 90 ASP cc_start: 0.8251 (t0) cc_final: 0.7850 (m-30) REVERT: B 133 GLN cc_start: 0.8176 (OUTLIER) cc_final: 0.7343 (pp30) REVERT: B 281 GLN cc_start: 0.8077 (pp30) cc_final: 0.7454 (pt0) REVERT: C 96 LYS cc_start: 0.8812 (mttt) cc_final: 0.7819 (mmmt) REVERT: C 154 MET cc_start: 0.8352 (mmm) cc_final: 0.8061 (mmm) REVERT: C 193 THR cc_start: 0.8913 (OUTLIER) cc_final: 0.8644 (p) REVERT: C 280 LYS cc_start: 0.8167 (ttmt) cc_final: 0.6696 (tptt) REVERT: C 285 GLN cc_start: 0.7763 (OUTLIER) cc_final: 0.6918 (mp10) REVERT: C 420 GLU cc_start: 0.6992 (mt-10) cc_final: 0.6550 (mp0) REVERT: S 546 ARG cc_start: 0.8122 (OUTLIER) cc_final: 0.7714 (ptm-80) REVERT: S 567 LEU cc_start: 0.7966 (mt) cc_final: 0.7529 (mt) outliers start: 25 outliers final: 7 residues processed: 132 average time/residue: 0.6062 time to fit residues: 85.7761 Evaluate side-chains 131 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 116 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 133 GLN Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain B residue 133 GLN Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 285 GLN Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain S residue 546 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 101 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 94 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 108 optimal weight: 0.9980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 HIS C 18 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.110530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.091419 restraints weight = 14116.994| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 2.00 r_work: 0.3067 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.3331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 10957 Z= 0.197 Angle : 0.580 11.416 14876 Z= 0.296 Chirality : 0.046 0.252 1626 Planarity : 0.004 0.052 1932 Dihedral : 11.126 177.562 1607 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.71 % Allowed : 18.13 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.23), residues: 1328 helix: 2.09 (0.21), residues: 635 sheet: 0.79 (0.33), residues: 228 loop : -0.65 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 84 TYR 0.013 0.001 TYR B 312 PHE 0.023 0.002 PHE A 255 TRP 0.012 0.002 TRP A 21 HIS 0.006 0.001 HIS C 266 Details of bonding type rmsd covalent geometry : bond 0.00469 (10954) covalent geometry : angle 0.57951 (14876) hydrogen bonds : bond 0.05773 ( 539) hydrogen bonds : angle 4.16694 ( 1554) metal coordination : bond 0.00070 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 115 time to evaluate : 0.283 Fit side-chains revert: symmetry clash REVERT: A 133 GLN cc_start: 0.7735 (OUTLIER) cc_final: 0.7373 (pm20) REVERT: A 193 THR cc_start: 0.8265 (OUTLIER) cc_final: 0.8031 (t) REVERT: A 248 LEU cc_start: 0.8336 (mt) cc_final: 0.8040 (mp) REVERT: A 313 MET cc_start: 0.8971 (OUTLIER) cc_final: 0.8765 (mtt) REVERT: A 372 GLN cc_start: 0.8350 (mm110) cc_final: 0.7733 (mp10) REVERT: A 377 MET cc_start: 0.9180 (OUTLIER) cc_final: 0.8819 (ttm) REVERT: B 31 ASP cc_start: 0.7610 (m-30) cc_final: 0.7300 (m-30) REVERT: B 47 GLU cc_start: 0.8638 (tt0) cc_final: 0.8379 (tt0) REVERT: B 76 ASP cc_start: 0.7666 (m-30) cc_final: 0.7262 (m-30) REVERT: B 90 ASP cc_start: 0.8262 (t0) cc_final: 0.7877 (m-30) REVERT: B 133 GLN cc_start: 0.8383 (OUTLIER) cc_final: 0.7467 (pp30) REVERT: C 96 LYS cc_start: 0.8831 (mttt) cc_final: 0.7818 (mmmt) REVERT: C 193 THR cc_start: 0.8962 (OUTLIER) cc_final: 0.8693 (p) REVERT: C 245 ASP cc_start: 0.7727 (t0) cc_final: 0.7402 (p0) REVERT: C 280 LYS cc_start: 0.8170 (ttmt) cc_final: 0.6739 (tptt) REVERT: C 285 GLN cc_start: 0.7796 (OUTLIER) cc_final: 0.7013 (mm-40) REVERT: C 420 GLU cc_start: 0.7046 (mt-10) cc_final: 0.6623 (mp0) REVERT: S 567 LEU cc_start: 0.8034 (mt) cc_final: 0.7587 (mt) outliers start: 31 outliers final: 10 residues processed: 134 average time/residue: 0.6335 time to fit residues: 91.0588 Evaluate side-chains 128 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 111 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 GLN Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 133 GLN Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 285 GLN Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 435 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 116 optimal weight: 0.9980 chunk 105 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 101 optimal weight: 4.9990 chunk 117 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 57 optimal weight: 7.9990 chunk 25 optimal weight: 5.9990 chunk 2 optimal weight: 0.8980 chunk 46 optimal weight: 5.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 394 GLN S 553 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.110827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.091755 restraints weight = 14076.755| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 1.99 r_work: 0.3072 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.3453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10957 Z= 0.176 Angle : 0.568 11.100 14876 Z= 0.290 Chirality : 0.046 0.242 1626 Planarity : 0.004 0.055 1932 Dihedral : 11.081 176.138 1607 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.28 % Allowed : 18.39 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.23), residues: 1328 helix: 2.05 (0.21), residues: 633 sheet: 0.67 (0.34), residues: 219 loop : -0.74 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 84 TYR 0.011 0.001 TYR B 312 PHE 0.022 0.001 PHE S 534 TRP 0.013 0.002 TRP A 21 HIS 0.005 0.001 HIS C 266 Details of bonding type rmsd covalent geometry : bond 0.00418 (10954) covalent geometry : angle 0.56802 (14876) hydrogen bonds : bond 0.05452 ( 539) hydrogen bonds : angle 4.17142 ( 1554) metal coordination : bond 0.00092 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 111 time to evaluate : 0.285 Fit side-chains revert: symmetry clash REVERT: A 117 LEU cc_start: 0.7227 (OUTLIER) cc_final: 0.6945 (tt) REVERT: A 133 GLN cc_start: 0.7914 (OUTLIER) cc_final: 0.7573 (pm20) REVERT: A 193 THR cc_start: 0.8454 (OUTLIER) cc_final: 0.8217 (t) REVERT: A 372 GLN cc_start: 0.8380 (mm110) cc_final: 0.7804 (mp10) REVERT: A 377 MET cc_start: 0.9225 (OUTLIER) cc_final: 0.8887 (ttm) REVERT: A 392 ASP cc_start: 0.7936 (m-30) cc_final: 0.7695 (m-30) REVERT: B 47 GLU cc_start: 0.8654 (tt0) cc_final: 0.8401 (tt0) REVERT: B 76 ASP cc_start: 0.7736 (m-30) cc_final: 0.7326 (m-30) REVERT: B 90 ASP cc_start: 0.8274 (t0) cc_final: 0.7933 (m-30) REVERT: B 116 ASP cc_start: 0.7670 (m-30) cc_final: 0.7167 (p0) REVERT: B 133 GLN cc_start: 0.8422 (OUTLIER) cc_final: 0.7514 (pp30) REVERT: C 96 LYS cc_start: 0.8863 (mttt) cc_final: 0.7861 (mmmt) REVERT: C 193 THR cc_start: 0.9030 (OUTLIER) cc_final: 0.8755 (p) REVERT: C 245 ASP cc_start: 0.7831 (t0) cc_final: 0.7579 (p0) REVERT: C 280 LYS cc_start: 0.8201 (ttmt) cc_final: 0.6662 (tptt) REVERT: C 285 GLN cc_start: 0.7836 (OUTLIER) cc_final: 0.7095 (mm-40) REVERT: C 420 GLU cc_start: 0.7133 (mt-10) cc_final: 0.6699 (mp0) REVERT: S 567 LEU cc_start: 0.8105 (mt) cc_final: 0.7678 (mt) outliers start: 26 outliers final: 11 residues processed: 127 average time/residue: 0.5679 time to fit residues: 77.6266 Evaluate side-chains 128 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 110 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 133 GLN Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 133 GLN Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 285 GLN Chi-restraints excluded: chain C residue 435 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 91 optimal weight: 0.6980 chunk 121 optimal weight: 0.7980 chunk 80 optimal weight: 0.9980 chunk 13 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 61 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 553 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.112409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.093101 restraints weight = 14037.319| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 2.01 r_work: 0.3110 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.3563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10957 Z= 0.126 Angle : 0.538 13.157 14876 Z= 0.269 Chirality : 0.044 0.222 1626 Planarity : 0.004 0.057 1932 Dihedral : 10.849 175.759 1607 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.58 % Allowed : 19.26 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.23), residues: 1328 helix: 2.11 (0.21), residues: 636 sheet: 0.75 (0.33), residues: 228 loop : -0.71 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 84 TYR 0.009 0.001 TYR B 312 PHE 0.025 0.001 PHE S 534 TRP 0.013 0.002 TRP A 21 HIS 0.004 0.001 HIS C 266 Details of bonding type rmsd covalent geometry : bond 0.00283 (10954) covalent geometry : angle 0.53825 (14876) hydrogen bonds : bond 0.04561 ( 539) hydrogen bonds : angle 4.02935 ( 1554) metal coordination : bond 0.00071 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 115 time to evaluate : 0.433 Fit side-chains revert: symmetry clash REVERT: A 35 GLN cc_start: 0.7892 (mt0) cc_final: 0.7289 (mp10) REVERT: A 133 GLN cc_start: 0.7868 (OUTLIER) cc_final: 0.7475 (pm20) REVERT: A 372 GLN cc_start: 0.8346 (mm110) cc_final: 0.7754 (mp10) REVERT: A 392 ASP cc_start: 0.7836 (m-30) cc_final: 0.7598 (m-30) REVERT: B 47 GLU cc_start: 0.8620 (tt0) cc_final: 0.8372 (tt0) REVERT: B 76 ASP cc_start: 0.7666 (m-30) cc_final: 0.7259 (m-30) REVERT: B 90 ASP cc_start: 0.8255 (t0) cc_final: 0.7925 (m-30) REVERT: B 116 ASP cc_start: 0.7533 (m-30) cc_final: 0.7036 (p0) REVERT: B 133 GLN cc_start: 0.8300 (OUTLIER) cc_final: 0.7383 (pp30) REVERT: C 96 LYS cc_start: 0.8841 (mttt) cc_final: 0.7833 (mmmt) REVERT: C 154 MET cc_start: 0.8499 (mmm) cc_final: 0.8237 (mmm) REVERT: C 193 THR cc_start: 0.8976 (OUTLIER) cc_final: 0.8690 (p) REVERT: C 245 ASP cc_start: 0.7805 (t0) cc_final: 0.7534 (p0) REVERT: C 280 LYS cc_start: 0.8155 (ttmt) cc_final: 0.6609 (tptt) REVERT: C 285 GLN cc_start: 0.7811 (OUTLIER) cc_final: 0.7047 (mm-40) REVERT: C 420 GLU cc_start: 0.7034 (mt-10) cc_final: 0.6624 (mp0) REVERT: S 567 LEU cc_start: 0.8061 (mt) cc_final: 0.7629 (mt) outliers start: 18 outliers final: 9 residues processed: 127 average time/residue: 0.6294 time to fit residues: 85.7524 Evaluate side-chains 126 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 113 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 133 GLN Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 133 GLN Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 285 GLN Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 435 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 35 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 81 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 85 optimal weight: 6.9990 chunk 75 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 GLN S 553 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.112621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.093411 restraints weight = 13996.657| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 1.98 r_work: 0.3113 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.3603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10957 Z= 0.125 Angle : 0.549 13.923 14876 Z= 0.273 Chirality : 0.044 0.224 1626 Planarity : 0.004 0.060 1932 Dihedral : 10.797 176.386 1607 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.23 % Allowed : 19.35 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.23), residues: 1328 helix: 2.12 (0.21), residues: 636 sheet: 0.73 (0.35), residues: 216 loop : -0.72 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG C 84 TYR 0.009 0.001 TYR B 312 PHE 0.017 0.001 PHE A 255 TRP 0.013 0.002 TRP A 21 HIS 0.004 0.001 HIS C 266 Details of bonding type rmsd covalent geometry : bond 0.00281 (10954) covalent geometry : angle 0.54915 (14876) hydrogen bonds : bond 0.04538 ( 539) hydrogen bonds : angle 4.03095 ( 1554) metal coordination : bond 0.00059 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 113 time to evaluate : 0.452 Fit side-chains revert: symmetry clash REVERT: A 35 GLN cc_start: 0.7998 (mt0) cc_final: 0.7412 (mp10) REVERT: A 133 GLN cc_start: 0.7928 (OUTLIER) cc_final: 0.7672 (pm20) REVERT: A 372 GLN cc_start: 0.8428 (mm110) cc_final: 0.7870 (mp10) REVERT: B 47 GLU cc_start: 0.8655 (tt0) cc_final: 0.8443 (tt0) REVERT: B 76 ASP cc_start: 0.7715 (m-30) cc_final: 0.7389 (m-30) REVERT: B 90 ASP cc_start: 0.8314 (t0) cc_final: 0.8021 (m-30) REVERT: B 116 ASP cc_start: 0.7613 (m-30) cc_final: 0.7147 (p0) REVERT: B 133 GLN cc_start: 0.8319 (OUTLIER) cc_final: 0.7401 (pp30) REVERT: C 96 LYS cc_start: 0.8874 (mttt) cc_final: 0.7896 (mmmt) REVERT: C 154 MET cc_start: 0.8563 (mmm) cc_final: 0.8307 (mmm) REVERT: C 193 THR cc_start: 0.9046 (OUTLIER) cc_final: 0.8750 (p) REVERT: C 245 ASP cc_start: 0.7811 (t0) cc_final: 0.7607 (p0) REVERT: C 280 LYS cc_start: 0.8242 (ttmt) cc_final: 0.6732 (tptt) REVERT: C 285 GLN cc_start: 0.7869 (OUTLIER) cc_final: 0.7132 (mm-40) REVERT: C 420 GLU cc_start: 0.7169 (mt-10) cc_final: 0.6733 (mp0) REVERT: S 567 LEU cc_start: 0.8058 (mt) cc_final: 0.7659 (mt) outliers start: 14 outliers final: 10 residues processed: 123 average time/residue: 0.6192 time to fit residues: 81.8109 Evaluate side-chains 126 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 133 GLN Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 133 GLN Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 255 PHE Chi-restraints excluded: chain C residue 285 GLN Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 435 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 95 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 115 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 chunk 3 optimal weight: 0.7980 chunk 99 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 101 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 GLN S 553 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.111656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.092413 restraints weight = 14283.824| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 1.99 r_work: 0.3098 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10957 Z= 0.144 Angle : 0.549 13.089 14876 Z= 0.277 Chirality : 0.044 0.227 1626 Planarity : 0.004 0.064 1932 Dihedral : 10.843 176.956 1607 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.58 % Allowed : 19.26 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.23), residues: 1328 helix: 2.16 (0.21), residues: 633 sheet: 0.72 (0.33), residues: 228 loop : -0.73 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 84 TYR 0.010 0.001 TYR B 312 PHE 0.020 0.001 PHE A 255 TRP 0.012 0.001 TRP A 21 HIS 0.005 0.001 HIS C 266 Details of bonding type rmsd covalent geometry : bond 0.00334 (10954) covalent geometry : angle 0.54935 (14876) hydrogen bonds : bond 0.04804 ( 539) hydrogen bonds : angle 4.05520 ( 1554) metal coordination : bond 0.00080 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3305.91 seconds wall clock time: 57 minutes 7.11 seconds (3427.11 seconds total)