Starting phenix.real_space_refine on Sat Feb 7 02:44:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vkq_65139/02_2026/9vkq_65139.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vkq_65139/02_2026/9vkq_65139.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9vkq_65139/02_2026/9vkq_65139.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vkq_65139/02_2026/9vkq_65139.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vkq_65139/02_2026/9vkq_65139.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vkq_65139/02_2026/9vkq_65139.map" } resolution = 3.41 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.015 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: 6 Type Number sf(0) Gaussians P 16 5.49 5 Mg 5 5.21 5 S 71 5.16 5 C 18240 2.51 5 N 5101 2.21 5 O 5771 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29204 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 3874 Classifications: {'peptide': 511} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 487} Chain: "C" Number of atoms: 3912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 3912 Classifications: {'peptide': 517} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 494} Chain: "D" Number of atoms: 3566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3566 Classifications: {'peptide': 466} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 441} Chain: "E" Number of atoms: 3566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3566 Classifications: {'peptide': 465} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 440} Chain: "F" Number of atoms: 3561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3561 Classifications: {'peptide': 465} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 439} Chain: "G" Number of atoms: 2311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2311 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 11, 'TRANS': 293} Chain: "H" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 920 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "b" Number of atoms: 588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 588 Classifications: {'peptide': 80} Link IDs: {'TRANS': 79} Chain: "d" Number of atoms: 2774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2774 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 8, 'TRANS': 361} Chain breaks: 1 Chain: "B" Number of atoms: 3949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 3949 Classifications: {'peptide': 521} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 497} Chain breaks: 2 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.84, per 1000 atoms: 0.23 Number of scatterers: 29204 At special positions: 0 Unit cell: (123.88, 144.4, 187.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 71 16.00 P 16 15.00 Mg 5 11.99 O 5771 8.00 N 5101 7.00 C 18240 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: 2.53 Conformation dependent library (CDL) restraints added in 1.4 seconds 7590 Ramachandran restraints generated. 3795 Oldfield, 0 Emsley, 3795 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7000 Finding SS restraints... Secondary structure from input PDB file: 156 helices and 32 sheets defined 49.0% alpha, 13.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'A' and resid 11 through 21 removed outlier: 3.677A pdb=" N ILE A 15 " --> pdb=" O ILE A 11 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N THR A 21 " --> pdb=" O GLN A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 107 removed outlier: 4.100A pdb=" N PHE A 106 " --> pdb=" O GLY A 103 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LEU A 107 " --> pdb=" O ASP A 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 103 through 107' Processing helix chain 'A' and resid 138 through 142 removed outlier: 3.876A pdb=" N ARG A 142 " --> pdb=" O VAL A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 158 removed outlier: 3.863A pdb=" N SER A 158 " --> pdb=" O LYS A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 188 removed outlier: 3.714A pdb=" N CYS A 182 " --> pdb=" O LYS A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 194 Processing helix chain 'A' and resid 212 through 226 Processing helix chain 'A' and resid 227 through 230 removed outlier: 4.058A pdb=" N GLU A 230 " --> pdb=" O GLY A 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 227 through 230' Processing helix chain 'A' and resid 244 through 262 Proline residue: A 250 - end of helix removed outlier: 3.663A pdb=" N TRP A 260 " --> pdb=" O LEU A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 288 removed outlier: 3.811A pdb=" N ILE A 284 " --> pdb=" O ALA A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 297 Processing helix chain 'A' and resid 298 through 300 No H-bonds generated for 'chain 'A' and resid 298 through 300' Processing helix chain 'A' and resid 301 through 310 removed outlier: 3.961A pdb=" N HIS A 305 " --> pdb=" O VAL A 301 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N ARG A 307 " --> pdb=" O TYR A 303 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LEU A 308 " --> pdb=" O LEU A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 346 removed outlier: 3.839A pdb=" N ILE A 346 " --> pdb=" O PRO A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 363 removed outlier: 3.658A pdb=" N PHE A 360 " --> pdb=" O GLN A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 391 removed outlier: 3.696A pdb=" N GLU A 388 " --> pdb=" O LYS A 384 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N VAL A 389 " --> pdb=" O ALA A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 401 removed outlier: 3.790A pdb=" N GLN A 399 " --> pdb=" O LEU A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 431 removed outlier: 3.880A pdb=" N LYS A 418 " --> pdb=" O ASP A 414 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ALA A 419 " --> pdb=" O ALA A 415 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU A 422 " --> pdb=" O LYS A 418 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG A 426 " --> pdb=" O GLU A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 450 removed outlier: 3.906A pdb=" N VAL A 446 " --> pdb=" O GLU A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 479 removed outlier: 3.636A pdb=" N ASP A 473 " --> pdb=" O GLN A 469 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY A 477 " --> pdb=" O ASP A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 490 removed outlier: 3.581A pdb=" N LEU A 483 " --> pdb=" O HIS A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 510 removed outlier: 3.595A pdb=" N ASN A 502 " --> pdb=" O THR A 498 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N SER A 510 " --> pdb=" O ALA A 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 21 Processing helix chain 'C' and resid 103 through 107 removed outlier: 4.048A pdb=" N PHE C 106 " --> pdb=" O GLY C 103 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LEU C 107 " --> pdb=" O ASP C 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 103 through 107' Processing helix chain 'C' and resid 154 through 159 removed outlier: 3.635A pdb=" N GLN C 159 " --> pdb=" O ALA C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 189 removed outlier: 3.883A pdb=" N VAL C 181 " --> pdb=" O GLY C 177 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N CYS C 182 " --> pdb=" O LYS C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 196 removed outlier: 4.129A pdb=" N GLY C 196 " --> pdb=" O ALA C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 226 removed outlier: 3.539A pdb=" N ALA C 226 " --> pdb=" O THR C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 230 No H-bonds generated for 'chain 'C' and resid 228 through 230' Processing helix chain 'C' and resid 242 through 263 removed outlier: 3.565A pdb=" N LYS C 246 " --> pdb=" O ALA C 242 " (cutoff:3.500A) Proline residue: C 250 - end of helix Processing helix chain 'C' and resid 273 through 288 removed outlier: 3.810A pdb=" N GLN C 277 " --> pdb=" O ASP C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 297 Processing helix chain 'C' and resid 300 through 309 removed outlier: 3.561A pdb=" N LEU C 308 " --> pdb=" O LEU C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 349 Processing helix chain 'C' and resid 356 through 361 Processing helix chain 'C' and resid 377 through 382 removed outlier: 3.872A pdb=" N ALA C 380 " --> pdb=" O VAL C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 390 Processing helix chain 'C' and resid 392 through 403 Processing helix chain 'C' and resid 414 through 431 Processing helix chain 'C' and resid 440 through 453 removed outlier: 3.528A pdb=" N GLY C 451 " --> pdb=" O ALA C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 462 No H-bonds generated for 'chain 'C' and resid 460 through 462' Processing helix chain 'C' and resid 463 through 479 Processing helix chain 'C' and resid 479 through 490 removed outlier: 4.033A pdb=" N LEU C 483 " --> pdb=" O HIS C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 493 through 511 removed outlier: 4.032A pdb=" N LYS C 509 " --> pdb=" O ASN C 505 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N SER C 510 " --> pdb=" O ALA C 506 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 96 removed outlier: 3.599A pdb=" N VAL D 95 " --> pdb=" O GLY D 92 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYS D 96 " --> pdb=" O ASP D 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 92 through 96' Processing helix chain 'D' and resid 127 through 131 removed outlier: 3.608A pdb=" N LEU D 131 " --> pdb=" O PHE D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 149 Processing helix chain 'D' and resid 166 through 181 removed outlier: 3.570A pdb=" N LEU D 170 " --> pdb=" O GLY D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 208 Processing helix chain 'D' and resid 210 through 212 No H-bonds generated for 'chain 'D' and resid 210 through 212' Processing helix chain 'D' and resid 226 through 245 removed outlier: 3.804A pdb=" N ARG D 230 " --> pdb=" O GLY D 226 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL D 231 " --> pdb=" O THR D 227 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N ALA D 232 " --> pdb=" O ARG D 228 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N LEU D 233 " --> pdb=" O MET D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 272 removed outlier: 3.674A pdb=" N THR D 261 " --> pdb=" O ILE D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 280 Processing helix chain 'D' and resid 283 through 293 Processing helix chain 'D' and resid 311 through 315 Processing helix chain 'D' and resid 318 through 325 Processing helix chain 'D' and resid 335 through 342 Processing helix chain 'D' and resid 358 through 363 Processing helix chain 'D' and resid 363 through 383 Processing helix chain 'D' and resid 396 through 413 removed outlier: 3.698A pdb=" N ARG D 411 " --> pdb=" O ARG D 407 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 423 removed outlier: 3.834A pdb=" N GLU D 421 " --> pdb=" O MET D 418 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLN D 422 " --> pdb=" O ALA D 419 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 445 Processing helix chain 'D' and resid 461 through 473 Processing helix chain 'E' and resid 127 through 131 Processing helix chain 'E' and resid 142 through 148 Processing helix chain 'E' and resid 167 through 179 Processing helix chain 'E' and resid 194 through 207 removed outlier: 3.922A pdb=" N GLY E 198 " --> pdb=" O ARG E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 210 through 212 No H-bonds generated for 'chain 'E' and resid 210 through 212' Processing helix chain 'E' and resid 224 through 230 Processing helix chain 'E' and resid 231 through 245 removed outlier: 3.921A pdb=" N ALA E 235 " --> pdb=" O VAL E 231 " (cutoff:3.500A) Processing helix chain 'E' and resid 257 through 272 removed outlier: 3.810A pdb=" N THR E 261 " --> pdb=" O ILE E 257 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY E 272 " --> pdb=" O SER E 268 " (cutoff:3.500A) Processing helix chain 'E' and resid 276 through 280 Processing helix chain 'E' and resid 284 through 293 Processing helix chain 'E' and resid 311 through 315 removed outlier: 3.566A pdb=" N ASP E 314 " --> pdb=" O VAL E 311 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 325 removed outlier: 3.849A pdb=" N THR E 324 " --> pdb=" O ALA E 320 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE E 325 " --> pdb=" O PRO E 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 341 Processing helix chain 'E' and resid 363 through 382 Processing helix chain 'E' and resid 383 through 391 Processing helix chain 'E' and resid 392 through 395 Processing helix chain 'E' and resid 396 through 413 removed outlier: 3.675A pdb=" N ARG E 408 " --> pdb=" O GLY E 404 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ARG E 411 " --> pdb=" O ARG E 407 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU E 413 " --> pdb=" O ILE E 409 " (cutoff:3.500A) Processing helix chain 'E' and resid 417 through 421 removed outlier: 4.146A pdb=" N GLU E 421 " --> pdb=" O MET E 418 " (cutoff:3.500A) Processing helix chain 'E' and resid 432 through 445 Processing helix chain 'E' and resid 452 through 457 Processing helix chain 'E' and resid 461 through 472 Processing helix chain 'F' and resid 92 through 96 removed outlier: 3.529A pdb=" N VAL F 95 " --> pdb=" O GLY F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 149 Processing helix chain 'F' and resid 166 through 179 Processing helix chain 'F' and resid 180 through 182 No H-bonds generated for 'chain 'F' and resid 180 through 182' Processing helix chain 'F' and resid 194 through 208 Processing helix chain 'F' and resid 210 through 214 Processing helix chain 'F' and resid 224 through 229 removed outlier: 3.848A pdb=" N MET F 229 " --> pdb=" O GLY F 226 " (cutoff:3.500A) Processing helix chain 'F' and resid 230 through 246 Processing helix chain 'F' and resid 257 through 272 removed outlier: 3.976A pdb=" N THR F 261 " --> pdb=" O ILE F 257 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU F 270 " --> pdb=" O GLU F 266 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLY F 272 " --> pdb=" O SER F 268 " (cutoff:3.500A) Processing helix chain 'F' and resid 276 through 280 Processing helix chain 'F' and resid 283 through 293 Processing helix chain 'F' and resid 311 through 315 removed outlier: 3.502A pdb=" N ASP F 314 " --> pdb=" O VAL F 311 " (cutoff:3.500A) Processing helix chain 'F' and resid 318 through 323 Processing helix chain 'F' and resid 324 through 328 removed outlier: 3.866A pdb=" N LEU F 328 " --> pdb=" O PHE F 325 " (cutoff:3.500A) Processing helix chain 'F' and resid 335 through 341 Processing helix chain 'F' and resid 363 through 383 Processing helix chain 'F' and resid 383 through 390 removed outlier: 4.044A pdb=" N ILE F 387 " --> pdb=" O LEU F 383 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA F 388 " --> pdb=" O GLN F 384 " (cutoff:3.500A) Processing helix chain 'F' and resid 391 through 395 removed outlier: 3.504A pdb=" N GLU F 394 " --> pdb=" O GLY F 391 " (cutoff:3.500A) Processing helix chain 'F' and resid 396 through 413 Processing helix chain 'F' and resid 432 through 446 Processing helix chain 'F' and resid 452 through 456 removed outlier: 3.977A pdb=" N PHE F 456 " --> pdb=" O GLU F 453 " (cutoff:3.500A) Processing helix chain 'F' and resid 462 through 472 Processing helix chain 'G' and resid 3 through 43 removed outlier: 3.732A pdb=" N ALA G 17 " --> pdb=" O LYS G 13 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE G 18 " --> pdb=" O SER G 14 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS G 23 " --> pdb=" O LYS G 19 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA G 34 " --> pdb=" O THR G 30 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA G 43 " --> pdb=" O ARG G 39 " (cutoff:3.500A) Processing helix chain 'G' and resid 44 through 58 removed outlier: 3.726A pdb=" N THR G 48 " --> pdb=" O ARG G 44 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 110 Processing helix chain 'G' and resid 120 through 130 removed outlier: 3.525A pdb=" N LEU G 124 " --> pdb=" O GLY G 120 " (cutoff:3.500A) Processing helix chain 'G' and resid 146 through 167 removed outlier: 4.013A pdb=" N ALA G 150 " --> pdb=" O GLU G 146 " (cutoff:3.500A) Processing helix chain 'G' and resid 226 through 306 removed outlier: 3.765A pdb=" N LEU G 230 " --> pdb=" O ASP G 226 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU G 235 " --> pdb=" O PHE G 231 " (cutoff:3.500A) Proline residue: G 236 - end of helix removed outlier: 4.251A pdb=" N ALA G 252 " --> pdb=" O LEU G 248 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SER G 253 " --> pdb=" O GLU G 249 " (cutoff:3.500A) Processing helix chain 'H' and resid 91 through 100 Processing helix chain 'H' and resid 105 through 113 removed outlier: 3.802A pdb=" N GLN H 109 " --> pdb=" O ARG H 105 " (cutoff:3.500A) Processing helix chain 'b' and resid 90 through 102 removed outlier: 3.744A pdb=" N ALA b 100 " --> pdb=" O ALA b 96 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ALA b 102 " --> pdb=" O GLY b 98 " (cutoff:3.500A) Processing helix chain 'b' and resid 103 through 145 removed outlier: 3.813A pdb=" N ALA b 107 " --> pdb=" O VAL b 103 " (cutoff:3.500A) Processing helix chain 'b' and resid 151 through 165 removed outlier: 3.813A pdb=" N LEU b 155 " --> pdb=" O ASN b 151 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLY b 165 " --> pdb=" O GLU b 161 " (cutoff:3.500A) Processing helix chain 'd' and resid 67 through 136 removed outlier: 3.610A pdb=" N ALA d 123 " --> pdb=" O GLY d 119 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N GLU d 124 " --> pdb=" O ASP d 120 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER d 125 " --> pdb=" O LEU d 121 " (cutoff:3.500A) Processing helix chain 'd' and resid 141 through 154 Processing helix chain 'd' and resid 182 through 194 Processing helix chain 'd' and resid 198 through 211 Processing helix chain 'd' and resid 212 through 219 removed outlier: 3.779A pdb=" N LEU d 216 " --> pdb=" O VAL d 212 " (cutoff:3.500A) Processing helix chain 'd' and resid 220 through 228 Processing helix chain 'd' and resid 234 through 246 removed outlier: 3.728A pdb=" N LYS d 238 " --> pdb=" O GLU d 234 " (cutoff:3.500A) Processing helix chain 'd' and resid 251 through 263 removed outlier: 3.689A pdb=" N THR d 263 " --> pdb=" O ARG d 259 " (cutoff:3.500A) Processing helix chain 'd' and resid 268 through 291 Processing helix chain 'd' and resid 293 through 309 Processing helix chain 'd' and resid 311 through 319 removed outlier: 3.586A pdb=" N SER d 319 " --> pdb=" O ALA d 315 " (cutoff:3.500A) Processing helix chain 'd' and resid 324 through 333 removed outlier: 3.833A pdb=" N ARG d 328 " --> pdb=" O PRO d 324 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA d 330 " --> pdb=" O GLN d 326 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LEU d 331 " --> pdb=" O GLY d 327 " (cutoff:3.500A) Processing helix chain 'd' and resid 341 through 354 removed outlier: 4.418A pdb=" N LEU d 354 " --> pdb=" O GLN d 350 " (cutoff:3.500A) Processing helix chain 'd' and resid 359 through 375 Processing helix chain 'd' and resid 389 through 404 Processing helix chain 'd' and resid 434 through 445 removed outlier: 3.707A pdb=" N ARG d 438 " --> pdb=" O SER d 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 19 Processing helix chain 'B' and resid 138 through 142 removed outlier: 3.620A pdb=" N ARG B 142 " --> pdb=" O VAL B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 158 removed outlier: 3.563A pdb=" N SER B 158 " --> pdb=" O LYS B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 188 Processing helix chain 'B' and resid 189 through 196 removed outlier: 4.015A pdb=" N GLY B 196 " --> pdb=" O ALA B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 227 Processing helix chain 'B' and resid 228 through 230 No H-bonds generated for 'chain 'B' and resid 228 through 230' Processing helix chain 'B' and resid 242 through 264 removed outlier: 3.651A pdb=" N LYS B 246 " --> pdb=" O ALA B 242 " (cutoff:3.500A) Proline residue: B 250 - end of helix removed outlier: 3.682A pdb=" N TRP B 260 " --> pdb=" O LEU B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 288 Processing helix chain 'B' and resid 293 through 297 removed outlier: 3.676A pdb=" N ALA B 296 " --> pdb=" O GLY B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 310 removed outlier: 4.048A pdb=" N HIS B 305 " --> pdb=" O VAL B 301 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N ARG B 307 " --> pdb=" O TYR B 303 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LEU B 308 " --> pdb=" O LEU B 304 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU B 310 " --> pdb=" O SER B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 320 Processing helix chain 'B' and resid 339 through 347 Processing helix chain 'B' and resid 356 through 362 removed outlier: 3.667A pdb=" N PHE B 360 " --> pdb=" O GLN B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 382 removed outlier: 3.696A pdb=" N ALA B 380 " --> pdb=" O VAL B 377 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA B 381 " --> pdb=" O GLY B 378 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN B 382 " --> pdb=" O GLY B 379 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 377 through 382' Processing helix chain 'B' and resid 383 through 390 Processing helix chain 'B' and resid 392 through 407 Processing helix chain 'B' and resid 420 through 431 Processing helix chain 'B' and resid 440 through 453 Processing helix chain 'B' and resid 460 through 462 No H-bonds generated for 'chain 'B' and resid 460 through 462' Processing helix chain 'B' and resid 463 through 478 Processing helix chain 'B' and resid 480 through 490 Processing helix chain 'B' and resid 493 through 510 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 4.866A pdb=" N GLU A 29 " --> pdb=" O GLU d 430 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLU d 430 " --> pdb=" O GLU A 29 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'E' and resid 48 through 50 removed outlier: 3.801A pdb=" N LYS E 48 " --> pdb=" O ILE E 41 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N GLU E 40 " --> pdb=" O ASP E 79 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ASP E 79 " --> pdb=" O GLU E 40 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 62 through 69 current: chain 'E' and resid 63 through 67 removed outlier: 6.806A pdb=" N ARG E 64 " --> pdb=" O ALA E 55 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 48 through 50 removed outlier: 3.801A pdb=" N LYS E 48 " --> pdb=" O ILE E 41 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N GLU E 40 " --> pdb=" O ASP E 79 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ASP E 79 " --> pdb=" O GLU E 40 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 11 through 17 current: chain 'A' and resid 41 through 45 removed outlier: 7.005A pdb=" N HIS A 43 " --> pdb=" O SER A 35 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS A 92 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL A 62 " --> pdb=" O PHE A 58 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 62 through 69 current: chain 'E' and resid 63 through 67 removed outlier: 6.806A pdb=" N ARG E 64 " --> pdb=" O ALA E 55 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 99 through 102 removed outlier: 3.520A pdb=" N THR A 128 " --> pdb=" O VAL A 102 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 110 through 111 removed outlier: 6.218A pdb=" N ARG A 203 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N VAL A 270 " --> pdb=" O ARG A 203 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ILE A 205 " --> pdb=" O VAL A 270 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N ASP A 272 " --> pdb=" O ILE A 205 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N VAL A 207 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE A 271 " --> pdb=" O LEU A 327 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N PHE A 354 " --> pdb=" O ASN A 369 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 148 through 149 removed outlier: 4.563A pdb=" N ILE A 162 " --> pdb=" O LEU A 149 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 55 through 57 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 11 through 17 current: chain 'C' and resid 41 through 45 removed outlier: 6.681A pdb=" N HIS C 43 " --> pdb=" O SER C 35 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 55 through 57 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 63 through 69 current: chain 'D' and resid 36 through 41 removed outlier: 3.703A pdb=" N ILE D 41 " --> pdb=" O LYS D 48 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LYS D 48 " --> pdb=" O ILE D 41 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ARG D 64 " --> pdb=" O ALA D 55 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N HIS D 57 " --> pdb=" O LEU D 62 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N LEU D 62 " --> pdb=" O HIS D 57 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N VAL D 20 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N VAL D 16 " --> pdb=" O VAL D 20 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ASP D 22 " --> pdb=" O VAL D 14 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 11 through 17 current: chain 'C' and resid 41 through 45 removed outlier: 6.681A pdb=" N HIS C 43 " --> pdb=" O SER C 35 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 99 through 102 Processing sheet with id=AB1, first strand: chain 'C' and resid 110 through 111 removed outlier: 3.946A pdb=" N VAL C 209 " --> pdb=" O ASP C 272 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 329 through 331 removed outlier: 3.567A pdb=" N ILE C 171 " --> pdb=" O CYS C 353 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 88 through 91 removed outlier: 4.353A pdb=" N GLU D 117 " --> pdb=" O VAL D 91 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 99 through 100 removed outlier: 6.211A pdb=" N PHE D 100 " --> pdb=" O PHE D 218 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N GLN D 220 " --> pdb=" O PHE D 100 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE D 254 " --> pdb=" O MET D 306 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 99 through 100 removed outlier: 6.211A pdb=" N PHE D 100 " --> pdb=" O PHE D 218 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N GLN D 220 " --> pdb=" O PHE D 100 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE D 254 " --> pdb=" O MET D 306 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N ILE D 157 " --> pdb=" O GLN D 307 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N LYS D 156 " --> pdb=" O ALA D 330 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N THR D 332 " --> pdb=" O LYS D 156 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N ALA D 158 " --> pdb=" O THR D 332 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 137 through 138 removed outlier: 4.593A pdb=" N TYR D 151 " --> pdb=" O LEU D 138 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 88 through 90 Processing sheet with id=AB8, first strand: chain 'E' and resid 99 through 100 removed outlier: 3.633A pdb=" N GLY E 219 " --> pdb=" O GLY E 190 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N THR E 185 " --> pdb=" O LEU E 251 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N PHE E 253 " --> pdb=" O THR E 185 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL E 187 " --> pdb=" O PHE E 253 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 137 through 138 removed outlier: 4.532A pdb=" N TYR E 151 " --> pdb=" O LEU E 138 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 157 through 160 removed outlier: 3.620A pdb=" N ALA E 158 " --> pdb=" O ALA E 330 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 11 through 16 removed outlier: 6.693A pdb=" N ASP F 22 " --> pdb=" O VAL F 14 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N VAL F 16 " --> pdb=" O VAL F 20 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N VAL F 20 " --> pdb=" O VAL F 16 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N LEU F 62 " --> pdb=" O HIS F 57 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N HIS F 57 " --> pdb=" O LEU F 62 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ARG F 64 " --> pdb=" O ALA F 55 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 88 through 91 removed outlier: 4.070A pdb=" N GLU F 117 " --> pdb=" O VAL F 91 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 137 through 138 removed outlier: 4.269A pdb=" N TYR F 151 " --> pdb=" O LEU F 138 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 217 through 220 removed outlier: 6.945A pdb=" N VAL F 250 " --> pdb=" O THR F 304 " (cutoff:3.500A) removed outlier: 8.219A pdb=" N MET F 306 " --> pdb=" O VAL F 250 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LEU F 252 " --> pdb=" O MET F 306 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 134 through 138 removed outlier: 10.857A pdb=" N GLU G 136 " --> pdb=" O PRO G 114 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N VAL G 116 " --> pdb=" O GLU G 136 " (cutoff:3.500A) removed outlier: 8.798A pdb=" N TRP G 138 " --> pdb=" O VAL G 116 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL G 118 " --> pdb=" O TRP G 138 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ALA G 77 " --> pdb=" O VAL G 115 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N TYR G 117 " --> pdb=" O ALA G 77 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N VAL G 79 " --> pdb=" O TYR G 117 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N VAL G 119 " --> pdb=" O VAL G 79 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ILE G 81 " --> pdb=" O VAL G 119 " (cutoff:3.500A) removed outlier: 8.831A pdb=" N HIS G 184 " --> pdb=" O ARG G 76 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N GLY G 78 " --> pdb=" O HIS G 184 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N VAL G 186 " --> pdb=" O GLY G 78 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU G 80 " --> pdb=" O VAL G 186 " (cutoff:3.500A) removed outlier: 8.900A pdb=" N THR G 188 " --> pdb=" O LEU G 80 " (cutoff:3.500A) removed outlier: 9.228A pdb=" N VAL G 82 " --> pdb=" O THR G 188 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA G 197 " --> pdb=" O GLU G 189 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 207 through 211 removed outlier: 6.454A pdb=" N GLU G 207 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N VAL B 541 " --> pdb=" O GLU G 207 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N GLU G 209 " --> pdb=" O VAL B 541 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'H' and resid 5 through 9 removed outlier: 3.707A pdb=" N TRP H 16 " --> pdb=" O ILE H 8 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 42 through 44 Processing sheet with id=AD1, first strand: chain 'H' and resid 64 through 65 Processing sheet with id=AD2, first strand: chain 'B' and resid 55 through 58 removed outlier: 3.638A pdb=" N VAL B 62 " --> pdb=" O PHE B 58 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N GLY B 64 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LEU B 79 " --> pdb=" O GLY B 64 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N ALA B 66 " --> pdb=" O VAL B 77 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N VAL B 77 " --> pdb=" O ALA B 66 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASP B 36 " --> pdb=" O HIS B 43 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N GLU B 45 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N VAL B 34 " --> pdb=" O GLU B 45 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 99 through 102 removed outlier: 3.550A pdb=" N THR B 128 " --> pdb=" O VAL B 102 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 110 through 111 removed outlier: 6.447A pdb=" N ARG B 203 " --> pdb=" O LEU B 268 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N VAL B 270 " --> pdb=" O ARG B 203 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ILE B 205 " --> pdb=" O VAL B 270 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N ASP B 272 " --> pdb=" O ILE B 205 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N VAL B 207 " --> pdb=" O ASP B 272 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE B 271 " --> pdb=" O LEU B 327 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 329 through 331 removed outlier: 6.512A pdb=" N ILE B 170 " --> pdb=" O ILE B 330 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL B 374 " --> pdb=" O GLN B 352 " (cutoff:3.500A) 1401 hydrogen bonds defined for protein. 4020 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: 5.74 Time building geometry restraints manager: 3.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9625 1.34 - 1.45: 3118 1.45 - 1.57: 16757 1.57 - 1.69: 26 1.69 - 1.81: 126 Bond restraints: 29652 Sorted by residual: bond pdb=" C4 ADP F 600 " pdb=" C5 ADP F 600 " ideal model delta sigma weight residual 1.490 1.378 0.112 2.00e-02 2.50e+03 3.15e+01 bond pdb=" C4 ADP E 600 " pdb=" C5 ADP E 600 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.99e+01 bond pdb=" C ALA H 95 " pdb=" N LYS H 96 " ideal model delta sigma weight residual 1.334 1.275 0.059 1.23e-02 6.61e+03 2.26e+01 bond pdb=" CA PHE E 344 " pdb=" C PHE E 344 " ideal model delta sigma weight residual 1.522 1.483 0.039 8.40e-03 1.42e+04 2.14e+01 bond pdb=" C LYS H 96 " pdb=" N THR H 97 " ideal model delta sigma weight residual 1.335 1.393 -0.058 1.30e-02 5.92e+03 1.96e+01 ... (remaining 29647 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.43: 39669 2.43 - 4.86: 542 4.86 - 7.29: 38 7.29 - 9.72: 12 9.72 - 12.16: 3 Bond angle restraints: 40264 Sorted by residual: angle pdb=" PB ATP D 600 " pdb=" O3B ATP D 600 " pdb=" PG ATP D 600 " ideal model delta sigma weight residual 139.87 132.08 7.79 1.00e+00 1.00e+00 6.06e+01 angle pdb=" PB ATP A 600 " pdb=" O3B ATP A 600 " pdb=" PG ATP A 600 " ideal model delta sigma weight residual 139.87 132.23 7.64 1.00e+00 1.00e+00 5.83e+01 angle pdb=" PB ATP B 600 " pdb=" O3B ATP B 600 " pdb=" PG ATP B 600 " ideal model delta sigma weight residual 139.87 133.04 6.83 1.00e+00 1.00e+00 4.67e+01 angle pdb=" PA ATP B 600 " pdb=" O3A ATP B 600 " pdb=" PB ATP B 600 " ideal model delta sigma weight residual 136.83 130.19 6.64 1.00e+00 1.00e+00 4.41e+01 angle pdb=" PB ATP C 600 " pdb=" O3B ATP C 600 " pdb=" PG ATP C 600 " ideal model delta sigma weight residual 139.87 133.80 6.07 1.00e+00 1.00e+00 3.68e+01 ... (remaining 40259 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.03: 17564 27.03 - 54.05: 432 54.05 - 81.08: 55 81.08 - 108.11: 3 108.11 - 135.13: 2 Dihedral angle restraints: 18056 sinusoidal: 7168 harmonic: 10888 Sorted by residual: dihedral pdb=" O2A ADP E 600 " pdb=" O3A ADP E 600 " pdb=" PA ADP E 600 " pdb=" PB ADP E 600 " ideal model delta sinusoidal sigma weight residual -60.00 75.14 -135.13 1 2.00e+01 2.50e-03 4.10e+01 dihedral pdb=" O1B ADP E 600 " pdb=" O3A ADP E 600 " pdb=" PB ADP E 600 " pdb=" PA ADP E 600 " ideal model delta sinusoidal sigma weight residual -60.00 -176.20 116.19 1 2.00e+01 2.50e-03 3.46e+01 dihedral pdb=" CA ARG H 113 " pdb=" C ARG H 113 " pdb=" N LEU H 114 " pdb=" CA LEU H 114 " ideal model delta harmonic sigma weight residual -180.00 -151.18 -28.82 0 5.00e+00 4.00e-02 3.32e+01 ... (remaining 18053 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 3888 0.055 - 0.109: 653 0.109 - 0.164: 117 0.164 - 0.219: 19 0.219 - 0.273: 4 Chirality restraints: 4681 Sorted by residual: chirality pdb=" CG LEU H 70 " pdb=" CB LEU H 70 " pdb=" CD1 LEU H 70 " pdb=" CD2 LEU H 70 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" CG LEU H 117 " pdb=" CB LEU H 117 " pdb=" CD1 LEU H 117 " pdb=" CD2 LEU H 117 " both_signs ideal model delta sigma weight residual False -2.59 -2.82 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CB ILE D 392 " pdb=" CA ILE D 392 " pdb=" CG1 ILE D 392 " pdb=" CG2 ILE D 392 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 4678 not shown) Planarity restraints: 5292 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA d 323 " -0.063 5.00e-02 4.00e+02 9.72e-02 1.51e+01 pdb=" N PRO d 324 " 0.168 5.00e-02 4.00e+02 pdb=" CA PRO d 324 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO d 324 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 376 " 0.288 9.50e-02 1.11e+02 1.29e-01 1.02e+01 pdb=" NE ARG A 376 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARG A 376 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG A 376 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 376 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG d 134 " 0.268 9.50e-02 1.11e+02 1.20e-01 8.92e+00 pdb=" NE ARG d 134 " -0.017 2.00e-02 2.50e+03 pdb=" CZ ARG d 134 " 0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG d 134 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG d 134 " 0.008 2.00e-02 2.50e+03 ... (remaining 5289 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 14 2.46 - 3.07: 19812 3.07 - 3.68: 41303 3.68 - 4.29: 59958 4.29 - 4.90: 103515 Nonbonded interactions: 224602 Sorted by model distance: nonbonded pdb=" O2G ATP A 600 " pdb="MG MG A 601 " model vdw 1.852 2.170 nonbonded pdb=" OG1 THR E 168 " pdb="MG MG E 601 " model vdw 1.926 2.170 nonbonded pdb=" OG1 THR B 179 " pdb="MG MG B 601 " model vdw 1.976 2.170 nonbonded pdb=" OG1 THR C 179 " pdb="MG MG C 601 " model vdw 2.093 2.170 nonbonded pdb=" O3B ADP F 600 " pdb="MG MG F 601 " model vdw 2.183 2.170 ... (remaining 224597 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 11 through 19 or resid 27 through 515 or resid 517 or resi \ d 519 through 601)) selection = (chain 'B' and (resid 11 through 514 or resid 530 or resid 532 or resid 534 or r \ esid 537 or resid 541 or resid 600 through 601)) selection = (chain 'C' and (resid 11 through 19 or resid 27 through 515 or resid 517 or resi \ d 519 through 521 or resid 600 through 601)) } ncs_group { reference = (chain 'D' and resid 9 through 472) selection = (chain 'E' and resid 9 through 472) selection = (chain 'F' and resid 9 through 472) } 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: 26.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.550 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 27.360 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.060 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.112 29652 Z= 0.288 Angle : 0.635 12.156 40264 Z= 0.396 Chirality : 0.044 0.273 4681 Planarity : 0.006 0.129 5292 Dihedral : 11.607 135.135 11056 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.36 % Allowed : 5.74 % Favored : 93.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % Cis-general : 0.08 % 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: 0.20 (0.14), residues: 3795 helix: 1.61 (0.13), residues: 1645 sheet: -0.13 (0.25), residues: 486 loop : -1.34 (0.15), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 405 TYR 0.013 0.001 TYR G 92 PHE 0.014 0.001 PHE G 141 TRP 0.012 0.001 TRP d 266 HIS 0.003 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00437 (29652) covalent geometry : angle 0.63478 (40264) hydrogen bonds : bond 0.17837 ( 1369) hydrogen bonds : angle 6.35379 ( 4020) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7590 Ramachandran restraints generated. 3795 Oldfield, 0 Emsley, 3795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7590 Ramachandran restraints generated. 3795 Oldfield, 0 Emsley, 3795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 3065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 327 time to evaluate : 1.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 470 GLU cc_start: 0.8208 (mt-10) cc_final: 0.7972 (mm-30) REVERT: C 82 PHE cc_start: 0.8638 (t80) cc_final: 0.8416 (t80) REVERT: C 403 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8924 (pp) REVERT: E 68 MET cc_start: 0.9018 (mmt) cc_final: 0.8684 (mmt) REVERT: F 68 MET cc_start: 0.8544 (mmm) cc_final: 0.8227 (mmt) REVERT: G 57 LEU cc_start: 0.7869 (mt) cc_final: 0.7496 (tt) REVERT: G 101 GLU cc_start: 0.8724 (tp30) cc_final: 0.8351 (tp30) REVERT: G 104 TYR cc_start: 0.8353 (m-10) cc_final: 0.8062 (m-80) REVERT: H 1 MET cc_start: 0.5328 (ptp) cc_final: 0.4998 (ptp) REVERT: H 47 ASP cc_start: 0.7738 (p0) cc_final: 0.7479 (p0) REVERT: d 88 ARG cc_start: 0.5601 (mmp-170) cc_final: 0.5317 (tpp80) REVERT: d 190 PHE cc_start: 0.3046 (OUTLIER) cc_final: 0.2794 (t80) REVERT: d 303 ARG cc_start: 0.5722 (mmp80) cc_final: 0.5177 (mtp85) REVERT: d 306 ARG cc_start: 0.7167 (mtm110) cc_final: 0.6770 (ptm-80) REVERT: d 328 ARG cc_start: 0.3145 (OUTLIER) cc_final: 0.1811 (mtt-85) REVERT: d 356 TYR cc_start: 0.5102 (p90) cc_final: 0.4760 (t80) outliers start: 11 outliers final: 2 residues processed: 336 average time/residue: 0.2529 time to fit residues: 125.8144 Evaluate side-chains 188 residues out of total 3065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 183 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain D residue 386 ILE Chi-restraints excluded: chain d residue 190 PHE Chi-restraints excluded: chain d residue 328 ARG Chi-restraints excluded: chain B residue 418 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 0.0270 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 6.9990 overall best weight: 2.5844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN A 399 GLN ** A 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 159 GLN E 209 ASN G 131 ASN d 313 GLN d 326 GLN B 159 GLN B 399 GLN B 479 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.101392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.070112 restraints weight = 68734.841| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 2.68 r_work: 0.2903 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 29652 Z= 0.198 Angle : 0.576 10.195 40264 Z= 0.299 Chirality : 0.043 0.239 4681 Planarity : 0.004 0.057 5292 Dihedral : 6.877 114.125 4302 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 1.47 % Allowed : 8.29 % Favored : 90.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % Cis-general : 0.08 % 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: 0.20 (0.14), residues: 3795 helix: 1.68 (0.13), residues: 1651 sheet: -0.24 (0.24), residues: 498 loop : -1.40 (0.15), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG d 406 TYR 0.026 0.002 TYR d 172 PHE 0.015 0.001 PHE F 260 TRP 0.012 0.001 TRP E 202 HIS 0.006 0.001 HIS A 259 Details of bonding type rmsd covalent geometry : bond 0.00471 (29652) covalent geometry : angle 0.57551 (40264) hydrogen bonds : bond 0.04979 ( 1369) hydrogen bonds : angle 4.68909 ( 4020) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7590 Ramachandran restraints generated. 3795 Oldfield, 0 Emsley, 3795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7590 Ramachandran restraints generated. 3795 Oldfield, 0 Emsley, 3795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 3065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 188 time to evaluate : 1.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 374 VAL cc_start: 0.8194 (OUTLIER) cc_final: 0.7975 (m) REVERT: A 470 GLU cc_start: 0.8781 (mt-10) cc_final: 0.8472 (tt0) REVERT: C 82 PHE cc_start: 0.8980 (t80) cc_final: 0.8699 (t80) REVERT: E 27 ARG cc_start: 0.8191 (tpt170) cc_final: 0.7955 (ttm110) REVERT: E 68 MET cc_start: 0.9263 (mmt) cc_final: 0.8836 (mmt) REVERT: E 209 ASN cc_start: 0.8595 (OUTLIER) cc_final: 0.8114 (t0) REVERT: F 68 MET cc_start: 0.8818 (mmm) cc_final: 0.8125 (mmt) REVERT: G 57 LEU cc_start: 0.7941 (mt) cc_final: 0.7547 (tt) REVERT: G 101 GLU cc_start: 0.8859 (tp30) cc_final: 0.8417 (tp30) REVERT: G 104 TYR cc_start: 0.8412 (m-10) cc_final: 0.7996 (m-80) REVERT: G 249 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7488 (mp0) REVERT: H 1 MET cc_start: 0.5743 (ptp) cc_final: 0.5459 (ptt) REVERT: d 136 HIS cc_start: 0.5268 (t70) cc_final: 0.4498 (m90) REVERT: d 190 PHE cc_start: 0.2843 (OUTLIER) cc_final: 0.2524 (t80) REVERT: d 356 TYR cc_start: 0.5806 (p90) cc_final: 0.5035 (t80) REVERT: d 381 HIS cc_start: 0.4293 (m-70) cc_final: 0.3940 (m90) REVERT: d 418 LEU cc_start: 0.4769 (OUTLIER) cc_final: 0.4483 (mm) outliers start: 45 outliers final: 23 residues processed: 226 average time/residue: 0.2007 time to fit residues: 73.0055 Evaluate side-chains 186 residues out of total 3065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 158 time to evaluate : 1.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain D residue 386 ILE Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 209 ASN Chi-restraints excluded: chain E residue 269 THR Chi-restraints excluded: chain E residue 471 SER Chi-restraints excluded: chain F residue 185 THR Chi-restraints excluded: chain F residue 221 MET Chi-restraints excluded: chain F residue 444 THR Chi-restraints excluded: chain G residue 195 THR Chi-restraints excluded: chain G residue 226 ASP Chi-restraints excluded: chain G residue 228 THR Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 249 GLU Chi-restraints excluded: chain G residue 296 VAL Chi-restraints excluded: chain d residue 190 PHE Chi-restraints excluded: chain d residue 294 ILE Chi-restraints excluded: chain d residue 308 LEU Chi-restraints excluded: chain d residue 414 VAL Chi-restraints excluded: chain d residue 418 LEU Chi-restraints excluded: chain d residue 426 ILE Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 418 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 304 optimal weight: 4.9990 chunk 290 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 128 optimal weight: 0.6980 chunk 255 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 chunk 84 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 258 optimal weight: 10.0000 chunk 250 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 143 GLN ** E 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 220 GLN ** d 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.102826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.071461 restraints weight = 68582.659| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 2.68 r_work: 0.2936 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 29652 Z= 0.105 Angle : 0.487 11.535 40264 Z= 0.248 Chirality : 0.040 0.221 4681 Planarity : 0.004 0.054 5292 Dihedral : 6.417 91.837 4296 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.01 % Allowed : 9.89 % Favored : 89.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % Cis-general : 0.08 % 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: 0.48 (0.14), residues: 3795 helix: 1.96 (0.13), residues: 1646 sheet: -0.04 (0.24), residues: 500 loop : -1.31 (0.15), residues: 1649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 121 TYR 0.012 0.001 TYR A 449 PHE 0.011 0.001 PHE G 141 TRP 0.007 0.001 TRP E 202 HIS 0.003 0.000 HIS H 37 Details of bonding type rmsd covalent geometry : bond 0.00224 (29652) covalent geometry : angle 0.48729 (40264) hydrogen bonds : bond 0.04236 ( 1369) hydrogen bonds : angle 4.31960 ( 4020) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7590 Ramachandran restraints generated. 3795 Oldfield, 0 Emsley, 3795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7590 Ramachandran restraints generated. 3795 Oldfield, 0 Emsley, 3795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 3065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 173 time to evaluate : 1.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 470 GLU cc_start: 0.8820 (mt-10) cc_final: 0.8459 (tt0) REVERT: C 82 PHE cc_start: 0.8953 (t80) cc_final: 0.8653 (t80) REVERT: C 160 THR cc_start: 0.8918 (m) cc_final: 0.8526 (p) REVERT: E 68 MET cc_start: 0.9279 (mmt) cc_final: 0.8844 (mmt) REVERT: E 209 ASN cc_start: 0.8459 (t0) cc_final: 0.7956 (t0) REVERT: G 33 ILE cc_start: 0.8600 (OUTLIER) cc_final: 0.8326 (mm) REVERT: G 57 LEU cc_start: 0.7936 (mt) cc_final: 0.7705 (tt) REVERT: G 101 GLU cc_start: 0.8857 (tp30) cc_final: 0.8494 (tp30) REVERT: G 104 TYR cc_start: 0.8375 (m-10) cc_final: 0.8045 (m-80) REVERT: G 249 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7528 (mp0) REVERT: H 1 MET cc_start: 0.5661 (ptp) cc_final: 0.5449 (ptt) REVERT: d 136 HIS cc_start: 0.5269 (t70) cc_final: 0.4512 (m90) REVERT: d 190 PHE cc_start: 0.2860 (OUTLIER) cc_final: 0.2567 (t80) REVERT: d 356 TYR cc_start: 0.5753 (p90) cc_final: 0.4948 (t80) REVERT: d 418 LEU cc_start: 0.4661 (OUTLIER) cc_final: 0.4361 (mm) outliers start: 31 outliers final: 18 residues processed: 196 average time/residue: 0.2012 time to fit residues: 63.2284 Evaluate side-chains 177 residues out of total 3065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 155 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain D residue 386 ILE Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 269 THR Chi-restraints excluded: chain F residue 185 THR Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 195 THR Chi-restraints excluded: chain G residue 226 ASP Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 249 GLU Chi-restraints excluded: chain H residue 59 ASP Chi-restraints excluded: chain d residue 190 PHE Chi-restraints excluded: chain d residue 294 ILE Chi-restraints excluded: chain d residue 308 LEU Chi-restraints excluded: chain d residue 414 VAL Chi-restraints excluded: chain d residue 418 LEU Chi-restraints excluded: chain d residue 426 ILE Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 418 LYS Chi-restraints excluded: chain B residue 509 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 114 optimal weight: 7.9990 chunk 157 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 122 optimal weight: 0.1980 chunk 212 optimal weight: 9.9990 chunk 291 optimal weight: 9.9990 chunk 60 optimal weight: 0.9980 chunk 302 optimal weight: 7.9990 chunk 220 optimal weight: 8.9990 chunk 257 optimal weight: 20.0000 chunk 15 optimal weight: 5.9990 overall best weight: 3.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 356 GLN ** E 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 381 HIS d 425 ASN B 143 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.098619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.067877 restraints weight = 67733.102| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 2.65 r_work: 0.2842 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 29652 Z= 0.271 Angle : 0.614 10.050 40264 Z= 0.317 Chirality : 0.045 0.232 4681 Planarity : 0.005 0.054 5292 Dihedral : 6.882 89.476 4296 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 1.83 % Allowed : 10.44 % Favored : 87.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % Cis-general : 0.08 % 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: 0.06 (0.14), residues: 3795 helix: 1.57 (0.13), residues: 1652 sheet: -0.33 (0.23), residues: 512 loop : -1.49 (0.15), residues: 1631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 93 TYR 0.017 0.002 TYR E 112 PHE 0.026 0.002 PHE G 223 TRP 0.015 0.001 TRP E 202 HIS 0.005 0.001 HIS A 259 Details of bonding type rmsd covalent geometry : bond 0.00660 (29652) covalent geometry : angle 0.61415 (40264) hydrogen bonds : bond 0.05576 ( 1369) hydrogen bonds : angle 4.63845 ( 4020) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7590 Ramachandran restraints generated. 3795 Oldfield, 0 Emsley, 3795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7590 Ramachandran restraints generated. 3795 Oldfield, 0 Emsley, 3795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 3065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 157 time to evaluate : 1.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 ARG cc_start: 0.9195 (OUTLIER) cc_final: 0.8485 (ptp90) REVERT: E 68 MET cc_start: 0.9302 (mmt) cc_final: 0.8811 (mmt) REVERT: E 209 ASN cc_start: 0.8457 (t0) cc_final: 0.7841 (t0) REVERT: F 426 GLN cc_start: 0.8059 (mm110) cc_final: 0.7796 (mp10) REVERT: G 33 ILE cc_start: 0.8692 (OUTLIER) cc_final: 0.8398 (mm) REVERT: G 249 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7638 (mp0) REVERT: H 7 GLU cc_start: 0.4924 (OUTLIER) cc_final: 0.4487 (pm20) REVERT: d 136 HIS cc_start: 0.5453 (t70) cc_final: 0.4565 (m90) REVERT: d 190 PHE cc_start: 0.2654 (OUTLIER) cc_final: 0.2292 (t80) REVERT: d 307 VAL cc_start: 0.4630 (OUTLIER) cc_final: 0.4141 (p) REVERT: d 356 TYR cc_start: 0.5595 (p90) cc_final: 0.4497 (t80) REVERT: d 383 LYS cc_start: 0.5252 (mtmt) cc_final: 0.4811 (tmtt) REVERT: d 418 LEU cc_start: 0.4802 (OUTLIER) cc_final: 0.3781 (pp) outliers start: 56 outliers final: 34 residues processed: 205 average time/residue: 0.1905 time to fit residues: 64.1603 Evaluate side-chains 187 residues out of total 3065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 146 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 ARG Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 438 GLU Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 269 THR Chi-restraints excluded: chain E residue 392 ILE Chi-restraints excluded: chain E residue 471 SER Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 185 THR Chi-restraints excluded: chain F residue 221 MET Chi-restraints excluded: chain F residue 444 THR Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 195 THR Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 226 ASP Chi-restraints excluded: chain G residue 228 THR Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 249 GLU Chi-restraints excluded: chain G residue 296 VAL Chi-restraints excluded: chain H residue 7 GLU Chi-restraints excluded: chain d residue 190 PHE Chi-restraints excluded: chain d residue 294 ILE Chi-restraints excluded: chain d residue 307 VAL Chi-restraints excluded: chain d residue 370 LEU Chi-restraints excluded: chain d residue 414 VAL Chi-restraints excluded: chain d residue 418 LEU Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 418 LYS Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 509 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 164 optimal weight: 0.7980 chunk 312 optimal weight: 3.9990 chunk 150 optimal weight: 3.9990 chunk 221 optimal weight: 0.9980 chunk 103 optimal weight: 0.0370 chunk 66 optimal weight: 5.9990 chunk 274 optimal weight: 20.0000 chunk 104 optimal weight: 1.9990 chunk 7 optimal weight: 0.0030 chunk 285 optimal weight: 7.9990 chunk 160 optimal weight: 3.9990 overall best weight: 0.7670 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 479 HIS ** E 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.101915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.070581 restraints weight = 66793.882| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 2.75 r_work: 0.2899 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 29652 Z= 0.100 Angle : 0.494 11.141 40264 Z= 0.249 Chirality : 0.040 0.271 4681 Planarity : 0.003 0.049 5292 Dihedral : 6.340 87.694 4294 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.40 % Allowed : 11.39 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % Cis-general : 0.08 % 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: 0.43 (0.14), residues: 3795 helix: 2.00 (0.13), residues: 1628 sheet: -0.22 (0.23), residues: 521 loop : -1.36 (0.15), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 72 TYR 0.011 0.001 TYR G 92 PHE 0.012 0.001 PHE G 141 TRP 0.007 0.001 TRP C 247 HIS 0.004 0.000 HIS A 479 Details of bonding type rmsd covalent geometry : bond 0.00207 (29652) covalent geometry : angle 0.49375 (40264) hydrogen bonds : bond 0.04143 ( 1369) hydrogen bonds : angle 4.18560 ( 4020) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7590 Ramachandran restraints generated. 3795 Oldfield, 0 Emsley, 3795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7590 Ramachandran restraints generated. 3795 Oldfield, 0 Emsley, 3795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 3065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 160 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 ARG cc_start: 0.9148 (OUTLIER) cc_final: 0.8377 (ptp90) REVERT: A 470 GLU cc_start: 0.8915 (mt-10) cc_final: 0.8571 (tt0) REVERT: C 45 GLU cc_start: 0.8013 (mp0) cc_final: 0.7419 (mp0) REVERT: C 82 PHE cc_start: 0.8947 (t80) cc_final: 0.8640 (t80) REVERT: C 160 THR cc_start: 0.8948 (m) cc_final: 0.8543 (p) REVERT: E 68 MET cc_start: 0.9235 (mmt) cc_final: 0.8747 (mmt) REVERT: E 209 ASN cc_start: 0.8417 (t0) cc_final: 0.7763 (t0) REVERT: G 33 ILE cc_start: 0.8587 (OUTLIER) cc_final: 0.8345 (mm) REVERT: G 104 TYR cc_start: 0.8401 (m-10) cc_final: 0.8042 (m-80) REVERT: H 1 MET cc_start: 0.4889 (ttt) cc_final: 0.3669 (ttm) REVERT: H 7 GLU cc_start: 0.4863 (OUTLIER) cc_final: 0.4345 (pm20) REVERT: H 31 GLU cc_start: 0.6863 (pt0) cc_final: 0.6486 (pm20) REVERT: H 74 ASP cc_start: 0.8068 (t0) cc_final: 0.7752 (m-30) REVERT: d 136 HIS cc_start: 0.5398 (t70) cc_final: 0.4521 (m90) REVERT: d 356 TYR cc_start: 0.5628 (p90) cc_final: 0.4678 (t80) REVERT: d 383 LYS cc_start: 0.5142 (mtmt) cc_final: 0.4760 (tmtt) REVERT: d 418 LEU cc_start: 0.4658 (OUTLIER) cc_final: 0.3708 (pp) outliers start: 43 outliers final: 19 residues processed: 199 average time/residue: 0.1787 time to fit residues: 57.4831 Evaluate side-chains 172 residues out of total 3065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 149 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 ARG Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 438 GLU Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 269 THR Chi-restraints excluded: chain E residue 471 SER Chi-restraints excluded: chain F residue 185 THR Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 195 THR Chi-restraints excluded: chain G residue 226 ASP Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain H residue 7 GLU Chi-restraints excluded: chain d residue 222 LEU Chi-restraints excluded: chain d residue 294 ILE Chi-restraints excluded: chain d residue 418 LEU Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 418 LYS Chi-restraints excluded: chain B residue 509 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 128 optimal weight: 6.9990 chunk 301 optimal weight: 20.0000 chunk 39 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 13 optimal weight: 9.9990 chunk 292 optimal weight: 3.9990 chunk 243 optimal weight: 1.9990 chunk 167 optimal weight: 3.9990 chunk 151 optimal weight: 4.9990 chunk 122 optimal weight: 0.6980 chunk 184 optimal weight: 0.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 426 GLN B 143 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.100497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.069029 restraints weight = 67126.074| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 2.77 r_work: 0.2860 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 29652 Z= 0.171 Angle : 0.525 9.179 40264 Z= 0.268 Chirality : 0.041 0.216 4681 Planarity : 0.004 0.048 5292 Dihedral : 6.365 88.505 4292 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 1.53 % Allowed : 11.42 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.14), residues: 3795 helix: 1.93 (0.13), residues: 1632 sheet: -0.21 (0.24), residues: 512 loop : -1.40 (0.15), residues: 1651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 72 TYR 0.012 0.001 TYR G 92 PHE 0.012 0.001 PHE F 260 TRP 0.008 0.001 TRP E 202 HIS 0.004 0.001 HIS A 479 Details of bonding type rmsd covalent geometry : bond 0.00410 (29652) covalent geometry : angle 0.52468 (40264) hydrogen bonds : bond 0.04648 ( 1369) hydrogen bonds : angle 4.26793 ( 4020) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7590 Ramachandran restraints generated. 3795 Oldfield, 0 Emsley, 3795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7590 Ramachandran restraints generated. 3795 Oldfield, 0 Emsley, 3795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 3065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 157 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 ARG cc_start: 0.9148 (OUTLIER) cc_final: 0.8344 (ptp90) REVERT: A 470 GLU cc_start: 0.8921 (mt-10) cc_final: 0.8589 (tp30) REVERT: C 82 PHE cc_start: 0.8962 (t80) cc_final: 0.8705 (t80) REVERT: E 68 MET cc_start: 0.9243 (mmt) cc_final: 0.8746 (mmt) REVERT: E 209 ASN cc_start: 0.8419 (t0) cc_final: 0.7740 (t0) REVERT: F 426 GLN cc_start: 0.8104 (mm110) cc_final: 0.7783 (mp10) REVERT: G 33 ILE cc_start: 0.8556 (OUTLIER) cc_final: 0.8288 (mm) REVERT: G 104 TYR cc_start: 0.8410 (m-10) cc_final: 0.8048 (m-80) REVERT: H 7 GLU cc_start: 0.4902 (OUTLIER) cc_final: 0.4390 (pm20) REVERT: H 89 ASP cc_start: 0.6752 (m-30) cc_final: 0.6417 (t0) REVERT: d 136 HIS cc_start: 0.5427 (t70) cc_final: 0.4596 (m90) REVERT: d 356 TYR cc_start: 0.5551 (p90) cc_final: 0.4529 (t80) REVERT: d 418 LEU cc_start: 0.4757 (OUTLIER) cc_final: 0.4256 (mm) outliers start: 47 outliers final: 30 residues processed: 198 average time/residue: 0.1633 time to fit residues: 54.0023 Evaluate side-chains 180 residues out of total 3065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 146 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 307 ARG Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain D residue 221 MET Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 438 GLU Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 144 VAL Chi-restraints excluded: chain E residue 269 THR Chi-restraints excluded: chain E residue 471 SER Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 185 THR Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 195 THR Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 226 ASP Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 270 ASP Chi-restraints excluded: chain H residue 7 GLU Chi-restraints excluded: chain d residue 294 ILE Chi-restraints excluded: chain d residue 418 LEU Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 418 LYS Chi-restraints excluded: chain B residue 509 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 320 optimal weight: 20.0000 chunk 364 optimal weight: 1.9990 chunk 338 optimal weight: 10.0000 chunk 240 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 303 optimal weight: 5.9990 chunk 221 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 135 optimal weight: 3.9990 chunk 144 optimal weight: 6.9990 chunk 227 optimal weight: 0.0070 overall best weight: 1.9804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 184 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.100684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.069296 restraints weight = 67156.208| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 2.75 r_work: 0.2865 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 29652 Z= 0.150 Angle : 0.523 13.060 40264 Z= 0.265 Chirality : 0.041 0.214 4681 Planarity : 0.004 0.045 5292 Dihedral : 6.294 89.759 4292 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.53 % Allowed : 11.71 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % Cis-general : 0.08 % 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: 0.35 (0.14), residues: 3795 helix: 1.90 (0.13), residues: 1639 sheet: -0.22 (0.24), residues: 512 loop : -1.40 (0.15), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 72 TYR 0.012 0.001 TYR G 92 PHE 0.011 0.001 PHE F 260 TRP 0.007 0.001 TRP E 202 HIS 0.003 0.001 HIS A 479 Details of bonding type rmsd covalent geometry : bond 0.00353 (29652) covalent geometry : angle 0.52335 (40264) hydrogen bonds : bond 0.04459 ( 1369) hydrogen bonds : angle 4.22174 ( 4020) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7590 Ramachandran restraints generated. 3795 Oldfield, 0 Emsley, 3795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7590 Ramachandran restraints generated. 3795 Oldfield, 0 Emsley, 3795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 3065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 153 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 ARG cc_start: 0.9156 (OUTLIER) cc_final: 0.8370 (ptp90) REVERT: A 470 GLU cc_start: 0.8871 (mt-10) cc_final: 0.8556 (tp30) REVERT: C 45 GLU cc_start: 0.8025 (mp0) cc_final: 0.7387 (mp0) REVERT: C 82 PHE cc_start: 0.8957 (t80) cc_final: 0.8677 (t80) REVERT: E 68 MET cc_start: 0.9244 (mmt) cc_final: 0.8738 (mmt) REVERT: E 209 ASN cc_start: 0.8419 (t0) cc_final: 0.7724 (t0) REVERT: G 33 ILE cc_start: 0.8560 (OUTLIER) cc_final: 0.8301 (mm) REVERT: G 104 TYR cc_start: 0.8413 (m-10) cc_final: 0.8085 (m-80) REVERT: G 116 VAL cc_start: 0.8662 (t) cc_final: 0.8365 (p) REVERT: H 7 GLU cc_start: 0.4923 (OUTLIER) cc_final: 0.4432 (pm20) REVERT: H 89 ASP cc_start: 0.6862 (m-30) cc_final: 0.6432 (t0) REVERT: d 356 TYR cc_start: 0.5524 (p90) cc_final: 0.4464 (t80) REVERT: d 418 LEU cc_start: 0.4755 (OUTLIER) cc_final: 0.4256 (mm) outliers start: 47 outliers final: 34 residues processed: 195 average time/residue: 0.1753 time to fit residues: 55.7253 Evaluate side-chains 188 residues out of total 3065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 150 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 307 ARG Chi-restraints excluded: chain A residue 352 GLN Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain D residue 221 MET Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 438 GLU Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 144 VAL Chi-restraints excluded: chain E residue 269 THR Chi-restraints excluded: chain E residue 471 SER Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 185 THR Chi-restraints excluded: chain F residue 306 MET Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 195 THR Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 226 ASP Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 270 ASP Chi-restraints excluded: chain H residue 7 GLU Chi-restraints excluded: chain b residue 93 LEU Chi-restraints excluded: chain d residue 294 ILE Chi-restraints excluded: chain d residue 414 VAL Chi-restraints excluded: chain d residue 418 LEU Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 418 LYS Chi-restraints excluded: chain B residue 509 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 287 optimal weight: 0.0040 chunk 217 optimal weight: 4.9990 chunk 127 optimal weight: 3.9990 chunk 179 optimal weight: 0.0980 chunk 42 optimal weight: 0.3980 chunk 360 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 238 optimal weight: 5.9990 chunk 237 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 overall best weight: 0.4392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 85 GLN B 143 GLN B 455 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.102942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.071724 restraints weight = 67421.841| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 2.77 r_work: 0.2922 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 29652 Z= 0.089 Angle : 0.485 13.491 40264 Z= 0.244 Chirality : 0.039 0.205 4681 Planarity : 0.003 0.045 5292 Dihedral : 5.896 87.716 4292 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.01 % Allowed : 12.27 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % Cis-general : 0.08 % 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: 0.64 (0.14), residues: 3795 helix: 2.16 (0.13), residues: 1632 sheet: -0.07 (0.24), residues: 510 loop : -1.25 (0.15), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 72 TYR 0.011 0.001 TYR d 278 PHE 0.012 0.001 PHE G 141 TRP 0.009 0.001 TRP G 138 HIS 0.004 0.000 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00180 (29652) covalent geometry : angle 0.48533 (40264) hydrogen bonds : bond 0.03524 ( 1369) hydrogen bonds : angle 3.90536 ( 4020) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7590 Ramachandran restraints generated. 3795 Oldfield, 0 Emsley, 3795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7590 Ramachandran restraints generated. 3795 Oldfield, 0 Emsley, 3795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 3065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 169 time to evaluate : 1.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 ARG cc_start: 0.9164 (OUTLIER) cc_final: 0.8303 (ptp90) REVERT: A 470 GLU cc_start: 0.8929 (mt-10) cc_final: 0.8510 (tp30) REVERT: C 45 GLU cc_start: 0.8032 (mp0) cc_final: 0.7461 (mp0) REVERT: C 82 PHE cc_start: 0.8883 (t80) cc_final: 0.8576 (t80) REVERT: C 160 THR cc_start: 0.8969 (m) cc_final: 0.8550 (p) REVERT: E 68 MET cc_start: 0.9253 (mmt) cc_final: 0.8802 (mmt) REVERT: E 209 ASN cc_start: 0.8438 (t0) cc_final: 0.7758 (t0) REVERT: G 65 HIS cc_start: 0.8246 (OUTLIER) cc_final: 0.7998 (t-90) REVERT: G 104 TYR cc_start: 0.8388 (m-10) cc_final: 0.8119 (m-10) REVERT: G 116 VAL cc_start: 0.8655 (t) cc_final: 0.8381 (p) REVERT: H 7 GLU cc_start: 0.4877 (OUTLIER) cc_final: 0.4450 (pm20) REVERT: H 74 ASP cc_start: 0.8070 (t0) cc_final: 0.7735 (t70) REVERT: H 89 ASP cc_start: 0.6835 (m-30) cc_final: 0.6465 (t0) REVERT: d 356 TYR cc_start: 0.5531 (p90) cc_final: 0.4605 (t80) REVERT: d 383 LYS cc_start: 0.5341 (mtmt) cc_final: 0.4965 (tmtt) REVERT: d 418 LEU cc_start: 0.4728 (OUTLIER) cc_final: 0.3766 (pp) REVERT: B 414 ASP cc_start: 0.7248 (p0) cc_final: 0.6794 (p0) outliers start: 31 outliers final: 23 residues processed: 197 average time/residue: 0.1851 time to fit residues: 59.2294 Evaluate side-chains 183 residues out of total 3065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 156 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 307 ARG Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 386 ILE Chi-restraints excluded: chain D residue 438 GLU Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 144 VAL Chi-restraints excluded: chain E residue 471 SER Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain G residue 65 HIS Chi-restraints excluded: chain H residue 7 GLU Chi-restraints excluded: chain b residue 93 LEU Chi-restraints excluded: chain d residue 222 LEU Chi-restraints excluded: chain d residue 294 ILE Chi-restraints excluded: chain d residue 414 VAL Chi-restraints excluded: chain d residue 418 LEU Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 418 LYS Chi-restraints excluded: chain B residue 509 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 198 optimal weight: 5.9990 chunk 270 optimal weight: 20.0000 chunk 360 optimal weight: 3.9990 chunk 163 optimal weight: 4.9990 chunk 114 optimal weight: 0.7980 chunk 377 optimal weight: 20.0000 chunk 9 optimal weight: 4.9990 chunk 160 optimal weight: 3.9990 chunk 233 optimal weight: 1.9990 chunk 251 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.099526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.068340 restraints weight = 68070.678| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 2.74 r_work: 0.2851 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 29652 Z= 0.214 Angle : 0.564 10.785 40264 Z= 0.288 Chirality : 0.043 0.236 4681 Planarity : 0.004 0.045 5292 Dihedral : 6.211 88.385 4292 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.31 % Allowed : 12.40 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % Cis-general : 0.08 % 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: 0.38 (0.14), residues: 3795 helix: 1.92 (0.13), residues: 1638 sheet: -0.22 (0.23), residues: 513 loop : -1.37 (0.15), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG b 112 TYR 0.012 0.001 TYR E 112 PHE 0.014 0.001 PHE F 260 TRP 0.010 0.001 TRP E 202 HIS 0.005 0.001 HIS E 327 Details of bonding type rmsd covalent geometry : bond 0.00518 (29652) covalent geometry : angle 0.56400 (40264) hydrogen bonds : bond 0.04743 ( 1369) hydrogen bonds : angle 4.25765 ( 4020) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7590 Ramachandran restraints generated. 3795 Oldfield, 0 Emsley, 3795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7590 Ramachandran restraints generated. 3795 Oldfield, 0 Emsley, 3795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 3065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 145 time to evaluate : 1.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 ARG cc_start: 0.9165 (OUTLIER) cc_final: 0.8298 (ptp90) REVERT: A 470 GLU cc_start: 0.8881 (mt-10) cc_final: 0.8470 (tp30) REVERT: C 82 PHE cc_start: 0.8941 (t80) cc_final: 0.8675 (t80) REVERT: E 68 MET cc_start: 0.9254 (mmt) cc_final: 0.8808 (mmt) REVERT: E 209 ASN cc_start: 0.8421 (t0) cc_final: 0.7727 (t0) REVERT: G 65 HIS cc_start: 0.8201 (OUTLIER) cc_final: 0.7874 (t-90) REVERT: G 104 TYR cc_start: 0.8405 (m-10) cc_final: 0.8100 (m-80) REVERT: H 7 GLU cc_start: 0.4906 (OUTLIER) cc_final: 0.4394 (pm20) REVERT: H 89 ASP cc_start: 0.7059 (m-30) cc_final: 0.6648 (t0) REVERT: d 328 ARG cc_start: 0.3087 (OUTLIER) cc_final: 0.1230 (mtt180) REVERT: d 356 TYR cc_start: 0.5512 (p90) cc_final: 0.4322 (t80) outliers start: 40 outliers final: 30 residues processed: 182 average time/residue: 0.1758 time to fit residues: 52.8049 Evaluate side-chains 178 residues out of total 3065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 144 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 307 ARG Chi-restraints excluded: chain A residue 352 GLN Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 386 ILE Chi-restraints excluded: chain D residue 436 THR Chi-restraints excluded: chain D residue 438 GLU Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 144 VAL Chi-restraints excluded: chain E residue 471 SER Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain G residue 65 HIS Chi-restraints excluded: chain G residue 195 THR Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain H residue 7 GLU Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain b residue 93 LEU Chi-restraints excluded: chain d residue 294 ILE Chi-restraints excluded: chain d residue 328 ARG Chi-restraints excluded: chain d residue 414 VAL Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 418 LYS Chi-restraints excluded: chain B residue 509 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 374 optimal weight: 4.9990 chunk 103 optimal weight: 6.9990 chunk 47 optimal weight: 6.9990 chunk 105 optimal weight: 4.9990 chunk 165 optimal weight: 0.0470 chunk 59 optimal weight: 0.4980 chunk 53 optimal weight: 0.0670 chunk 111 optimal weight: 5.9990 chunk 201 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 329 optimal weight: 3.9990 overall best weight: 1.3220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 425 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.100937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.069756 restraints weight = 67330.545| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 2.75 r_work: 0.2881 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 29652 Z= 0.120 Angle : 0.505 11.333 40264 Z= 0.256 Chirality : 0.040 0.211 4681 Planarity : 0.003 0.043 5292 Dihedral : 6.081 89.908 4292 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.01 % Allowed : 12.72 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % Cis-general : 0.08 % 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: 0.50 (0.14), residues: 3795 helix: 2.05 (0.13), residues: 1635 sheet: -0.22 (0.24), residues: 518 loop : -1.31 (0.15), residues: 1642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 72 TYR 0.012 0.001 TYR G 92 PHE 0.014 0.001 PHE H 22 TRP 0.007 0.001 TRP C 247 HIS 0.003 0.001 HIS A 259 Details of bonding type rmsd covalent geometry : bond 0.00275 (29652) covalent geometry : angle 0.50474 (40264) hydrogen bonds : bond 0.04129 ( 1369) hydrogen bonds : angle 4.08121 ( 4020) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7590 Ramachandran restraints generated. 3795 Oldfield, 0 Emsley, 3795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7590 Ramachandran restraints generated. 3795 Oldfield, 0 Emsley, 3795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 3065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 153 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 ARG cc_start: 0.9149 (OUTLIER) cc_final: 0.8350 (ptp90) REVERT: A 470 GLU cc_start: 0.8907 (mt-10) cc_final: 0.8551 (tp30) REVERT: C 45 GLU cc_start: 0.8040 (mp0) cc_final: 0.7406 (mp0) REVERT: C 82 PHE cc_start: 0.8910 (t80) cc_final: 0.8629 (t80) REVERT: E 68 MET cc_start: 0.9246 (mmt) cc_final: 0.8799 (mmt) REVERT: E 209 ASN cc_start: 0.8401 (t0) cc_final: 0.7708 (t0) REVERT: G 65 HIS cc_start: 0.8220 (OUTLIER) cc_final: 0.7903 (t-90) REVERT: G 104 TYR cc_start: 0.8401 (m-10) cc_final: 0.8158 (m-80) REVERT: H 7 GLU cc_start: 0.4827 (OUTLIER) cc_final: 0.4346 (pm20) REVERT: H 89 ASP cc_start: 0.7062 (m-30) cc_final: 0.6627 (t0) REVERT: d 249 LYS cc_start: 0.3871 (mtmp) cc_final: 0.3122 (tmtt) REVERT: d 328 ARG cc_start: 0.3139 (OUTLIER) cc_final: 0.1331 (mtt180) REVERT: d 356 TYR cc_start: 0.5539 (p90) cc_final: 0.4418 (t80) REVERT: d 383 LYS cc_start: 0.5387 (mtmt) cc_final: 0.5000 (tmtt) outliers start: 31 outliers final: 27 residues processed: 181 average time/residue: 0.1870 time to fit residues: 55.3552 Evaluate side-chains 181 residues out of total 3065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 150 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 307 ARG Chi-restraints excluded: chain A residue 352 GLN Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 386 ILE Chi-restraints excluded: chain D residue 438 GLU Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 144 VAL Chi-restraints excluded: chain E residue 471 SER Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain G residue 65 HIS Chi-restraints excluded: chain G residue 195 THR Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain H residue 7 GLU Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain b residue 93 LEU Chi-restraints excluded: chain d residue 294 ILE Chi-restraints excluded: chain d residue 328 ARG Chi-restraints excluded: chain d residue 414 VAL Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 418 LYS Chi-restraints excluded: chain B residue 509 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 160 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 129 optimal weight: 0.0370 chunk 267 optimal weight: 3.9990 chunk 175 optimal weight: 0.9990 chunk 259 optimal weight: 3.9990 chunk 39 optimal weight: 8.9990 chunk 377 optimal weight: 20.0000 chunk 357 optimal weight: 2.9990 chunk 272 optimal weight: 0.9980 chunk 205 optimal weight: 3.9990 overall best weight: 0.9662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 292 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.101643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.070596 restraints weight = 67583.895| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 2.76 r_work: 0.2899 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 29652 Z= 0.103 Angle : 0.489 11.091 40264 Z= 0.246 Chirality : 0.040 0.210 4681 Planarity : 0.003 0.044 5292 Dihedral : 5.926 89.594 4292 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.21 % Allowed : 12.53 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % Cis-general : 0.08 % 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: 0.62 (0.14), residues: 3795 helix: 2.15 (0.13), residues: 1630 sheet: -0.18 (0.24), residues: 520 loop : -1.24 (0.15), residues: 1645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 72 TYR 0.010 0.001 TYR G 92 PHE 0.011 0.001 PHE G 141 TRP 0.007 0.001 TRP G 138 HIS 0.002 0.000 HIS B 259 Details of bonding type rmsd covalent geometry : bond 0.00229 (29652) covalent geometry : angle 0.48898 (40264) hydrogen bonds : bond 0.03846 ( 1369) hydrogen bonds : angle 3.96471 ( 4020) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6754.69 seconds wall clock time: 116 minutes 36.49 seconds (6996.49 seconds total)