Starting phenix.real_space_refine on Fri Mar 6 16:31:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6y5a_10692/03_2026/6y5a_10692_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/6y5a_10692/03_2026/6y5a_10692.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6y5a_10692/03_2026/6y5a_10692_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6y5a_10692/03_2026/6y5a_10692_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6y5a_10692/03_2026/6y5a_10692.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6y5a_10692/03_2026/6y5a_10692.map" } resolution = 2.8 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= 0.002 sd= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 45 5.16 5 C 10638 2.51 5 N 2633 2.21 5 O 2815 1.98 5 H 16272 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 91 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32403 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 6465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 6465 Classifications: {'peptide': 388} Link IDs: {'PTRANS': 20, 'TRANS': 367} Chain breaks: 1 Chain: "C" Number of atoms: 6439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 6439 Classifications: {'peptide': 386} Link IDs: {'PTRANS': 20, 'TRANS': 365} Chain breaks: 1 Chain: "D" Number of atoms: 6504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 6504 Classifications: {'peptide': 390} Link IDs: {'PTRANS': 20, 'TRANS': 369} Chain breaks: 1 Chain: "B" Number of atoms: 6465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 6465 Classifications: {'peptide': 388} Link IDs: {'PTRANS': 20, 'TRANS': 367} Chain breaks: 1 Chain: "E" Number of atoms: 6465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 6465 Classifications: {'peptide': 388} Link IDs: {'PTRANS': 20, 'TRANS': 367} Chain breaks: 1 Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'SRO': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'SRO': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'SRO': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'SRO': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'SRO': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.49, per 1000 atoms: 0.20 Number of scatterers: 32403 At special positions: 0 Unit cell: (101.504, 97.344, 163.904, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 45 16.00 O 2815 8.00 N 2633 7.00 C 10638 6.00 H 16272 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 135 " - pdb=" SG CYS A 149 " distance=2.03 Simple disulfide: pdb=" SG CYS C 135 " - pdb=" SG CYS C 149 " distance=2.03 Simple disulfide: pdb=" SG CYS D 135 " - pdb=" SG CYS D 149 " distance=2.03 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS E 135 " - pdb=" SG CYS E 149 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.04 Conformation dependent library (CDL) restraints added in 894.7 milliseconds 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3772 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 13 sheets defined 45.4% alpha, 20.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'A' and resid 10 through 21 removed outlier: 3.707A pdb=" N HIS A 18 " --> pdb=" O ARG A 14 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA A 21 " --> pdb=" O ASP A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 81 removed outlier: 3.971A pdb=" N ASP A 81 " --> pdb=" O GLU A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 93 Processing helix chain 'A' and resid 170 through 176 Processing helix chain 'A' and resid 220 through 244 removed outlier: 4.175A pdb=" N LEU A 229 " --> pdb=" O VAL A 225 " (cutoff:3.500A) Proline residue: A 230 - end of helix removed outlier: 3.550A pdb=" N VAL A 237 " --> pdb=" O PHE A 233 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N ASP A 238 " --> pdb=" O LEU A 234 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ILE A 239 " --> pdb=" O MET A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 273 removed outlier: 3.602A pdb=" N VAL A 252 " --> pdb=" O SER A 248 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR A 257 " --> pdb=" O SER A 253 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU A 258 " --> pdb=" O PHE A 254 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU A 260 " --> pdb=" O ILE A 256 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY A 261 " --> pdb=" O THR A 257 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE A 268 " --> pdb=" O VAL A 264 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER A 270 " --> pdb=" O LEU A 266 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASP A 271 " --> pdb=" O ILE A 267 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N THR A 272 " --> pdb=" O ILE A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 309 removed outlier: 3.619A pdb=" N TYR A 286 " --> pdb=" O LEU A 282 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE A 287 " --> pdb=" O ILE A 283 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL A 288 " --> pdb=" O GLY A 284 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU A 294 " --> pdb=" O CYS A 290 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE A 302 " --> pdb=" O LEU A 298 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE A 303 " --> pdb=" O ALA A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 333 Processing helix chain 'A' and resid 402 through 415 Processing helix chain 'A' and resid 416 through 418 No H-bonds generated for 'chain 'A' and resid 416 through 418' Processing helix chain 'A' and resid 420 through 462 removed outlier: 3.683A pdb=" N ARG A 424 " --> pdb=" O ARG A 420 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY A 430 " --> pdb=" O TRP A 426 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL A 432 " --> pdb=" O ARG A 428 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LEU A 433 " --> pdb=" O VAL A 429 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASP A 434 " --> pdb=" O GLY A 430 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG A 435 " --> pdb=" O TYR A 431 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU A 436 " --> pdb=" O VAL A 432 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ARG A 439 " --> pdb=" O ARG A 435 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU A 452 " --> pdb=" O TYR A 448 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL A 453 " --> pdb=" O SER A 449 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR A 454 " --> pdb=" O ILE A 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 21 removed outlier: 3.503A pdb=" N SER C 16 " --> pdb=" O LEU C 12 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N HIS C 18 " --> pdb=" O ARG C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 93 removed outlier: 3.545A pdb=" N SER C 92 " --> pdb=" O PRO C 89 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE C 93 " --> pdb=" O THR C 90 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 89 through 93' Processing helix chain 'C' and resid 170 through 176 Processing helix chain 'C' and resid 220 through 227 Processing helix chain 'C' and resid 227 through 244 removed outlier: 3.645A pdb=" N VAL C 237 " --> pdb=" O PHE C 233 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N VAL C 240 " --> pdb=" O VAL C 236 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY C 241 " --> pdb=" O VAL C 237 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N PHE C 242 " --> pdb=" O ASP C 238 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N CYS C 243 " --> pdb=" O ILE C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 271 removed outlier: 3.828A pdb=" N PHE C 254 " --> pdb=" O GLU C 250 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N THR C 257 " --> pdb=" O SER C 253 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP C 271 " --> pdb=" O ILE C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 308 removed outlier: 3.540A pdb=" N VAL C 288 " --> pdb=" O GLY C 284 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL C 289 " --> pdb=" O VAL C 285 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU C 294 " --> pdb=" O CYS C 290 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE C 303 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL C 305 " --> pdb=" O THR C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 333 removed outlier: 4.479A pdb=" N ASP C 327 " --> pdb=" O HIS C 323 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARG C 328 " --> pdb=" O LEU C 324 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA C 330 " --> pdb=" O LEU C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 417 removed outlier: 4.146A pdb=" N SER C 408 " --> pdb=" O GLN C 404 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LEU C 413 " --> pdb=" O ILE C 409 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N GLU C 414 " --> pdb=" O ARG C 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 462 removed outlier: 3.553A pdb=" N LEU C 436 " --> pdb=" O VAL C 432 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU C 437 " --> pdb=" O LEU C 433 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU C 443 " --> pdb=" O ARG C 439 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU C 452 " --> pdb=" O TYR C 448 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL C 453 " --> pdb=" O SER C 449 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR C 454 " --> pdb=" O ILE C 450 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 21 removed outlier: 3.541A pdb=" N HIS D 18 " --> pdb=" O ARG D 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 93 No H-bonds generated for 'chain 'D' and resid 91 through 93' Processing helix chain 'D' and resid 170 through 176 Processing helix chain 'D' and resid 220 through 244 removed outlier: 4.034A pdb=" N LEU D 229 " --> pdb=" O VAL D 225 " (cutoff:3.500A) Proline residue: D 230 - end of helix removed outlier: 3.709A pdb=" N VAL D 237 " --> pdb=" O PHE D 233 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE D 239 " --> pdb=" O MET D 235 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE D 242 " --> pdb=" O ASP D 238 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N CYS D 243 " --> pdb=" O ILE D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 273 removed outlier: 3.843A pdb=" N PHE D 254 " --> pdb=" O GLU D 250 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ILE D 256 " --> pdb=" O VAL D 252 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N THR D 257 " --> pdb=" O SER D 253 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU D 260 " --> pdb=" O ILE D 256 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLY D 261 " --> pdb=" O THR D 257 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE D 268 " --> pdb=" O VAL D 264 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL D 269 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N SER D 270 " --> pdb=" O LEU D 266 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASP D 271 " --> pdb=" O ILE D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 311 removed outlier: 3.950A pdb=" N LEU D 298 " --> pdb=" O LEU D 294 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG D 306 " --> pdb=" O ILE D 302 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N LEU D 307 " --> pdb=" O PHE D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 333 removed outlier: 4.052A pdb=" N ARG D 328 " --> pdb=" O LEU D 324 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA D 330 " --> pdb=" O LEU D 326 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N TRP D 331 " --> pdb=" O ASP D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 400 through 404 removed outlier: 3.537A pdb=" N GLN D 404 " --> pdb=" O ARG D 400 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 400 through 404' Processing helix chain 'D' and resid 404 through 418 removed outlier: 3.604A pdb=" N GLU D 418 " --> pdb=" O GLU D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 462 removed outlier: 4.264A pdb=" N TRP D 426 " --> pdb=" O VAL D 422 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL D 429 " --> pdb=" O ASP D 425 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLY D 430 " --> pdb=" O TRP D 426 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU D 433 " --> pdb=" O VAL D 429 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASP D 434 " --> pdb=" O GLY D 430 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ARG D 439 " --> pdb=" O ARG D 435 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE D 440 " --> pdb=" O LEU D 436 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU D 442 " --> pdb=" O PHE D 438 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N LEU D 443 " --> pdb=" O ARG D 439 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL D 453 " --> pdb=" O SER D 449 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR D 454 " --> pdb=" O ILE D 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 21 removed outlier: 3.568A pdb=" N ASP B 17 " --> pdb=" O LEU B 13 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N HIS B 18 " --> pdb=" O ARG B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 93 removed outlier: 3.653A pdb=" N SER B 92 " --> pdb=" O PRO B 89 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE B 93 " --> pdb=" O THR B 90 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 89 through 93' Processing helix chain 'B' and resid 170 through 176 Processing helix chain 'B' and resid 220 through 227 Processing helix chain 'B' and resid 227 through 244 removed outlier: 3.858A pdb=" N VAL B 237 " --> pdb=" O PHE B 233 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASP B 238 " --> pdb=" O LEU B 234 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY B 241 " --> pdb=" O VAL B 237 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N PHE B 242 " --> pdb=" O ASP B 238 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N CYS B 243 " --> pdb=" O ILE B 239 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU B 244 " --> pdb=" O VAL B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 273 removed outlier: 5.101A pdb=" N SER B 253 " --> pdb=" O GLY B 249 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N PHE B 254 " --> pdb=" O GLU B 250 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N THR B 257 " --> pdb=" O SER B 253 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLY B 261 " --> pdb=" O THR B 257 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N SER B 270 " --> pdb=" O LEU B 266 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP B 271 " --> pdb=" O ILE B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 309 removed outlier: 3.594A pdb=" N LEU B 307 " --> pdb=" O PHE B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 333 removed outlier: 3.747A pdb=" N ASP B 327 " --> pdb=" O HIS B 323 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG B 328 " --> pdb=" O LEU B 324 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE B 329 " --> pdb=" O VAL B 325 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA B 330 " --> pdb=" O LEU B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 418 removed outlier: 3.691A pdb=" N SER B 407 " --> pdb=" O LEU B 403 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ILE B 409 " --> pdb=" O GLU B 405 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG B 410 " --> pdb=" O LEU B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 462 removed outlier: 4.063A pdb=" N VAL B 429 " --> pdb=" O ASP B 425 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLY B 430 " --> pdb=" O TRP B 426 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU B 433 " --> pdb=" O VAL B 429 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASP B 434 " --> pdb=" O GLY B 430 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG B 435 " --> pdb=" O TYR B 431 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE B 440 " --> pdb=" O LEU B 436 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER B 449 " --> pdb=" O VAL B 445 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU B 452 " --> pdb=" O TYR B 448 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR B 454 " --> pdb=" O ILE B 450 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 21 removed outlier: 3.705A pdb=" N ASP E 17 " --> pdb=" O LEU E 13 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N HIS E 18 " --> pdb=" O ARG E 14 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 81 removed outlier: 3.841A pdb=" N ASP E 81 " --> pdb=" O GLU E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 170 through 177 Processing helix chain 'E' and resid 220 through 227 Processing helix chain 'E' and resid 227 through 241 removed outlier: 3.601A pdb=" N VAL E 237 " --> pdb=" O PHE E 233 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ASP E 238 " --> pdb=" O LEU E 234 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE E 239 " --> pdb=" O MET E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 273 removed outlier: 3.751A pdb=" N GLY E 261 " --> pdb=" O THR E 257 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N SER E 270 " --> pdb=" O LEU E 266 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N THR E 272 " --> pdb=" O ILE E 268 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 309 removed outlier: 3.644A pdb=" N LEU E 298 " --> pdb=" O LEU E 294 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE E 304 " --> pdb=" O GLU E 300 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ARG E 306 " --> pdb=" O ILE E 302 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N LEU E 307 " --> pdb=" O PHE E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 319 through 332 removed outlier: 3.575A pdb=" N LEU E 324 " --> pdb=" O TRP E 320 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N VAL E 325 " --> pdb=" O LEU E 321 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ALA E 330 " --> pdb=" O LEU E 326 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TRP E 331 " --> pdb=" O ASP E 327 " (cutoff:3.500A) Processing helix chain 'E' and resid 402 through 416 removed outlier: 4.098A pdb=" N GLU E 414 " --> pdb=" O ARG E 410 " (cutoff:3.500A) Processing helix chain 'E' and resid 421 through 462 removed outlier: 3.514A pdb=" N ASP E 425 " --> pdb=" O GLU E 421 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG E 428 " --> pdb=" O ARG E 424 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL E 429 " --> pdb=" O ASP E 425 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY E 430 " --> pdb=" O TRP E 426 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N LEU E 433 " --> pdb=" O VAL E 429 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ASP E 434 " --> pdb=" O GLY E 430 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ARG E 435 " --> pdb=" O TYR E 431 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU E 452 " --> pdb=" O TYR E 448 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR E 454 " --> pdb=" O ILE E 450 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 88 removed outlier: 4.537A pdb=" N GLU A 122 " --> pdb=" O HIS A 118 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N VAL A 57 " --> pdb=" O ASN A 50 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N ASN A 50 " --> pdb=" O VAL A 57 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N THR A 59 " --> pdb=" O ILE A 48 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N ILE A 48 " --> pdb=" O THR A 59 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N TYR A 61 " --> pdb=" O TYR A 46 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N VAL A 39 " --> pdb=" O THR A 166 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 98 through 100 removed outlier: 4.852A pdb=" N SER A 155 " --> pdb=" O ALA A 208 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N ALA A 208 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N TYR A 207 " --> pdb=" O GLU A 198 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N GLU A 198 " --> pdb=" O TYR A 207 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N GLU A 209 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N PHE A 196 " --> pdb=" O GLU A 209 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N LYS A 211 " --> pdb=" O PRO A 194 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N TYR A 213 " --> pdb=" O VAL A 192 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N VAL A 192 " --> pdb=" O TYR A 213 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ILE A 215 " --> pdb=" O LEU A 190 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 85 through 88 removed outlier: 4.103A pdb=" N GLU C 122 " --> pdb=" O HIS C 118 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N VAL C 57 " --> pdb=" O ASN C 50 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N ASN C 50 " --> pdb=" O VAL C 57 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N THR C 59 " --> pdb=" O ILE C 48 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N ILE C 48 " --> pdb=" O THR C 59 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N TYR C 61 " --> pdb=" O TYR C 46 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N THR C 69 " --> pdb=" O THR C 38 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N THR C 38 " --> pdb=" O THR C 69 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N THR C 37 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N THR C 166 " --> pdb=" O THR C 37 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N VAL C 39 " --> pdb=" O THR C 166 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 98 through 100 Processing sheet with id=AA5, first strand: chain 'C' and resid 146 through 150 removed outlier: 5.253A pdb=" N TYR C 207 " --> pdb=" O GLU C 198 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLU C 198 " --> pdb=" O TYR C 207 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N GLU C 209 " --> pdb=" O PHE C 196 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N PHE C 196 " --> pdb=" O GLU C 209 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LYS C 211 " --> pdb=" O PRO C 194 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N TYR C 213 " --> pdb=" O VAL C 192 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N VAL C 192 " --> pdb=" O TYR C 213 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ILE C 215 " --> pdb=" O LEU C 190 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 85 through 89 removed outlier: 7.137A pdb=" N TYR D 114 " --> pdb=" O TYR D 126 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N TYR D 126 " --> pdb=" O TYR D 114 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N GLU D 122 " --> pdb=" O HIS D 118 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N VAL D 57 " --> pdb=" O ASN D 50 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N ASN D 50 " --> pdb=" O VAL D 57 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N THR D 59 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N ILE D 48 " --> pdb=" O THR D 59 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N TYR D 61 " --> pdb=" O TYR D 46 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N VAL D 39 " --> pdb=" O THR D 166 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 98 through 100 Processing sheet with id=AA8, first strand: chain 'D' and resid 146 through 150 removed outlier: 3.611A pdb=" N GLU D 191 " --> pdb=" O ILE D 215 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ARG D 217 " --> pdb=" O LEU D 189 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N LEU D 189 " --> pdb=" O ARG D 217 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 85 through 88 removed outlier: 4.493A pdb=" N GLU B 122 " --> pdb=" O HIS B 118 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TRP B 68 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N VAL B 57 " --> pdb=" O ASN B 50 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N ASN B 50 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N THR B 59 " --> pdb=" O ILE B 48 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N ILE B 48 " --> pdb=" O THR B 59 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N TYR B 61 " --> pdb=" O TYR B 46 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG B 65 " --> pdb=" O ASP B 42 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N THR B 69 " --> pdb=" O THR B 38 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N THR B 38 " --> pdb=" O THR B 69 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N THR B 37 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N THR B 166 " --> pdb=" O THR B 37 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N VAL B 39 " --> pdb=" O THR B 166 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 98 through 100 Processing sheet with id=AB2, first strand: chain 'B' and resid 146 through 149 removed outlier: 6.127A pdb=" N ARG B 217 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N LEU B 189 " --> pdb=" O ARG B 217 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 85 through 89 removed outlier: 7.168A pdb=" N TYR E 114 " --> pdb=" O TYR E 126 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N TYR E 126 " --> pdb=" O TYR E 114 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N VAL E 57 " --> pdb=" O ASN E 50 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N ASN E 50 " --> pdb=" O VAL E 57 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N THR E 59 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N ILE E 48 " --> pdb=" O THR E 59 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N TYR E 61 " --> pdb=" O TYR E 46 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N VAL E 39 " --> pdb=" O THR E 166 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 98 through 100 removed outlier: 3.613A pdb=" N GLN E 147 " --> pdb=" O ILE E 216 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE E 216 " --> pdb=" O GLN E 147 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N SER E 155 " --> pdb=" O ALA E 208 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ALA E 208 " --> pdb=" O SER E 155 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N TYR E 207 " --> pdb=" O GLU E 198 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N GLU E 198 " --> pdb=" O TYR E 207 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N GLU E 209 " --> pdb=" O PHE E 196 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N PHE E 196 " --> pdb=" O GLU E 209 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LYS E 211 " --> pdb=" O PRO E 194 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N TYR E 213 " --> pdb=" O VAL E 192 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N VAL E 192 " --> pdb=" O TYR E 213 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ILE E 215 " --> pdb=" O LEU E 190 " (cutoff:3.500A) 708 hydrogen bonds defined for protein. 2094 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: 7.28 Time building geometry restraints manager: 4.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 16262 1.03 - 1.23: 124 1.23 - 1.43: 6938 1.43 - 1.62: 9459 1.62 - 1.82: 70 Bond restraints: 32853 Sorted by residual: bond pdb=" CD1 SRO E 501 " pdb=" NE1 SRO E 501 " ideal model delta sigma weight residual 1.377 1.239 0.138 2.00e-02 2.50e+03 4.79e+01 bond pdb=" CD1 SRO B 501 " pdb=" NE1 SRO B 501 " ideal model delta sigma weight residual 1.377 1.239 0.138 2.00e-02 2.50e+03 4.73e+01 bond pdb=" CD1 SRO A 501 " pdb=" NE1 SRO A 501 " ideal model delta sigma weight residual 1.377 1.240 0.137 2.00e-02 2.50e+03 4.69e+01 bond pdb=" CD1 SRO D 501 " pdb=" NE1 SRO D 501 " ideal model delta sigma weight residual 1.377 1.241 0.136 2.00e-02 2.50e+03 4.63e+01 bond pdb=" CD1 SRO C 501 " pdb=" NE1 SRO C 501 " ideal model delta sigma weight residual 1.377 1.242 0.135 2.00e-02 2.50e+03 4.53e+01 ... (remaining 32848 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.46: 59024 3.46 - 6.92: 432 6.92 - 10.39: 36 10.39 - 13.85: 1 13.85 - 17.31: 5 Bond angle restraints: 59498 Sorted by residual: angle pdb=" CD1 SRO B 501 " pdb=" NE1 SRO B 501 " pdb=" CE2 SRO B 501 " ideal model delta sigma weight residual 109.10 126.41 -17.31 3.00e+00 1.11e-01 3.33e+01 angle pdb=" CD1 SRO C 501 " pdb=" NE1 SRO C 501 " pdb=" CE2 SRO C 501 " ideal model delta sigma weight residual 109.10 126.37 -17.27 3.00e+00 1.11e-01 3.31e+01 angle pdb=" CD1 SRO D 501 " pdb=" NE1 SRO D 501 " pdb=" CE2 SRO D 501 " ideal model delta sigma weight residual 109.10 126.30 -17.20 3.00e+00 1.11e-01 3.29e+01 angle pdb=" CD1 SRO E 501 " pdb=" NE1 SRO E 501 " pdb=" CE2 SRO E 501 " ideal model delta sigma weight residual 109.10 126.26 -17.16 3.00e+00 1.11e-01 3.27e+01 angle pdb=" CD1 SRO A 501 " pdb=" NE1 SRO A 501 " pdb=" CE2 SRO A 501 " ideal model delta sigma weight residual 109.10 126.26 -17.16 3.00e+00 1.11e-01 3.27e+01 ... (remaining 59493 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 14125 17.61 - 35.22: 899 35.22 - 52.83: 276 52.83 - 70.44: 67 70.44 - 88.05: 18 Dihedral angle restraints: 15385 sinusoidal: 8248 harmonic: 7137 Sorted by residual: dihedral pdb=" CA ILE D 304 " pdb=" C ILE D 304 " pdb=" N VAL D 305 " pdb=" CA VAL D 305 " ideal model delta harmonic sigma weight residual -180.00 -154.76 -25.24 0 5.00e+00 4.00e-02 2.55e+01 dihedral pdb=" CA ASP B 319 " pdb=" C ASP B 319 " pdb=" N TRP B 320 " pdb=" CA TRP B 320 " ideal model delta harmonic sigma weight residual 180.00 155.69 24.31 0 5.00e+00 4.00e-02 2.36e+01 dihedral pdb=" CA VAL D 317 " pdb=" C VAL D 317 " pdb=" N PRO D 318 " pdb=" CA PRO D 318 " ideal model delta harmonic sigma weight residual 180.00 157.91 22.09 0 5.00e+00 4.00e-02 1.95e+01 ... (remaining 15382 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1663 0.038 - 0.075: 690 0.075 - 0.113: 219 0.113 - 0.151: 43 0.151 - 0.188: 1 Chirality restraints: 2616 Sorted by residual: chirality pdb=" CA VAL B 317 " pdb=" N VAL B 317 " pdb=" C VAL B 317 " pdb=" CB VAL B 317 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.85e-01 chirality pdb=" CA VAL D 192 " pdb=" N VAL D 192 " pdb=" C VAL D 192 " pdb=" CB VAL D 192 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.11e-01 chirality pdb=" CA VAL B 192 " pdb=" N VAL B 192 " pdb=" C VAL B 192 " pdb=" CB VAL B 192 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.07e-01 ... (remaining 2613 not shown) Planarity restraints: 4606 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN D 66 " -0.164 2.00e-02 2.50e+03 1.79e-01 4.79e+02 pdb=" CD GLN D 66 " 0.014 2.00e-02 2.50e+03 pdb=" OE1 GLN D 66 " 0.155 2.00e-02 2.50e+03 pdb=" NE2 GLN D 66 " 0.001 2.00e-02 2.50e+03 pdb="HE21 GLN D 66 " 0.262 2.00e-02 2.50e+03 pdb="HE22 GLN D 66 " -0.268 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN C 66 " -0.162 2.00e-02 2.50e+03 1.76e-01 4.63e+02 pdb=" CD GLN C 66 " 0.014 2.00e-02 2.50e+03 pdb=" OE1 GLN C 66 " 0.153 2.00e-02 2.50e+03 pdb=" NE2 GLN C 66 " 0.002 2.00e-02 2.50e+03 pdb="HE21 GLN C 66 " 0.257 2.00e-02 2.50e+03 pdb="HE22 GLN C 66 " -0.264 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN B 66 " -0.144 2.00e-02 2.50e+03 1.54e-01 3.57e+02 pdb=" CD GLN B 66 " 0.013 2.00e-02 2.50e+03 pdb=" OE1 GLN B 66 " 0.135 2.00e-02 2.50e+03 pdb=" NE2 GLN B 66 " 0.000 2.00e-02 2.50e+03 pdb="HE21 GLN B 66 " 0.225 2.00e-02 2.50e+03 pdb="HE22 GLN B 66 " -0.230 2.00e-02 2.50e+03 ... (remaining 4603 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.10: 641 2.10 - 2.73: 58781 2.73 - 3.35: 91966 3.35 - 3.98: 118284 3.98 - 4.60: 188206 Nonbonded interactions: 457878 Sorted by model distance: nonbonded pdb="HD12 LEU A 244 " pdb=" HE1 PHE E 303 " model vdw 1.481 2.270 nonbonded pdb=" HG1 THR A 159 " pdb=" OE1 GLN A 161 " model vdw 1.605 2.450 nonbonded pdb=" HG1 THR E 154 " pdb=" O ALA E 208 " model vdw 1.605 2.450 nonbonded pdb=" OE2 GLU B 102 " pdb=" HG1 THR B 152 " model vdw 1.632 2.450 nonbonded pdb=" OD1 ASP E 42 " pdb=" HE ARG E 169 " model vdw 1.633 2.450 ... (remaining 457873 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 8 through 333 or resid 403 through 501)) selection = (chain 'B' and (resid 8 through 333 or resid 403 through 501)) selection = chain 'C' selection = (chain 'D' and (resid 8 through 333 or resid 403 through 501)) selection = (chain 'E' and (resid 8 through 333 or resid 403 through 501)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.790 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: 0.170 Extract box with map and model: 0.430 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 30.990 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 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 : 0.008 0.138 16586 Z= 0.346 Angle : 0.802 17.310 22663 Z= 0.391 Chirality : 0.045 0.188 2616 Planarity : 0.005 0.062 2776 Dihedral : 13.422 88.050 5969 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.99 (0.17), residues: 1920 helix: -2.66 (0.15), residues: 679 sheet: -3.38 (0.19), residues: 421 loop : -1.96 (0.23), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 251 TYR 0.022 0.002 TYR A 67 PHE 0.013 0.002 PHE D 254 TRP 0.018 0.001 TRP D 459 HIS 0.004 0.001 HIS C 309 Details of bonding type rmsd covalent geometry : bond 0.00779 (16581) covalent geometry : angle 0.80189 (22653) SS BOND : bond 0.00120 ( 5) SS BOND : angle 0.39017 ( 10) hydrogen bonds : bond 0.28391 ( 708) hydrogen bonds : angle 9.49070 ( 2094) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.956 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: symmetry clash 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: symmetry clash 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: symmetry clash revert: symmetry clash REVERT: D 435 ARG cc_start: 0.8400 (tpp80) cc_final: 0.7823 (tmm160) REVERT: B 233 PHE cc_start: 0.8944 (t80) cc_final: 0.8456 (t80) REVERT: B 235 MET cc_start: 0.8505 (mtt) cc_final: 0.8014 (mtt) REVERT: E 331 TRP cc_start: 0.7752 (m100) cc_final: 0.7506 (m100) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 1.7612 time to fit residues: 254.9426 Evaluate side-chains 83 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.4980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 9.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 184 GLN C 195 GLN E 184 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.048489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.037470 restraints weight = 233398.047| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 3.18 r_work: 0.2788 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8957 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16586 Z= 0.177 Angle : 0.605 6.360 22663 Z= 0.322 Chirality : 0.044 0.169 2616 Planarity : 0.006 0.081 2776 Dihedral : 6.893 77.826 2146 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.66 % Allowed : 6.28 % Favored : 93.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.79 (0.18), residues: 1920 helix: -1.13 (0.17), residues: 758 sheet: -2.74 (0.20), residues: 439 loop : -1.79 (0.25), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 420 TYR 0.014 0.001 TYR A 67 PHE 0.018 0.001 PHE B 438 TRP 0.014 0.001 TRP D 426 HIS 0.005 0.001 HIS C 309 Details of bonding type rmsd covalent geometry : bond 0.00370 (16581) covalent geometry : angle 0.60535 (22653) SS BOND : bond 0.00109 ( 5) SS BOND : angle 0.39143 ( 10) hydrogen bonds : bond 0.05996 ( 708) hydrogen bonds : angle 5.89152 ( 2094) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 104 time to evaluate : 0.955 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 419 MET cc_start: 0.8126 (tpp) cc_final: 0.7599 (tpt) REVERT: A 438 PHE cc_start: 0.8659 (t80) cc_final: 0.8358 (t80) REVERT: C 315 ARG cc_start: 0.8816 (mmm160) cc_final: 0.8569 (mmm-85) REVERT: D 319 ASP cc_start: 0.8748 (m-30) cc_final: 0.8446 (t0) REVERT: D 435 ARG cc_start: 0.8591 (tpp80) cc_final: 0.7802 (tmm-80) REVERT: B 233 PHE cc_start: 0.9114 (t80) cc_final: 0.8621 (t80) REVERT: B 235 MET cc_start: 0.8867 (mtt) cc_final: 0.8634 (mtt) REVERT: E 331 TRP cc_start: 0.7868 (m100) cc_final: 0.7534 (m100) outliers start: 12 outliers final: 7 residues processed: 111 average time/residue: 1.3448 time to fit residues: 166.1159 Evaluate side-chains 85 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 78 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain C residue 309 HIS Chi-restraints excluded: chain D residue 431 TYR Chi-restraints excluded: chain B residue 323 HIS Chi-restraints excluded: chain E residue 141 ASN Chi-restraints excluded: chain E residue 243 CYS Chi-restraints excluded: chain E residue 406 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 50 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 42 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 166 optimal weight: 0.9990 chunk 36 optimal weight: 7.9990 chunk 11 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 158 optimal weight: 3.9990 chunk 150 optimal weight: 8.9990 chunk 91 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.047443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.036325 restraints weight = 235077.473| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 3.17 r_work: 0.2748 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8981 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16586 Z= 0.184 Angle : 0.548 5.704 22663 Z= 0.290 Chirality : 0.042 0.174 2616 Planarity : 0.005 0.045 2776 Dihedral : 5.180 45.615 2146 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 0.94 % Allowed : 7.54 % Favored : 91.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.97 (0.19), residues: 1920 helix: -0.20 (0.18), residues: 779 sheet: -2.40 (0.21), residues: 427 loop : -1.63 (0.25), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 315 TYR 0.013 0.001 TYR A 67 PHE 0.024 0.001 PHE B 303 TRP 0.013 0.001 TRP D 426 HIS 0.004 0.001 HIS C 309 Details of bonding type rmsd covalent geometry : bond 0.00394 (16581) covalent geometry : angle 0.54819 (22653) SS BOND : bond 0.00027 ( 5) SS BOND : angle 0.26481 ( 10) hydrogen bonds : bond 0.04896 ( 708) hydrogen bonds : angle 5.28852 ( 2094) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 0.847 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: symmetry clash 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: symmetry clash REVERT: A 438 PHE cc_start: 0.8715 (t80) cc_final: 0.8414 (t80) REVERT: C 315 ARG cc_start: 0.8939 (mmm160) cc_final: 0.8679 (mmm-85) REVERT: D 319 ASP cc_start: 0.8842 (m-30) cc_final: 0.8547 (t0) REVERT: D 435 ARG cc_start: 0.8652 (tpp80) cc_final: 0.7796 (tmm-80) REVERT: B 235 MET cc_start: 0.8975 (mtt) cc_final: 0.8617 (mtt) REVERT: E 331 TRP cc_start: 0.7844 (m100) cc_final: 0.7488 (m100) outliers start: 17 outliers final: 11 residues processed: 99 average time/residue: 1.3172 time to fit residues: 146.6039 Evaluate side-chains 87 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain C residue 309 HIS Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain D residue 431 TYR Chi-restraints excluded: chain B residue 323 HIS Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain E residue 141 ASN Chi-restraints excluded: chain E residue 243 CYS Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 406 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 107 optimal weight: 0.9990 chunk 106 optimal weight: 6.9990 chunk 190 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 16 optimal weight: 0.5980 chunk 152 optimal weight: 5.9990 chunk 165 optimal weight: 0.8980 chunk 118 optimal weight: 0.9980 chunk 182 optimal weight: 8.9990 chunk 28 optimal weight: 5.9990 chunk 168 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.048070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.036790 restraints weight = 233066.092| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 3.14 r_work: 0.2766 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8970 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 16586 Z= 0.113 Angle : 0.500 6.450 22663 Z= 0.260 Chirality : 0.042 0.154 2616 Planarity : 0.004 0.048 2776 Dihedral : 4.761 25.389 2146 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.88 % Allowed : 8.43 % Favored : 90.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.19), residues: 1920 helix: 0.37 (0.18), residues: 778 sheet: -2.33 (0.21), residues: 429 loop : -1.53 (0.25), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 328 TYR 0.016 0.001 TYR A 262 PHE 0.024 0.001 PHE B 438 TRP 0.011 0.001 TRP E 320 HIS 0.003 0.001 HIS C 309 Details of bonding type rmsd covalent geometry : bond 0.00242 (16581) covalent geometry : angle 0.49966 (22653) SS BOND : bond 0.00047 ( 5) SS BOND : angle 0.15983 ( 10) hydrogen bonds : bond 0.04010 ( 708) hydrogen bonds : angle 4.93191 ( 2094) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 0.895 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 438 PHE cc_start: 0.8689 (t80) cc_final: 0.8358 (t80) REVERT: C 315 ARG cc_start: 0.8908 (mmm160) cc_final: 0.8673 (mmm-85) REVERT: D 319 ASP cc_start: 0.8858 (m-30) cc_final: 0.8561 (t0) REVERT: D 435 ARG cc_start: 0.8671 (tpp80) cc_final: 0.7838 (tmm-80) REVERT: B 235 MET cc_start: 0.8961 (mtt) cc_final: 0.8587 (mtt) REVERT: E 331 TRP cc_start: 0.7828 (m100) cc_final: 0.7407 (m100) REVERT: E 442 LEU cc_start: 0.9178 (tt) cc_final: 0.8900 (mm) outliers start: 16 outliers final: 11 residues processed: 98 average time/residue: 1.2608 time to fit residues: 138.2356 Evaluate side-chains 87 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain C residue 309 HIS Chi-restraints excluded: chain C residue 434 ASP Chi-restraints excluded: chain D residue 431 TYR Chi-restraints excluded: chain D residue 439 ARG Chi-restraints excluded: chain B residue 323 HIS Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain E residue 141 ASN Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 406 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 22 optimal weight: 4.9990 chunk 125 optimal weight: 0.9980 chunk 175 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 67 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 chunk 64 optimal weight: 0.2980 chunk 2 optimal weight: 0.9990 chunk 186 optimal weight: 9.9990 chunk 34 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.048105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.037081 restraints weight = 233359.861| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 3.17 r_work: 0.2769 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8958 moved from start: 0.3297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 16586 Z= 0.102 Angle : 0.485 6.373 22663 Z= 0.251 Chirality : 0.041 0.149 2616 Planarity : 0.004 0.043 2776 Dihedral : 4.561 23.471 2146 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.88 % Allowed : 9.09 % Favored : 90.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.20), residues: 1920 helix: 0.83 (0.19), residues: 771 sheet: -2.21 (0.22), residues: 425 loop : -1.47 (0.25), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 328 TYR 0.012 0.001 TYR A 67 PHE 0.029 0.001 PHE B 438 TRP 0.012 0.001 TRP E 320 HIS 0.003 0.000 HIS C 309 Details of bonding type rmsd covalent geometry : bond 0.00225 (16581) covalent geometry : angle 0.48500 (22653) SS BOND : bond 0.00036 ( 5) SS BOND : angle 0.15654 ( 10) hydrogen bonds : bond 0.03682 ( 708) hydrogen bonds : angle 4.73886 ( 2094) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 0.892 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 438 PHE cc_start: 0.8697 (t80) cc_final: 0.8371 (t80) REVERT: C 315 ARG cc_start: 0.8938 (mmm160) cc_final: 0.8717 (mmm-85) REVERT: D 319 ASP cc_start: 0.8814 (m-30) cc_final: 0.8570 (t0) REVERT: D 435 ARG cc_start: 0.8661 (tpp80) cc_final: 0.7875 (tmm-80) REVERT: B 235 MET cc_start: 0.8970 (mtt) cc_final: 0.8595 (mtt) REVERT: E 331 TRP cc_start: 0.7734 (m100) cc_final: 0.7342 (m100) REVERT: E 442 LEU cc_start: 0.9220 (tt) cc_final: 0.8959 (mm) outliers start: 16 outliers final: 12 residues processed: 100 average time/residue: 1.5312 time to fit residues: 169.9661 Evaluate side-chains 91 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain C residue 309 HIS Chi-restraints excluded: chain D residue 291 MET Chi-restraints excluded: chain D residue 431 TYR Chi-restraints excluded: chain D residue 439 ARG Chi-restraints excluded: chain B residue 323 HIS Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain E residue 141 ASN Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 406 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 3 optimal weight: 6.9990 chunk 159 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 135 optimal weight: 6.9990 chunk 145 optimal weight: 9.9990 chunk 74 optimal weight: 5.9990 chunk 92 optimal weight: 0.9990 chunk 120 optimal weight: 4.9990 chunk 164 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 GLN B 147 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.046753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.035732 restraints weight = 236730.996| |-----------------------------------------------------------------------------| r_work (start): 0.2830 rms_B_bonded: 3.14 r_work: 0.2725 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9001 moved from start: 0.3591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16586 Z= 0.199 Angle : 0.533 6.809 22663 Z= 0.281 Chirality : 0.042 0.141 2616 Planarity : 0.005 0.091 2776 Dihedral : 4.710 29.165 2146 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.16 % Allowed : 9.14 % Favored : 89.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.20), residues: 1920 helix: 0.94 (0.18), residues: 794 sheet: -2.08 (0.22), residues: 416 loop : -1.47 (0.25), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG C 328 TYR 0.011 0.001 TYR A 67 PHE 0.022 0.001 PHE B 438 TRP 0.013 0.001 TRP E 320 HIS 0.004 0.001 HIS C 309 Details of bonding type rmsd covalent geometry : bond 0.00431 (16581) covalent geometry : angle 0.53356 (22653) SS BOND : bond 0.00101 ( 5) SS BOND : angle 0.20872 ( 10) hydrogen bonds : bond 0.03783 ( 708) hydrogen bonds : angle 4.81102 ( 2094) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 85 time to evaluate : 0.905 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: symmetry clash 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: symmetry clash revert: symmetry clash REVERT: A 415 LYS cc_start: 0.8922 (mmtt) cc_final: 0.8692 (ptmt) REVERT: C 244 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8131 (mm) REVERT: C 315 ARG cc_start: 0.9010 (mmm160) cc_final: 0.8731 (mmm-85) REVERT: D 319 ASP cc_start: 0.8881 (m-30) cc_final: 0.8634 (t0) REVERT: D 435 ARG cc_start: 0.8683 (tpp80) cc_final: 0.7848 (tmm-80) REVERT: B 235 MET cc_start: 0.8998 (mtt) cc_final: 0.8607 (mtt) REVERT: E 331 TRP cc_start: 0.7805 (m100) cc_final: 0.7429 (m100) outliers start: 21 outliers final: 14 residues processed: 98 average time/residue: 1.4703 time to fit residues: 160.2794 Evaluate side-chains 91 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 309 HIS Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain D residue 291 MET Chi-restraints excluded: chain D residue 431 TYR Chi-restraints excluded: chain B residue 323 HIS Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain E residue 141 ASN Chi-restraints excluded: chain E residue 243 CYS Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 406 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 132 optimal weight: 4.9990 chunk 151 optimal weight: 5.9990 chunk 148 optimal weight: 10.0000 chunk 134 optimal weight: 0.5980 chunk 137 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 163 optimal weight: 0.8980 chunk 179 optimal weight: 4.9990 chunk 188 optimal weight: 3.9990 chunk 90 optimal weight: 6.9990 chunk 98 optimal weight: 0.0020 overall best weight: 1.8992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.047188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.036036 restraints weight = 237532.363| |-----------------------------------------------------------------------------| r_work (start): 0.2843 rms_B_bonded: 3.15 r_work: 0.2738 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8991 moved from start: 0.3725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16586 Z= 0.130 Angle : 0.496 6.941 22663 Z= 0.257 Chirality : 0.041 0.146 2616 Planarity : 0.004 0.087 2776 Dihedral : 4.573 25.582 2146 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.83 % Allowed : 9.64 % Favored : 89.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.20), residues: 1920 helix: 1.21 (0.18), residues: 794 sheet: -2.01 (0.23), residues: 416 loop : -1.40 (0.25), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG C 328 TYR 0.011 0.001 TYR A 67 PHE 0.026 0.001 PHE B 438 TRP 0.014 0.001 TRP E 320 HIS 0.003 0.001 HIS C 309 Details of bonding type rmsd covalent geometry : bond 0.00286 (16581) covalent geometry : angle 0.49574 (22653) SS BOND : bond 0.00021 ( 5) SS BOND : angle 0.15734 ( 10) hydrogen bonds : bond 0.03484 ( 708) hydrogen bonds : angle 4.62726 ( 2094) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 84 time to evaluate : 0.917 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 319 ASP cc_start: 0.8874 (m-30) cc_final: 0.8612 (t0) REVERT: D 435 ARG cc_start: 0.8685 (tpp80) cc_final: 0.7849 (tmm-80) REVERT: B 235 MET cc_start: 0.8961 (mtt) cc_final: 0.8571 (mtt) REVERT: E 331 TRP cc_start: 0.7742 (m100) cc_final: 0.7364 (m100) outliers start: 15 outliers final: 10 residues processed: 95 average time/residue: 1.3576 time to fit residues: 145.1615 Evaluate side-chains 87 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 77 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain C residue 309 HIS Chi-restraints excluded: chain D residue 431 TYR Chi-restraints excluded: chain B residue 323 HIS Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain E residue 141 ASN Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 406 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 151 optimal weight: 6.9990 chunk 166 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 chunk 32 optimal weight: 7.9990 chunk 135 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.046368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.035409 restraints weight = 237209.323| |-----------------------------------------------------------------------------| r_work (start): 0.2819 rms_B_bonded: 3.13 r_work: 0.2715 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9006 moved from start: 0.3887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16586 Z= 0.198 Angle : 0.533 7.525 22663 Z= 0.278 Chirality : 0.042 0.140 2616 Planarity : 0.005 0.107 2776 Dihedral : 4.680 29.039 2146 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 1.16 % Allowed : 9.58 % Favored : 89.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.20), residues: 1920 helix: 1.30 (0.18), residues: 794 sheet: -1.94 (0.23), residues: 416 loop : -1.43 (0.25), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG C 328 TYR 0.010 0.001 TYR A 67 PHE 0.024 0.001 PHE B 438 TRP 0.014 0.001 TRP E 320 HIS 0.004 0.001 HIS C 309 Details of bonding type rmsd covalent geometry : bond 0.00432 (16581) covalent geometry : angle 0.53305 (22653) SS BOND : bond 0.00111 ( 5) SS BOND : angle 0.21929 ( 10) hydrogen bonds : bond 0.03612 ( 708) hydrogen bonds : angle 4.70673 ( 2094) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 77 time to evaluate : 0.998 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: symmetry clash 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: symmetry clash revert: symmetry clash REVERT: D 319 ASP cc_start: 0.8865 (m-30) cc_final: 0.8601 (t0) REVERT: D 438 PHE cc_start: 0.8662 (t80) cc_final: 0.8403 (t80) REVERT: D 462 SER cc_start: 0.9272 (m) cc_final: 0.9047 (p) REVERT: B 235 MET cc_start: 0.8995 (mtt) cc_final: 0.8607 (mtt) REVERT: E 331 TRP cc_start: 0.7823 (m100) cc_final: 0.7434 (m100) outliers start: 21 outliers final: 13 residues processed: 90 average time/residue: 1.2643 time to fit residues: 129.2085 Evaluate side-chains 87 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 309 HIS Chi-restraints excluded: chain C residue 434 ASP Chi-restraints excluded: chain D residue 431 TYR Chi-restraints excluded: chain B residue 323 HIS Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain E residue 141 ASN Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 406 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 113 optimal weight: 3.9990 chunk 126 optimal weight: 5.9990 chunk 136 optimal weight: 4.9990 chunk 160 optimal weight: 4.9990 chunk 92 optimal weight: 0.2980 chunk 82 optimal weight: 5.9990 chunk 103 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 153 optimal weight: 0.7980 chunk 18 optimal weight: 4.9990 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.047089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.036236 restraints weight = 233459.534| |-----------------------------------------------------------------------------| r_work (start): 0.2845 rms_B_bonded: 3.11 r_work: 0.2737 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8982 moved from start: 0.3994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 16586 Z= 0.112 Angle : 0.500 7.835 22663 Z= 0.257 Chirality : 0.042 0.148 2616 Planarity : 0.005 0.106 2776 Dihedral : 4.524 24.287 2146 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.72 % Allowed : 10.35 % Favored : 88.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.20), residues: 1920 helix: 1.48 (0.18), residues: 799 sheet: -1.85 (0.23), residues: 421 loop : -1.33 (0.26), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG C 328 TYR 0.016 0.001 TYR C 262 PHE 0.026 0.001 PHE B 438 TRP 0.015 0.001 TRP E 320 HIS 0.003 0.000 HIS C 309 Details of bonding type rmsd covalent geometry : bond 0.00250 (16581) covalent geometry : angle 0.49992 (22653) SS BOND : bond 0.00025 ( 5) SS BOND : angle 0.15095 ( 10) hydrogen bonds : bond 0.03323 ( 708) hydrogen bonds : angle 4.53838 ( 2094) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 0.930 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 319 ASP cc_start: 0.8871 (m-30) cc_final: 0.8605 (t0) REVERT: D 435 ARG cc_start: 0.8621 (tpp-160) cc_final: 0.7721 (tmm-80) REVERT: D 462 SER cc_start: 0.9260 (m) cc_final: 0.9053 (p) REVERT: B 235 MET cc_start: 0.8979 (mtt) cc_final: 0.8581 (mtt) REVERT: E 331 TRP cc_start: 0.7768 (m100) cc_final: 0.7372 (m100) outliers start: 13 outliers final: 11 residues processed: 97 average time/residue: 1.2634 time to fit residues: 138.7194 Evaluate side-chains 89 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain C residue 309 HIS Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain D residue 431 TYR Chi-restraints excluded: chain B residue 323 HIS Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain E residue 141 ASN Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 406 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 59 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 110 optimal weight: 0.9990 chunk 178 optimal weight: 4.9990 chunk 28 optimal weight: 7.9990 chunk 117 optimal weight: 0.4980 chunk 27 optimal weight: 0.9990 chunk 169 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 overall best weight: 1.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.047451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.036397 restraints weight = 235379.575| |-----------------------------------------------------------------------------| r_work (start): 0.2854 rms_B_bonded: 3.13 r_work: 0.2748 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8981 moved from start: 0.4111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 16586 Z= 0.101 Angle : 0.493 8.642 22663 Z= 0.251 Chirality : 0.041 0.145 2616 Planarity : 0.005 0.119 2776 Dihedral : 4.430 23.149 2146 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.72 % Allowed : 10.57 % Favored : 88.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.20), residues: 1920 helix: 1.60 (0.18), residues: 802 sheet: -1.81 (0.23), residues: 421 loop : -1.33 (0.26), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.000 ARG C 328 TYR 0.011 0.001 TYR C 262 PHE 0.025 0.001 PHE B 438 TRP 0.016 0.001 TRP E 320 HIS 0.003 0.001 HIS C 309 Details of bonding type rmsd covalent geometry : bond 0.00229 (16581) covalent geometry : angle 0.49359 (22653) SS BOND : bond 0.00026 ( 5) SS BOND : angle 0.16045 ( 10) hydrogen bonds : bond 0.03189 ( 708) hydrogen bonds : angle 4.43669 ( 2094) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.976 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 416 ARG cc_start: 0.8515 (ptm160) cc_final: 0.8286 (mpp80) REVERT: D 319 ASP cc_start: 0.8884 (m-30) cc_final: 0.8622 (t0) REVERT: D 435 ARG cc_start: 0.8667 (tpp-160) cc_final: 0.7726 (tmm-80) REVERT: B 235 MET cc_start: 0.8953 (mtt) cc_final: 0.8562 (mtt) REVERT: E 331 TRP cc_start: 0.7721 (m100) cc_final: 0.7307 (m100) outliers start: 13 outliers final: 11 residues processed: 91 average time/residue: 1.3878 time to fit residues: 142.5555 Evaluate side-chains 89 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain C residue 309 HIS Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain D residue 141 ASN Chi-restraints excluded: chain D residue 431 TYR Chi-restraints excluded: chain B residue 323 HIS Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain E residue 141 ASN Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 406 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 158 optimal weight: 4.9990 chunk 14 optimal weight: 6.9990 chunk 172 optimal weight: 4.9990 chunk 46 optimal weight: 0.6980 chunk 33 optimal weight: 10.0000 chunk 121 optimal weight: 3.9990 chunk 151 optimal weight: 5.9990 chunk 141 optimal weight: 5.9990 chunk 183 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.046264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.035170 restraints weight = 239584.528| |-----------------------------------------------------------------------------| r_work (start): 0.2813 rms_B_bonded: 3.12 r_work: 0.2709 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9017 moved from start: 0.4168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 16586 Z= 0.222 Angle : 0.541 9.345 22663 Z= 0.283 Chirality : 0.042 0.139 2616 Planarity : 0.005 0.088 2776 Dihedral : 4.632 29.174 2146 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.83 % Allowed : 10.52 % Favored : 88.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.20), residues: 1920 helix: 1.53 (0.18), residues: 805 sheet: -1.81 (0.23), residues: 423 loop : -1.36 (0.26), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG C 328 TYR 0.014 0.001 TYR C 262 PHE 0.023 0.001 PHE B 438 TRP 0.014 0.001 TRP E 320 HIS 0.006 0.001 HIS A 411 Details of bonding type rmsd covalent geometry : bond 0.00487 (16581) covalent geometry : angle 0.54098 (22653) SS BOND : bond 0.00117 ( 5) SS BOND : angle 0.23979 ( 10) hydrogen bonds : bond 0.03478 ( 708) hydrogen bonds : angle 4.64748 ( 2094) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7985.12 seconds wall clock time: 136 minutes 5.42 seconds (8165.42 seconds total)