Starting phenix.real_space_refine on Wed Mar 4 06:35:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ksw_0775/03_2026/6ksw_0775.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ksw_0775/03_2026/6ksw_0775.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6ksw_0775/03_2026/6ksw_0775.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ksw_0775/03_2026/6ksw_0775.map" model { file = "/net/cci-nas-00/data/ceres_data/6ksw_0775/03_2026/6ksw_0775.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ksw_0775/03_2026/6ksw_0775.cif" } resolution = 3.6 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= 0.001 sd= 0.009 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: 4 Type Number sf(0) Gaussians S 63 5.16 5 C 7740 2.51 5 N 1863 2.21 5 O 1995 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11661 Number of models: 1 Model: "" Number of chains: 1 Chain: "C" Number of atoms: 3887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 3887 Classifications: {'peptide': 513} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 18, 'TRANS': 494} Chain breaks: 1 Unresolved non-hydrogen bonds: 166 Unresolved non-hydrogen angles: 212 Unresolved non-hydrogen dihedrals: 155 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'TRP:plan': 4, 'PHE:plan': 1, 'TYR:plan': 1, 'GLU:plan': 3, 'ARG:plan': 3, 'ASP:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 97 Restraints were copied for chains: A, B Time building chain proxies: 2.79, per 1000 atoms: 0.24 Number of scatterers: 11661 At special positions: 0 Unit cell: (123.76, 125.84, 72.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 63 16.00 O 1995 8.00 N 1863 7.00 C 7740 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.73 Conformation dependent library (CDL) restraints added in 468.9 milliseconds 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2850 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 0 sheets defined 82.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'C' and resid 102 through 124 removed outlier: 4.229A pdb=" N ILE C 106 " --> pdb=" O LEU C 102 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA C 121 " --> pdb=" O MET C 117 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL C 123 " --> pdb=" O ILE C 119 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU C 124 " --> pdb=" O SER C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 152 removed outlier: 3.590A pdb=" N VAL C 143 " --> pdb=" O ALA C 139 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N MET C 149 " --> pdb=" O TRP C 145 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA C 150 " --> pdb=" O ASP C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 159 removed outlier: 3.618A pdb=" N ASP C 157 " --> pdb=" O GLU C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 190 removed outlier: 3.766A pdb=" N LEU C 166 " --> pdb=" O PRO C 162 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N PHE C 172 " --> pdb=" O ASN C 168 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N TRP C 173 " --> pdb=" O SER C 169 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N TRP C 176 " --> pdb=" O PHE C 172 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N TRP C 179 " --> pdb=" O LYS C 175 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N SER C 180 " --> pdb=" O TRP C 176 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU C 182 " --> pdb=" O ILE C 178 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N VAL C 183 " --> pdb=" O TRP C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 198 Processing helix chain 'C' and resid 200 through 217 removed outlier: 3.501A pdb=" N MET C 210 " --> pdb=" O GLY C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 245 removed outlier: 4.427A pdb=" N VAL C 230 " --> pdb=" O TYR C 226 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TRP C 232 " --> pdb=" O ARG C 228 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ILE C 234 " --> pdb=" O VAL C 230 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN C 237 " --> pdb=" O GLY C 233 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU C 243 " --> pdb=" O LEU C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 268 removed outlier: 3.614A pdb=" N VAL C 261 " --> pdb=" O LEU C 257 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE C 264 " --> pdb=" O GLN C 260 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU C 266 " --> pdb=" O GLN C 262 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR C 268 " --> pdb=" O PHE C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 276 Processing helix chain 'C' and resid 277 through 282 removed outlier: 4.495A pdb=" N LYS C 281 " --> pdb=" O GLU C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 288 Processing helix chain 'C' and resid 288 through 306 removed outlier: 3.597A pdb=" N SER C 301 " --> pdb=" O SER C 297 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N MET C 302 " --> pdb=" O THR C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 325 removed outlier: 3.565A pdb=" N ILE C 313 " --> pdb=" O MET C 309 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR C 323 " --> pdb=" O ILE C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 337 Processing helix chain 'C' and resid 352 through 356 removed outlier: 3.745A pdb=" N ILE C 356 " --> pdb=" O LEU C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 371 removed outlier: 3.565A pdb=" N THR C 371 " --> pdb=" O ALA C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 384 removed outlier: 3.851A pdb=" N GLY C 384 " --> pdb=" O TYR C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 409 removed outlier: 3.932A pdb=" N ALA C 398 " --> pdb=" O SER C 394 " (cutoff:3.500A) Proline residue: C 399 - end of helix removed outlier: 4.168A pdb=" N LEU C 407 " --> pdb=" O ALA C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 443 removed outlier: 3.536A pdb=" N ALA C 436 " --> pdb=" O ASN C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 444 through 474 removed outlier: 3.728A pdb=" N LEU C 459 " --> pdb=" O LEU C 455 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER C 470 " --> pdb=" O ASN C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 477 No H-bonds generated for 'chain 'C' and resid 475 through 477' Processing helix chain 'C' and resid 482 through 491 Processing helix chain 'C' and resid 491 through 498 Processing helix chain 'C' and resid 501 through 518 removed outlier: 4.146A pdb=" N PHE C 506 " --> pdb=" O TRP C 502 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N MET C 507 " --> pdb=" O GLN C 503 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ARG C 510 " --> pdb=" O PHE C 506 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LEU C 511 " --> pdb=" O MET C 507 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 536 removed outlier: 3.849A pdb=" N ALA C 523 " --> pdb=" O ASN C 519 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N TRP C 530 " --> pdb=" O HIS C 526 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 560 Processing helix chain 'C' and resid 568 through 579 removed outlier: 4.034A pdb=" N ILE C 572 " --> pdb=" O GLY C 568 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 583 No H-bonds generated for 'chain 'C' and resid 581 through 583' Processing helix chain 'C' and resid 584 through 613 removed outlier: 4.654A pdb=" N VAL C 593 " --> pdb=" O ALA C 589 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ARG C 594 " --> pdb=" O SER C 590 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ILE C 597 " --> pdb=" O VAL C 593 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR C 606 " --> pdb=" O ALA C 602 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE C 609 " --> pdb=" O MET C 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 124 removed outlier: 4.230A pdb=" N ILE A 106 " --> pdb=" O LEU A 102 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA A 121 " --> pdb=" O MET A 117 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL A 123 " --> pdb=" O ILE A 119 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU A 124 " --> pdb=" O SER A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 152 removed outlier: 3.589A pdb=" N VAL A 143 " --> pdb=" O ALA A 139 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N MET A 149 " --> pdb=" O TRP A 145 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA A 150 " --> pdb=" O ASP A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 159 removed outlier: 3.618A pdb=" N ASP A 157 " --> pdb=" O GLU A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 190 removed outlier: 3.765A pdb=" N LEU A 166 " --> pdb=" O PRO A 162 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N PHE A 172 " --> pdb=" O ASN A 168 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N TRP A 173 " --> pdb=" O SER A 169 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N TRP A 176 " --> pdb=" O PHE A 172 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N TRP A 179 " --> pdb=" O LYS A 175 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N SER A 180 " --> pdb=" O TRP A 176 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU A 182 " --> pdb=" O ILE A 178 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N VAL A 183 " --> pdb=" O TRP A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 198 Processing helix chain 'A' and resid 200 through 217 removed outlier: 3.501A pdb=" N MET A 210 " --> pdb=" O GLY A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 245 removed outlier: 4.428A pdb=" N VAL A 230 " --> pdb=" O TYR A 226 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TRP A 232 " --> pdb=" O ARG A 228 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ILE A 234 " --> pdb=" O VAL A 230 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN A 237 " --> pdb=" O GLY A 233 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU A 243 " --> pdb=" O LEU A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 268 removed outlier: 3.615A pdb=" N VAL A 261 " --> pdb=" O LEU A 257 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE A 264 " --> pdb=" O GLN A 260 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU A 266 " --> pdb=" O GLN A 262 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR A 268 " --> pdb=" O PHE A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 276 Processing helix chain 'A' and resid 277 through 282 removed outlier: 4.494A pdb=" N LYS A 281 " --> pdb=" O GLU A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 288 Processing helix chain 'A' and resid 288 through 306 removed outlier: 3.598A pdb=" N SER A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N MET A 302 " --> pdb=" O THR A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 325 removed outlier: 3.564A pdb=" N ILE A 313 " --> pdb=" O MET A 309 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR A 323 " --> pdb=" O ILE A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 337 Processing helix chain 'A' and resid 352 through 356 removed outlier: 3.745A pdb=" N ILE A 356 " --> pdb=" O LEU A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 371 removed outlier: 3.565A pdb=" N THR A 371 " --> pdb=" O ALA A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 384 removed outlier: 3.851A pdb=" N GLY A 384 " --> pdb=" O TYR A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 409 removed outlier: 3.934A pdb=" N ALA A 398 " --> pdb=" O SER A 394 " (cutoff:3.500A) Proline residue: A 399 - end of helix removed outlier: 4.168A pdb=" N LEU A 407 " --> pdb=" O ALA A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 443 removed outlier: 3.535A pdb=" N ALA A 436 " --> pdb=" O ASN A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 474 removed outlier: 3.728A pdb=" N LEU A 459 " --> pdb=" O LEU A 455 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N SER A 470 " --> pdb=" O ASN A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 477 No H-bonds generated for 'chain 'A' and resid 475 through 477' Processing helix chain 'A' and resid 482 through 491 Processing helix chain 'A' and resid 491 through 498 Processing helix chain 'A' and resid 501 through 518 removed outlier: 4.146A pdb=" N PHE A 506 " --> pdb=" O TRP A 502 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N MET A 507 " --> pdb=" O GLN A 503 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ARG A 510 " --> pdb=" O PHE A 506 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LEU A 511 " --> pdb=" O MET A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 536 removed outlier: 3.848A pdb=" N ALA A 523 " --> pdb=" O ASN A 519 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N TRP A 530 " --> pdb=" O HIS A 526 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ARG A 534 " --> pdb=" O TRP A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 560 Processing helix chain 'A' and resid 568 through 579 removed outlier: 4.034A pdb=" N ILE A 572 " --> pdb=" O GLY A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 583 No H-bonds generated for 'chain 'A' and resid 581 through 583' Processing helix chain 'A' and resid 584 through 613 removed outlier: 4.654A pdb=" N VAL A 593 " --> pdb=" O ALA A 589 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N ARG A 594 " --> pdb=" O SER A 590 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ILE A 597 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR A 606 " --> pdb=" O ALA A 602 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE A 609 " --> pdb=" O MET A 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 124 removed outlier: 4.230A pdb=" N ILE B 106 " --> pdb=" O LEU B 102 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA B 121 " --> pdb=" O MET B 117 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL B 123 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU B 124 " --> pdb=" O SER B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 152 removed outlier: 3.589A pdb=" N VAL B 143 " --> pdb=" O ALA B 139 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N MET B 149 " --> pdb=" O TRP B 145 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA B 150 " --> pdb=" O ASP B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 159 removed outlier: 3.618A pdb=" N ASP B 157 " --> pdb=" O GLU B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 190 removed outlier: 3.767A pdb=" N LEU B 166 " --> pdb=" O PRO B 162 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N PHE B 172 " --> pdb=" O ASN B 168 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N TRP B 173 " --> pdb=" O SER B 169 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N TRP B 176 " --> pdb=" O PHE B 172 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N TRP B 179 " --> pdb=" O LYS B 175 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N SER B 180 " --> pdb=" O TRP B 176 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU B 182 " --> pdb=" O ILE B 178 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N VAL B 183 " --> pdb=" O TRP B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 198 Processing helix chain 'B' and resid 200 through 217 removed outlier: 3.501A pdb=" N MET B 210 " --> pdb=" O GLY B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 245 removed outlier: 4.427A pdb=" N VAL B 230 " --> pdb=" O TYR B 226 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TRP B 232 " --> pdb=" O ARG B 228 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ILE B 234 " --> pdb=" O VAL B 230 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLN B 237 " --> pdb=" O GLY B 233 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU B 243 " --> pdb=" O LEU B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 268 removed outlier: 3.614A pdb=" N VAL B 261 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE B 264 " --> pdb=" O GLN B 260 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU B 266 " --> pdb=" O GLN B 262 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR B 268 " --> pdb=" O PHE B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 276 Processing helix chain 'B' and resid 277 through 282 removed outlier: 4.495A pdb=" N LYS B 281 " --> pdb=" O GLU B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 288 Processing helix chain 'B' and resid 288 through 306 removed outlier: 3.597A pdb=" N SER B 301 " --> pdb=" O SER B 297 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N MET B 302 " --> pdb=" O THR B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 325 removed outlier: 3.564A pdb=" N ILE B 313 " --> pdb=" O MET B 309 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR B 323 " --> pdb=" O ILE B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 337 Processing helix chain 'B' and resid 352 through 356 removed outlier: 3.744A pdb=" N ILE B 356 " --> pdb=" O LEU B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 371 removed outlier: 3.565A pdb=" N THR B 371 " --> pdb=" O ALA B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 384 removed outlier: 3.850A pdb=" N GLY B 384 " --> pdb=" O TYR B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 409 removed outlier: 3.933A pdb=" N ALA B 398 " --> pdb=" O SER B 394 " (cutoff:3.500A) Proline residue: B 399 - end of helix removed outlier: 4.168A pdb=" N LEU B 407 " --> pdb=" O ALA B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 443 removed outlier: 3.534A pdb=" N ALA B 436 " --> pdb=" O ASN B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 474 removed outlier: 3.728A pdb=" N LEU B 459 " --> pdb=" O LEU B 455 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N SER B 470 " --> pdb=" O ASN B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 477 No H-bonds generated for 'chain 'B' and resid 475 through 477' Processing helix chain 'B' and resid 482 through 491 Processing helix chain 'B' and resid 491 through 498 Processing helix chain 'B' and resid 501 through 518 removed outlier: 4.145A pdb=" N PHE B 506 " --> pdb=" O TRP B 502 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N MET B 507 " --> pdb=" O GLN B 503 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ARG B 510 " --> pdb=" O PHE B 506 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LEU B 511 " --> pdb=" O MET B 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 536 removed outlier: 3.849A pdb=" N ALA B 523 " --> pdb=" O ASN B 519 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N TRP B 530 " --> pdb=" O HIS B 526 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ARG B 534 " --> pdb=" O TRP B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 560 Processing helix chain 'B' and resid 568 through 579 removed outlier: 4.033A pdb=" N ILE B 572 " --> pdb=" O GLY B 568 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 583 No H-bonds generated for 'chain 'B' and resid 581 through 583' Processing helix chain 'B' and resid 584 through 613 removed outlier: 4.654A pdb=" N VAL B 593 " --> pdb=" O ALA B 589 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ARG B 594 " --> pdb=" O SER B 590 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ILE B 597 " --> pdb=" O VAL B 593 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR B 606 " --> pdb=" O ALA B 602 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE B 609 " --> pdb=" O MET B 605 " (cutoff:3.500A) 772 hydrogen bonds defined for protein. 2289 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.80 Time building geometry restraints manager: 1.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2628 1.33 - 1.45: 2763 1.45 - 1.57: 6471 1.57 - 1.69: 0 1.69 - 1.81: 114 Bond restraints: 11976 Sorted by residual: bond pdb=" CG LEU A 265 " pdb=" CD1 LEU A 265 " ideal model delta sigma weight residual 1.521 1.450 0.071 3.30e-02 9.18e+02 4.66e+00 bond pdb=" CG LEU C 265 " pdb=" CD1 LEU C 265 " ideal model delta sigma weight residual 1.521 1.450 0.071 3.30e-02 9.18e+02 4.58e+00 bond pdb=" CG LEU B 265 " pdb=" CD1 LEU B 265 " ideal model delta sigma weight residual 1.521 1.451 0.070 3.30e-02 9.18e+02 4.47e+00 bond pdb=" CG LEU A 455 " pdb=" CD2 LEU A 455 " ideal model delta sigma weight residual 1.521 1.469 0.052 3.30e-02 9.18e+02 2.44e+00 bond pdb=" CG LEU C 455 " pdb=" CD2 LEU C 455 " ideal model delta sigma weight residual 1.521 1.470 0.051 3.30e-02 9.18e+02 2.36e+00 ... (remaining 11971 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 15019 1.77 - 3.54: 1040 3.54 - 5.31: 174 5.31 - 7.08: 42 7.08 - 8.85: 39 Bond angle restraints: 16314 Sorted by residual: angle pdb=" C PRO C 479 " pdb=" N GLN C 480 " pdb=" CA GLN C 480 " ideal model delta sigma weight residual 125.66 134.07 -8.41 1.85e+00 2.92e-01 2.07e+01 angle pdb=" C PRO B 479 " pdb=" N GLN B 480 " pdb=" CA GLN B 480 " ideal model delta sigma weight residual 125.66 134.04 -8.38 1.85e+00 2.92e-01 2.05e+01 angle pdb=" C PRO A 479 " pdb=" N GLN A 480 " pdb=" CA GLN A 480 " ideal model delta sigma weight residual 125.66 134.04 -8.38 1.85e+00 2.92e-01 2.05e+01 angle pdb=" N SER B 161 " pdb=" CA SER B 161 " pdb=" C SER B 161 " ideal model delta sigma weight residual 109.81 118.20 -8.39 2.21e+00 2.05e-01 1.44e+01 angle pdb=" N SER A 161 " pdb=" CA SER A 161 " pdb=" C SER A 161 " ideal model delta sigma weight residual 109.81 118.15 -8.34 2.21e+00 2.05e-01 1.42e+01 ... (remaining 16309 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.96: 6352 14.96 - 29.91: 371 29.91 - 44.87: 120 44.87 - 59.82: 6 59.82 - 74.78: 6 Dihedral angle restraints: 6855 sinusoidal: 2421 harmonic: 4434 Sorted by residual: dihedral pdb=" CA HIS C 283 " pdb=" C HIS C 283 " pdb=" N PHE C 284 " pdb=" CA PHE C 284 " ideal model delta harmonic sigma weight residual 180.00 -156.30 -23.70 0 5.00e+00 4.00e-02 2.25e+01 dihedral pdb=" CA HIS B 283 " pdb=" C HIS B 283 " pdb=" N PHE B 284 " pdb=" CA PHE B 284 " ideal model delta harmonic sigma weight residual -180.00 -156.39 -23.61 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CA HIS A 283 " pdb=" C HIS A 283 " pdb=" N PHE A 284 " pdb=" CA PHE A 284 " ideal model delta harmonic sigma weight residual -180.00 -156.42 -23.58 0 5.00e+00 4.00e-02 2.22e+01 ... (remaining 6852 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1090 0.042 - 0.085: 604 0.085 - 0.127: 147 0.127 - 0.170: 49 0.170 - 0.212: 15 Chirality restraints: 1905 Sorted by residual: chirality pdb=" CA ARG C 350 " pdb=" N ARG C 350 " pdb=" C ARG C 350 " pdb=" CB ARG C 350 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA ARG A 350 " pdb=" N ARG A 350 " pdb=" C ARG A 350 " pdb=" CB ARG A 350 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA ARG B 350 " pdb=" N ARG B 350 " pdb=" C ARG B 350 " pdb=" CB ARG B 350 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 1902 not shown) Planarity restraints: 1995 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 290 " 0.050 5.00e-02 4.00e+02 7.46e-02 8.91e+00 pdb=" N PRO B 291 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO B 291 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 291 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 290 " -0.050 5.00e-02 4.00e+02 7.43e-02 8.83e+00 pdb=" N PRO A 291 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO A 291 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 291 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 290 " -0.050 5.00e-02 4.00e+02 7.42e-02 8.80e+00 pdb=" N PRO C 291 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO C 291 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO C 291 " -0.042 5.00e-02 4.00e+02 ... (remaining 1992 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 3224 2.78 - 3.31: 11263 3.31 - 3.84: 20191 3.84 - 4.37: 24356 4.37 - 4.90: 40130 Nonbonded interactions: 99164 Sorted by model distance: nonbonded pdb=" O LEU C 243 " pdb=" OG1 THR C 247 " model vdw 2.245 3.040 nonbonded pdb=" O LEU B 243 " pdb=" OG1 THR B 247 " model vdw 2.245 3.040 nonbonded pdb=" O LEU A 243 " pdb=" OG1 THR A 247 " model vdw 2.245 3.040 nonbonded pdb=" OH TYR A 380 " pdb=" OE2 GLU A 520 " model vdw 2.329 3.040 nonbonded pdb=" OH TYR B 380 " pdb=" OE2 GLU B 520 " model vdw 2.329 3.040 ... (remaining 99159 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: 0.03 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 11.160 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 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 0.071 11976 Z= 0.342 Angle : 1.083 8.854 16314 Z= 0.589 Chirality : 0.056 0.212 1905 Planarity : 0.008 0.075 1995 Dihedral : 11.373 74.778 4005 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 0.25 % Allowed : 4.83 % Favored : 94.91 % 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: -5.90 (0.13), residues: 1527 helix: -3.95 (0.08), residues: 1113 sheet: None (None), residues: 0 loop : -2.98 (0.27), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 510 TYR 0.029 0.004 TYR B 478 PHE 0.039 0.004 PHE B 383 TRP 0.029 0.004 TRP A 530 HIS 0.008 0.001 HIS A 389 Details of bonding type rmsd covalent geometry : bond 0.00834 (11976) covalent geometry : angle 1.08257 (16314) hydrogen bonds : bond 0.31650 ( 772) hydrogen bonds : angle 11.14282 ( 2289) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 540 time to evaluate : 0.393 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: C 103 ARG cc_start: 0.7463 (ttm-80) cc_final: 0.5701 (ptp90) REVERT: C 106 ILE cc_start: 0.8216 (mp) cc_final: 0.8013 (pt) REVERT: C 183 VAL cc_start: 0.9108 (t) cc_final: 0.8856 (p) REVERT: C 228 ARG cc_start: 0.8132 (tmm-80) cc_final: 0.7013 (mmm160) REVERT: C 280 TYR cc_start: 0.8608 (p90) cc_final: 0.8334 (p90) REVERT: C 337 ASN cc_start: 0.9011 (m-40) cc_final: 0.8651 (m-40) REVERT: C 370 SER cc_start: 0.8947 (m) cc_final: 0.8740 (p) REVERT: C 515 LYS cc_start: 0.8643 (tmmt) cc_final: 0.8202 (ttpp) REVERT: C 549 ILE cc_start: 0.8925 (mp) cc_final: 0.8662 (mt) REVERT: C 555 ILE cc_start: 0.8700 (mt) cc_final: 0.8390 (mm) REVERT: C 569 SER cc_start: 0.8624 (m) cc_final: 0.7891 (t) REVERT: C 600 THR cc_start: 0.8905 (m) cc_final: 0.8676 (p) REVERT: A 103 ARG cc_start: 0.7407 (ttm-80) cc_final: 0.5630 (ptp90) REVERT: A 183 VAL cc_start: 0.9083 (t) cc_final: 0.8849 (p) REVERT: A 211 TYR cc_start: 0.8259 (m-80) cc_final: 0.7796 (m-80) REVERT: A 228 ARG cc_start: 0.8075 (tmm-80) cc_final: 0.6940 (mtp180) REVERT: A 300 MET cc_start: 0.7736 (mmm) cc_final: 0.7499 (mmt) REVERT: A 337 ASN cc_start: 0.8999 (m-40) cc_final: 0.8752 (m-40) REVERT: A 390 LEU cc_start: 0.9328 (tt) cc_final: 0.9037 (tt) REVERT: A 549 ILE cc_start: 0.8849 (mp) cc_final: 0.8007 (mt) REVERT: A 555 ILE cc_start: 0.8819 (mt) cc_final: 0.8449 (mm) REVERT: B 103 ARG cc_start: 0.7085 (ttm-80) cc_final: 0.5310 (ptp90) REVERT: B 228 ARG cc_start: 0.8206 (tmm-80) cc_final: 0.6902 (mtp180) REVERT: B 476 PHE cc_start: 0.7687 (m-80) cc_final: 0.7461 (m-80) REVERT: B 500 VAL cc_start: 0.8569 (t) cc_final: 0.8274 (t) REVERT: B 600 THR cc_start: 0.8831 (m) cc_final: 0.8509 (p) outliers start: 3 outliers final: 0 residues processed: 540 average time/residue: 0.1079 time to fit residues: 81.7765 Evaluate side-chains 371 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 371 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.0980 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 4.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 547 GLN A 547 GLN B 104 HIS ** B 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 262 GLN B 547 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.137285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.116524 restraints weight = 18977.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.119427 restraints weight = 9718.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.121097 restraints weight = 6295.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.122320 restraints weight = 4882.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.122952 restraints weight = 4125.718| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.3592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11976 Z= 0.170 Angle : 0.709 7.717 16314 Z= 0.367 Chirality : 0.042 0.178 1905 Planarity : 0.006 0.052 1995 Dihedral : 5.448 22.480 1626 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.73 % Allowed : 15.27 % Favored : 81.00 % 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: -3.03 (0.18), residues: 1527 helix: -1.68 (0.13), residues: 1140 sheet: None (None), residues: 0 loop : -2.47 (0.29), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 350 TYR 0.019 0.002 TYR C 211 PHE 0.020 0.002 PHE A 251 TRP 0.017 0.002 TRP C 530 HIS 0.009 0.001 HIS A 532 Details of bonding type rmsd covalent geometry : bond 0.00382 (11976) covalent geometry : angle 0.70950 (16314) hydrogen bonds : bond 0.04304 ( 772) hydrogen bonds : angle 5.59895 ( 2289) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 418 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 211 TYR cc_start: 0.8162 (m-80) cc_final: 0.7540 (m-80) REVERT: C 370 SER cc_start: 0.8897 (m) cc_final: 0.8544 (p) REVERT: C 555 ILE cc_start: 0.8550 (mt) cc_final: 0.8337 (mm) REVERT: C 601 VAL cc_start: 0.9318 (t) cc_final: 0.9099 (m) REVERT: A 211 TYR cc_start: 0.8212 (m-80) cc_final: 0.7385 (m-80) REVERT: A 216 PHE cc_start: 0.8411 (t80) cc_final: 0.8170 (t80) REVERT: A 300 MET cc_start: 0.7909 (mmm) cc_final: 0.7658 (mmt) REVERT: A 302 MET cc_start: 0.8164 (mtp) cc_final: 0.7941 (mtm) REVERT: A 435 GLU cc_start: 0.7280 (tt0) cc_final: 0.7020 (tt0) REVERT: A 533 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8469 (tt) REVERT: A 549 ILE cc_start: 0.8827 (mp) cc_final: 0.8102 (mt) REVERT: A 555 ILE cc_start: 0.8780 (mt) cc_final: 0.8506 (mm) REVERT: B 220 LYS cc_start: 0.3952 (mttp) cc_final: 0.3686 (mmtm) REVERT: B 392 THR cc_start: 0.9056 (m) cc_final: 0.8728 (p) outliers start: 44 outliers final: 12 residues processed: 444 average time/residue: 0.0758 time to fit residues: 53.2637 Evaluate side-chains 359 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 346 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 490 ILE Chi-restraints excluded: chain C residue 512 ILE Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 587 ASP Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 390 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 135 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 68 optimal weight: 0.0970 chunk 152 optimal weight: 0.5980 chunk 104 optimal weight: 5.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 HIS C 127 HIS ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 466 ASN C 532 HIS A 532 HIS B 127 HIS B 532 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.138580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.117798 restraints weight = 19356.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.120702 restraints weight = 9808.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.122519 restraints weight = 6351.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.123516 restraints weight = 4865.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.124275 restraints weight = 4177.718| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.4355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11976 Z= 0.143 Angle : 0.662 7.594 16314 Z= 0.336 Chirality : 0.042 0.142 1905 Planarity : 0.005 0.047 1995 Dihedral : 4.921 22.506 1626 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.90 % Allowed : 19.17 % Favored : 76.93 % 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: -1.61 (0.20), residues: 1527 helix: -0.56 (0.14), residues: 1146 sheet: None (None), residues: 0 loop : -2.28 (0.29), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 552 TYR 0.015 0.001 TYR B 559 PHE 0.023 0.002 PHE C 188 TRP 0.015 0.001 TRP C 530 HIS 0.004 0.001 HIS B 526 Details of bonding type rmsd covalent geometry : bond 0.00325 (11976) covalent geometry : angle 0.66151 (16314) hydrogen bonds : bond 0.03837 ( 772) hydrogen bonds : angle 4.94097 ( 2289) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 386 time to evaluate : 0.365 Fit side-chains revert: symmetry clash REVERT: C 205 PHE cc_start: 0.8879 (t80) cc_final: 0.8650 (t80) REVERT: C 211 TYR cc_start: 0.8156 (m-80) cc_final: 0.7271 (m-80) REVERT: C 220 LYS cc_start: 0.4172 (mttm) cc_final: 0.3803 (mmtm) REVERT: C 243 LEU cc_start: 0.7709 (OUTLIER) cc_final: 0.7185 (mt) REVERT: C 549 ILE cc_start: 0.8754 (mt) cc_final: 0.8395 (mt) REVERT: C 555 ILE cc_start: 0.8507 (mt) cc_final: 0.8217 (mm) REVERT: A 210 MET cc_start: 0.8142 (tmm) cc_final: 0.7832 (tmm) REVERT: A 211 TYR cc_start: 0.8241 (m-80) cc_final: 0.7494 (m-80) REVERT: A 300 MET cc_start: 0.7981 (mmm) cc_final: 0.7736 (mmt) REVERT: A 435 GLU cc_start: 0.7295 (tt0) cc_final: 0.7010 (tt0) REVERT: A 502 TRP cc_start: 0.8262 (t-100) cc_final: 0.7683 (t60) REVERT: A 533 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8371 (tt) REVERT: A 555 ILE cc_start: 0.8763 (mt) cc_final: 0.8496 (mm) REVERT: B 220 LYS cc_start: 0.4032 (mttp) cc_final: 0.3479 (mmtm) REVERT: B 243 LEU cc_start: 0.7788 (OUTLIER) cc_final: 0.7531 (mt) REVERT: B 252 ILE cc_start: 0.8817 (tt) cc_final: 0.8405 (pt) REVERT: B 549 ILE cc_start: 0.8817 (mt) cc_final: 0.8094 (mt) outliers start: 46 outliers final: 17 residues processed: 414 average time/residue: 0.0769 time to fit residues: 50.3431 Evaluate side-chains 364 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 344 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 340 VAL Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 551 ILE Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 587 ASP Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 551 ILE Chi-restraints excluded: chain B residue 587 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 42 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 114 optimal weight: 0.9990 chunk 6 optimal weight: 8.9990 chunk 115 optimal weight: 0.7980 chunk 89 optimal weight: 5.9990 chunk 104 optimal weight: 0.7980 chunk 83 optimal weight: 0.0770 chunk 21 optimal weight: 0.0030 chunk 103 optimal weight: 5.9990 chunk 71 optimal weight: 0.9990 overall best weight: 0.4748 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 HIS C 127 HIS ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 532 HIS B 127 HIS B 200 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.140489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.120004 restraints weight = 19280.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.123007 restraints weight = 9793.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.124847 restraints weight = 6264.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.125855 restraints weight = 4753.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.126677 restraints weight = 4080.359| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.4828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11976 Z= 0.129 Angle : 0.638 7.403 16314 Z= 0.321 Chirality : 0.041 0.159 1905 Planarity : 0.004 0.047 1995 Dihedral : 4.711 20.165 1626 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 3.39 % Allowed : 22.14 % Favored : 74.47 % 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: -0.91 (0.21), residues: 1527 helix: -0.01 (0.15), residues: 1137 sheet: None (None), residues: 0 loop : -2.16 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 552 TYR 0.011 0.001 TYR B 548 PHE 0.034 0.002 PHE C 188 TRP 0.017 0.001 TRP B 318 HIS 0.006 0.001 HIS B 526 Details of bonding type rmsd covalent geometry : bond 0.00288 (11976) covalent geometry : angle 0.63845 (16314) hydrogen bonds : bond 0.03525 ( 772) hydrogen bonds : angle 4.72078 ( 2289) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 380 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 220 LYS cc_start: 0.3929 (mttm) cc_final: 0.3546 (mmtm) REVERT: C 228 ARG cc_start: 0.8034 (tmm-80) cc_final: 0.6699 (mmm160) REVERT: C 243 LEU cc_start: 0.7769 (OUTLIER) cc_final: 0.7183 (mt) REVERT: C 435 GLU cc_start: 0.7454 (tt0) cc_final: 0.7209 (pt0) REVERT: A 435 GLU cc_start: 0.7313 (tt0) cc_final: 0.7026 (tt0) REVERT: A 502 TRP cc_start: 0.8150 (t-100) cc_final: 0.7789 (t60) REVERT: A 533 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8431 (tt) REVERT: B 252 ILE cc_start: 0.8762 (tt) cc_final: 0.8374 (pt) REVERT: B 484 GLU cc_start: 0.8361 (mt-10) cc_final: 0.7953 (mt-10) REVERT: B 549 ILE cc_start: 0.8438 (mt) cc_final: 0.8110 (mt) outliers start: 40 outliers final: 22 residues processed: 404 average time/residue: 0.0755 time to fit residues: 48.0070 Evaluate side-chains 365 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 341 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 340 VAL Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain C residue 397 SER Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 551 ILE Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 587 ASP Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 397 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 101 optimal weight: 2.9990 chunk 43 optimal weight: 7.9990 chunk 127 optimal weight: 1.9990 chunk 63 optimal weight: 0.0670 chunk 102 optimal weight: 20.0000 chunk 81 optimal weight: 5.9990 chunk 96 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 31 optimal weight: 20.0000 chunk 123 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 overall best weight: 1.3524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 503 GLN A 389 HIS A 474 ASN B 127 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.135281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.114434 restraints weight = 19200.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.117302 restraints weight = 9832.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.119069 restraints weight = 6380.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.120214 restraints weight = 4894.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.120638 restraints weight = 4160.945| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.4986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11976 Z= 0.166 Angle : 0.668 10.485 16314 Z= 0.339 Chirality : 0.044 0.212 1905 Planarity : 0.005 0.055 1995 Dihedral : 4.755 21.959 1626 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 4.24 % Allowed : 22.05 % Favored : 73.71 % 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: -0.48 (0.22), residues: 1527 helix: 0.23 (0.15), residues: 1149 sheet: None (None), residues: 0 loop : -1.80 (0.34), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 103 TYR 0.014 0.001 TYR B 559 PHE 0.026 0.002 PHE A 188 TRP 0.015 0.001 TRP B 318 HIS 0.014 0.001 HIS C 104 Details of bonding type rmsd covalent geometry : bond 0.00389 (11976) covalent geometry : angle 0.66770 (16314) hydrogen bonds : bond 0.03559 ( 772) hydrogen bonds : angle 4.67977 ( 2289) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 353 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 104 HIS cc_start: 0.7213 (OUTLIER) cc_final: 0.6152 (p-80) REVERT: C 220 LYS cc_start: 0.4324 (mttm) cc_final: 0.3972 (mmtm) REVERT: C 240 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7786 (tt) REVERT: C 401 SER cc_start: 0.8818 (OUTLIER) cc_final: 0.8519 (p) REVERT: C 497 MET cc_start: 0.8070 (tpp) cc_final: 0.7732 (tpp) REVERT: C 549 ILE cc_start: 0.8556 (mt) cc_final: 0.7982 (mt) REVERT: A 205 PHE cc_start: 0.9056 (t80) cc_final: 0.8686 (t80) REVERT: A 211 TYR cc_start: 0.7905 (m-80) cc_final: 0.7529 (m-80) REVERT: A 254 PHE cc_start: 0.8813 (m-80) cc_final: 0.8485 (m-80) REVERT: A 435 GLU cc_start: 0.7321 (tt0) cc_final: 0.7064 (tt0) REVERT: A 475 MET cc_start: 0.7769 (mmp) cc_final: 0.7553 (mmm) REVERT: A 502 TRP cc_start: 0.8392 (t-100) cc_final: 0.7541 (t60) REVERT: A 533 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8487 (tt) REVERT: B 201 GLN cc_start: 0.8611 (OUTLIER) cc_final: 0.7269 (mp10) REVERT: B 210 MET cc_start: 0.8414 (OUTLIER) cc_final: 0.8162 (tmm) REVERT: B 252 ILE cc_start: 0.8765 (tt) cc_final: 0.8489 (pt) outliers start: 50 outliers final: 30 residues processed: 384 average time/residue: 0.0763 time to fit residues: 46.4960 Evaluate side-chains 357 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 321 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 340 VAL Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain C residue 397 SER Chi-restraints excluded: chain C residue 401 SER Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 551 ILE Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 586 ARG Chi-restraints excluded: chain A residue 587 ASP Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 201 GLN Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 397 SER Chi-restraints excluded: chain B residue 578 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 74 optimal weight: 0.9980 chunk 23 optimal weight: 5.9990 chunk 67 optimal weight: 0.6980 chunk 109 optimal weight: 8.9990 chunk 146 optimal weight: 0.8980 chunk 142 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 131 optimal weight: 0.9990 chunk 91 optimal weight: 0.7980 chunk 53 optimal weight: 8.9990 chunk 83 optimal weight: 9.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 HIS ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 127 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.138049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.117004 restraints weight = 19183.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.119916 restraints weight = 9880.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.121640 restraints weight = 6445.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.122703 restraints weight = 4994.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.123505 restraints weight = 4298.228| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.5237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11976 Z= 0.142 Angle : 0.648 6.739 16314 Z= 0.329 Chirality : 0.042 0.160 1905 Planarity : 0.004 0.054 1995 Dihedral : 4.637 23.155 1626 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 3.99 % Allowed : 23.32 % Favored : 72.69 % 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: -0.29 (0.22), residues: 1527 helix: 0.38 (0.15), residues: 1164 sheet: None (None), residues: 0 loop : -1.88 (0.33), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 552 TYR 0.012 0.001 TYR B 548 PHE 0.036 0.002 PHE A 188 TRP 0.014 0.001 TRP C 502 HIS 0.008 0.001 HIS A 526 Details of bonding type rmsd covalent geometry : bond 0.00330 (11976) covalent geometry : angle 0.64840 (16314) hydrogen bonds : bond 0.03392 ( 772) hydrogen bonds : angle 4.62466 ( 2289) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 365 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 104 HIS cc_start: 0.7234 (OUTLIER) cc_final: 0.5966 (p90) REVERT: C 201 GLN cc_start: 0.8342 (OUTLIER) cc_final: 0.7825 (mp10) REVERT: C 220 LYS cc_start: 0.4337 (mttm) cc_final: 0.3829 (mmtm) REVERT: C 240 LEU cc_start: 0.8120 (OUTLIER) cc_final: 0.7805 (tt) REVERT: C 390 LEU cc_start: 0.9410 (OUTLIER) cc_final: 0.9057 (tt) REVERT: C 439 GLN cc_start: 0.8030 (mm110) cc_final: 0.7818 (mm-40) REVERT: C 504 ASP cc_start: 0.8161 (t0) cc_final: 0.7723 (t0) REVERT: A 205 PHE cc_start: 0.9021 (t80) cc_final: 0.8596 (t80) REVERT: A 211 TYR cc_start: 0.7847 (m-80) cc_final: 0.7433 (m-80) REVERT: A 254 PHE cc_start: 0.8730 (m-80) cc_final: 0.8464 (m-80) REVERT: A 502 TRP cc_start: 0.8288 (t-100) cc_final: 0.7590 (t60) REVERT: A 533 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8394 (tt) REVERT: B 201 GLN cc_start: 0.8545 (OUTLIER) cc_final: 0.7254 (mp10) REVERT: B 252 ILE cc_start: 0.8770 (tt) cc_final: 0.8403 (pt) outliers start: 47 outliers final: 34 residues processed: 392 average time/residue: 0.0716 time to fit residues: 44.4838 Evaluate side-chains 365 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 325 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 201 GLN Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 340 VAL Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 397 SER Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 551 ILE Chi-restraints excluded: chain C residue 609 ILE Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 587 ASP Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 201 GLN Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 397 SER Chi-restraints excluded: chain B residue 554 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 24 optimal weight: 0.0010 chunk 151 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 128 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 26 optimal weight: 5.9990 chunk 131 optimal weight: 0.8980 chunk 2 optimal weight: 8.9990 overall best weight: 0.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 HIS ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 154 HIS B 127 HIS B 200 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.139881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.118728 restraints weight = 19153.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.121698 restraints weight = 9858.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.123516 restraints weight = 6411.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.124544 restraints weight = 4920.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.125234 restraints weight = 4241.976| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.5439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11976 Z= 0.140 Angle : 0.667 8.559 16314 Z= 0.337 Chirality : 0.043 0.180 1905 Planarity : 0.004 0.056 1995 Dihedral : 4.596 22.960 1626 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 4.58 % Allowed : 23.58 % Favored : 71.84 % 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: -0.14 (0.22), residues: 1527 helix: 0.49 (0.15), residues: 1164 sheet: None (None), residues: 0 loop : -1.80 (0.34), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 552 TYR 0.011 0.001 TYR B 548 PHE 0.031 0.001 PHE B 251 TRP 0.014 0.001 TRP C 530 HIS 0.011 0.001 HIS C 104 Details of bonding type rmsd covalent geometry : bond 0.00324 (11976) covalent geometry : angle 0.66650 (16314) hydrogen bonds : bond 0.03372 ( 772) hydrogen bonds : angle 4.63559 ( 2289) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 363 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 104 HIS cc_start: 0.7395 (OUTLIER) cc_final: 0.5983 (p90) REVERT: C 201 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.7900 (mp10) REVERT: C 211 TYR cc_start: 0.7700 (m-80) cc_final: 0.7389 (m-80) REVERT: C 220 LYS cc_start: 0.4307 (mttm) cc_final: 0.3758 (mmtm) REVERT: C 240 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7803 (tt) REVERT: C 252 ILE cc_start: 0.8760 (tt) cc_final: 0.8497 (pt) REVERT: C 390 LEU cc_start: 0.9435 (OUTLIER) cc_final: 0.9086 (tt) REVERT: C 392 THR cc_start: 0.9156 (m) cc_final: 0.8732 (p) REVERT: C 401 SER cc_start: 0.8735 (OUTLIER) cc_final: 0.8431 (p) REVERT: C 439 GLN cc_start: 0.8015 (mm110) cc_final: 0.7686 (mm-40) REVERT: A 135 ILE cc_start: 0.8913 (tp) cc_final: 0.8685 (tp) REVERT: A 182 LEU cc_start: 0.8686 (mm) cc_final: 0.8404 (pp) REVERT: A 205 PHE cc_start: 0.8950 (t80) cc_final: 0.8504 (t80) REVERT: A 211 TYR cc_start: 0.7905 (m-80) cc_final: 0.7453 (m-80) REVERT: A 220 LYS cc_start: 0.3538 (mttm) cc_final: 0.3243 (mmtt) REVERT: A 254 PHE cc_start: 0.8711 (m-80) cc_final: 0.8475 (m-80) REVERT: A 502 TRP cc_start: 0.8290 (t-100) cc_final: 0.7624 (t60) REVERT: A 533 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8505 (tt) REVERT: B 117 MET cc_start: 0.7275 (tpp) cc_final: 0.6925 (tpp) REVERT: B 201 GLN cc_start: 0.8464 (OUTLIER) cc_final: 0.7956 (mp10) REVERT: B 252 ILE cc_start: 0.8738 (tt) cc_final: 0.8367 (pt) REVERT: B 435 GLU cc_start: 0.7989 (tm-30) cc_final: 0.7619 (tt0) outliers start: 54 outliers final: 36 residues processed: 393 average time/residue: 0.0781 time to fit residues: 48.7771 Evaluate side-chains 371 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 328 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 201 GLN Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 340 VAL Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 397 SER Chi-restraints excluded: chain C residue 401 SER Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 551 ILE Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 609 ILE Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 587 ASP Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 200 GLN Chi-restraints excluded: chain B residue 201 GLN Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 397 SER Chi-restraints excluded: chain B residue 476 PHE Chi-restraints excluded: chain B residue 554 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 11 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 96 optimal weight: 0.7980 chunk 66 optimal weight: 0.0970 chunk 59 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 143 optimal weight: 0.7980 chunk 88 optimal weight: 0.0020 chunk 74 optimal weight: 0.9990 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 HIS ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 154 HIS ** A 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 127 HIS B 200 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.140362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.119706 restraints weight = 18977.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.122658 restraints weight = 9735.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.124486 restraints weight = 6300.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.125573 restraints weight = 4809.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.125966 restraints weight = 4110.370| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.5601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11976 Z= 0.135 Angle : 0.671 10.010 16314 Z= 0.339 Chirality : 0.043 0.264 1905 Planarity : 0.004 0.057 1995 Dihedral : 4.535 25.859 1626 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 4.50 % Allowed : 24.00 % Favored : 71.50 % 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: -0.07 (0.22), residues: 1527 helix: 0.61 (0.15), residues: 1143 sheet: None (None), residues: 0 loop : -1.89 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 552 TYR 0.010 0.001 TYR C 211 PHE 0.035 0.001 PHE A 188 TRP 0.012 0.001 TRP C 530 HIS 0.011 0.001 HIS C 104 Details of bonding type rmsd covalent geometry : bond 0.00309 (11976) covalent geometry : angle 0.67094 (16314) hydrogen bonds : bond 0.03352 ( 772) hydrogen bonds : angle 4.60899 ( 2289) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 346 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 104 HIS cc_start: 0.7448 (OUTLIER) cc_final: 0.6077 (p90) REVERT: C 201 GLN cc_start: 0.8328 (OUTLIER) cc_final: 0.7791 (mp10) REVERT: C 211 TYR cc_start: 0.7555 (m-80) cc_final: 0.7319 (m-80) REVERT: C 240 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7802 (tt) REVERT: C 252 ILE cc_start: 0.8674 (tt) cc_final: 0.8408 (pt) REVERT: C 392 THR cc_start: 0.9156 (m) cc_final: 0.8740 (p) REVERT: A 135 ILE cc_start: 0.8945 (tp) cc_final: 0.8706 (tp) REVERT: A 182 LEU cc_start: 0.8677 (mm) cc_final: 0.8451 (pp) REVERT: A 205 PHE cc_start: 0.8860 (t80) cc_final: 0.8358 (t80) REVERT: A 211 TYR cc_start: 0.7711 (m-80) cc_final: 0.7268 (m-80) REVERT: A 254 PHE cc_start: 0.8688 (m-80) cc_final: 0.8446 (m-80) REVERT: A 407 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8497 (tt) REVERT: A 475 MET cc_start: 0.7572 (mmp) cc_final: 0.7335 (mmm) REVERT: A 502 TRP cc_start: 0.8160 (t-100) cc_final: 0.7616 (t60) REVERT: A 533 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8380 (tp) REVERT: B 201 GLN cc_start: 0.8382 (OUTLIER) cc_final: 0.7863 (mp10) REVERT: B 252 ILE cc_start: 0.8703 (tt) cc_final: 0.8288 (pt) REVERT: B 435 GLU cc_start: 0.7984 (tm-30) cc_final: 0.7514 (tt0) outliers start: 53 outliers final: 31 residues processed: 378 average time/residue: 0.0699 time to fit residues: 42.9250 Evaluate side-chains 367 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 330 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 201 GLN Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 340 VAL Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain C residue 397 SER Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 609 ILE Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 587 ASP Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 201 GLN Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 397 SER Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 554 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 78 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 chunk 118 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 131 optimal weight: 0.9980 chunk 1 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 22 optimal weight: 0.0770 chunk 114 optimal weight: 0.0570 chunk 107 optimal weight: 9.9990 overall best weight: 0.8058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 127 HIS B 200 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.139505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.118797 restraints weight = 18907.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.121687 restraints weight = 9798.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.123511 restraints weight = 6375.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.124549 restraints weight = 4870.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.124999 restraints weight = 4167.875| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.5708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 11976 Z= 0.148 Angle : 0.689 10.665 16314 Z= 0.351 Chirality : 0.043 0.224 1905 Planarity : 0.004 0.059 1995 Dihedral : 4.564 30.576 1626 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 4.58 % Allowed : 24.94 % Favored : 70.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.04 (0.22), residues: 1527 helix: 0.64 (0.15), residues: 1137 sheet: None (None), residues: 0 loop : -1.91 (0.32), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 552 TYR 0.010 0.001 TYR B 548 PHE 0.020 0.001 PHE C 254 TRP 0.021 0.001 TRP A 502 HIS 0.009 0.001 HIS C 104 Details of bonding type rmsd covalent geometry : bond 0.00348 (11976) covalent geometry : angle 0.68933 (16314) hydrogen bonds : bond 0.03408 ( 772) hydrogen bonds : angle 4.62521 ( 2289) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 335 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 104 HIS cc_start: 0.7155 (OUTLIER) cc_final: 0.5769 (p-80) REVERT: C 201 GLN cc_start: 0.8242 (OUTLIER) cc_final: 0.7762 (mp10) REVERT: C 240 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7791 (tt) REVERT: C 252 ILE cc_start: 0.8714 (tt) cc_final: 0.8448 (pt) REVERT: C 392 THR cc_start: 0.9137 (m) cc_final: 0.8723 (p) REVERT: C 401 SER cc_start: 0.8779 (OUTLIER) cc_final: 0.8389 (p) REVERT: A 135 ILE cc_start: 0.8951 (tp) cc_final: 0.8707 (tp) REVERT: A 182 LEU cc_start: 0.8686 (mm) cc_final: 0.8453 (pp) REVERT: A 205 PHE cc_start: 0.8856 (t80) cc_final: 0.8390 (t80) REVERT: A 211 TYR cc_start: 0.7771 (m-80) cc_final: 0.7283 (m-80) REVERT: A 216 PHE cc_start: 0.7961 (t80) cc_final: 0.7696 (m-80) REVERT: A 254 PHE cc_start: 0.8697 (m-80) cc_final: 0.8428 (m-80) REVERT: A 390 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8948 (tt) REVERT: A 475 MET cc_start: 0.7392 (mmp) cc_final: 0.7064 (mmm) REVERT: A 502 TRP cc_start: 0.8155 (t-100) cc_final: 0.7381 (t60) REVERT: A 525 GLU cc_start: 0.8542 (pp20) cc_final: 0.8062 (pp20) REVERT: A 533 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8477 (tp) REVERT: B 200 GLN cc_start: 0.8920 (OUTLIER) cc_final: 0.8511 (mm-40) REVERT: B 201 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.7951 (mp10) REVERT: B 205 PHE cc_start: 0.8816 (t80) cc_final: 0.8547 (t80) REVERT: B 252 ILE cc_start: 0.8712 (tt) cc_final: 0.8333 (pt) REVERT: B 435 GLU cc_start: 0.8030 (tm-30) cc_final: 0.7526 (tt0) outliers start: 54 outliers final: 33 residues processed: 370 average time/residue: 0.0718 time to fit residues: 42.7648 Evaluate side-chains 363 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 322 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 201 GLN Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 340 VAL Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain C residue 397 SER Chi-restraints excluded: chain C residue 401 SER Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 609 ILE Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 586 ARG Chi-restraints excluded: chain A residue 587 ASP Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 200 GLN Chi-restraints excluded: chain B residue 201 GLN Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 397 SER Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 554 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 32 optimal weight: 10.0000 chunk 36 optimal weight: 0.6980 chunk 61 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 44 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 111 optimal weight: 5.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 HIS ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 127 HIS B 200 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.137477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.116237 restraints weight = 19214.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.119109 restraints weight = 9979.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.120923 restraints weight = 6529.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.121868 restraints weight = 5035.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.122648 restraints weight = 4366.234| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.5665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11976 Z= 0.180 Angle : 0.724 10.809 16314 Z= 0.369 Chirality : 0.045 0.223 1905 Planarity : 0.004 0.059 1995 Dihedral : 4.671 30.843 1626 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 3.82 % Allowed : 26.29 % Favored : 69.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.08 (0.22), residues: 1527 helix: 0.62 (0.15), residues: 1134 sheet: None (None), residues: 0 loop : -1.93 (0.33), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 350 TYR 0.011 0.001 TYR B 548 PHE 0.037 0.002 PHE A 188 TRP 0.016 0.001 TRP C 471 HIS 0.005 0.001 HIS A 526 Details of bonding type rmsd covalent geometry : bond 0.00431 (11976) covalent geometry : angle 0.72373 (16314) hydrogen bonds : bond 0.03525 ( 772) hydrogen bonds : angle 4.67265 ( 2289) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 329 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 104 HIS cc_start: 0.7324 (OUTLIER) cc_final: 0.5983 (p90) REVERT: C 201 GLN cc_start: 0.8370 (OUTLIER) cc_final: 0.8073 (mp10) REVERT: C 240 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7823 (tt) REVERT: C 252 ILE cc_start: 0.8713 (tt) cc_final: 0.8446 (pt) REVERT: C 392 THR cc_start: 0.9154 (m) cc_final: 0.8816 (p) REVERT: C 401 SER cc_start: 0.8911 (OUTLIER) cc_final: 0.8430 (p) REVERT: A 135 ILE cc_start: 0.8956 (tp) cc_final: 0.8716 (tp) REVERT: A 182 LEU cc_start: 0.8680 (mm) cc_final: 0.8450 (pp) REVERT: A 205 PHE cc_start: 0.8910 (t80) cc_final: 0.8384 (t80) REVERT: A 211 TYR cc_start: 0.7854 (m-80) cc_final: 0.7378 (m-80) REVERT: A 220 LYS cc_start: 0.3762 (mttm) cc_final: 0.3535 (mmtt) REVERT: A 254 PHE cc_start: 0.8705 (m-80) cc_final: 0.8468 (m-80) REVERT: A 390 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.9041 (tt) REVERT: A 411 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7621 (tp30) REVERT: A 475 MET cc_start: 0.7518 (mmp) cc_final: 0.7162 (mmm) REVERT: A 502 TRP cc_start: 0.8016 (t-100) cc_final: 0.7147 (t60) REVERT: A 533 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8468 (tt) REVERT: B 200 GLN cc_start: 0.8948 (OUTLIER) cc_final: 0.8616 (mm-40) REVERT: B 201 GLN cc_start: 0.8579 (OUTLIER) cc_final: 0.8128 (mp10) REVERT: B 205 PHE cc_start: 0.8832 (t80) cc_final: 0.8622 (t80) REVERT: B 252 ILE cc_start: 0.8738 (tt) cc_final: 0.8354 (pt) REVERT: B 484 GLU cc_start: 0.8373 (mt-10) cc_final: 0.7985 (mt-10) outliers start: 45 outliers final: 34 residues processed: 359 average time/residue: 0.0696 time to fit residues: 40.1248 Evaluate side-chains 360 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 318 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 201 GLN Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 340 VAL Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain C residue 397 SER Chi-restraints excluded: chain C residue 401 SER Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 609 ILE Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 586 ARG Chi-restraints excluded: chain A residue 587 ASP Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 200 GLN Chi-restraints excluded: chain B residue 201 GLN Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 397 SER Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 554 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 123 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 chunk 55 optimal weight: 0.4980 chunk 134 optimal weight: 9.9990 chunk 43 optimal weight: 7.9990 chunk 51 optimal weight: 20.0000 chunk 42 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 150 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 127 HIS B 200 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.139521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.118424 restraints weight = 19148.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.121323 restraints weight = 9968.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.123136 restraints weight = 6509.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.124156 restraints weight = 5015.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.124784 restraints weight = 4322.625| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.5779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 11976 Z= 0.150 Angle : 0.706 10.783 16314 Z= 0.359 Chirality : 0.044 0.218 1905 Planarity : 0.004 0.056 1995 Dihedral : 4.628 27.155 1626 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 4.16 % Allowed : 25.95 % Favored : 69.89 % 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: -0.02 (0.22), residues: 1527 helix: 0.68 (0.15), residues: 1134 sheet: None (None), residues: 0 loop : -1.94 (0.33), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 350 TYR 0.010 0.001 TYR B 548 PHE 0.026 0.001 PHE B 188 TRP 0.016 0.001 TRP C 530 HIS 0.010 0.001 HIS C 104 Details of bonding type rmsd covalent geometry : bond 0.00356 (11976) covalent geometry : angle 0.70586 (16314) hydrogen bonds : bond 0.03482 ( 772) hydrogen bonds : angle 4.66598 ( 2289) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1898.86 seconds wall clock time: 33 minutes 38.83 seconds (2018.83 seconds total)