Starting phenix.real_space_refine on Tue Jul 29 17:50:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ksw_0775/07_2025/6ksw_0775.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ksw_0775/07_2025/6ksw_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_0775/07_2025/6ksw_0775.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ksw_0775/07_2025/6ksw_0775.map" model { file = "/net/cci-nas-00/data/ceres_data/6ksw_0775/07_2025/6ksw_0775.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ksw_0775/07_2025/6ksw_0775.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 11661 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" 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: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 4, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 97 Restraints were copied for chains: C, B Time building chain proxies: 7.12, per 1000 atoms: 0.61 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: 2.72 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 1.08 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: 3.22 Time building geometry restraints manager: 3.23 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' 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: 0.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 27.450 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.510 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.029 0.004 TRP A 530 HIS 0.008 0.001 HIS A 389 PHE 0.039 0.004 PHE B 383 TYR 0.029 0.004 TYR B 478 ARG 0.006 0.001 ARG B 510 Details of bonding type rmsd hydrogen bonds : bond 0.31650 ( 772) hydrogen bonds : angle 11.14282 ( 2289) covalent geometry : bond 0.00834 (11976) covalent geometry : angle 1.08257 (16314) *********************** 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 : 1.287 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: C 103 ARG cc_start: 0.7463 (ttm-80) cc_final: 0.5699 (ptp90) REVERT: C 106 ILE cc_start: 0.8217 (mp) cc_final: 0.8014 (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: 0.7016 (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: 0.8742 (p) REVERT: C 515 LYS cc_start: 0.8643 (tmmt) cc_final: 0.8201 (ttpp) REVERT: C 549 ILE cc_start: 0.8925 (mp) cc_final: 0.8646 (mt) REVERT: C 555 ILE cc_start: 0.8700 (mt) cc_final: 0.8392 (mm) REVERT: C 569 SER cc_start: 0.8624 (m) cc_final: 0.7890 (t) REVERT: C 600 THR cc_start: 0.8905 (m) cc_final: 0.8680 (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: 0.8842 (p) REVERT: A 211 TYR cc_start: 0.8259 (m-80) cc_final: 0.7801 (m-80) REVERT: A 228 ARG cc_start: 0.8075 (tmm-80) cc_final: 0.6939 (mtp180) REVERT: A 300 MET cc_start: 0.7736 (mmm) cc_final: 0.7496 (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 477 ASP cc_start: 0.7761 (m-30) cc_final: 0.7504 (m-30) REVERT: A 549 ILE cc_start: 0.8849 (mp) cc_final: 0.7986 (mt) REVERT: A 555 ILE cc_start: 0.8819 (mt) cc_final: 0.8448 (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: 0.6903 (mtp180) REVERT: B 500 VAL cc_start: 0.8569 (t) cc_final: 0.8320 (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: 0.2409 time to fit residues: 180.7851 Evaluate side-chains 370 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 370 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 129 optimal weight: 0.1980 chunk 115 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 39 optimal weight: 10.0000 chunk 78 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 119 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 89 optimal weight: 0.9980 chunk 138 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 310 GLN C 547 GLN A 547 GLN 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 = 0.3660 r_free = 0.3660 target = 0.138206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.117762 restraints weight = 18752.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.120671 restraints weight = 9567.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.122474 restraints weight = 6173.962| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 11976 Z= 0.158 Angle : 0.708 8.027 16314 Z= 0.364 Chirality : 0.042 0.174 1905 Planarity : 0.006 0.053 1995 Dihedral : 5.447 22.706 1626 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 3.73 % Allowed : 15.35 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.97 (0.18), residues: 1527 helix: -1.69 (0.13), residues: 1134 sheet: None (None), residues: 0 loop : -2.26 (0.30), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 530 HIS 0.009 0.001 HIS A 532 PHE 0.019 0.002 PHE A 251 TYR 0.019 0.002 TYR C 211 ARG 0.006 0.001 ARG B 350 Details of bonding type rmsd hydrogen bonds : bond 0.04352 ( 772) hydrogen bonds : angle 5.63674 ( 2289) covalent geometry : bond 0.00350 (11976) covalent geometry : angle 0.70813 (16314) *********************** 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 472 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 428 time to evaluate : 1.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 188 PHE cc_start: 0.7857 (m-10) cc_final: 0.7608 (m-80) REVERT: C 201 GLN cc_start: 0.7106 (mt0) cc_final: 0.6884 (mt0) REVERT: C 211 TYR cc_start: 0.8143 (m-80) cc_final: 0.7554 (m-80) REVERT: C 370 SER cc_start: 0.8876 (m) cc_final: 0.8628 (p) REVERT: C 501 GLU cc_start: 0.7419 (tp30) cc_final: 0.7188 (tm-30) REVERT: C 515 LYS cc_start: 0.8638 (tmmt) cc_final: 0.8373 (ttpp) REVERT: A 211 TYR cc_start: 0.8154 (m-80) cc_final: 0.7497 (m-80) REVERT: A 216 PHE cc_start: 0.8391 (t80) cc_final: 0.8153 (t80) REVERT: A 300 MET cc_start: 0.7856 (mmm) cc_final: 0.7621 (mmt) REVERT: A 302 MET cc_start: 0.8163 (mtp) cc_final: 0.7929 (mtm) REVERT: A 312 ILE cc_start: 0.8588 (mt) cc_final: 0.8368 (mt) REVERT: A 435 GLU cc_start: 0.7295 (tt0) cc_final: 0.7071 (tt0) REVERT: A 533 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8442 (tt) REVERT: A 549 ILE cc_start: 0.8775 (mp) cc_final: 0.7999 (mt) REVERT: A 555 ILE cc_start: 0.8795 (mt) cc_final: 0.8529 (mm) REVERT: B 392 THR cc_start: 0.9050 (m) cc_final: 0.8743 (p) outliers start: 44 outliers final: 13 residues processed: 454 average time/residue: 0.1753 time to fit residues: 121.8155 Evaluate side-chains 368 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 354 time to evaluate : 1.297 ------------------------------------------------------------------------------- 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 C residue 533 LEU 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 98 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 8 optimal weight: 5.9990 chunk 2 optimal weight: 0.4980 chunk 33 optimal weight: 0.9980 chunk 127 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 chunk 7 optimal weight: 6.9990 chunk 85 optimal weight: 0.5980 chunk 139 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 C 466 ASN C 532 HIS A 104 HIS ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 532 HIS B 127 HIS B 503 GLN B 532 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.138199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.117880 restraints weight = 19380.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.120809 restraints weight = 9796.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.122488 restraints weight = 6258.992| |-----------------------------------------------------------------------------| r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.4372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11976 Z= 0.143 Angle : 0.657 7.569 16314 Z= 0.333 Chirality : 0.041 0.138 1905 Planarity : 0.005 0.047 1995 Dihedral : 4.969 21.599 1626 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 3.73 % Allowed : 19.76 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.20), residues: 1527 helix: -0.59 (0.14), residues: 1146 sheet: None (None), residues: 0 loop : -2.22 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 318 HIS 0.004 0.001 HIS B 526 PHE 0.022 0.002 PHE C 518 TYR 0.015 0.001 TYR B 559 ARG 0.003 0.001 ARG B 246 Details of bonding type rmsd hydrogen bonds : bond 0.03823 ( 772) hydrogen bonds : angle 4.97319 ( 2289) covalent geometry : bond 0.00324 (11976) covalent geometry : angle 0.65670 (16314) *********************** 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 438 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 394 time to evaluate : 1.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 216 PHE cc_start: 0.8307 (t80) cc_final: 0.8082 (t80) REVERT: C 220 LYS cc_start: 0.4116 (mttm) cc_final: 0.3783 (mmtm) REVERT: C 243 LEU cc_start: 0.7732 (OUTLIER) cc_final: 0.7275 (mt) REVERT: C 549 ILE cc_start: 0.8683 (mt) cc_final: 0.8153 (mt) REVERT: A 211 TYR cc_start: 0.8283 (m-80) cc_final: 0.7378 (m-80) REVERT: A 214 LEU cc_start: 0.8832 (mt) cc_final: 0.8420 (mt) REVERT: A 300 MET cc_start: 0.7912 (mmm) cc_final: 0.7617 (mmt) REVERT: A 435 GLU cc_start: 0.7345 (tt0) cc_final: 0.7068 (tt0) REVERT: A 502 TRP cc_start: 0.8191 (t-100) cc_final: 0.7650 (t60) REVERT: A 533 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8350 (tt) REVERT: A 555 ILE cc_start: 0.8831 (mt) cc_final: 0.8570 (mm) REVERT: B 243 LEU cc_start: 0.7777 (OUTLIER) cc_final: 0.7531 (mt) REVERT: B 252 ILE cc_start: 0.8823 (tt) cc_final: 0.8402 (pt) REVERT: B 330 GLU cc_start: 0.7382 (tp30) cc_final: 0.7176 (tp30) REVERT: B 361 LEU cc_start: 0.9490 (tp) cc_final: 0.9213 (tp) REVERT: B 525 GLU cc_start: 0.8080 (tm-30) cc_final: 0.7810 (pp20) outliers start: 44 outliers final: 16 residues processed: 419 average time/residue: 0.1792 time to fit residues: 116.2902 Evaluate side-chains 360 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 341 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain C residue 512 ILE 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 481 LEU 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 151 optimal weight: 4.9990 chunk 76 optimal weight: 0.9980 chunk 142 optimal weight: 0.7980 chunk 141 optimal weight: 0.9990 chunk 98 optimal weight: 0.9980 chunk 57 optimal weight: 6.9990 chunk 117 optimal weight: 0.5980 chunk 20 optimal weight: 5.9990 chunk 18 optimal weight: 0.5980 chunk 66 optimal weight: 0.8980 chunk 135 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 503 GLN C 532 HIS A 532 HIS B 104 HIS B 127 HIS B 474 ASN B 546 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.138232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.117687 restraints weight = 19191.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.120653 restraints weight = 9771.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.122535 restraints weight = 6283.498| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.4750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11976 Z= 0.138 Angle : 0.639 7.028 16314 Z= 0.322 Chirality : 0.042 0.155 1905 Planarity : 0.004 0.050 1995 Dihedral : 4.747 20.220 1626 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 3.73 % Allowed : 21.20 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.21), residues: 1527 helix: 0.02 (0.15), residues: 1134 sheet: None (None), residues: 0 loop : -2.04 (0.30), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 471 HIS 0.006 0.001 HIS C 104 PHE 0.029 0.002 PHE C 483 TYR 0.009 0.001 TYR B 548 ARG 0.003 0.000 ARG B 246 Details of bonding type rmsd hydrogen bonds : bond 0.03572 ( 772) hydrogen bonds : angle 4.73311 ( 2289) covalent geometry : bond 0.00317 (11976) covalent geometry : angle 0.63851 (16314) *********************** 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 423 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 379 time to evaluate : 1.250 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 211 TYR cc_start: 0.8092 (m-80) cc_final: 0.7619 (m-80) REVERT: C 216 PHE cc_start: 0.8270 (t80) cc_final: 0.8048 (t80) REVERT: C 220 LYS cc_start: 0.4180 (mttm) cc_final: 0.3873 (mmtm) REVERT: C 243 LEU cc_start: 0.7822 (OUTLIER) cc_final: 0.7196 (mt) REVERT: C 435 GLU cc_start: 0.7527 (tt0) cc_final: 0.7278 (pt0) REVERT: C 549 ILE cc_start: 0.8393 (OUTLIER) cc_final: 0.7588 (mt) REVERT: A 205 PHE cc_start: 0.8911 (t80) cc_final: 0.8577 (t80) REVERT: A 211 TYR cc_start: 0.8144 (m-80) cc_final: 0.7556 (m-80) REVERT: A 435 GLU cc_start: 0.7330 (tt0) cc_final: 0.7035 (tt0) REVERT: A 502 TRP cc_start: 0.8194 (t-100) cc_final: 0.7776 (t60) REVERT: A 533 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8397 (tt) REVERT: A 555 ILE cc_start: 0.8689 (mt) cc_final: 0.8485 (mm) REVERT: B 252 ILE cc_start: 0.8784 (tt) cc_final: 0.8396 (pt) REVERT: B 330 GLU cc_start: 0.7445 (tp30) cc_final: 0.7160 (tp30) REVERT: B 546 GLN cc_start: 0.6724 (OUTLIER) cc_final: 0.6465 (mt0) outliers start: 44 outliers final: 24 residues processed: 406 average time/residue: 0.1723 time to fit residues: 108.6660 Evaluate side-chains 381 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 353 time to evaluate : 1.122 ------------------------------------------------------------------------------- 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 215 LEU 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 397 SER Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 549 ILE Chi-restraints excluded: chain C residue 551 ILE 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 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 340 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 397 SER Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 546 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 53 optimal weight: 7.9990 chunk 42 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 26 optimal weight: 6.9990 chunk 1 optimal weight: 4.9990 chunk 127 optimal weight: 3.9990 chunk 145 optimal weight: 0.9980 chunk 76 optimal weight: 0.8980 chunk 103 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 127 HIS ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 ASN B 127 HIS B 546 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.134483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.113851 restraints weight = 19049.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.116687 restraints weight = 9673.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.118452 restraints weight = 6203.098| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.4914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11976 Z= 0.176 Angle : 0.657 6.217 16314 Z= 0.336 Chirality : 0.044 0.179 1905 Planarity : 0.004 0.053 1995 Dihedral : 4.817 22.304 1626 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 4.33 % Allowed : 22.48 % Favored : 73.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.22), residues: 1527 helix: 0.19 (0.15), residues: 1143 sheet: None (None), residues: 0 loop : -1.73 (0.34), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 318 HIS 0.012 0.001 HIS C 104 PHE 0.037 0.002 PHE C 188 TYR 0.015 0.001 TYR B 548 ARG 0.004 0.000 ARG C 103 Details of bonding type rmsd hydrogen bonds : bond 0.03562 ( 772) hydrogen bonds : angle 4.71860 ( 2289) covalent geometry : bond 0.00414 (11976) covalent geometry : angle 0.65701 (16314) *********************** 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 416 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 365 time to evaluate : 1.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 104 HIS cc_start: 0.7088 (OUTLIER) cc_final: 0.5971 (p-80) REVERT: C 117 MET cc_start: 0.8096 (tpp) cc_final: 0.7827 (tpp) REVERT: C 211 TYR cc_start: 0.8100 (m-80) cc_final: 0.7687 (m-80) REVERT: C 240 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.7949 (tt) REVERT: C 504 ASP cc_start: 0.7812 (m-30) cc_final: 0.7380 (t0) REVERT: C 532 HIS cc_start: 0.7038 (m90) cc_final: 0.6809 (m-70) REVERT: A 205 PHE cc_start: 0.8977 (t80) cc_final: 0.8645 (t80) REVERT: A 211 TYR cc_start: 0.8238 (m-80) cc_final: 0.7835 (m-80) REVERT: A 220 LYS cc_start: 0.4231 (mmtt) cc_final: 0.3982 (mttm) REVERT: A 300 MET cc_start: 0.7807 (mmm) cc_final: 0.7556 (mmp) REVERT: A 435 GLU cc_start: 0.7359 (tt0) cc_final: 0.7077 (tt0) REVERT: A 475 MET cc_start: 0.7974 (mmp) cc_final: 0.7701 (mmm) REVERT: A 502 TRP cc_start: 0.8406 (t-100) cc_final: 0.7566 (t60) REVERT: A 525 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.8162 (pp20) REVERT: A 533 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8408 (tt) REVERT: A 555 ILE cc_start: 0.8624 (mt) cc_final: 0.8422 (mm) REVERT: B 145 TRP cc_start: 0.7046 (t60) cc_final: 0.6647 (t-100) REVERT: B 252 ILE cc_start: 0.8782 (tt) cc_final: 0.8472 (pt) REVERT: B 546 GLN cc_start: 0.6999 (OUTLIER) cc_final: 0.6717 (mt0) outliers start: 51 outliers final: 34 residues processed: 395 average time/residue: 0.1754 time to fit residues: 107.6152 Evaluate side-chains 366 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 327 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 215 LEU 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 321 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 578 THR Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 124 LEU 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 306 LEU Chi-restraints excluded: chain A residue 321 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 525 GLU 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 B residue 110 LEU Chi-restraints excluded: chain B residue 124 LEU 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 481 LEU Chi-restraints excluded: chain B residue 546 GLN 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 20 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 147 optimal weight: 0.1980 chunk 81 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 7 optimal weight: 8.9990 chunk 74 optimal weight: 0.9980 chunk 9 optimal weight: 10.0000 chunk 119 optimal weight: 0.9990 chunk 137 optimal weight: 0.5980 chunk 133 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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** B 127 HIS B 200 GLN B 546 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.137032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.116105 restraints weight = 19214.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.119053 restraints weight = 9796.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.120907 restraints weight = 6318.155| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.5186 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= 0.144 Angle : 0.645 11.015 16314 Z= 0.326 Chirality : 0.042 0.174 1905 Planarity : 0.004 0.055 1995 Dihedral : 4.635 20.324 1626 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 4.50 % Allowed : 23.16 % Favored : 72.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.22), residues: 1527 helix: 0.35 (0.15), residues: 1161 sheet: None (None), residues: 0 loop : -1.75 (0.34), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 318 HIS 0.007 0.001 HIS C 526 PHE 0.040 0.002 PHE A 188 TYR 0.014 0.001 TYR B 548 ARG 0.003 0.000 ARG A 552 Details of bonding type rmsd hydrogen bonds : bond 0.03414 ( 772) hydrogen bonds : angle 4.65895 ( 2289) covalent geometry : bond 0.00335 (11976) covalent geometry : angle 0.64472 (16314) *********************** 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 419 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 366 time to evaluate : 1.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 104 HIS cc_start: 0.7248 (OUTLIER) cc_final: 0.6114 (p90) REVERT: C 211 TYR cc_start: 0.8017 (m-80) cc_final: 0.7667 (m-80) REVERT: C 220 LYS cc_start: 0.4307 (mttm) cc_final: 0.3951 (mmtm) REVERT: C 390 LEU cc_start: 0.9407 (OUTLIER) cc_final: 0.9073 (tt) REVERT: A 117 MET cc_start: 0.7223 (tpp) cc_final: 0.6921 (tpp) REVERT: A 135 ILE cc_start: 0.8918 (tp) cc_final: 0.8715 (tp) REVERT: A 205 PHE cc_start: 0.8957 (t80) cc_final: 0.8558 (t80) REVERT: A 211 TYR cc_start: 0.8238 (m-80) cc_final: 0.7676 (m-80) REVERT: A 254 PHE cc_start: 0.8775 (m-80) cc_final: 0.8496 (m-80) REVERT: A 435 GLU cc_start: 0.7358 (tt0) cc_final: 0.7108 (tt0) REVERT: A 465 MET cc_start: 0.7456 (mmt) cc_final: 0.7236 (mmt) REVERT: A 475 MET cc_start: 0.7743 (mmp) cc_final: 0.7529 (mmm) REVERT: A 502 TRP cc_start: 0.8266 (t-100) cc_final: 0.7633 (t60) REVERT: A 525 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.8247 (pp20) REVERT: A 533 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8336 (tt) REVERT: B 252 ILE cc_start: 0.8734 (tt) cc_final: 0.8394 (pt) REVERT: B 525 GLU cc_start: 0.8319 (tm-30) cc_final: 0.7821 (pp20) outliers start: 53 outliers final: 39 residues processed: 395 average time/residue: 0.2225 time to fit residues: 135.0354 Evaluate side-chains 384 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 341 time to evaluate : 1.457 ------------------------------------------------------------------------------- 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 215 LEU Chi-restraints excluded: chain C residue 230 VAL 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 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 554 GLU Chi-restraints excluded: chain C residue 578 THR Chi-restraints excluded: chain C residue 609 ILE Chi-restraints excluded: chain A residue 110 LEU 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 292 ILE Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 321 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 525 GLU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 554 GLU 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 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 481 LEU Chi-restraints excluded: chain B residue 578 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 87 optimal weight: 0.7980 chunk 93 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 19 optimal weight: 0.6980 chunk 67 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 118 optimal weight: 0.7980 chunk 60 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 51 optimal weight: 20.0000 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 127 HIS ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 154 HIS A 389 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 = 0.3647 r_free = 0.3647 target = 0.137682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.116730 restraints weight = 19400.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.119653 restraints weight = 9886.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.121502 restraints weight = 6412.194| |-----------------------------------------------------------------------------| r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.5366 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= 0.139 Angle : 0.637 6.794 16314 Z= 0.324 Chirality : 0.043 0.258 1905 Planarity : 0.004 0.056 1995 Dihedral : 4.607 21.906 1626 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 4.83 % Allowed : 22.82 % Favored : 72.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.22), residues: 1527 helix: 0.49 (0.15), residues: 1164 sheet: None (None), residues: 0 loop : -1.66 (0.34), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 530 HIS 0.015 0.001 HIS C 104 PHE 0.036 0.002 PHE C 188 TYR 0.011 0.001 TYR B 559 ARG 0.003 0.000 ARG B 128 Details of bonding type rmsd hydrogen bonds : bond 0.03360 ( 772) hydrogen bonds : angle 4.62067 ( 2289) covalent geometry : bond 0.00320 (11976) covalent geometry : angle 0.63741 (16314) *********************** 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 414 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 357 time to evaluate : 2.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 104 HIS cc_start: 0.7163 (OUTLIER) cc_final: 0.5972 (p-80) REVERT: C 211 TYR cc_start: 0.7978 (m-80) cc_final: 0.7549 (m-80) REVERT: C 214 LEU cc_start: 0.8537 (mt) cc_final: 0.8243 (mt) REVERT: C 220 LYS cc_start: 0.4281 (mttm) cc_final: 0.3923 (mmtm) REVERT: C 240 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.7913 (tt) REVERT: C 252 ILE cc_start: 0.8713 (tt) cc_final: 0.8441 (pt) REVERT: C 390 LEU cc_start: 0.9411 (OUTLIER) cc_final: 0.9079 (tt) REVERT: C 504 ASP cc_start: 0.8266 (t0) cc_final: 0.7776 (t0) REVERT: A 135 ILE cc_start: 0.8926 (tp) cc_final: 0.8695 (tp) REVERT: A 182 LEU cc_start: 0.8713 (mm) cc_final: 0.8395 (pp) REVERT: A 205 PHE cc_start: 0.8908 (t80) cc_final: 0.8445 (t80) REVERT: A 211 TYR cc_start: 0.8148 (m-80) cc_final: 0.7733 (m-80) REVERT: A 220 LYS cc_start: 0.3521 (mttm) cc_final: 0.3273 (mmtt) REVERT: A 254 PHE cc_start: 0.8747 (m-80) cc_final: 0.8465 (m-80) REVERT: A 475 MET cc_start: 0.7607 (mmp) cc_final: 0.7370 (mmm) REVERT: A 501 GLU cc_start: 0.7235 (tm-30) cc_final: 0.6749 (tm-30) REVERT: A 502 TRP cc_start: 0.8120 (t-100) cc_final: 0.7445 (t60) REVERT: A 525 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.8186 (pp20) REVERT: A 533 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8424 (tt) REVERT: B 201 GLN cc_start: 0.8304 (OUTLIER) cc_final: 0.7855 (mp10) REVERT: B 220 LYS cc_start: 0.4454 (mmtm) cc_final: 0.4210 (mttm) REVERT: B 252 ILE cc_start: 0.8724 (tt) cc_final: 0.8369 (pt) REVERT: B 525 GLU cc_start: 0.8306 (tm-30) cc_final: 0.7924 (pp20) outliers start: 57 outliers final: 33 residues processed: 392 average time/residue: 0.2833 time to fit residues: 172.4613 Evaluate side-chains 378 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 339 time to evaluate : 1.253 ------------------------------------------------------------------------------- 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 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 533 LEU Chi-restraints excluded: chain C residue 609 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 292 ILE Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 321 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 525 GLU 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 124 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 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 481 LEU Chi-restraints excluded: chain B residue 578 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 129 optimal weight: 7.9990 chunk 95 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 141 optimal weight: 0.8980 chunk 139 optimal weight: 0.0470 chunk 91 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 chunk 17 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 133 optimal weight: 0.0370 overall best weight: 0.5758 ------------------------------------------------------------------------------- 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 A 154 HIS ** A 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 200 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.139793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.119367 restraints weight = 19192.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.122333 restraints weight = 9716.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.124140 restraints weight = 6221.502| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.5572 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= 0.133 Angle : 0.653 9.958 16314 Z= 0.328 Chirality : 0.043 0.244 1905 Planarity : 0.004 0.058 1995 Dihedral : 4.549 23.883 1626 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 4.16 % Allowed : 24.17 % Favored : 71.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.22), residues: 1527 helix: 0.58 (0.15), residues: 1167 sheet: None (None), residues: 0 loop : -1.78 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 530 HIS 0.006 0.001 HIS A 154 PHE 0.035 0.002 PHE A 188 TYR 0.007 0.001 TYR C 305 ARG 0.002 0.000 ARG A 552 Details of bonding type rmsd hydrogen bonds : bond 0.03334 ( 772) hydrogen bonds : angle 4.61063 ( 2289) covalent geometry : bond 0.00303 (11976) covalent geometry : angle 0.65256 (16314) *********************** 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 404 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 355 time to evaluate : 2.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 104 HIS cc_start: 0.7205 (OUTLIER) cc_final: 0.6174 (p90) REVERT: C 182 LEU cc_start: 0.8750 (mm) cc_final: 0.8522 (pp) REVERT: C 211 TYR cc_start: 0.7888 (m-80) cc_final: 0.7570 (m-80) REVERT: C 220 LYS cc_start: 0.4334 (mttm) cc_final: 0.3985 (mmtm) REVERT: C 240 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.7878 (tt) REVERT: C 252 ILE cc_start: 0.8672 (tt) cc_final: 0.8413 (pt) REVERT: C 390 LEU cc_start: 0.9400 (OUTLIER) cc_final: 0.9068 (tt) REVERT: C 392 THR cc_start: 0.9231 (m) cc_final: 0.8792 (p) REVERT: C 504 ASP cc_start: 0.8375 (t0) cc_final: 0.7959 (t0) REVERT: C 531 ILE cc_start: 0.7872 (OUTLIER) cc_final: 0.7617 (mm) REVERT: A 135 ILE cc_start: 0.8961 (tp) cc_final: 0.8727 (tp) REVERT: A 182 LEU cc_start: 0.8673 (mm) cc_final: 0.8438 (pp) REVERT: A 210 MET cc_start: 0.7995 (ptm) cc_final: 0.7729 (ptp) REVERT: A 211 TYR cc_start: 0.8187 (m-80) cc_final: 0.7733 (m-80) REVERT: A 254 PHE cc_start: 0.8723 (m-80) cc_final: 0.8471 (m-80) REVERT: A 396 MET cc_start: 0.8832 (ptm) cc_final: 0.8529 (ptp) REVERT: A 502 TRP cc_start: 0.8030 (t-100) cc_final: 0.7342 (t60) REVERT: A 525 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.8126 (pp20) REVERT: A 533 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8408 (tt) REVERT: B 117 MET cc_start: 0.7397 (tpp) cc_final: 0.6918 (tpp) REVERT: B 201 GLN cc_start: 0.8124 (OUTLIER) cc_final: 0.7815 (mp10) REVERT: B 220 LYS cc_start: 0.4304 (mmtm) cc_final: 0.4061 (mttm) REVERT: B 228 ARG cc_start: 0.7913 (tmm-80) cc_final: 0.6280 (mtp180) REVERT: B 252 ILE cc_start: 0.8715 (tt) cc_final: 0.8339 (pt) REVERT: B 555 ILE cc_start: 0.8777 (mm) cc_final: 0.8559 (mm) outliers start: 49 outliers final: 34 residues processed: 386 average time/residue: 0.3853 time to fit residues: 229.0924 Evaluate side-chains 372 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 331 time to evaluate : 3.110 ------------------------------------------------------------------------------- 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 230 VAL Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 254 PHE 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 531 ILE 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 140 ILE 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 321 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 525 GLU Chi-restraints excluded: chain A residue 533 LEU 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 118 VAL Chi-restraints excluded: chain B residue 200 GLN Chi-restraints excluded: chain B residue 201 GLN 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 407 LEU Chi-restraints excluded: chain B residue 481 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 94 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 135 optimal weight: 0.8980 chunk 76 optimal weight: 0.7980 chunk 125 optimal weight: 1.9990 chunk 116 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 9 optimal weight: 9.9990 chunk 149 optimal weight: 0.8980 chunk 30 optimal weight: 0.0370 chunk 91 optimal weight: 1.9990 overall best weight: 0.7058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 127 HIS ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 342 GLN B 200 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.139689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.119210 restraints weight = 19186.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.122167 restraints weight = 9732.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.123981 restraints weight = 6233.814| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.5698 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= 0.139 Angle : 0.673 12.020 16314 Z= 0.339 Chirality : 0.043 0.240 1905 Planarity : 0.004 0.058 1995 Dihedral : 4.517 23.249 1626 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 3.99 % Allowed : 25.28 % Favored : 70.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.22), residues: 1527 helix: 0.67 (0.15), residues: 1164 sheet: None (None), residues: 0 loop : -1.80 (0.33), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 502 HIS 0.010 0.001 HIS C 104 PHE 0.021 0.001 PHE C 254 TYR 0.008 0.001 TYR A 548 ARG 0.002 0.000 ARG B 350 Details of bonding type rmsd hydrogen bonds : bond 0.03360 ( 772) hydrogen bonds : angle 4.61355 ( 2289) covalent geometry : bond 0.00323 (11976) covalent geometry : angle 0.67306 (16314) *********************** 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 384 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 337 time to evaluate : 1.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 104 HIS cc_start: 0.7176 (OUTLIER) cc_final: 0.5868 (p-80) REVERT: C 211 TYR cc_start: 0.7828 (m-80) cc_final: 0.7607 (m-80) REVERT: C 240 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.7883 (tt) REVERT: C 252 ILE cc_start: 0.8665 (tt) cc_final: 0.8407 (pt) REVERT: C 304 TYR cc_start: 0.7718 (t80) cc_final: 0.7164 (t80) REVERT: C 390 LEU cc_start: 0.9411 (OUTLIER) cc_final: 0.9072 (tt) REVERT: C 392 THR cc_start: 0.9224 (m) cc_final: 0.8815 (p) REVERT: C 504 ASP cc_start: 0.8375 (t0) cc_final: 0.7957 (t0) REVERT: A 135 ILE cc_start: 0.8992 (tp) cc_final: 0.8750 (tp) REVERT: A 182 LEU cc_start: 0.8704 (mm) cc_final: 0.8455 (pp) REVERT: A 210 MET cc_start: 0.8030 (ptm) cc_final: 0.7736 (ptp) REVERT: A 211 TYR cc_start: 0.8217 (m-80) cc_final: 0.7756 (m-80) REVERT: A 254 PHE cc_start: 0.8701 (m-80) cc_final: 0.8437 (m-80) REVERT: A 396 MET cc_start: 0.8833 (ptm) cc_final: 0.8540 (ptp) REVERT: A 435 GLU cc_start: 0.7984 (tm-30) cc_final: 0.7372 (tt0) REVERT: A 502 TRP cc_start: 0.7777 (t-100) cc_final: 0.7207 (t60) REVERT: A 525 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.8115 (pp20) REVERT: A 533 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8456 (tt) REVERT: B 201 GLN cc_start: 0.8209 (OUTLIER) cc_final: 0.7926 (mp10) REVERT: B 205 PHE cc_start: 0.8770 (t80) cc_final: 0.8506 (t80) REVERT: B 220 LYS cc_start: 0.4272 (mmtm) cc_final: 0.4032 (mttm) REVERT: B 228 ARG cc_start: 0.7918 (tmm-80) cc_final: 0.6283 (mtp180) REVERT: B 252 ILE cc_start: 0.8717 (tt) cc_final: 0.8357 (pt) REVERT: B 525 GLU cc_start: 0.8289 (tm-30) cc_final: 0.7904 (pp20) REVERT: B 546 GLN cc_start: 0.7016 (mm-40) cc_final: 0.6571 (mt0) REVERT: B 555 ILE cc_start: 0.8711 (mm) cc_final: 0.8470 (mm) outliers start: 47 outliers final: 33 residues processed: 367 average time/residue: 0.2573 time to fit residues: 149.0379 Evaluate side-chains 367 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 328 time to evaluate : 2.492 ------------------------------------------------------------------------------- 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 230 VAL Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 254 PHE 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 533 LEU Chi-restraints excluded: chain C residue 551 ILE Chi-restraints excluded: chain C residue 609 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 265 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 321 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 525 GLU 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 201 GLN 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 481 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 151 optimal weight: 3.9990 chunk 131 optimal weight: 0.8980 chunk 86 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 37 optimal weight: 0.5980 chunk 146 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 150 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 B 546 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.139807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.119220 restraints weight = 19060.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.122118 restraints weight = 9766.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.123929 restraints weight = 6329.599| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.5764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11976 Z= 0.143 Angle : 0.681 12.599 16314 Z= 0.342 Chirality : 0.043 0.226 1905 Planarity : 0.004 0.059 1995 Dihedral : 4.545 23.862 1626 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 3.99 % Allowed : 24.77 % Favored : 71.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.22), residues: 1527 helix: 0.79 (0.15), residues: 1152 sheet: None (None), residues: 0 loop : -1.84 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 502 HIS 0.005 0.001 HIS C 104 PHE 0.037 0.002 PHE A 188 TYR 0.008 0.001 TYR C 559 ARG 0.002 0.000 ARG A 350 Details of bonding type rmsd hydrogen bonds : bond 0.03369 ( 772) hydrogen bonds : angle 4.60866 ( 2289) covalent geometry : bond 0.00335 (11976) covalent geometry : angle 0.68084 (16314) ********************** 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 388 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 341 time to evaluate : 1.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 104 HIS cc_start: 0.7287 (OUTLIER) cc_final: 0.6323 (p90) REVERT: C 205 PHE cc_start: 0.8824 (t80) cc_final: 0.8610 (t80) REVERT: C 210 MET cc_start: 0.8401 (OUTLIER) cc_final: 0.8145 (ptm) REVERT: C 211 TYR cc_start: 0.8035 (m-80) cc_final: 0.7323 (m-80) REVERT: C 240 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.7883 (tt) REVERT: C 252 ILE cc_start: 0.8720 (tt) cc_final: 0.8465 (pt) REVERT: C 304 TYR cc_start: 0.7689 (t80) cc_final: 0.7133 (t80) REVERT: C 392 THR cc_start: 0.9226 (m) cc_final: 0.8889 (p) REVERT: C 504 ASP cc_start: 0.8292 (t0) cc_final: 0.7893 (t0) REVERT: A 117 MET cc_start: 0.8334 (tpp) cc_final: 0.8112 (tpp) REVERT: A 135 ILE cc_start: 0.8974 (tp) cc_final: 0.8742 (tp) REVERT: A 182 LEU cc_start: 0.8724 (mm) cc_final: 0.8476 (pp) REVERT: A 210 MET cc_start: 0.7935 (ptm) cc_final: 0.7623 (ptp) REVERT: A 211 TYR cc_start: 0.8179 (m-80) cc_final: 0.7663 (m-80) REVERT: A 254 PHE cc_start: 0.8692 (m-80) cc_final: 0.8438 (m-80) REVERT: A 396 MET cc_start: 0.8834 (ptm) cc_final: 0.8513 (ptp) REVERT: A 475 MET cc_start: 0.7656 (mmp) cc_final: 0.7455 (mmm) REVERT: A 502 TRP cc_start: 0.7652 (t-100) cc_final: 0.7021 (t60) REVERT: A 525 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.8047 (pp20) REVERT: A 533 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8452 (tt) REVERT: B 201 GLN cc_start: 0.8209 (OUTLIER) cc_final: 0.7892 (mp10) REVERT: B 205 PHE cc_start: 0.8752 (t80) cc_final: 0.8440 (t80) REVERT: B 220 LYS cc_start: 0.4283 (mmtm) cc_final: 0.4049 (mttm) REVERT: B 228 ARG cc_start: 0.7957 (tmm-80) cc_final: 0.6425 (mtp180) REVERT: B 252 ILE cc_start: 0.8707 (tt) cc_final: 0.8371 (pt) REVERT: B 525 GLU cc_start: 0.8267 (tm-30) cc_final: 0.7887 (pp20) outliers start: 47 outliers final: 34 residues processed: 370 average time/residue: 0.1775 time to fit residues: 102.1503 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 : 1.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 210 MET 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 254 PHE 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 402 LEU Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 551 ILE Chi-restraints excluded: chain A residue 124 LEU 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 265 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 321 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 525 GLU 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 201 GLN 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 481 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 38 optimal weight: 1.9990 chunk 91 optimal weight: 0.1980 chunk 106 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 139 optimal weight: 0.0270 chunk 96 optimal weight: 0.5980 chunk 49 optimal weight: 0.8980 chunk 93 optimal weight: 0.9980 chunk 142 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 127 HIS ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 310 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.142141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.121544 restraints weight = 19075.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.124490 restraints weight = 9801.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.126298 restraints weight = 6355.906| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.5941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11976 Z= 0.134 Angle : 0.687 12.644 16314 Z= 0.344 Chirality : 0.044 0.268 1905 Planarity : 0.004 0.055 1995 Dihedral : 4.519 25.425 1626 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 3.65 % Allowed : 25.45 % Favored : 70.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.22), residues: 1527 helix: 0.87 (0.16), residues: 1152 sheet: None (None), residues: 0 loop : -1.86 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 530 HIS 0.013 0.001 HIS C 104 PHE 0.036 0.001 PHE C 188 TYR 0.010 0.001 TYR A 211 ARG 0.007 0.000 ARG C 350 Details of bonding type rmsd hydrogen bonds : bond 0.03373 ( 772) hydrogen bonds : angle 4.61894 ( 2289) covalent geometry : bond 0.00305 (11976) covalent geometry : angle 0.68654 (16314) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4551.88 seconds wall clock time: 86 minutes 14.82 seconds (5174.82 seconds total)