Starting phenix.real_space_refine on Tue Aug 26 23:03:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sp8_40676/08_2025/8sp8_40676_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sp8_40676/08_2025/8sp8_40676.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8sp8_40676/08_2025/8sp8_40676_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sp8_40676/08_2025/8sp8_40676_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8sp8_40676/08_2025/8sp8_40676.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sp8_40676/08_2025/8sp8_40676.map" } resolution = 2.79 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.045 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: 8 Type Number sf(0) Gaussians Ca 1 9.91 5 P 12 5.49 5 S 160 5.16 5 Cl 1 4.86 5 C 13920 2.51 5 N 3336 2.21 5 O 3652 1.98 5 H 19860 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 84 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 40942 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 9877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 9877 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 26, 'TRANS': 585} Chain: "B" Number of atoms: 9877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 9877 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 26, 'TRANS': 585} Chain: "C" Number of atoms: 9877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 9877 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 26, 'TRANS': 585} Chain: "D" Number of atoms: 9877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 9877 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 26, 'TRANS': 585} Chain: "A" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 360 Unusual residues: {' CA': 1, ' CL': 1, 'I8E': 2, 'POV': 7, 'Y01': 3} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 153 Unresolved non-hydrogen angles: 187 Unresolved non-hydrogen dihedrals: 136 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'POV:plan-1': 3, 'POV:plan-2': 3, 'POV:plan-3': 3} Unresolved non-hydrogen planarities: 34 Chain: "B" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 358 Unusual residues: {'I8E': 2, 'POV': 7, 'Y01': 3} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 153 Unresolved non-hydrogen angles: 187 Unresolved non-hydrogen dihedrals: 136 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'POV:plan-1': 3, 'POV:plan-2': 3, 'POV:plan-3': 3} Unresolved non-hydrogen planarities: 34 Chain: "C" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 358 Unusual residues: {'I8E': 2, 'POV': 7, 'Y01': 3} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 153 Unresolved non-hydrogen angles: 187 Unresolved non-hydrogen dihedrals: 136 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'POV:plan-1': 3, 'POV:plan-2': 3, 'POV:plan-3': 3} Unresolved non-hydrogen planarities: 34 Chain: "D" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 358 Unusual residues: {'I8E': 2, 'POV': 7, 'Y01': 3} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 153 Unresolved non-hydrogen angles: 187 Unresolved non-hydrogen dihedrals: 136 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'POV:plan-1': 3, 'POV:plan-2': 3, 'POV:plan-3': 3} Unresolved non-hydrogen planarities: 34 Time building chain proxies: 6.82, per 1000 atoms: 0.17 Number of scatterers: 40942 At special positions: 0 Unit cell: (149.325, 149.325, 121.275, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Ca 1 19.99 Cl 1 17.00 S 160 16.00 P 12 15.00 O 3652 8.00 N 3336 7.00 C 13920 6.00 H 19860 1.00 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: 2.76 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 476.8 nanoseconds 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4624 Finding SS restraints... Secondary structure from input PDB file: 148 helices and 8 sheets defined 63.6% alpha, 2.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid 27 through 46 removed outlier: 3.504A pdb=" N ASP A 34 " --> pdb=" O ALA A 30 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN A 36 " --> pdb=" O SER A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 56 removed outlier: 3.555A pdb=" N LEU A 51 " --> pdb=" O SER A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 68 removed outlier: 3.796A pdb=" N LYS A 63 " --> pdb=" O GLN A 59 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU A 64 " --> pdb=" O ALA A 60 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLU A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 89 removed outlier: 3.651A pdb=" N ILE A 85 " --> pdb=" O THR A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 102 removed outlier: 3.821A pdb=" N VAL A 97 " --> pdb=" O GLU A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 106 removed outlier: 3.793A pdb=" N VAL A 106 " --> pdb=" O PRO A 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 103 through 106' Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.708A pdb=" N ILE A 123 " --> pdb=" O THR A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 139 removed outlier: 3.857A pdb=" N ALA A 135 " --> pdb=" O ASN A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 173 removed outlier: 3.598A pdb=" N CYS A 172 " --> pdb=" O SER A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 185 removed outlier: 3.597A pdb=" N ILE A 183 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N HIS A 185 " --> pdb=" O LEU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 203 Processing helix chain 'A' and resid 204 through 206 No H-bonds generated for 'chain 'A' and resid 204 through 206' Processing helix chain 'A' and resid 209 through 222 removed outlier: 4.055A pdb=" N GLN A 214 " --> pdb=" O THR A 210 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N MET A 215 " --> pdb=" O PHE A 211 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU A 220 " --> pdb=" O TYR A 216 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TYR A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 235 Processing helix chain 'A' and resid 242 through 250 removed outlier: 3.599A pdb=" N GLY A 248 " --> pdb=" O PHE A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 259 Processing helix chain 'A' and resid 291 through 298 removed outlier: 3.584A pdb=" N ILE A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 310 Processing helix chain 'A' and resid 313 through 325 removed outlier: 3.909A pdb=" N LEU A 319 " --> pdb=" O GLU A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 331 Processing helix chain 'A' and resid 336 through 349 removed outlier: 3.654A pdb=" N CYS A 342 " --> pdb=" O LEU A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 377 removed outlier: 3.528A pdb=" N TYR A 377 " --> pdb=" O LEU A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 403 removed outlier: 3.672A pdb=" N ARG A 385 " --> pdb=" O LYS A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 410 Processing helix chain 'A' and resid 415 through 420 Processing helix chain 'A' and resid 424 through 445 removed outlier: 3.627A pdb=" N ILE A 430 " --> pdb=" O HIS A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 464 removed outlier: 3.588A pdb=" N VAL A 459 " --> pdb=" O SER A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 467 No H-bonds generated for 'chain 'A' and resid 465 through 467' Processing helix chain 'A' and resid 469 through 473 Processing helix chain 'A' and resid 478 through 485 removed outlier: 3.723A pdb=" N ILE A 482 " --> pdb=" O PHE A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 491 removed outlier: 6.597A pdb=" N ASP A 489 " --> pdb=" O ILE A 486 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU A 490 " --> pdb=" O PHE A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 512 removed outlier: 3.530A pdb=" N ILE A 510 " --> pdb=" O SER A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 538 Processing helix chain 'A' and resid 552 through 570 removed outlier: 4.017A pdb=" N SER A 556 " --> pdb=" O PRO A 552 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE A 557 " --> pdb=" O PHE A 553 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR A 558 " --> pdb=" O MET A 554 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE A 564 " --> pdb=" O ALA A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 580 Processing helix chain 'A' and resid 587 through 608 removed outlier: 3.809A pdb=" N ARG A 594 " --> pdb=" O ASP A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 624 removed outlier: 3.809A pdb=" N GLY A 624 " --> pdb=" O ARG A 621 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 46 removed outlier: 3.504A pdb=" N ASP B 34 " --> pdb=" O ALA B 30 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN B 36 " --> pdb=" O SER B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 56 removed outlier: 3.555A pdb=" N LEU B 51 " --> pdb=" O SER B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 68 removed outlier: 3.797A pdb=" N LYS B 63 " --> pdb=" O GLN B 59 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU B 64 " --> pdb=" O ALA B 60 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLU B 68 " --> pdb=" O LEU B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 89 removed outlier: 3.652A pdb=" N ILE B 85 " --> pdb=" O THR B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 102 removed outlier: 3.821A pdb=" N VAL B 97 " --> pdb=" O GLU B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 106 removed outlier: 3.792A pdb=" N VAL B 106 " --> pdb=" O PRO B 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 103 through 106' Processing helix chain 'B' and resid 119 through 127 removed outlier: 3.707A pdb=" N ILE B 123 " --> pdb=" O THR B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 139 removed outlier: 3.858A pdb=" N ALA B 135 " --> pdb=" O ASN B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 173 removed outlier: 3.599A pdb=" N CYS B 172 " --> pdb=" O SER B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 185 removed outlier: 3.597A pdb=" N ILE B 183 " --> pdb=" O VAL B 179 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N HIS B 185 " --> pdb=" O LEU B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 203 Processing helix chain 'B' and resid 204 through 206 No H-bonds generated for 'chain 'B' and resid 204 through 206' Processing helix chain 'B' and resid 209 through 222 removed outlier: 4.055A pdb=" N GLN B 214 " --> pdb=" O THR B 210 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N MET B 215 " --> pdb=" O PHE B 211 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU B 220 " --> pdb=" O TYR B 216 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TYR B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 235 Processing helix chain 'B' and resid 242 through 250 removed outlier: 3.599A pdb=" N GLY B 248 " --> pdb=" O PHE B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 259 Processing helix chain 'B' and resid 291 through 298 removed outlier: 3.585A pdb=" N ILE B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 310 Processing helix chain 'B' and resid 313 through 325 removed outlier: 3.909A pdb=" N LEU B 319 " --> pdb=" O GLU B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 331 Processing helix chain 'B' and resid 336 through 349 removed outlier: 3.654A pdb=" N CYS B 342 " --> pdb=" O LEU B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 377 removed outlier: 3.529A pdb=" N TYR B 377 " --> pdb=" O LEU B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 403 removed outlier: 3.673A pdb=" N ARG B 385 " --> pdb=" O LYS B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 410 Processing helix chain 'B' and resid 415 through 420 Processing helix chain 'B' and resid 424 through 445 removed outlier: 3.627A pdb=" N ILE B 430 " --> pdb=" O HIS B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 464 removed outlier: 3.588A pdb=" N VAL B 459 " --> pdb=" O SER B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 467 No H-bonds generated for 'chain 'B' and resid 465 through 467' Processing helix chain 'B' and resid 469 through 473 Processing helix chain 'B' and resid 478 through 485 removed outlier: 3.722A pdb=" N ILE B 482 " --> pdb=" O PHE B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 491 removed outlier: 6.597A pdb=" N ASP B 489 " --> pdb=" O ILE B 486 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU B 490 " --> pdb=" O PHE B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 512 removed outlier: 3.529A pdb=" N ILE B 510 " --> pdb=" O SER B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 538 Processing helix chain 'B' and resid 552 through 570 removed outlier: 4.017A pdb=" N SER B 556 " --> pdb=" O PRO B 552 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE B 557 " --> pdb=" O PHE B 553 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR B 558 " --> pdb=" O MET B 554 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE B 564 " --> pdb=" O ALA B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 580 Processing helix chain 'B' and resid 587 through 608 removed outlier: 3.808A pdb=" N ARG B 594 " --> pdb=" O ASP B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 620 through 624 removed outlier: 3.810A pdb=" N GLY B 624 " --> pdb=" O ARG B 621 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 46 removed outlier: 3.504A pdb=" N ASP C 34 " --> pdb=" O ALA C 30 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN C 36 " --> pdb=" O SER C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 56 removed outlier: 3.555A pdb=" N LEU C 51 " --> pdb=" O SER C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 68 removed outlier: 3.796A pdb=" N LYS C 63 " --> pdb=" O GLN C 59 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU C 64 " --> pdb=" O ALA C 60 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLU C 68 " --> pdb=" O LEU C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 removed outlier: 3.651A pdb=" N ILE C 85 " --> pdb=" O THR C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 102 removed outlier: 3.821A pdb=" N VAL C 97 " --> pdb=" O GLU C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 106 removed outlier: 3.793A pdb=" N VAL C 106 " --> pdb=" O PRO C 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 103 through 106' Processing helix chain 'C' and resid 119 through 127 removed outlier: 3.707A pdb=" N ILE C 123 " --> pdb=" O THR C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 139 removed outlier: 3.859A pdb=" N ALA C 135 " --> pdb=" O ASN C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 173 removed outlier: 3.598A pdb=" N CYS C 172 " --> pdb=" O SER C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 185 removed outlier: 3.597A pdb=" N ILE C 183 " --> pdb=" O VAL C 179 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N HIS C 185 " --> pdb=" O LEU C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 203 Processing helix chain 'C' and resid 204 through 206 No H-bonds generated for 'chain 'C' and resid 204 through 206' Processing helix chain 'C' and resid 209 through 222 removed outlier: 4.054A pdb=" N GLN C 214 " --> pdb=" O THR C 210 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N MET C 215 " --> pdb=" O PHE C 211 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU C 220 " --> pdb=" O TYR C 216 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TYR C 222 " --> pdb=" O LEU C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 235 Processing helix chain 'C' and resid 242 through 250 removed outlier: 3.599A pdb=" N GLY C 248 " --> pdb=" O PHE C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 259 Processing helix chain 'C' and resid 291 through 298 removed outlier: 3.585A pdb=" N ILE C 297 " --> pdb=" O LEU C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 310 Processing helix chain 'C' and resid 313 through 325 removed outlier: 3.909A pdb=" N LEU C 319 " --> pdb=" O GLU C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 331 Processing helix chain 'C' and resid 336 through 349 removed outlier: 3.654A pdb=" N CYS C 342 " --> pdb=" O LEU C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 377 removed outlier: 3.528A pdb=" N TYR C 377 " --> pdb=" O LEU C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 403 removed outlier: 3.672A pdb=" N ARG C 385 " --> pdb=" O LYS C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 410 Processing helix chain 'C' and resid 415 through 420 Processing helix chain 'C' and resid 424 through 445 removed outlier: 3.626A pdb=" N ILE C 430 " --> pdb=" O HIS C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 464 removed outlier: 3.588A pdb=" N VAL C 459 " --> pdb=" O SER C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 467 No H-bonds generated for 'chain 'C' and resid 465 through 467' Processing helix chain 'C' and resid 469 through 473 Processing helix chain 'C' and resid 478 through 485 removed outlier: 3.722A pdb=" N ILE C 482 " --> pdb=" O PHE C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 491 removed outlier: 6.597A pdb=" N ASP C 489 " --> pdb=" O ILE C 486 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU C 490 " --> pdb=" O PHE C 487 " (cutoff:3.500A) Processing helix chain 'C' and resid 497 through 512 removed outlier: 3.530A pdb=" N ILE C 510 " --> pdb=" O SER C 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 538 Processing helix chain 'C' and resid 552 through 570 removed outlier: 4.017A pdb=" N SER C 556 " --> pdb=" O PRO C 552 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE C 557 " --> pdb=" O PHE C 553 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR C 558 " --> pdb=" O MET C 554 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE C 564 " --> pdb=" O ALA C 560 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 580 Processing helix chain 'C' and resid 587 through 608 removed outlier: 3.809A pdb=" N ARG C 594 " --> pdb=" O ASP C 590 " (cutoff:3.500A) Processing helix chain 'C' and resid 620 through 624 removed outlier: 3.809A pdb=" N GLY C 624 " --> pdb=" O ARG C 621 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 46 removed outlier: 3.504A pdb=" N ASP D 34 " --> pdb=" O ALA D 30 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN D 36 " --> pdb=" O SER D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 56 removed outlier: 3.554A pdb=" N LEU D 51 " --> pdb=" O SER D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 68 removed outlier: 3.796A pdb=" N LYS D 63 " --> pdb=" O GLN D 59 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU D 64 " --> pdb=" O ALA D 60 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLU D 68 " --> pdb=" O LEU D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 89 removed outlier: 3.651A pdb=" N ILE D 85 " --> pdb=" O THR D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 102 removed outlier: 3.822A pdb=" N VAL D 97 " --> pdb=" O GLU D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 106 removed outlier: 3.793A pdb=" N VAL D 106 " --> pdb=" O PRO D 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 103 through 106' Processing helix chain 'D' and resid 119 through 127 removed outlier: 3.708A pdb=" N ILE D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 139 removed outlier: 3.858A pdb=" N ALA D 135 " --> pdb=" O ASN D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 173 removed outlier: 3.599A pdb=" N CYS D 172 " --> pdb=" O SER D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 185 removed outlier: 3.597A pdb=" N ILE D 183 " --> pdb=" O VAL D 179 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N HIS D 185 " --> pdb=" O LEU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 203 Processing helix chain 'D' and resid 204 through 206 No H-bonds generated for 'chain 'D' and resid 204 through 206' Processing helix chain 'D' and resid 209 through 222 removed outlier: 4.054A pdb=" N GLN D 214 " --> pdb=" O THR D 210 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N MET D 215 " --> pdb=" O PHE D 211 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU D 220 " --> pdb=" O TYR D 216 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TYR D 222 " --> pdb=" O LEU D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 235 Processing helix chain 'D' and resid 242 through 250 removed outlier: 3.599A pdb=" N GLY D 248 " --> pdb=" O PHE D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 259 Processing helix chain 'D' and resid 291 through 298 removed outlier: 3.584A pdb=" N ILE D 297 " --> pdb=" O LEU D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 310 Processing helix chain 'D' and resid 313 through 325 removed outlier: 3.909A pdb=" N LEU D 319 " --> pdb=" O GLU D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 331 Processing helix chain 'D' and resid 336 through 349 removed outlier: 3.654A pdb=" N CYS D 342 " --> pdb=" O LEU D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 377 removed outlier: 3.527A pdb=" N TYR D 377 " --> pdb=" O LEU D 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 379 through 403 removed outlier: 3.672A pdb=" N ARG D 385 " --> pdb=" O LYS D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 410 Processing helix chain 'D' and resid 415 through 420 Processing helix chain 'D' and resid 424 through 445 removed outlier: 3.628A pdb=" N ILE D 430 " --> pdb=" O HIS D 426 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 464 removed outlier: 3.588A pdb=" N VAL D 459 " --> pdb=" O SER D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 467 No H-bonds generated for 'chain 'D' and resid 465 through 467' Processing helix chain 'D' and resid 469 through 473 Processing helix chain 'D' and resid 478 through 485 removed outlier: 3.723A pdb=" N ILE D 482 " --> pdb=" O PHE D 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 486 through 491 removed outlier: 6.598A pdb=" N ASP D 489 " --> pdb=" O ILE D 486 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU D 490 " --> pdb=" O PHE D 487 " (cutoff:3.500A) Processing helix chain 'D' and resid 497 through 512 removed outlier: 3.529A pdb=" N ILE D 510 " --> pdb=" O SER D 506 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 538 Processing helix chain 'D' and resid 552 through 570 removed outlier: 4.017A pdb=" N SER D 556 " --> pdb=" O PRO D 552 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE D 557 " --> pdb=" O PHE D 553 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR D 558 " --> pdb=" O MET D 554 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE D 564 " --> pdb=" O ALA D 560 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 580 Processing helix chain 'D' and resid 587 through 608 removed outlier: 3.808A pdb=" N ARG D 594 " --> pdb=" O ASP D 590 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL D 598 " --> pdb=" O ARG D 594 " (cutoff:3.500A) Processing helix chain 'D' and resid 620 through 624 removed outlier: 3.809A pdb=" N GLY D 624 " --> pdb=" O ARG D 621 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 269 through 270 Processing sheet with id=AA2, first strand: chain 'A' and resid 353 through 354 Processing sheet with id=AA3, first strand: chain 'B' and resid 269 through 270 Processing sheet with id=AA4, first strand: chain 'B' and resid 353 through 354 Processing sheet with id=AA5, first strand: chain 'C' and resid 269 through 270 Processing sheet with id=AA6, first strand: chain 'C' and resid 353 through 354 Processing sheet with id=AA7, first strand: chain 'D' and resid 269 through 270 Processing sheet with id=AA8, first strand: chain 'D' and resid 353 through 354 892 hydrogen bonds defined for protein. 2508 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: 8.67 Time building geometry restraints manager: 3.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.25: 22721 1.25 - 1.67: 18407 1.67 - 2.09: 272 2.09 - 2.50: 4 2.50 - 2.92: 12 Bond restraints: 41416 Sorted by residual: bond pdb=" CB ASP A 638 " pdb=" HB2 ASP A 638 " ideal model delta sigma weight residual 0.970 2.923 -1.953 2.00e-02 2.50e+03 9.54e+03 bond pdb=" CB ASP C 638 " pdb=" HB2 ASP C 638 " ideal model delta sigma weight residual 0.970 2.915 -1.945 2.00e-02 2.50e+03 9.46e+03 bond pdb=" CB ASP B 638 " pdb=" HB2 ASP B 638 " ideal model delta sigma weight residual 0.970 2.911 -1.941 2.00e-02 2.50e+03 9.42e+03 bond pdb=" CB ASP D 638 " pdb=" HB2 ASP D 638 " ideal model delta sigma weight residual 0.970 2.910 -1.940 2.00e-02 2.50e+03 9.41e+03 bond pdb=" CB ASP D 638 " pdb=" HB3 ASP D 638 " ideal model delta sigma weight residual 0.970 2.809 -1.839 2.00e-02 2.50e+03 8.46e+03 ... (remaining 41411 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.99: 73991 5.99 - 11.98: 113 11.98 - 17.98: 24 17.98 - 23.97: 8 23.97 - 29.96: 4 Bond angle restraints: 74140 Sorted by residual: angle pdb=" HB2 ASP A 638 " pdb=" CB ASP A 638 " pdb=" HB3 ASP A 638 " ideal model delta sigma weight residual 110.00 80.04 29.96 3.00e+00 1.11e-01 9.97e+01 angle pdb=" HB2 ASP C 638 " pdb=" CB ASP C 638 " pdb=" HB3 ASP C 638 " ideal model delta sigma weight residual 110.00 80.20 29.80 3.00e+00 1.11e-01 9.87e+01 angle pdb=" HB2 ASP B 638 " pdb=" CB ASP B 638 " pdb=" HB3 ASP B 638 " ideal model delta sigma weight residual 110.00 80.21 29.79 3.00e+00 1.11e-01 9.86e+01 angle pdb=" HB2 ASP D 638 " pdb=" CB ASP D 638 " pdb=" HB3 ASP D 638 " ideal model delta sigma weight residual 110.00 80.24 29.76 3.00e+00 1.11e-01 9.84e+01 angle pdb=" C ASP D 638 " pdb=" CA ASP D 638 " pdb=" HA ASP D 638 " ideal model delta sigma weight residual 109.00 88.36 20.64 3.00e+00 1.11e-01 4.73e+01 ... (remaining 74135 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.09: 19860 32.09 - 64.18: 560 64.18 - 96.27: 44 96.27 - 128.35: 40 128.35 - 160.44: 4 Dihedral angle restraints: 20508 sinusoidal: 11960 harmonic: 8548 Sorted by residual: dihedral pdb=" CA GLY D 411 " pdb=" C GLY D 411 " pdb=" N VAL D 412 " pdb=" CA VAL D 412 " ideal model delta harmonic sigma weight residual -180.00 -154.01 -25.99 0 5.00e+00 4.00e-02 2.70e+01 dihedral pdb=" CA GLY B 411 " pdb=" C GLY B 411 " pdb=" N VAL B 412 " pdb=" CA VAL B 412 " ideal model delta harmonic sigma weight residual -180.00 -154.02 -25.98 0 5.00e+00 4.00e-02 2.70e+01 dihedral pdb=" CA GLY C 411 " pdb=" C GLY C 411 " pdb=" N VAL C 412 " pdb=" CA VAL C 412 " ideal model delta harmonic sigma weight residual -180.00 -154.02 -25.98 0 5.00e+00 4.00e-02 2.70e+01 ... (remaining 20505 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 2848 0.091 - 0.181: 327 0.181 - 0.272: 33 0.272 - 0.362: 4 0.362 - 0.453: 8 Chirality restraints: 3220 Sorted by residual: chirality pdb=" CG LEU C 475 " pdb=" CB LEU C 475 " pdb=" CD1 LEU C 475 " pdb=" CD2 LEU C 475 " both_signs ideal model delta sigma weight residual False -2.59 -2.14 -0.45 2.00e-01 2.50e+01 5.13e+00 chirality pdb=" CG LEU B 475 " pdb=" CB LEU B 475 " pdb=" CD1 LEU B 475 " pdb=" CD2 LEU B 475 " both_signs ideal model delta sigma weight residual False -2.59 -2.14 -0.45 2.00e-01 2.50e+01 5.12e+00 chirality pdb=" CG LEU A 475 " pdb=" CB LEU A 475 " pdb=" CD1 LEU A 475 " pdb=" CD2 LEU A 475 " both_signs ideal model delta sigma weight residual False -2.59 -2.14 -0.45 2.00e-01 2.50e+01 5.10e+00 ... (remaining 3217 not shown) Planarity restraints: 5872 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C28 POV C 709 " -0.143 2.00e-02 2.50e+03 2.59e-01 6.73e+02 pdb=" C29 POV C 709 " 0.340 2.00e-02 2.50e+03 pdb="C210 POV C 709 " -0.337 2.00e-02 2.50e+03 pdb="C211 POV C 709 " 0.140 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV B 709 " -0.143 2.00e-02 2.50e+03 2.59e-01 6.70e+02 pdb=" C29 POV B 709 " 0.339 2.00e-02 2.50e+03 pdb="C210 POV B 709 " -0.336 2.00e-02 2.50e+03 pdb="C211 POV B 709 " 0.139 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV D 711 " 0.142 2.00e-02 2.50e+03 2.59e-01 6.70e+02 pdb=" C29 POV D 711 " -0.339 2.00e-02 2.50e+03 pdb="C210 POV D 711 " 0.336 2.00e-02 2.50e+03 pdb="C211 POV D 711 " -0.140 2.00e-02 2.50e+03 ... (remaining 5869 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.23: 3084 2.23 - 2.82: 89818 2.82 - 3.41: 104517 3.41 - 4.01: 146895 4.01 - 4.60: 230678 Nonbonded interactions: 574992 Sorted by model distance: nonbonded pdb="HH12 ARG A 470 " pdb=" OE1 GLN A 596 " model vdw 1.636 2.450 nonbonded pdb="HH12 ARG D 470 " pdb=" OE1 GLN D 596 " model vdw 1.636 2.450 nonbonded pdb="HH12 ARG C 470 " pdb=" OE1 GLN C 596 " model vdw 1.636 2.450 nonbonded pdb="HH12 ARG B 470 " pdb=" OE1 GLN B 596 " model vdw 1.636 2.450 nonbonded pdb="HH12 ARG B 355 " pdb=" OD2 ASP B 364 " model vdw 1.656 2.450 ... (remaining 574987 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 27 through 638) selection = (chain 'B' and resid 27 through 638) selection = (chain 'C' and resid 27 through 638) selection = (chain 'D' and resid 27 through 638) } 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=0.45 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.910 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: 0.150 Extract box with map and model: 0.440 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 32.230 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 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 : 0.014 0.176 21556 Z= 0.531 Angle : 1.173 21.550 29140 Z= 0.554 Chirality : 0.065 0.453 3220 Planarity : 0.012 0.259 3532 Dihedral : 16.364 160.443 9180 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.84 (0.14), residues: 2440 helix: -3.54 (0.09), residues: 1384 sheet: -3.59 (0.37), residues: 124 loop : -2.27 (0.20), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 492 TYR 0.022 0.003 TYR C 547 PHE 0.021 0.003 PHE D 537 TRP 0.013 0.003 TRP A 629 HIS 0.010 0.002 HIS A 582 Details of bonding type rmsd covalent geometry : bond 0.01357 (21556) covalent geometry : angle 1.17342 (29140) hydrogen bonds : bond 0.29168 ( 892) hydrogen bonds : angle 9.86009 ( 2508) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 538 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 ASN cc_start: 0.7348 (t0) cc_final: 0.6874 (t0) REVERT: A 195 LEU cc_start: 0.7827 (mt) cc_final: 0.7620 (mt) REVERT: A 208 ASN cc_start: 0.8227 (t0) cc_final: 0.7993 (t0) REVERT: A 262 LYS cc_start: 0.8602 (tttm) cc_final: 0.7909 (ttpp) REVERT: A 300 LYS cc_start: 0.8439 (mttm) cc_final: 0.8238 (mttm) REVERT: A 306 GLN cc_start: 0.7720 (mm-40) cc_final: 0.7485 (mt0) REVERT: A 318 SER cc_start: 0.8072 (t) cc_final: 0.7780 (m) REVERT: A 322 LYS cc_start: 0.7937 (tmmt) cc_final: 0.7587 (mtpm) REVERT: A 328 TYR cc_start: 0.8453 (m-10) cc_final: 0.8226 (m-80) REVERT: A 554 MET cc_start: 0.8864 (tpt) cc_final: 0.8636 (tpt) REVERT: A 577 MET cc_start: 0.7129 (mtm) cc_final: 0.6832 (mtp) REVERT: A 628 ARG cc_start: 0.8118 (mtt-85) cc_final: 0.7455 (mtp180) REVERT: A 635 ASP cc_start: 0.7232 (t70) cc_final: 0.6802 (p0) REVERT: B 174 ASN cc_start: 0.7367 (t0) cc_final: 0.6988 (t0) REVERT: B 195 LEU cc_start: 0.8019 (mt) cc_final: 0.7801 (mt) REVERT: B 211 PHE cc_start: 0.8731 (m-10) cc_final: 0.8489 (m-10) REVERT: B 262 LYS cc_start: 0.8652 (tttm) cc_final: 0.7961 (ttpp) REVERT: B 306 GLN cc_start: 0.7743 (mm-40) cc_final: 0.7539 (mt0) REVERT: B 318 SER cc_start: 0.8195 (t) cc_final: 0.7834 (m) REVERT: B 322 LYS cc_start: 0.7957 (tmmt) cc_final: 0.7606 (mtpm) REVERT: B 328 TYR cc_start: 0.8498 (m-10) cc_final: 0.8255 (m-10) REVERT: B 602 VAL cc_start: 0.7695 (t) cc_final: 0.7492 (m) REVERT: B 628 ARG cc_start: 0.8179 (mtt-85) cc_final: 0.7545 (mpp-170) REVERT: B 635 ASP cc_start: 0.7102 (t70) cc_final: 0.6789 (p0) REVERT: C 113 GLU cc_start: 0.8239 (tt0) cc_final: 0.8017 (tt0) REVERT: C 174 ASN cc_start: 0.7331 (t0) cc_final: 0.6922 (t0) REVERT: C 195 LEU cc_start: 0.7936 (mt) cc_final: 0.7720 (mt) REVERT: C 208 ASN cc_start: 0.8305 (t0) cc_final: 0.8083 (t0) REVERT: C 262 LYS cc_start: 0.8629 (tttm) cc_final: 0.7921 (ttpp) REVERT: C 300 LYS cc_start: 0.8434 (mttm) cc_final: 0.8226 (mttm) REVERT: C 306 GLN cc_start: 0.7718 (mm-40) cc_final: 0.7489 (mt0) REVERT: C 318 SER cc_start: 0.8140 (t) cc_final: 0.7787 (m) REVERT: C 322 LYS cc_start: 0.7962 (tmmt) cc_final: 0.7552 (mtpm) REVERT: C 328 TYR cc_start: 0.8512 (m-10) cc_final: 0.8251 (m-10) REVERT: C 577 MET cc_start: 0.7178 (mtm) cc_final: 0.6948 (mtp) REVERT: C 602 VAL cc_start: 0.7633 (t) cc_final: 0.7424 (m) REVERT: C 628 ARG cc_start: 0.8162 (mtt-85) cc_final: 0.7479 (mpp-170) REVERT: C 635 ASP cc_start: 0.7110 (t70) cc_final: 0.6750 (p0) REVERT: D 113 GLU cc_start: 0.8287 (tt0) cc_final: 0.7984 (tt0) REVERT: D 174 ASN cc_start: 0.7364 (t0) cc_final: 0.6958 (t0) REVERT: D 195 LEU cc_start: 0.7979 (mt) cc_final: 0.7745 (mt) REVERT: D 211 PHE cc_start: 0.8723 (m-10) cc_final: 0.8455 (m-10) REVERT: D 262 LYS cc_start: 0.8664 (tttm) cc_final: 0.7950 (ttpp) REVERT: D 300 LYS cc_start: 0.8412 (mttm) cc_final: 0.8209 (mttm) REVERT: D 303 GLU cc_start: 0.7602 (mp0) cc_final: 0.7138 (mp0) REVERT: D 306 GLN cc_start: 0.7722 (mm-40) cc_final: 0.7493 (mt0) REVERT: D 318 SER cc_start: 0.8182 (t) cc_final: 0.7826 (m) REVERT: D 322 LYS cc_start: 0.7989 (tmmt) cc_final: 0.7591 (mtpm) REVERT: D 328 TYR cc_start: 0.8482 (m-10) cc_final: 0.8184 (m-10) REVERT: D 577 MET cc_start: 0.7162 (mtm) cc_final: 0.6943 (mtp) REVERT: D 602 VAL cc_start: 0.7595 (t) cc_final: 0.7389 (m) REVERT: D 628 ARG cc_start: 0.8186 (mtt-85) cc_final: 0.7506 (mpp-170) REVERT: D 635 ASP cc_start: 0.7099 (t70) cc_final: 0.6735 (p0) outliers start: 0 outliers final: 0 residues processed: 538 average time/residue: 1.3057 time to fit residues: 792.5632 Evaluate side-chains 374 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 374 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 216 optimal weight: 0.8980 chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 8.9990 chunk 227 optimal weight: 0.8980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.7980 chunk 235 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN A 197 ASN A 357 ASN A 582 HIS B 118 GLN B 197 ASN ** B 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 357 ASN B 582 HIS C 118 GLN C 197 ASN ** C 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 357 ASN C 582 HIS D 31 GLN D 118 GLN D 197 ASN D 357 ASN D 582 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.186144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.132187 restraints weight = 66252.382| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 2.23 r_work: 0.3498 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3364 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3304 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3304 r_free = 0.3304 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3300 r_free = 0.3300 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3300 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 21556 Z= 0.162 Angle : 0.737 11.747 29140 Z= 0.373 Chirality : 0.040 0.231 3220 Planarity : 0.006 0.080 3532 Dihedral : 18.065 159.809 4456 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.86 % Favored : 93.98 % Rotamer: Outliers : 1.41 % Allowed : 11.96 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.81 (0.16), residues: 2440 helix: -1.64 (0.12), residues: 1420 sheet: -3.25 (0.37), residues: 124 loop : -1.73 (0.23), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 492 TYR 0.016 0.002 TYR D 377 PHE 0.016 0.002 PHE B 493 TRP 0.009 0.001 TRP A 593 HIS 0.005 0.001 HIS B 582 Details of bonding type rmsd covalent geometry : bond 0.00358 (21556) covalent geometry : angle 0.73660 (29140) hydrogen bonds : bond 0.06379 ( 892) hydrogen bonds : angle 5.61912 ( 2508) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 369 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 GLU cc_start: 0.6964 (tm-30) cc_final: 0.6716 (tm-30) REVERT: A 146 ARG cc_start: 0.7888 (mtp85) cc_final: 0.7537 (mtp-110) REVERT: A 174 ASN cc_start: 0.7613 (t0) cc_final: 0.7120 (t0) REVERT: A 208 ASN cc_start: 0.8237 (t0) cc_final: 0.7880 (t0) REVERT: A 262 LYS cc_start: 0.8721 (tttm) cc_final: 0.8041 (ttpp) REVERT: A 300 LYS cc_start: 0.8501 (mttm) cc_final: 0.8199 (mttm) REVERT: A 303 GLU cc_start: 0.7567 (mp0) cc_final: 0.7163 (mp0) REVERT: A 318 SER cc_start: 0.7893 (t) cc_final: 0.7378 (m) REVERT: A 322 LYS cc_start: 0.7941 (tmmt) cc_final: 0.7594 (mtpm) REVERT: A 554 MET cc_start: 0.8970 (tpt) cc_final: 0.8413 (tpt) REVERT: A 596 GLN cc_start: 0.6797 (mt0) cc_final: 0.6028 (mm-40) REVERT: A 628 ARG cc_start: 0.8157 (mtt-85) cc_final: 0.7307 (mpp-170) REVERT: A 635 ASP cc_start: 0.7498 (t70) cc_final: 0.6781 (p0) REVERT: B 174 ASN cc_start: 0.7580 (t0) cc_final: 0.7001 (t0) REVERT: B 262 LYS cc_start: 0.8744 (tttm) cc_final: 0.8065 (ttpp) REVERT: B 314 LYS cc_start: 0.7467 (ttpt) cc_final: 0.7090 (ttmm) REVERT: B 318 SER cc_start: 0.7922 (t) cc_final: 0.7699 (t) REVERT: B 322 LYS cc_start: 0.7944 (tmmt) cc_final: 0.7587 (mtpm) REVERT: B 328 TYR cc_start: 0.8805 (m-10) cc_final: 0.8601 (m-80) REVERT: B 596 GLN cc_start: 0.6742 (mt0) cc_final: 0.6503 (pt0) REVERT: B 602 VAL cc_start: 0.7488 (t) cc_final: 0.7243 (m) REVERT: B 628 ARG cc_start: 0.8194 (mtt-85) cc_final: 0.7311 (mpp-170) REVERT: B 635 ASP cc_start: 0.7398 (t70) cc_final: 0.6661 (p0) REVERT: C 113 GLU cc_start: 0.8423 (tt0) cc_final: 0.8222 (tt0) REVERT: C 174 ASN cc_start: 0.7554 (t0) cc_final: 0.6963 (t0) REVERT: C 208 ASN cc_start: 0.8302 (t0) cc_final: 0.7962 (t0) REVERT: C 211 PHE cc_start: 0.8804 (m-10) cc_final: 0.8489 (m-10) REVERT: C 262 LYS cc_start: 0.8749 (tttm) cc_final: 0.8075 (ttpp) REVERT: C 300 LYS cc_start: 0.8490 (mttm) cc_final: 0.8224 (mttm) REVERT: C 314 LYS cc_start: 0.7469 (ttpt) cc_final: 0.6859 (ttmm) REVERT: C 318 SER cc_start: 0.7867 (t) cc_final: 0.7314 (m) REVERT: C 322 LYS cc_start: 0.7906 (tmmt) cc_final: 0.7571 (mtpm) REVERT: C 596 GLN cc_start: 0.6697 (mt0) cc_final: 0.5950 (mm-40) REVERT: C 602 VAL cc_start: 0.7490 (t) cc_final: 0.7251 (m) REVERT: C 622 GLU cc_start: 0.7309 (pm20) cc_final: 0.7095 (pm20) REVERT: C 628 ARG cc_start: 0.8175 (mtt-85) cc_final: 0.7291 (mpp-170) REVERT: C 635 ASP cc_start: 0.7440 (t70) cc_final: 0.6674 (p0) REVERT: D 113 GLU cc_start: 0.8404 (tt0) cc_final: 0.8178 (tt0) REVERT: D 174 ASN cc_start: 0.7466 (t0) cc_final: 0.6976 (t0) REVERT: D 262 LYS cc_start: 0.8772 (tttm) cc_final: 0.8076 (ttpp) REVERT: D 300 LYS cc_start: 0.8466 (mttm) cc_final: 0.8230 (mttm) REVERT: D 303 GLU cc_start: 0.7629 (mp0) cc_final: 0.7213 (mp0) REVERT: D 318 SER cc_start: 0.7922 (t) cc_final: 0.7713 (t) REVERT: D 322 LYS cc_start: 0.7946 (tmmt) cc_final: 0.7603 (mtpm) REVERT: D 328 TYR cc_start: 0.8791 (m-10) cc_final: 0.8569 (m-80) REVERT: D 410 MET cc_start: 0.7344 (ttp) cc_final: 0.7080 (mtm) REVERT: D 554 MET cc_start: 0.9018 (tpt) cc_final: 0.8657 (tpt) REVERT: D 596 GLN cc_start: 0.6718 (mt0) cc_final: 0.6472 (pt0) REVERT: D 602 VAL cc_start: 0.7476 (t) cc_final: 0.7247 (m) REVERT: D 628 ARG cc_start: 0.8189 (mtt-85) cc_final: 0.7331 (mpp-170) REVERT: D 635 ASP cc_start: 0.7424 (t70) cc_final: 0.6671 (p0) outliers start: 30 outliers final: 12 residues processed: 391 average time/residue: 1.0940 time to fit residues: 493.3379 Evaluate side-chains 344 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 332 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 379 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 61 optimal weight: 10.0000 chunk 159 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 196 optimal weight: 6.9990 chunk 81 optimal weight: 0.3980 chunk 51 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 88 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 224 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 ASN B 546 ASN C 91 ASN C 118 GLN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 546 ASN D 91 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.182509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.126452 restraints weight = 66892.824| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 2.25 r_work: 0.3434 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3238 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3238 r_free = 0.3238 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3238 r_free = 0.3238 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3238 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 21556 Z= 0.164 Angle : 0.673 10.126 29140 Z= 0.332 Chirality : 0.039 0.200 3220 Planarity : 0.005 0.070 3532 Dihedral : 16.319 158.333 4456 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 2.02 % Allowed : 12.99 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.79 (0.17), residues: 2440 helix: -0.72 (0.13), residues: 1448 sheet: -2.99 (0.39), residues: 124 loop : -1.46 (0.23), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 492 TYR 0.012 0.001 TYR A 222 PHE 0.013 0.001 PHE B 493 TRP 0.007 0.001 TRP A 593 HIS 0.003 0.001 HIS B 426 Details of bonding type rmsd covalent geometry : bond 0.00385 (21556) covalent geometry : angle 0.67296 (29140) hydrogen bonds : bond 0.05239 ( 892) hydrogen bonds : angle 5.05517 ( 2508) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 371 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7570 (tt) REVERT: A 174 ASN cc_start: 0.7597 (t0) cc_final: 0.7119 (t0) REVERT: A 262 LYS cc_start: 0.8862 (tttm) cc_final: 0.8068 (ttpp) REVERT: A 300 LYS cc_start: 0.8498 (mttm) cc_final: 0.8214 (mttm) REVERT: A 303 GLU cc_start: 0.7707 (mp0) cc_final: 0.7208 (mp0) REVERT: A 314 LYS cc_start: 0.7439 (ttpt) cc_final: 0.7129 (ttmm) REVERT: A 318 SER cc_start: 0.7880 (t) cc_final: 0.7672 (t) REVERT: A 322 LYS cc_start: 0.7960 (tmmt) cc_final: 0.7633 (mtpm) REVERT: A 596 GLN cc_start: 0.6843 (mt0) cc_final: 0.6025 (mm-40) REVERT: A 628 ARG cc_start: 0.8140 (mtt-85) cc_final: 0.7266 (mpp-170) REVERT: A 635 ASP cc_start: 0.7595 (t70) cc_final: 0.6833 (p0) REVERT: B 51 LEU cc_start: 0.7949 (OUTLIER) cc_final: 0.7536 (tt) REVERT: B 174 ASN cc_start: 0.7702 (t0) cc_final: 0.7154 (t0) REVERT: B 262 LYS cc_start: 0.8793 (tttm) cc_final: 0.8114 (ttpp) REVERT: B 314 LYS cc_start: 0.7447 (ttpt) cc_final: 0.7161 (ttmm) REVERT: B 318 SER cc_start: 0.7964 (t) cc_final: 0.7754 (t) REVERT: B 322 LYS cc_start: 0.7972 (tmmt) cc_final: 0.7616 (mtpm) REVERT: B 332 LEU cc_start: 0.8255 (mt) cc_final: 0.8054 (mt) REVERT: B 596 GLN cc_start: 0.6725 (mt0) cc_final: 0.5952 (mm-40) REVERT: B 602 VAL cc_start: 0.7604 (t) cc_final: 0.7301 (m) REVERT: B 628 ARG cc_start: 0.8157 (mtt-85) cc_final: 0.7278 (mpp-170) REVERT: B 635 ASP cc_start: 0.7507 (t70) cc_final: 0.6797 (p0) REVERT: C 51 LEU cc_start: 0.7948 (OUTLIER) cc_final: 0.7542 (tt) REVERT: C 113 GLU cc_start: 0.8488 (tt0) cc_final: 0.8274 (tt0) REVERT: C 174 ASN cc_start: 0.7697 (t0) cc_final: 0.7115 (t0) REVERT: C 208 ASN cc_start: 0.8134 (t0) cc_final: 0.7805 (t0) REVERT: C 211 PHE cc_start: 0.8782 (m-10) cc_final: 0.8404 (m-10) REVERT: C 262 LYS cc_start: 0.8779 (tttm) cc_final: 0.8104 (ttpp) REVERT: C 300 LYS cc_start: 0.8500 (mttm) cc_final: 0.8234 (mttm) REVERT: C 314 LYS cc_start: 0.7430 (ttpt) cc_final: 0.7074 (ttmm) REVERT: C 315 GLU cc_start: 0.8259 (mp0) cc_final: 0.7534 (mp0) REVERT: C 318 SER cc_start: 0.7956 (t) cc_final: 0.7736 (t) REVERT: C 322 LYS cc_start: 0.7962 (tmmt) cc_final: 0.7589 (mtpm) REVERT: C 374 GLN cc_start: 0.8542 (mp-120) cc_final: 0.8331 (mm-40) REVERT: C 596 GLN cc_start: 0.6780 (mt0) cc_final: 0.6006 (mm-40) REVERT: C 602 VAL cc_start: 0.7659 (t) cc_final: 0.7347 (m) REVERT: C 622 GLU cc_start: 0.7477 (pm20) cc_final: 0.7245 (pm20) REVERT: C 628 ARG cc_start: 0.8131 (mtt-85) cc_final: 0.7245 (mpp-170) REVERT: C 635 ASP cc_start: 0.7556 (t70) cc_final: 0.6808 (p0) REVERT: D 51 LEU cc_start: 0.7954 (OUTLIER) cc_final: 0.7534 (tt) REVERT: D 113 GLU cc_start: 0.8441 (tt0) cc_final: 0.8200 (tt0) REVERT: D 174 ASN cc_start: 0.7387 (t0) cc_final: 0.7053 (t0) REVERT: D 262 LYS cc_start: 0.8883 (tttm) cc_final: 0.8181 (ttpp) REVERT: D 300 LYS cc_start: 0.8494 (mttm) cc_final: 0.8226 (mttm) REVERT: D 314 LYS cc_start: 0.7447 (ttpt) cc_final: 0.7155 (ttmm) REVERT: D 318 SER cc_start: 0.7965 (t) cc_final: 0.7750 (t) REVERT: D 322 LYS cc_start: 0.8010 (tmmt) cc_final: 0.7632 (mtpm) REVERT: D 474 MET cc_start: 0.2109 (OUTLIER) cc_final: 0.1839 (mtt) REVERT: D 596 GLN cc_start: 0.6727 (mt0) cc_final: 0.5961 (mm-40) REVERT: D 602 VAL cc_start: 0.7644 (t) cc_final: 0.7345 (m) REVERT: D 628 ARG cc_start: 0.8166 (mtt-85) cc_final: 0.7314 (mpp-170) REVERT: D 635 ASP cc_start: 0.7553 (t70) cc_final: 0.6821 (p0) outliers start: 43 outliers final: 27 residues processed: 398 average time/residue: 1.0534 time to fit residues: 488.8133 Evaluate side-chains 364 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 332 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 118 GLN Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 479 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 55 optimal weight: 9.9990 chunk 117 optimal weight: 10.0000 chunk 232 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 229 optimal weight: 8.9990 chunk 183 optimal weight: 10.0000 chunk 114 optimal weight: 2.9990 chunk 6 optimal weight: 9.9990 chunk 65 optimal weight: 20.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN A 118 GLN ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 ASN A 546 ASN ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 357 ASN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 357 ASN D 91 ASN D 118 GLN ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 357 ASN D 546 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.177733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.123192 restraints weight = 67308.672| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.16 r_work: 0.3406 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3168 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3168 r_free = 0.3168 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3168 r_free = 0.3168 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3168 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.3377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 21556 Z= 0.259 Angle : 0.700 9.096 29140 Z= 0.343 Chirality : 0.043 0.240 3220 Planarity : 0.005 0.056 3532 Dihedral : 16.464 152.314 4456 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 2.12 % Allowed : 13.94 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.52 (0.17), residues: 2440 helix: -0.45 (0.13), residues: 1456 sheet: -3.67 (0.48), residues: 84 loop : -1.48 (0.22), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 492 TYR 0.012 0.002 TYR A 222 PHE 0.012 0.002 PHE B 493 TRP 0.007 0.001 TRP A 593 HIS 0.005 0.001 HIS D 522 Details of bonding type rmsd covalent geometry : bond 0.00628 (21556) covalent geometry : angle 0.70036 (29140) hydrogen bonds : bond 0.04885 ( 892) hydrogen bonds : angle 4.91773 ( 2508) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 348 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LEU cc_start: 0.8006 (OUTLIER) cc_final: 0.7598 (tt) REVERT: A 174 ASN cc_start: 0.7731 (t0) cc_final: 0.7242 (t0) REVERT: A 262 LYS cc_start: 0.8941 (tttm) cc_final: 0.8478 (ttpt) REVERT: A 300 LYS cc_start: 0.8511 (mttm) cc_final: 0.8238 (mttm) REVERT: A 303 GLU cc_start: 0.7830 (mp0) cc_final: 0.7322 (mp0) REVERT: A 314 LYS cc_start: 0.7550 (ttpt) cc_final: 0.7247 (ttmm) REVERT: A 322 LYS cc_start: 0.8016 (tmmt) cc_final: 0.7675 (mtpm) REVERT: A 490 LEU cc_start: 0.5976 (OUTLIER) cc_final: 0.5746 (tt) REVERT: A 492 ARG cc_start: 0.5852 (tpp80) cc_final: 0.5278 (tpp80) REVERT: A 596 GLN cc_start: 0.6970 (mt0) cc_final: 0.6098 (mm-40) REVERT: A 628 ARG cc_start: 0.8141 (mtt-85) cc_final: 0.7289 (mpp-170) REVERT: A 635 ASP cc_start: 0.7675 (t70) cc_final: 0.6880 (p0) REVERT: B 51 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7560 (tt) REVERT: B 174 ASN cc_start: 0.7800 (t0) cc_final: 0.7198 (t0) REVERT: B 255 MET cc_start: 0.8558 (mmm) cc_final: 0.8256 (mtp) REVERT: B 262 LYS cc_start: 0.8930 (tttm) cc_final: 0.8168 (ttpp) REVERT: B 303 GLU cc_start: 0.7839 (mp0) cc_final: 0.7396 (mp0) REVERT: B 314 LYS cc_start: 0.7524 (ttpt) cc_final: 0.7227 (ttmm) REVERT: B 322 LYS cc_start: 0.7954 (tmmt) cc_final: 0.7603 (mtpm) REVERT: B 410 MET cc_start: 0.6994 (mtp) cc_final: 0.6745 (mtm) REVERT: B 596 GLN cc_start: 0.6851 (mt0) cc_final: 0.6043 (mm-40) REVERT: B 602 VAL cc_start: 0.7809 (t) cc_final: 0.7491 (m) REVERT: B 628 ARG cc_start: 0.8197 (mtt-85) cc_final: 0.7405 (mpp-170) REVERT: B 635 ASP cc_start: 0.7650 (t70) cc_final: 0.6873 (p0) REVERT: C 51 LEU cc_start: 0.7996 (OUTLIER) cc_final: 0.7557 (tt) REVERT: C 113 GLU cc_start: 0.8541 (tt0) cc_final: 0.8293 (tt0) REVERT: C 174 ASN cc_start: 0.7754 (t0) cc_final: 0.7203 (t0) REVERT: C 211 PHE cc_start: 0.8781 (m-10) cc_final: 0.8530 (m-10) REVERT: C 262 LYS cc_start: 0.8926 (tttm) cc_final: 0.8119 (ttpp) REVERT: C 300 LYS cc_start: 0.8518 (mttm) cc_final: 0.8271 (mttm) REVERT: C 314 LYS cc_start: 0.7530 (ttpt) cc_final: 0.7229 (ttmm) REVERT: C 322 LYS cc_start: 0.7983 (tmmt) cc_final: 0.7600 (mtpm) REVERT: C 374 GLN cc_start: 0.8564 (mp-120) cc_final: 0.8338 (mm-40) REVERT: C 378 MET cc_start: 0.8408 (mtm) cc_final: 0.8153 (mtm) REVERT: C 596 GLN cc_start: 0.6871 (mt0) cc_final: 0.6046 (mm-40) REVERT: C 602 VAL cc_start: 0.7829 (t) cc_final: 0.7518 (m) REVERT: C 622 GLU cc_start: 0.7697 (pm20) cc_final: 0.7410 (pm20) REVERT: C 628 ARG cc_start: 0.8201 (mtt-85) cc_final: 0.7371 (mpp-170) REVERT: C 635 ASP cc_start: 0.7685 (t70) cc_final: 0.6878 (p0) REVERT: D 51 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7551 (tt) REVERT: D 113 GLU cc_start: 0.8445 (tt0) cc_final: 0.8180 (tt0) REVERT: D 174 ASN cc_start: 0.7740 (t0) cc_final: 0.7245 (t0) REVERT: D 262 LYS cc_start: 0.8926 (tttm) cc_final: 0.8130 (ttpp) REVERT: D 300 LYS cc_start: 0.8522 (mttm) cc_final: 0.8284 (mttm) REVERT: D 314 LYS cc_start: 0.7547 (ttpt) cc_final: 0.7243 (ttmm) REVERT: D 322 LYS cc_start: 0.8017 (tmmt) cc_final: 0.7637 (mtpm) REVERT: D 378 MET cc_start: 0.8393 (mtm) cc_final: 0.8141 (mtm) REVERT: D 596 GLN cc_start: 0.6901 (mt0) cc_final: 0.6047 (mm-40) REVERT: D 602 VAL cc_start: 0.7719 (t) cc_final: 0.7416 (m) REVERT: D 628 ARG cc_start: 0.8183 (mtt-85) cc_final: 0.7392 (mpp-170) REVERT: D 635 ASP cc_start: 0.7626 (t70) cc_final: 0.6842 (p0) outliers start: 45 outliers final: 22 residues processed: 375 average time/residue: 1.2229 time to fit residues: 529.1036 Evaluate side-chains 356 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 329 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 118 GLN Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 490 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 66 optimal weight: 4.9990 chunk 163 optimal weight: 0.9990 chunk 139 optimal weight: 2.9990 chunk 122 optimal weight: 8.9990 chunk 44 optimal weight: 7.9990 chunk 206 optimal weight: 5.9990 chunk 14 optimal weight: 0.5980 chunk 108 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 144 optimal weight: 3.9990 chunk 115 optimal weight: 0.5980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 GLN A 357 ASN B 357 ASN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 357 ASN ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 357 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.180296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.126223 restraints weight = 66533.974| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 2.14 r_work: 0.3456 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3213 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3213 r_free = 0.3213 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3213 r_free = 0.3213 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3213 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.3585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21556 Z= 0.126 Angle : 0.616 7.963 29140 Z= 0.306 Chirality : 0.038 0.217 3220 Planarity : 0.004 0.057 3532 Dihedral : 15.262 150.965 4456 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.48 % Favored : 93.44 % Rotamer: Outliers : 1.93 % Allowed : 15.11 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.03 (0.17), residues: 2440 helix: -0.06 (0.14), residues: 1456 sheet: -3.70 (0.47), residues: 84 loop : -1.26 (0.22), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 75 TYR 0.009 0.001 TYR D 216 PHE 0.012 0.001 PHE B 493 TRP 0.007 0.001 TRP A 462 HIS 0.003 0.001 HIS B 201 Details of bonding type rmsd covalent geometry : bond 0.00296 (21556) covalent geometry : angle 0.61611 (29140) hydrogen bonds : bond 0.04269 ( 892) hydrogen bonds : angle 4.69233 ( 2508) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 346 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LEU cc_start: 0.7967 (OUTLIER) cc_final: 0.7537 (tt) REVERT: A 174 ASN cc_start: 0.7644 (t0) cc_final: 0.7188 (t0) REVERT: A 262 LYS cc_start: 0.8901 (tttm) cc_final: 0.8438 (ttpt) REVERT: A 300 LYS cc_start: 0.8492 (mttm) cc_final: 0.8218 (mttm) REVERT: A 303 GLU cc_start: 0.7876 (mp0) cc_final: 0.7383 (mp0) REVERT: A 314 LYS cc_start: 0.7451 (ttpt) cc_final: 0.7146 (ttmm) REVERT: A 322 LYS cc_start: 0.7932 (tmmt) cc_final: 0.7564 (mtpm) REVERT: A 378 MET cc_start: 0.8356 (mtm) cc_final: 0.8047 (mtm) REVERT: A 596 GLN cc_start: 0.6835 (mt0) cc_final: 0.5989 (mm-40) REVERT: A 628 ARG cc_start: 0.8118 (mtt-85) cc_final: 0.7266 (mpp-170) REVERT: A 635 ASP cc_start: 0.7537 (t70) cc_final: 0.6805 (p0) REVERT: B 51 LEU cc_start: 0.7966 (OUTLIER) cc_final: 0.7524 (tt) REVERT: B 174 ASN cc_start: 0.7699 (t0) cc_final: 0.7127 (t0) REVERT: B 262 LYS cc_start: 0.8912 (tttm) cc_final: 0.8136 (ttpp) REVERT: B 303 GLU cc_start: 0.7856 (mp0) cc_final: 0.7398 (mp0) REVERT: B 314 LYS cc_start: 0.7397 (ttpt) cc_final: 0.7116 (ttmm) REVERT: B 322 LYS cc_start: 0.7903 (tmmt) cc_final: 0.7517 (mtpm) REVERT: B 596 GLN cc_start: 0.6812 (mt0) cc_final: 0.5985 (mm-40) REVERT: B 602 VAL cc_start: 0.7781 (t) cc_final: 0.7465 (m) REVERT: B 628 ARG cc_start: 0.8139 (mtt-85) cc_final: 0.7296 (mpp-170) REVERT: B 635 ASP cc_start: 0.7535 (t70) cc_final: 0.6766 (p0) REVERT: C 51 LEU cc_start: 0.7949 (OUTLIER) cc_final: 0.7517 (tt) REVERT: C 113 GLU cc_start: 0.8502 (tt0) cc_final: 0.8253 (tt0) REVERT: C 174 ASN cc_start: 0.7690 (t0) cc_final: 0.7133 (t0) REVERT: C 255 MET cc_start: 0.8575 (mmm) cc_final: 0.8207 (mtp) REVERT: C 262 LYS cc_start: 0.8905 (tttm) cc_final: 0.8086 (ttpp) REVERT: C 300 LYS cc_start: 0.8499 (mttm) cc_final: 0.8258 (mttm) REVERT: C 303 GLU cc_start: 0.7855 (mp0) cc_final: 0.7400 (mp0) REVERT: C 314 LYS cc_start: 0.7389 (ttpt) cc_final: 0.7098 (ttmm) REVERT: C 318 SER cc_start: 0.7866 (t) cc_final: 0.7634 (t) REVERT: C 322 LYS cc_start: 0.7902 (tmmt) cc_final: 0.7527 (mtpm) REVERT: C 374 GLN cc_start: 0.8501 (mp-120) cc_final: 0.8209 (mm-40) REVERT: C 378 MET cc_start: 0.8397 (mtm) cc_final: 0.8019 (mtm) REVERT: C 490 LEU cc_start: 0.6010 (OUTLIER) cc_final: 0.5784 (tt) REVERT: C 596 GLN cc_start: 0.6842 (mt0) cc_final: 0.6007 (mm-40) REVERT: C 602 VAL cc_start: 0.7792 (t) cc_final: 0.7483 (m) REVERT: C 622 GLU cc_start: 0.7706 (pm20) cc_final: 0.7409 (pm20) REVERT: C 628 ARG cc_start: 0.8169 (mtt-85) cc_final: 0.7301 (mpp-170) REVERT: C 635 ASP cc_start: 0.7573 (t70) cc_final: 0.6815 (p0) REVERT: D 113 GLU cc_start: 0.8446 (tt0) cc_final: 0.8176 (tt0) REVERT: D 174 ASN cc_start: 0.7566 (t0) cc_final: 0.7125 (t0) REVERT: D 262 LYS cc_start: 0.8898 (tttm) cc_final: 0.8080 (ttpp) REVERT: D 300 LYS cc_start: 0.8506 (mttm) cc_final: 0.8270 (mttm) REVERT: D 303 GLU cc_start: 0.7807 (mp0) cc_final: 0.7372 (mp0) REVERT: D 314 LYS cc_start: 0.7414 (ttpt) cc_final: 0.7111 (ttmm) REVERT: D 322 LYS cc_start: 0.7932 (tmmt) cc_final: 0.7562 (mtpm) REVERT: D 378 MET cc_start: 0.8390 (mtm) cc_final: 0.8168 (mtm) REVERT: D 490 LEU cc_start: 0.5918 (OUTLIER) cc_final: 0.5684 (tt) REVERT: D 596 GLN cc_start: 0.6691 (mt0) cc_final: 0.5875 (mm-40) REVERT: D 602 VAL cc_start: 0.7705 (t) cc_final: 0.7415 (m) REVERT: D 628 ARG cc_start: 0.8166 (mtt-85) cc_final: 0.7319 (mpp-170) REVERT: D 635 ASP cc_start: 0.7509 (t70) cc_final: 0.6779 (p0) outliers start: 41 outliers final: 24 residues processed: 376 average time/residue: 1.1648 time to fit residues: 505.8476 Evaluate side-chains 357 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 328 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 490 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 206 optimal weight: 0.4980 chunk 209 optimal weight: 6.9990 chunk 75 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 219 optimal weight: 3.9990 chunk 55 optimal weight: 7.9990 chunk 76 optimal weight: 0.9990 chunk 4 optimal weight: 0.1980 chunk 80 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 ASN B 357 ASN C 118 GLN C 357 ASN ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 357 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.181297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.126974 restraints weight = 66805.393| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 2.15 r_work: 0.3466 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3340 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3236 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3236 r_free = 0.3236 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3236 r_free = 0.3236 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3236 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.3730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21556 Z= 0.111 Angle : 0.584 7.656 29140 Z= 0.291 Chirality : 0.038 0.191 3220 Planarity : 0.004 0.057 3532 Dihedral : 14.196 146.164 4456 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 2.17 % Allowed : 15.35 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.61 (0.18), residues: 2440 helix: 0.31 (0.14), residues: 1452 sheet: -3.64 (0.47), residues: 84 loop : -1.13 (0.22), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 492 TYR 0.012 0.001 TYR A 216 PHE 0.009 0.001 PHE D 493 TRP 0.007 0.001 TRP A 593 HIS 0.003 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00258 (21556) covalent geometry : angle 0.58352 (29140) hydrogen bonds : bond 0.03899 ( 892) hydrogen bonds : angle 4.50274 ( 2508) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 345 time to evaluate : 1.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LEU cc_start: 0.7982 (OUTLIER) cc_final: 0.7536 (tt) REVERT: A 174 ASN cc_start: 0.7649 (t0) cc_final: 0.7192 (t0) REVERT: A 262 LYS cc_start: 0.8874 (tttm) cc_final: 0.8036 (ttpp) REVERT: A 300 LYS cc_start: 0.8484 (mttm) cc_final: 0.8217 (mttm) REVERT: A 303 GLU cc_start: 0.7899 (mp0) cc_final: 0.7389 (mp0) REVERT: A 314 LYS cc_start: 0.7436 (ttpt) cc_final: 0.7115 (ttmm) REVERT: A 318 SER cc_start: 0.7853 (t) cc_final: 0.7603 (t) REVERT: A 322 LYS cc_start: 0.7925 (tmmt) cc_final: 0.7546 (mtpm) REVERT: A 378 MET cc_start: 0.8356 (mtm) cc_final: 0.8029 (mtm) REVERT: A 596 GLN cc_start: 0.6854 (mt0) cc_final: 0.5968 (mm-40) REVERT: A 628 ARG cc_start: 0.8120 (mtt-85) cc_final: 0.7270 (mpp-170) REVERT: A 635 ASP cc_start: 0.7541 (t70) cc_final: 0.6847 (p0) REVERT: B 51 LEU cc_start: 0.7970 (OUTLIER) cc_final: 0.7513 (tt) REVERT: B 167 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7816 (tp) REVERT: B 174 ASN cc_start: 0.7724 (t0) cc_final: 0.7163 (t0) REVERT: B 262 LYS cc_start: 0.8909 (tttm) cc_final: 0.8148 (ttpp) REVERT: B 303 GLU cc_start: 0.7872 (mp0) cc_final: 0.7413 (mp0) REVERT: B 314 LYS cc_start: 0.7360 (ttpt) cc_final: 0.7061 (ttmm) REVERT: B 318 SER cc_start: 0.7850 (t) cc_final: 0.7609 (t) REVERT: B 322 LYS cc_start: 0.7899 (tmmt) cc_final: 0.7506 (mtpm) REVERT: B 492 ARG cc_start: 0.6030 (OUTLIER) cc_final: 0.4976 (tpp80) REVERT: B 596 GLN cc_start: 0.6883 (mt0) cc_final: 0.5967 (mm-40) REVERT: B 602 VAL cc_start: 0.7783 (t) cc_final: 0.7466 (m) REVERT: B 628 ARG cc_start: 0.8095 (mtt-85) cc_final: 0.7271 (mpp-170) REVERT: B 635 ASP cc_start: 0.7531 (t70) cc_final: 0.6797 (p0) REVERT: C 51 LEU cc_start: 0.7956 (OUTLIER) cc_final: 0.7513 (tt) REVERT: C 113 GLU cc_start: 0.8502 (tt0) cc_final: 0.8258 (tt0) REVERT: C 174 ASN cc_start: 0.7691 (t0) cc_final: 0.7153 (t0) REVERT: C 176 GLU cc_start: 0.8069 (mp0) cc_final: 0.7835 (mp0) REVERT: C 215 MET cc_start: 0.8504 (mmm) cc_final: 0.8301 (tpt) REVERT: C 262 LYS cc_start: 0.8912 (tttm) cc_final: 0.8104 (ttpp) REVERT: C 300 LYS cc_start: 0.8489 (mttm) cc_final: 0.8255 (mttm) REVERT: C 314 LYS cc_start: 0.7385 (ttpt) cc_final: 0.7082 (ttmm) REVERT: C 318 SER cc_start: 0.7856 (t) cc_final: 0.7613 (t) REVERT: C 322 LYS cc_start: 0.7895 (tmmt) cc_final: 0.7520 (mtpm) REVERT: C 374 GLN cc_start: 0.8504 (mp-120) cc_final: 0.8241 (mm-40) REVERT: C 378 MET cc_start: 0.8425 (mtm) cc_final: 0.8027 (mtm) REVERT: C 596 GLN cc_start: 0.6900 (mt0) cc_final: 0.5994 (mm-40) REVERT: C 602 VAL cc_start: 0.7765 (t) cc_final: 0.7471 (m) REVERT: C 628 ARG cc_start: 0.8113 (mtt-85) cc_final: 0.7279 (mpp-170) REVERT: C 635 ASP cc_start: 0.7543 (t70) cc_final: 0.6837 (p0) REVERT: D 51 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.7508 (tt) REVERT: D 113 GLU cc_start: 0.8492 (tt0) cc_final: 0.8229 (tt0) REVERT: D 167 LEU cc_start: 0.8055 (OUTLIER) cc_final: 0.7785 (tp) REVERT: D 174 ASN cc_start: 0.7559 (t0) cc_final: 0.7116 (t0) REVERT: D 215 MET cc_start: 0.8452 (OUTLIER) cc_final: 0.8181 (mmt) REVERT: D 262 LYS cc_start: 0.8904 (tttm) cc_final: 0.8104 (ttpp) REVERT: D 300 LYS cc_start: 0.8496 (mttm) cc_final: 0.8265 (mttm) REVERT: D 303 GLU cc_start: 0.7829 (mp0) cc_final: 0.7443 (mp0) REVERT: D 314 LYS cc_start: 0.7383 (ttpt) cc_final: 0.7081 (ttmm) REVERT: D 318 SER cc_start: 0.7871 (t) cc_final: 0.7625 (t) REVERT: D 322 LYS cc_start: 0.7921 (tmmt) cc_final: 0.7544 (mtpm) REVERT: D 378 MET cc_start: 0.8425 (mtm) cc_final: 0.8062 (mtm) REVERT: D 596 GLN cc_start: 0.6708 (mt0) cc_final: 0.5893 (mm-40) REVERT: D 602 VAL cc_start: 0.7697 (t) cc_final: 0.7423 (m) REVERT: D 621 ARG cc_start: 0.7614 (ttm110) cc_final: 0.7392 (ttp-110) REVERT: D 628 ARG cc_start: 0.8117 (mtt-85) cc_final: 0.7309 (mpp-170) REVERT: D 635 ASP cc_start: 0.7515 (t70) cc_final: 0.6800 (p0) outliers start: 46 outliers final: 31 residues processed: 377 average time/residue: 1.0569 time to fit residues: 463.5816 Evaluate side-chains 370 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 331 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 492 ARG Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 215 MET Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 490 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 82 optimal weight: 2.9990 chunk 211 optimal weight: 1.9990 chunk 172 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 236 optimal weight: 1.9990 chunk 161 optimal weight: 0.8980 chunk 227 optimal weight: 2.9990 chunk 132 optimal weight: 9.9990 chunk 108 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 ASN ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 357 ASN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 357 ASN ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 357 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.181369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.127274 restraints weight = 66701.774| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 2.12 r_work: 0.3460 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3335 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3226 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3226 r_free = 0.3226 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3226 r_free = 0.3226 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3226 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.3803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 21556 Z= 0.136 Angle : 0.587 7.384 29140 Z= 0.292 Chirality : 0.038 0.193 3220 Planarity : 0.004 0.057 3532 Dihedral : 14.000 141.988 4456 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.39 % Favored : 93.52 % Rotamer: Outliers : 2.21 % Allowed : 15.21 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.46 (0.18), residues: 2440 helix: 0.46 (0.14), residues: 1448 sheet: -3.62 (0.47), residues: 84 loop : -1.11 (0.22), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 621 TYR 0.011 0.001 TYR A 216 PHE 0.008 0.001 PHE D 493 TRP 0.006 0.001 TRP B 593 HIS 0.003 0.001 HIS C 426 Details of bonding type rmsd covalent geometry : bond 0.00331 (21556) covalent geometry : angle 0.58732 (29140) hydrogen bonds : bond 0.03893 ( 892) hydrogen bonds : angle 4.45538 ( 2508) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 352 time to evaluate : 1.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7531 (tt) REVERT: A 174 ASN cc_start: 0.7653 (t0) cc_final: 0.7202 (t0) REVERT: A 262 LYS cc_start: 0.8876 (tttm) cc_final: 0.8414 (ttpt) REVERT: A 300 LYS cc_start: 0.8482 (mttm) cc_final: 0.8218 (mttm) REVERT: A 303 GLU cc_start: 0.7919 (mp0) cc_final: 0.7397 (mp0) REVERT: A 314 LYS cc_start: 0.7427 (ttpt) cc_final: 0.7106 (ttmm) REVERT: A 318 SER cc_start: 0.7862 (t) cc_final: 0.7614 (t) REVERT: A 322 LYS cc_start: 0.7906 (tmmt) cc_final: 0.7546 (mtpm) REVERT: A 378 MET cc_start: 0.8391 (mtm) cc_final: 0.8065 (mtm) REVERT: A 596 GLN cc_start: 0.6912 (mt0) cc_final: 0.5957 (mm-40) REVERT: A 628 ARG cc_start: 0.8134 (mtt-85) cc_final: 0.7271 (mpp-170) REVERT: A 635 ASP cc_start: 0.7540 (t70) cc_final: 0.6844 (p0) REVERT: B 51 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7488 (tt) REVERT: B 167 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7833 (tp) REVERT: B 174 ASN cc_start: 0.7727 (t0) cc_final: 0.7181 (t0) REVERT: B 262 LYS cc_start: 0.8934 (tttm) cc_final: 0.8175 (ttpp) REVERT: B 303 GLU cc_start: 0.7886 (mp0) cc_final: 0.7394 (mp0) REVERT: B 314 LYS cc_start: 0.7399 (ttpt) cc_final: 0.7079 (ttmm) REVERT: B 318 SER cc_start: 0.7821 (t) cc_final: 0.7584 (t) REVERT: B 322 LYS cc_start: 0.7901 (tmmt) cc_final: 0.7504 (mtpm) REVERT: B 378 MET cc_start: 0.8558 (mtm) cc_final: 0.8201 (mtm) REVERT: B 492 ARG cc_start: 0.6069 (OUTLIER) cc_final: 0.4984 (tpp80) REVERT: B 596 GLN cc_start: 0.6930 (mt0) cc_final: 0.6007 (mm-40) REVERT: B 602 VAL cc_start: 0.7800 (t) cc_final: 0.7497 (m) REVERT: B 628 ARG cc_start: 0.8096 (mtt-85) cc_final: 0.7264 (mpp-170) REVERT: B 635 ASP cc_start: 0.7519 (t70) cc_final: 0.6782 (p0) REVERT: C 51 LEU cc_start: 0.7947 (OUTLIER) cc_final: 0.7482 (tt) REVERT: C 113 GLU cc_start: 0.8509 (tt0) cc_final: 0.8266 (tt0) REVERT: C 167 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7844 (tp) REVERT: C 174 ASN cc_start: 0.7736 (t0) cc_final: 0.7173 (t0) REVERT: C 176 GLU cc_start: 0.7975 (mp0) cc_final: 0.7738 (mp0) REVERT: C 262 LYS cc_start: 0.8907 (tttm) cc_final: 0.8095 (ttpp) REVERT: C 300 LYS cc_start: 0.8489 (mttm) cc_final: 0.8257 (mttm) REVERT: C 314 LYS cc_start: 0.7434 (ttpt) cc_final: 0.7110 (ttmm) REVERT: C 318 SER cc_start: 0.7845 (t) cc_final: 0.7607 (t) REVERT: C 322 LYS cc_start: 0.7917 (tmmt) cc_final: 0.7526 (mtpm) REVERT: C 596 GLN cc_start: 0.6910 (mt0) cc_final: 0.5998 (mm-40) REVERT: C 602 VAL cc_start: 0.7788 (t) cc_final: 0.7491 (m) REVERT: C 628 ARG cc_start: 0.8094 (mtt-85) cc_final: 0.7246 (mpp-170) REVERT: C 635 ASP cc_start: 0.7547 (t70) cc_final: 0.6808 (p0) REVERT: D 51 LEU cc_start: 0.7956 (OUTLIER) cc_final: 0.7501 (tt) REVERT: D 113 GLU cc_start: 0.8480 (tt0) cc_final: 0.8220 (tt0) REVERT: D 167 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7828 (tp) REVERT: D 174 ASN cc_start: 0.7524 (t0) cc_final: 0.7135 (t0) REVERT: D 262 LYS cc_start: 0.8900 (tttm) cc_final: 0.8084 (ttpp) REVERT: D 300 LYS cc_start: 0.8493 (mttm) cc_final: 0.8252 (mttm) REVERT: D 303 GLU cc_start: 0.7862 (mp0) cc_final: 0.7461 (mp0) REVERT: D 314 LYS cc_start: 0.7411 (ttpt) cc_final: 0.7089 (ttmm) REVERT: D 318 SER cc_start: 0.7842 (t) cc_final: 0.7600 (t) REVERT: D 322 LYS cc_start: 0.7926 (tmmt) cc_final: 0.7533 (mtpm) REVERT: D 378 MET cc_start: 0.8472 (mtm) cc_final: 0.8096 (mtm) REVERT: D 596 GLN cc_start: 0.6707 (mt0) cc_final: 0.5906 (mm-40) REVERT: D 602 VAL cc_start: 0.7725 (t) cc_final: 0.7444 (m) REVERT: D 621 ARG cc_start: 0.7616 (ttm110) cc_final: 0.7389 (ttp-110) REVERT: D 628 ARG cc_start: 0.8126 (mtt-85) cc_final: 0.7297 (mpp-170) REVERT: D 635 ASP cc_start: 0.7519 (t70) cc_final: 0.6796 (p0) outliers start: 47 outliers final: 27 residues processed: 384 average time/residue: 1.0982 time to fit residues: 492.2128 Evaluate side-chains 370 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 335 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 492 ARG Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 490 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 99 optimal weight: 0.0770 chunk 198 optimal weight: 6.9990 chunk 121 optimal weight: 6.9990 chunk 68 optimal weight: 8.9990 chunk 147 optimal weight: 6.9990 chunk 179 optimal weight: 4.9990 chunk 23 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 overall best weight: 1.7544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 ASN ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 357 ASN C 357 ASN ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 357 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.179954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.124930 restraints weight = 66925.571| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 2.16 r_work: 0.3441 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3218 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3218 r_free = 0.3218 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3218 r_free = 0.3218 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3218 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.3906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21556 Z= 0.141 Angle : 0.587 7.326 29140 Z= 0.292 Chirality : 0.038 0.190 3220 Planarity : 0.004 0.069 3532 Dihedral : 13.784 136.385 4456 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 2.31 % Allowed : 16.01 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.32 (0.18), residues: 2440 helix: 0.55 (0.14), residues: 1452 sheet: -3.59 (0.47), residues: 84 loop : -1.01 (0.22), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 75 TYR 0.012 0.001 TYR A 216 PHE 0.009 0.001 PHE B 493 TRP 0.006 0.001 TRP B 593 HIS 0.003 0.001 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00340 (21556) covalent geometry : angle 0.58736 (29140) hydrogen bonds : bond 0.03831 ( 892) hydrogen bonds : angle 4.41238 ( 2508) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 346 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7516 (tt) REVERT: A 174 ASN cc_start: 0.7685 (t0) cc_final: 0.7221 (t0) REVERT: A 262 LYS cc_start: 0.8905 (tttm) cc_final: 0.8330 (mttm) REVERT: A 300 LYS cc_start: 0.8498 (mttm) cc_final: 0.8239 (mttm) REVERT: A 303 GLU cc_start: 0.7948 (mp0) cc_final: 0.7406 (mp0) REVERT: A 314 LYS cc_start: 0.7460 (ttpt) cc_final: 0.7138 (ttmm) REVERT: A 322 LYS cc_start: 0.7937 (tmmt) cc_final: 0.7574 (mtpm) REVERT: A 378 MET cc_start: 0.8417 (mtm) cc_final: 0.8097 (mtm) REVERT: A 596 GLN cc_start: 0.6967 (mt0) cc_final: 0.6022 (mm-40) REVERT: A 628 ARG cc_start: 0.8130 (mtt-85) cc_final: 0.7280 (mpp-170) REVERT: A 635 ASP cc_start: 0.7578 (t70) cc_final: 0.6836 (p0) REVERT: B 51 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7496 (tt) REVERT: B 167 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7890 (tp) REVERT: B 174 ASN cc_start: 0.7725 (t0) cc_final: 0.7197 (t0) REVERT: B 262 LYS cc_start: 0.8896 (tttm) cc_final: 0.8141 (ttpp) REVERT: B 303 GLU cc_start: 0.7940 (mp0) cc_final: 0.7442 (mp0) REVERT: B 314 LYS cc_start: 0.7411 (ttpt) cc_final: 0.7086 (ttmm) REVERT: B 318 SER cc_start: 0.7863 (t) cc_final: 0.7629 (t) REVERT: B 322 LYS cc_start: 0.7918 (tmmt) cc_final: 0.7518 (mtpm) REVERT: B 378 MET cc_start: 0.8572 (mtm) cc_final: 0.8228 (mtm) REVERT: B 492 ARG cc_start: 0.5989 (OUTLIER) cc_final: 0.4821 (tpp80) REVERT: B 596 GLN cc_start: 0.6955 (mt0) cc_final: 0.6029 (mm-40) REVERT: B 602 VAL cc_start: 0.7812 (t) cc_final: 0.7511 (m) REVERT: B 628 ARG cc_start: 0.8094 (mtt-85) cc_final: 0.7262 (mpp-170) REVERT: B 635 ASP cc_start: 0.7533 (t70) cc_final: 0.6784 (p0) REVERT: C 51 LEU cc_start: 0.7956 (OUTLIER) cc_final: 0.7487 (tt) REVERT: C 113 GLU cc_start: 0.8518 (tt0) cc_final: 0.8279 (tt0) REVERT: C 167 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7859 (tp) REVERT: C 174 ASN cc_start: 0.7753 (t0) cc_final: 0.7206 (t0) REVERT: C 262 LYS cc_start: 0.8898 (tttm) cc_final: 0.8094 (ttpp) REVERT: C 300 LYS cc_start: 0.8497 (mttm) cc_final: 0.8257 (mttm) REVERT: C 303 GLU cc_start: 0.7939 (mp0) cc_final: 0.7444 (mp0) REVERT: C 314 LYS cc_start: 0.7459 (ttpt) cc_final: 0.7131 (ttmm) REVERT: C 318 SER cc_start: 0.7885 (t) cc_final: 0.7649 (t) REVERT: C 322 LYS cc_start: 0.7935 (tmmt) cc_final: 0.7547 (mtpm) REVERT: C 378 MET cc_start: 0.8612 (mtm) cc_final: 0.8284 (mtm) REVERT: C 410 MET cc_start: 0.6961 (mtm) cc_final: 0.6731 (mtp) REVERT: C 596 GLN cc_start: 0.6969 (mt0) cc_final: 0.6028 (mm-40) REVERT: C 602 VAL cc_start: 0.7810 (t) cc_final: 0.7527 (m) REVERT: C 628 ARG cc_start: 0.8116 (mtt-85) cc_final: 0.7277 (mpp-170) REVERT: C 635 ASP cc_start: 0.7575 (t70) cc_final: 0.6826 (p0) REVERT: D 51 LEU cc_start: 0.7939 (OUTLIER) cc_final: 0.7478 (tt) REVERT: D 113 GLU cc_start: 0.8475 (tt0) cc_final: 0.8219 (tt0) REVERT: D 167 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7899 (tp) REVERT: D 174 ASN cc_start: 0.7552 (t0) cc_final: 0.7231 (t0) REVERT: D 262 LYS cc_start: 0.8898 (tttm) cc_final: 0.8099 (ttpp) REVERT: D 300 LYS cc_start: 0.8471 (mttm) cc_final: 0.8235 (mttm) REVERT: D 303 GLU cc_start: 0.7931 (mp0) cc_final: 0.7510 (mp0) REVERT: D 314 LYS cc_start: 0.7412 (ttpt) cc_final: 0.7087 (ttmm) REVERT: D 318 SER cc_start: 0.7878 (t) cc_final: 0.7641 (t) REVERT: D 322 LYS cc_start: 0.7944 (tmmt) cc_final: 0.7560 (mtpm) REVERT: D 378 MET cc_start: 0.8504 (mtm) cc_final: 0.8140 (mtm) REVERT: D 474 MET cc_start: 0.1853 (mtt) cc_final: 0.1503 (mtt) REVERT: D 596 GLN cc_start: 0.6734 (mt0) cc_final: 0.5928 (mm-40) REVERT: D 602 VAL cc_start: 0.7776 (t) cc_final: 0.7487 (m) REVERT: D 621 ARG cc_start: 0.7593 (ttm110) cc_final: 0.7363 (ttp-110) REVERT: D 628 ARG cc_start: 0.8129 (mtt-85) cc_final: 0.7301 (mpp-170) REVERT: D 635 ASP cc_start: 0.7531 (t70) cc_final: 0.6784 (p0) outliers start: 49 outliers final: 30 residues processed: 379 average time/residue: 1.2226 time to fit residues: 536.0034 Evaluate side-chains 366 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 328 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 492 ARG Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 490 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 228 optimal weight: 6.9990 chunk 118 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 231 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 229 optimal weight: 5.9990 chunk 77 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 236 optimal weight: 0.9990 chunk 86 optimal weight: 6.9990 chunk 78 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 ASN ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 357 ASN C 357 ASN ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 357 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.179998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.125039 restraints weight = 67171.430| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 2.15 r_work: 0.3438 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3313 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3226 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3226 r_free = 0.3226 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3226 r_free = 0.3226 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3226 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.4011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 21556 Z= 0.134 Angle : 0.585 8.039 29140 Z= 0.293 Chirality : 0.038 0.181 3220 Planarity : 0.004 0.060 3532 Dihedral : 13.410 129.244 4456 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 1.93 % Allowed : 16.53 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.18), residues: 2440 helix: 0.58 (0.14), residues: 1468 sheet: -3.56 (0.47), residues: 84 loop : -0.86 (0.22), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 75 TYR 0.017 0.001 TYR A 216 PHE 0.008 0.001 PHE D 493 TRP 0.007 0.001 TRP A 593 HIS 0.003 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00324 (21556) covalent geometry : angle 0.58492 (29140) hydrogen bonds : bond 0.03744 ( 892) hydrogen bonds : angle 4.36328 ( 2508) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 339 time to evaluate : 1.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LEU cc_start: 0.7993 (OUTLIER) cc_final: 0.7510 (tt) REVERT: A 174 ASN cc_start: 0.7687 (t0) cc_final: 0.7379 (t0) REVERT: A 176 GLU cc_start: 0.7949 (mp0) cc_final: 0.7501 (pt0) REVERT: A 262 LYS cc_start: 0.8896 (tttm) cc_final: 0.8316 (mttm) REVERT: A 300 LYS cc_start: 0.8470 (mttm) cc_final: 0.8209 (mttm) REVERT: A 303 GLU cc_start: 0.7961 (mp0) cc_final: 0.7416 (mp0) REVERT: A 314 LYS cc_start: 0.7483 (ttpt) cc_final: 0.7117 (ttmm) REVERT: A 322 LYS cc_start: 0.7937 (tmmt) cc_final: 0.7564 (mtpm) REVERT: A 378 MET cc_start: 0.8472 (mtm) cc_final: 0.8122 (mtm) REVERT: A 596 GLN cc_start: 0.7006 (mt0) cc_final: 0.6027 (mm-40) REVERT: A 628 ARG cc_start: 0.8117 (mtt-85) cc_final: 0.7269 (mpp-170) REVERT: A 635 ASP cc_start: 0.7558 (t70) cc_final: 0.6816 (p0) REVERT: B 51 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7496 (tt) REVERT: B 160 ILE cc_start: 0.8661 (pp) cc_final: 0.8410 (pp) REVERT: B 174 ASN cc_start: 0.7687 (t0) cc_final: 0.7378 (t0) REVERT: B 176 GLU cc_start: 0.7999 (mp0) cc_final: 0.7397 (mt-10) REVERT: B 262 LYS cc_start: 0.8905 (tttm) cc_final: 0.8149 (ttpp) REVERT: B 303 GLU cc_start: 0.7960 (mp0) cc_final: 0.7440 (mp0) REVERT: B 314 LYS cc_start: 0.7395 (ttpt) cc_final: 0.7066 (ttmm) REVERT: B 318 SER cc_start: 0.7864 (t) cc_final: 0.7631 (t) REVERT: B 322 LYS cc_start: 0.7932 (tmmt) cc_final: 0.7527 (mtpm) REVERT: B 378 MET cc_start: 0.8573 (mtm) cc_final: 0.8219 (mtm) REVERT: B 492 ARG cc_start: 0.5952 (OUTLIER) cc_final: 0.4829 (tpp80) REVERT: B 596 GLN cc_start: 0.6948 (mt0) cc_final: 0.6009 (mm-40) REVERT: B 602 VAL cc_start: 0.7828 (t) cc_final: 0.7522 (m) REVERT: B 628 ARG cc_start: 0.8071 (mtt-85) cc_final: 0.7248 (mpp-170) REVERT: B 635 ASP cc_start: 0.7537 (t70) cc_final: 0.6772 (p0) REVERT: C 51 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.7489 (tt) REVERT: C 113 GLU cc_start: 0.8501 (tt0) cc_final: 0.8296 (tt0) REVERT: C 160 ILE cc_start: 0.8653 (pp) cc_final: 0.8401 (pp) REVERT: C 174 ASN cc_start: 0.7688 (t0) cc_final: 0.7376 (t0) REVERT: C 176 GLU cc_start: 0.7905 (mp0) cc_final: 0.7296 (mt-10) REVERT: C 262 LYS cc_start: 0.8903 (tttm) cc_final: 0.8101 (ttpp) REVERT: C 300 LYS cc_start: 0.8506 (mttm) cc_final: 0.8267 (mttm) REVERT: C 303 GLU cc_start: 0.7956 (mp0) cc_final: 0.7439 (mp0) REVERT: C 314 LYS cc_start: 0.7439 (ttpt) cc_final: 0.7109 (ttmm) REVERT: C 318 SER cc_start: 0.7896 (t) cc_final: 0.7662 (t) REVERT: C 322 LYS cc_start: 0.7926 (tmmt) cc_final: 0.7528 (mtpm) REVERT: C 378 MET cc_start: 0.8622 (mtm) cc_final: 0.8253 (mtm) REVERT: C 596 GLN cc_start: 0.6995 (mt0) cc_final: 0.6043 (mm-40) REVERT: C 602 VAL cc_start: 0.7822 (t) cc_final: 0.7536 (m) REVERT: C 628 ARG cc_start: 0.8108 (mtt-85) cc_final: 0.7260 (mpp-170) REVERT: C 635 ASP cc_start: 0.7579 (t70) cc_final: 0.6821 (p0) REVERT: D 51 LEU cc_start: 0.7950 (OUTLIER) cc_final: 0.7459 (tt) REVERT: D 113 GLU cc_start: 0.8480 (tt0) cc_final: 0.8226 (tt0) REVERT: D 174 ASN cc_start: 0.7586 (t0) cc_final: 0.7178 (t0) REVERT: D 176 GLU cc_start: 0.7974 (mp0) cc_final: 0.7735 (mp0) REVERT: D 262 LYS cc_start: 0.8905 (tttm) cc_final: 0.8106 (ttpp) REVERT: D 300 LYS cc_start: 0.8435 (mttm) cc_final: 0.8208 (mttm) REVERT: D 303 GLU cc_start: 0.7945 (mp0) cc_final: 0.7462 (mp0) REVERT: D 314 LYS cc_start: 0.7419 (ttpt) cc_final: 0.7091 (ttmm) REVERT: D 318 SER cc_start: 0.7880 (t) cc_final: 0.7643 (t) REVERT: D 322 LYS cc_start: 0.7941 (tmmt) cc_final: 0.7545 (mtpm) REVERT: D 474 MET cc_start: 0.1923 (mtt) cc_final: 0.1584 (mtt) REVERT: D 596 GLN cc_start: 0.6758 (mt0) cc_final: 0.5931 (mm-40) REVERT: D 602 VAL cc_start: 0.7838 (t) cc_final: 0.7565 (m) REVERT: D 621 ARG cc_start: 0.7616 (ttm110) cc_final: 0.7389 (ttp-110) REVERT: D 628 ARG cc_start: 0.8107 (mtt-85) cc_final: 0.7273 (mpp-170) REVERT: D 635 ASP cc_start: 0.7565 (t70) cc_final: 0.6772 (p0) outliers start: 41 outliers final: 28 residues processed: 367 average time/residue: 1.2923 time to fit residues: 547.8509 Evaluate side-chains 366 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 333 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 492 ARG Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 490 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 81 optimal weight: 0.6980 chunk 167 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 144 optimal weight: 3.9990 chunk 121 optimal weight: 5.9990 chunk 123 optimal weight: 2.9990 chunk 8 optimal weight: 10.0000 chunk 152 optimal weight: 0.7980 chunk 117 optimal weight: 10.0000 chunk 109 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 357 ASN C 357 ASN ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 357 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.180579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.125644 restraints weight = 66658.721| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 2.15 r_work: 0.3447 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3322 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3219 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3219 r_free = 0.3219 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3219 r_free = 0.3219 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3219 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.4076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 21556 Z= 0.122 Angle : 0.577 6.483 29140 Z= 0.289 Chirality : 0.037 0.179 3220 Planarity : 0.004 0.060 3532 Dihedral : 12.969 121.516 4456 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 1.88 % Allowed : 17.00 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.08 (0.18), residues: 2440 helix: 0.69 (0.14), residues: 1464 sheet: -3.51 (0.47), residues: 84 loop : -0.84 (0.22), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 621 TYR 0.014 0.001 TYR A 216 PHE 0.008 0.001 PHE D 493 TRP 0.009 0.001 TRP B 593 HIS 0.003 0.001 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00294 (21556) covalent geometry : angle 0.57687 (29140) hydrogen bonds : bond 0.03632 ( 892) hydrogen bonds : angle 4.33118 ( 2508) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 345 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7488 (tt) REVERT: A 75 ARG cc_start: 0.7477 (mtt90) cc_final: 0.7188 (mtt90) REVERT: A 174 ASN cc_start: 0.7669 (t0) cc_final: 0.7209 (t0) REVERT: A 262 LYS cc_start: 0.8888 (tttm) cc_final: 0.8296 (mttm) REVERT: A 300 LYS cc_start: 0.8469 (mttm) cc_final: 0.8204 (mttm) REVERT: A 303 GLU cc_start: 0.7934 (mp0) cc_final: 0.7353 (mp0) REVERT: A 314 LYS cc_start: 0.7456 (ttpt) cc_final: 0.7090 (ttmm) REVERT: A 322 LYS cc_start: 0.7922 (tmmt) cc_final: 0.7539 (mtpm) REVERT: A 378 MET cc_start: 0.8478 (mtm) cc_final: 0.8179 (mtm) REVERT: A 596 GLN cc_start: 0.6971 (mt0) cc_final: 0.5987 (mm-40) REVERT: A 628 ARG cc_start: 0.8069 (mtt-85) cc_final: 0.7211 (mpp-170) REVERT: A 635 ASP cc_start: 0.7545 (t70) cc_final: 0.6764 (p0) REVERT: B 51 LEU cc_start: 0.7976 (OUTLIER) cc_final: 0.7490 (tt) REVERT: B 160 ILE cc_start: 0.8620 (pp) cc_final: 0.8365 (pp) REVERT: B 174 ASN cc_start: 0.7693 (t0) cc_final: 0.7215 (t0) REVERT: B 262 LYS cc_start: 0.8897 (tttm) cc_final: 0.8142 (ttpp) REVERT: B 303 GLU cc_start: 0.7950 (mp0) cc_final: 0.7420 (mp0) REVERT: B 314 LYS cc_start: 0.7367 (ttpt) cc_final: 0.7035 (ttmm) REVERT: B 318 SER cc_start: 0.7819 (t) cc_final: 0.7584 (t) REVERT: B 322 LYS cc_start: 0.7905 (tmmt) cc_final: 0.7495 (mtpm) REVERT: B 378 MET cc_start: 0.8573 (mtm) cc_final: 0.8226 (mtm) REVERT: B 596 GLN cc_start: 0.6903 (mt0) cc_final: 0.5947 (mm-40) REVERT: B 602 VAL cc_start: 0.7782 (t) cc_final: 0.7483 (m) REVERT: B 628 ARG cc_start: 0.8056 (mtt-85) cc_final: 0.7201 (mpp-170) REVERT: B 635 ASP cc_start: 0.7536 (t70) cc_final: 0.6745 (p0) REVERT: C 51 LEU cc_start: 0.7945 (OUTLIER) cc_final: 0.7470 (tt) REVERT: C 113 GLU cc_start: 0.8479 (tt0) cc_final: 0.8277 (tt0) REVERT: C 160 ILE cc_start: 0.8623 (pp) cc_final: 0.8370 (pp) REVERT: C 174 ASN cc_start: 0.7685 (t0) cc_final: 0.7152 (t0) REVERT: C 262 LYS cc_start: 0.8894 (tttm) cc_final: 0.8085 (ttpp) REVERT: C 300 LYS cc_start: 0.8493 (mttm) cc_final: 0.8250 (mttm) REVERT: C 303 GLU cc_start: 0.7939 (mp0) cc_final: 0.7413 (mp0) REVERT: C 314 LYS cc_start: 0.7389 (ttpt) cc_final: 0.7056 (ttmm) REVERT: C 318 SER cc_start: 0.7844 (t) cc_final: 0.7608 (t) REVERT: C 322 LYS cc_start: 0.7910 (tmmt) cc_final: 0.7505 (mtpm) REVERT: C 378 MET cc_start: 0.8569 (mtm) cc_final: 0.8221 (mtm) REVERT: C 596 GLN cc_start: 0.6996 (mt0) cc_final: 0.6002 (mm-40) REVERT: C 602 VAL cc_start: 0.7826 (t) cc_final: 0.7560 (m) REVERT: C 628 ARG cc_start: 0.8076 (mtt-85) cc_final: 0.7221 (mpp-170) REVERT: C 635 ASP cc_start: 0.7546 (t70) cc_final: 0.6759 (p0) REVERT: D 51 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7445 (tt) REVERT: D 113 GLU cc_start: 0.8453 (tt0) cc_final: 0.8196 (tt0) REVERT: D 174 ASN cc_start: 0.7619 (t0) cc_final: 0.7180 (t0) REVERT: D 262 LYS cc_start: 0.8893 (tttm) cc_final: 0.8093 (ttpp) REVERT: D 300 LYS cc_start: 0.8449 (mttm) cc_final: 0.8209 (mttm) REVERT: D 303 GLU cc_start: 0.7937 (mp0) cc_final: 0.7428 (mp0) REVERT: D 314 LYS cc_start: 0.7361 (ttpt) cc_final: 0.7030 (ttmm) REVERT: D 318 SER cc_start: 0.7844 (t) cc_final: 0.7603 (t) REVERT: D 322 LYS cc_start: 0.7915 (tmmt) cc_final: 0.7515 (mtpm) REVERT: D 378 MET cc_start: 0.8585 (mtm) cc_final: 0.8212 (mtm) REVERT: D 474 MET cc_start: 0.1830 (mtt) cc_final: 0.1504 (mtt) REVERT: D 596 GLN cc_start: 0.6752 (mt0) cc_final: 0.5920 (mm-40) REVERT: D 602 VAL cc_start: 0.7824 (t) cc_final: 0.7552 (m) REVERT: D 621 ARG cc_start: 0.7580 (ttm110) cc_final: 0.7346 (ttp-110) REVERT: D 628 ARG cc_start: 0.8077 (mtt-85) cc_final: 0.7227 (mpp-170) REVERT: D 635 ASP cc_start: 0.7524 (t70) cc_final: 0.6700 (p0) outliers start: 40 outliers final: 29 residues processed: 372 average time/residue: 1.1359 time to fit residues: 490.7493 Evaluate side-chains 366 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 333 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 492 ARG Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 490 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 187 optimal weight: 8.9990 chunk 234 optimal weight: 1.9990 chunk 129 optimal weight: 10.0000 chunk 228 optimal weight: 6.9990 chunk 2 optimal weight: 6.9990 chunk 61 optimal weight: 10.0000 chunk 3 optimal weight: 4.9990 chunk 48 optimal weight: 0.2980 chunk 32 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 overall best weight: 2.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 357 ASN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 357 ASN ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 357 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.179387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.124154 restraints weight = 67332.745| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 2.15 r_work: 0.3432 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3217 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3217 r_free = 0.3217 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3217 r_free = 0.3217 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3217 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.4154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 21556 Z= 0.154 Angle : 0.587 6.493 29140 Z= 0.294 Chirality : 0.039 0.178 3220 Planarity : 0.004 0.059 3532 Dihedral : 12.975 112.982 4456 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 1.84 % Allowed : 17.18 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.12 (0.18), residues: 2440 helix: 0.66 (0.14), residues: 1468 sheet: -3.52 (0.47), residues: 84 loop : -0.84 (0.22), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 621 TYR 0.011 0.001 TYR A 216 PHE 0.008 0.001 PHE D 493 TRP 0.006 0.001 TRP B 613 HIS 0.003 0.001 HIS D 201 Details of bonding type rmsd covalent geometry : bond 0.00374 (21556) covalent geometry : angle 0.58729 (29140) hydrogen bonds : bond 0.03725 ( 892) hydrogen bonds : angle 4.36118 ( 2508) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16706.72 seconds wall clock time: 282 minutes 21.22 seconds (16941.22 seconds total)