Starting phenix.real_space_refine on Thu Dec 26 03:54:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sp8_40676/12_2024/8sp8_40676_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sp8_40676/12_2024/8sp8_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8sp8_40676/12_2024/8sp8_40676.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sp8_40676/12_2024/8sp8_40676.map" model { file = "/net/cci-nas-00/data/ceres_data/8sp8_40676/12_2024/8sp8_40676_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sp8_40676/12_2024/8sp8_40676_trim.cif" } resolution = 2.79 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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-3': 3, 'POV:plan-2': 3, 'POV:plan-1': 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-3': 3, 'POV:plan-2': 3, 'POV:plan-1': 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-3': 3, 'POV:plan-2': 3, 'POV:plan-1': 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-3': 3, 'POV:plan-2': 3, 'POV:plan-1': 3} Unresolved non-hydrogen planarities: 34 Time building chain proxies: 19.10, per 1000 atoms: 0.47 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: 11.63 Conformation dependent library (CDL) restraints added in 3.4 seconds 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: 3.21 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: 16.17 Time building geometry restraints manager: 13.08 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: 0.950 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: 0.700 Extract box with map and model: 1.630 Check model and map are aligned: 0.300 Set scattering table: 0.410 Process input model: 82.850 Find NCS groups from input model: 1.730 Set up NCS constraints: 0.150 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:13.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.140 ------------------------------------------------------------------------------- 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= 0.856 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 : 2.78 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.013 0.003 TRP A 629 HIS 0.010 0.002 HIS A 582 PHE 0.021 0.003 PHE D 537 TYR 0.022 0.003 TYR C 547 ARG 0.011 0.001 ARG A 492 *********************** 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 : 3.045 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: 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: 0.8237 (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: 0.7960 (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: 0.6790 (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: 0.8225 (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: 0.7786 (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: 0.6959 (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: 0.7951 (ttpp) REVERT: D 300 LYS cc_start: 0.8412 (mttm) cc_final: 0.8208 (mttm) REVERT: D 303 GLU cc_start: 0.7602 (mp0) cc_final: 0.7137 (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: 0.7825 (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: 0.6944 (mtp) REVERT: D 602 VAL cc_start: 0.7595 (t) cc_final: 0.7388 (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: 3.0074 time to fit residues: 1832.1671 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 : 3.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 206 optimal weight: 1.9990 chunk 184 optimal weight: 0.9990 chunk 102 optimal weight: 0.7980 chunk 63 optimal weight: 7.9990 chunk 124 optimal weight: 5.9990 chunk 98 optimal weight: 0.8980 chunk 191 optimal weight: 5.9990 chunk 74 optimal weight: 0.9980 chunk 116 optimal weight: 3.9990 chunk 142 optimal weight: 0.6980 chunk 221 optimal weight: 6.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN A 197 ASN A 357 ASN A 582 HIS A 637 GLN 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 C 637 GLN D 31 GLN D 118 GLN D 197 ASN D 357 ASN D 582 HIS D 637 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 21556 Z= 0.238 Angle : 0.737 12.339 29140 Z= 0.373 Chirality : 0.040 0.240 3220 Planarity : 0.006 0.077 3532 Dihedral : 18.155 159.863 4456 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.02 % Favored : 93.81 % Rotamer: Outliers : 1.51 % Allowed : 12.15 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.90 (0.16), residues: 2440 helix: -1.74 (0.12), residues: 1420 sheet: -3.28 (0.36), residues: 124 loop : -1.72 (0.23), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 593 HIS 0.005 0.001 HIS B 582 PHE 0.016 0.001 PHE B 493 TYR 0.015 0.002 TYR C 377 ARG 0.006 0.001 ARG B 492 *********************** 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 404 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 372 time to evaluate : 3.052 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 174 ASN cc_start: 0.7556 (t0) cc_final: 0.7018 (t0) REVERT: A 208 ASN cc_start: 0.8167 (t0) cc_final: 0.7869 (t0) REVERT: A 262 LYS cc_start: 0.8589 (tttm) cc_final: 0.7947 (ttpp) REVERT: A 300 LYS cc_start: 0.8421 (mttm) cc_final: 0.8201 (mttm) REVERT: A 303 GLU cc_start: 0.7456 (mp0) cc_final: 0.7115 (mp0) REVERT: A 318 SER cc_start: 0.7572 (t) cc_final: 0.7055 (m) REVERT: A 322 LYS cc_start: 0.7801 (tmmt) cc_final: 0.7450 (mtpm) REVERT: A 410 MET cc_start: 0.7091 (OUTLIER) cc_final: 0.6512 (mtp) REVERT: A 554 MET cc_start: 0.8906 (tpt) cc_final: 0.8254 (tpt) REVERT: A 596 GLN cc_start: 0.6744 (mt0) cc_final: 0.6083 (mm-40) REVERT: A 628 ARG cc_start: 0.8152 (mtt-85) cc_final: 0.7469 (mpp-170) REVERT: A 635 ASP cc_start: 0.7043 (t70) cc_final: 0.6621 (p0) REVERT: B 174 ASN cc_start: 0.7524 (t0) cc_final: 0.6850 (t0) REVERT: B 262 LYS cc_start: 0.8631 (tttm) cc_final: 0.8005 (ttpp) REVERT: B 314 LYS cc_start: 0.7390 (ttpt) cc_final: 0.7010 (ttmm) REVERT: B 315 GLU cc_start: 0.8093 (mp0) cc_final: 0.7301 (mp0) REVERT: B 318 SER cc_start: 0.7712 (t) cc_final: 0.7490 (t) REVERT: B 322 LYS cc_start: 0.7864 (tmmt) cc_final: 0.7509 (mtpm) REVERT: B 410 MET cc_start: 0.6604 (mtp) cc_final: 0.6402 (mtm) REVERT: B 602 VAL cc_start: 0.7677 (t) cc_final: 0.7460 (m) REVERT: B 628 ARG cc_start: 0.8189 (mtt-85) cc_final: 0.7536 (mpp-170) REVERT: B 635 ASP cc_start: 0.6982 (t70) cc_final: 0.6642 (p0) REVERT: C 174 ASN cc_start: 0.7489 (t0) cc_final: 0.6861 (t0) REVERT: C 208 ASN cc_start: 0.8237 (t0) cc_final: 0.7968 (t0) REVERT: C 211 PHE cc_start: 0.8777 (m-10) cc_final: 0.8522 (m-10) REVERT: C 262 LYS cc_start: 0.8610 (tttm) cc_final: 0.7962 (ttpp) REVERT: C 300 LYS cc_start: 0.8414 (mttm) cc_final: 0.8202 (mttm) REVERT: C 314 LYS cc_start: 0.7324 (ttpt) cc_final: 0.6687 (ttmm) REVERT: C 318 SER cc_start: 0.7592 (t) cc_final: 0.7037 (m) REVERT: C 322 LYS cc_start: 0.7795 (tmmt) cc_final: 0.7455 (mtpm) REVERT: C 328 TYR cc_start: 0.8569 (m-10) cc_final: 0.8365 (m-80) REVERT: C 596 GLN cc_start: 0.6617 (mt0) cc_final: 0.5996 (mm-40) REVERT: C 628 ARG cc_start: 0.8175 (mtt-85) cc_final: 0.7478 (mpp-170) REVERT: C 635 ASP cc_start: 0.6998 (t70) cc_final: 0.6569 (p0) REVERT: D 174 ASN cc_start: 0.7446 (t0) cc_final: 0.6906 (t0) REVERT: D 211 PHE cc_start: 0.8677 (m-10) cc_final: 0.8472 (m-10) REVERT: D 262 LYS cc_start: 0.8647 (tttm) cc_final: 0.7986 (ttpp) REVERT: D 303 GLU cc_start: 0.7480 (mp0) cc_final: 0.7114 (mp0) REVERT: D 314 LYS cc_start: 0.7344 (ttpt) cc_final: 0.6958 (ttmm) REVERT: D 315 GLU cc_start: 0.8082 (mp0) cc_final: 0.7167 (mp0) REVERT: D 318 SER cc_start: 0.7666 (t) cc_final: 0.7435 (t) REVERT: D 322 LYS cc_start: 0.7819 (tmmt) cc_final: 0.7475 (mtpm) REVERT: D 328 TYR cc_start: 0.8542 (m-10) cc_final: 0.8329 (m-80) REVERT: D 410 MET cc_start: 0.7133 (OUTLIER) cc_final: 0.6503 (mtp) REVERT: D 554 MET cc_start: 0.8919 (tpt) cc_final: 0.8430 (tpt) REVERT: D 596 GLN cc_start: 0.6716 (mt0) cc_final: 0.6105 (mm-40) REVERT: D 628 ARG cc_start: 0.8208 (mtt-85) cc_final: 0.7523 (mpp-170) REVERT: D 635 ASP cc_start: 0.6975 (t70) cc_final: 0.6649 (p0) outliers start: 32 outliers final: 12 residues processed: 394 average time/residue: 2.5774 time to fit residues: 1174.2306 Evaluate side-chains 347 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 333 time to evaluate : 3.016 ------------------------------------------------------------------------------- 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 A residue 410 MET 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 Chi-restraints excluded: chain D residue 410 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 123 optimal weight: 7.9990 chunk 68 optimal weight: 9.9990 chunk 184 optimal weight: 7.9990 chunk 150 optimal weight: 4.9990 chunk 61 optimal weight: 10.0000 chunk 221 optimal weight: 0.9990 chunk 239 optimal weight: 2.9990 chunk 197 optimal weight: 0.9990 chunk 220 optimal weight: 0.8980 chunk 75 optimal weight: 5.9990 chunk 178 optimal weight: 6.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 546 ASN C 91 ASN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 21556 Z= 0.274 Angle : 0.681 10.234 29140 Z= 0.335 Chirality : 0.040 0.205 3220 Planarity : 0.005 0.058 3532 Dihedral : 16.319 157.294 4456 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 1.98 % Allowed : 12.85 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.17), residues: 2440 helix: -0.67 (0.13), residues: 1444 sheet: -3.73 (0.48), residues: 84 loop : -1.42 (0.22), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 593 HIS 0.004 0.001 HIS B 426 PHE 0.014 0.001 PHE C 478 TYR 0.011 0.002 TYR A 324 ARG 0.007 0.001 ARG C 492 *********************** 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 413 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 371 time to evaluate : 3.328 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: 0.8057 (OUTLIER) cc_final: 0.7648 (tt) REVERT: A 174 ASN cc_start: 0.7595 (t0) cc_final: 0.7065 (t0) REVERT: A 262 LYS cc_start: 0.8757 (tttm) cc_final: 0.7950 (ttpp) REVERT: A 300 LYS cc_start: 0.8412 (mttm) cc_final: 0.8201 (mttm) REVERT: A 303 GLU cc_start: 0.7538 (mp0) cc_final: 0.7105 (mp0) REVERT: A 306 GLN cc_start: 0.8049 (mt0) cc_final: 0.7842 (mt0) REVERT: A 314 LYS cc_start: 0.7324 (ttpt) cc_final: 0.6914 (ttmm) REVERT: A 315 GLU cc_start: 0.7995 (mp0) cc_final: 0.7109 (mp0) REVERT: A 318 SER cc_start: 0.7615 (t) cc_final: 0.7395 (t) REVERT: A 322 LYS cc_start: 0.7814 (tmmt) cc_final: 0.7473 (mtpm) REVERT: A 492 ARG cc_start: 0.6109 (tpp80) cc_final: 0.5652 (tpp80) REVERT: A 596 GLN cc_start: 0.6675 (mt0) cc_final: 0.6006 (mm-40) REVERT: A 628 ARG cc_start: 0.8122 (mtt-85) cc_final: 0.7416 (mpp-170) REVERT: A 635 ASP cc_start: 0.7111 (t70) cc_final: 0.6638 (p0) REVERT: B 51 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7657 (tt) REVERT: B 174 ASN cc_start: 0.7637 (t0) cc_final: 0.7034 (t0) REVERT: B 262 LYS cc_start: 0.8686 (tttm) cc_final: 0.7997 (ttpp) REVERT: B 314 LYS cc_start: 0.7368 (ttpt) cc_final: 0.7066 (ttmm) REVERT: B 318 SER cc_start: 0.7789 (t) cc_final: 0.7573 (t) REVERT: B 322 LYS cc_start: 0.7825 (tmmt) cc_final: 0.7449 (mtpm) REVERT: B 602 VAL cc_start: 0.7766 (t) cc_final: 0.7483 (m) REVERT: B 628 ARG cc_start: 0.8165 (mtt-85) cc_final: 0.7508 (mpp-170) REVERT: B 635 ASP cc_start: 0.7072 (t70) cc_final: 0.6691 (p0) REVERT: C 51 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7626 (tt) REVERT: C 174 ASN cc_start: 0.7616 (t0) cc_final: 0.6996 (t0) REVERT: C 208 ASN cc_start: 0.8044 (t0) cc_final: 0.7763 (t0) REVERT: C 211 PHE cc_start: 0.8742 (m-10) cc_final: 0.8419 (m-10) REVERT: C 262 LYS cc_start: 0.8676 (tttm) cc_final: 0.7962 (ttpp) REVERT: C 314 LYS cc_start: 0.7282 (ttpt) cc_final: 0.6972 (ttmm) REVERT: C 318 SER cc_start: 0.7668 (t) cc_final: 0.7449 (t) REVERT: C 322 LYS cc_start: 0.7802 (tmmt) cc_final: 0.7387 (mtpm) REVERT: C 332 LEU cc_start: 0.8286 (mt) cc_final: 0.8075 (mt) REVERT: C 596 GLN cc_start: 0.6711 (mt0) cc_final: 0.6024 (mm-40) REVERT: C 628 ARG cc_start: 0.8148 (mtt-85) cc_final: 0.7447 (mpp-170) REVERT: C 635 ASP cc_start: 0.7069 (t70) cc_final: 0.6646 (p0) REVERT: D 51 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7650 (tt) REVERT: D 174 ASN cc_start: 0.7512 (t0) cc_final: 0.7072 (t0) REVERT: D 262 LYS cc_start: 0.8770 (tttm) cc_final: 0.8100 (ttpp) REVERT: D 303 GLU cc_start: 0.7569 (mp0) cc_final: 0.7038 (mp0) REVERT: D 314 LYS cc_start: 0.7313 (ttpt) cc_final: 0.7003 (ttmm) REVERT: D 318 SER cc_start: 0.7706 (t) cc_final: 0.7489 (t) REVERT: D 322 LYS cc_start: 0.7823 (tmmt) cc_final: 0.7416 (mtpm) REVERT: D 596 GLN cc_start: 0.6646 (mt0) cc_final: 0.5984 (mm-40) REVERT: D 628 ARG cc_start: 0.8180 (mtt-85) cc_final: 0.7486 (mpp-170) REVERT: D 635 ASP cc_start: 0.7073 (t70) cc_final: 0.6661 (p0) outliers start: 42 outliers final: 26 residues processed: 396 average time/residue: 2.4065 time to fit residues: 1112.6608 Evaluate side-chains 360 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 330 time to evaluate : 3.053 ------------------------------------------------------------------------------- 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 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 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 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 410 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 219 optimal weight: 2.9990 chunk 166 optimal weight: 5.9990 chunk 115 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 105 optimal weight: 6.9990 chunk 149 optimal weight: 5.9990 chunk 222 optimal weight: 9.9990 chunk 235 optimal weight: 1.9990 chunk 116 optimal weight: 0.6980 chunk 211 optimal weight: 0.7980 chunk 63 optimal weight: 7.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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** A 357 ASN B 31 GLN B 357 ASN ** B 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 357 ASN D 91 ASN D 357 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.3391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21556 Z= 0.216 Angle : 0.626 8.824 29140 Z= 0.307 Chirality : 0.038 0.196 3220 Planarity : 0.004 0.055 3532 Dihedral : 15.394 154.825 4456 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 2.02 % Allowed : 14.69 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.17), residues: 2440 helix: -0.15 (0.14), residues: 1448 sheet: -3.59 (0.49), residues: 84 loop : -1.21 (0.22), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 593 HIS 0.003 0.001 HIS B 426 PHE 0.011 0.001 PHE B 493 TYR 0.013 0.001 TYR C 216 ARG 0.005 0.000 ARG D 492 *********************** 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 382 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 339 time to evaluate : 3.357 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: 0.8104 (OUTLIER) cc_final: 0.7677 (tt) REVERT: A 174 ASN cc_start: 0.7609 (t0) cc_final: 0.7082 (t0) REVERT: A 262 LYS cc_start: 0.8765 (tttm) cc_final: 0.7946 (ttpp) REVERT: A 300 LYS cc_start: 0.8410 (mttm) cc_final: 0.8203 (mttm) REVERT: A 303 GLU cc_start: 0.7583 (mp0) cc_final: 0.7154 (mp0) REVERT: A 314 LYS cc_start: 0.7286 (ttpt) cc_final: 0.6973 (ttmm) REVERT: A 318 SER cc_start: 0.7548 (t) cc_final: 0.7326 (t) REVERT: A 322 LYS cc_start: 0.7784 (tmmt) cc_final: 0.7439 (mtpm) REVERT: A 492 ARG cc_start: 0.6075 (tpp80) cc_final: 0.5508 (tpp80) REVERT: A 596 GLN cc_start: 0.6709 (mt0) cc_final: 0.5982 (mm-40) REVERT: A 628 ARG cc_start: 0.8111 (mtt-85) cc_final: 0.7414 (mpp-170) REVERT: A 635 ASP cc_start: 0.7085 (t70) cc_final: 0.6638 (p0) REVERT: B 51 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7658 (tt) REVERT: B 174 ASN cc_start: 0.7657 (t0) cc_final: 0.7095 (t0) REVERT: B 255 MET cc_start: 0.8405 (mmm) cc_final: 0.8077 (mtp) REVERT: B 262 LYS cc_start: 0.8778 (tttm) cc_final: 0.8125 (ttpp) REVERT: B 314 LYS cc_start: 0.7342 (ttpt) cc_final: 0.7029 (ttmm) REVERT: B 318 SER cc_start: 0.7730 (t) cc_final: 0.7499 (t) REVERT: B 322 LYS cc_start: 0.7810 (tmmt) cc_final: 0.7447 (mtpm) REVERT: B 602 VAL cc_start: 0.7812 (t) cc_final: 0.7516 (m) REVERT: B 628 ARG cc_start: 0.8153 (mtt-85) cc_final: 0.7507 (mpp-170) REVERT: B 635 ASP cc_start: 0.7094 (t70) cc_final: 0.6692 (p0) REVERT: C 51 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7628 (tt) REVERT: C 174 ASN cc_start: 0.7612 (t0) cc_final: 0.7051 (t0) REVERT: C 211 PHE cc_start: 0.8743 (m-10) cc_final: 0.8517 (m-10) REVERT: C 262 LYS cc_start: 0.8771 (tttm) cc_final: 0.8085 (ttpp) REVERT: C 314 LYS cc_start: 0.7264 (ttpt) cc_final: 0.6945 (ttmm) REVERT: C 318 SER cc_start: 0.7612 (t) cc_final: 0.7377 (t) REVERT: C 322 LYS cc_start: 0.7744 (tmmt) cc_final: 0.7386 (mtpm) REVERT: C 410 MET cc_start: 0.7000 (mtp) cc_final: 0.6611 (mtm) REVERT: C 596 GLN cc_start: 0.6719 (mt0) cc_final: 0.6003 (mm-40) REVERT: C 628 ARG cc_start: 0.8130 (mtt-85) cc_final: 0.7437 (mpp-170) REVERT: C 635 ASP cc_start: 0.7068 (t70) cc_final: 0.6655 (p0) REVERT: D 51 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7632 (tt) REVERT: D 174 ASN cc_start: 0.7562 (t0) cc_final: 0.7036 (t0) REVERT: D 262 LYS cc_start: 0.8774 (tttm) cc_final: 0.8086 (ttpp) REVERT: D 303 GLU cc_start: 0.7641 (mp0) cc_final: 0.7236 (mp0) REVERT: D 314 LYS cc_start: 0.7279 (ttpt) cc_final: 0.6964 (ttmm) REVERT: D 318 SER cc_start: 0.7643 (t) cc_final: 0.7410 (t) REVERT: D 322 LYS cc_start: 0.7766 (tmmt) cc_final: 0.7417 (mtpm) REVERT: D 596 GLN cc_start: 0.6574 (mt0) cc_final: 0.5909 (mm-40) REVERT: D 628 ARG cc_start: 0.8144 (mtt-85) cc_final: 0.7479 (mpp-170) REVERT: D 635 ASP cc_start: 0.7073 (t70) cc_final: 0.6664 (p0) outliers start: 43 outliers final: 25 residues processed: 364 average time/residue: 2.4783 time to fit residues: 1051.6582 Evaluate side-chains 352 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 323 time to evaluate : 3.165 ------------------------------------------------------------------------------- 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 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 64 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 474 MET 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 196 optimal weight: 0.0050 chunk 133 optimal weight: 10.0000 chunk 3 optimal weight: 20.0000 chunk 175 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 201 optimal weight: 0.9980 chunk 163 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 120 optimal weight: 10.0000 chunk 211 optimal weight: 1.9990 chunk 59 optimal weight: 8.9990 overall best weight: 1.6000 ------------------------------------------------------------------------------- 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 230 GLN A 357 ASN A 546 ASN B 31 GLN B 357 ASN ** B 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 357 ASN D 357 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 21556 Z= 0.215 Angle : 0.605 8.219 29140 Z= 0.300 Chirality : 0.039 0.215 3220 Planarity : 0.004 0.056 3532 Dihedral : 14.599 150.809 4456 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 2.02 % Allowed : 15.16 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.17), residues: 2440 helix: 0.10 (0.14), residues: 1456 sheet: -3.63 (0.48), residues: 84 loop : -1.18 (0.22), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 593 HIS 0.003 0.001 HIS B 426 PHE 0.009 0.001 PHE D 493 TYR 0.010 0.001 TYR D 216 ARG 0.007 0.000 ARG D 621 *********************** 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 378 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 335 time to evaluate : 3.373 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: 0.8048 (OUTLIER) cc_final: 0.7591 (tt) REVERT: A 174 ASN cc_start: 0.7632 (t0) cc_final: 0.7272 (t0) REVERT: A 176 GLU cc_start: 0.7942 (mp0) cc_final: 0.7402 (pm20) REVERT: A 177 GLU cc_start: 0.7814 (mp0) cc_final: 0.7152 (mp0) REVERT: A 262 LYS cc_start: 0.8795 (tttm) cc_final: 0.8309 (ttpt) REVERT: A 300 LYS cc_start: 0.8411 (mttm) cc_final: 0.8206 (mttm) REVERT: A 303 GLU cc_start: 0.7624 (mp0) cc_final: 0.7208 (mp0) REVERT: A 314 LYS cc_start: 0.7310 (ttpt) cc_final: 0.6962 (ttmm) REVERT: A 318 SER cc_start: 0.7597 (t) cc_final: 0.7353 (t) REVERT: A 322 LYS cc_start: 0.7761 (tmmt) cc_final: 0.7394 (mtpm) REVERT: A 596 GLN cc_start: 0.6706 (mt0) cc_final: 0.5982 (mm-40) REVERT: A 628 ARG cc_start: 0.8114 (mtt-85) cc_final: 0.7411 (mpp-170) REVERT: A 635 ASP cc_start: 0.7102 (t70) cc_final: 0.6642 (p0) REVERT: B 51 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7611 (tt) REVERT: B 174 ASN cc_start: 0.7716 (t0) cc_final: 0.7103 (t0) REVERT: B 262 LYS cc_start: 0.8785 (tttm) cc_final: 0.8122 (ttpp) REVERT: B 314 LYS cc_start: 0.7338 (ttpt) cc_final: 0.7030 (ttmm) REVERT: B 318 SER cc_start: 0.7729 (t) cc_final: 0.7493 (t) REVERT: B 322 LYS cc_start: 0.7803 (tmmt) cc_final: 0.7434 (mtpm) REVERT: B 492 ARG cc_start: 0.6351 (tpp-160) cc_final: 0.5518 (tpp80) REVERT: B 602 VAL cc_start: 0.7909 (t) cc_final: 0.7615 (m) REVERT: B 628 ARG cc_start: 0.8137 (mtt-85) cc_final: 0.7477 (mpp-170) REVERT: B 635 ASP cc_start: 0.7093 (t70) cc_final: 0.6711 (p0) REVERT: C 51 LEU cc_start: 0.8071 (OUTLIER) cc_final: 0.7584 (tt) REVERT: C 174 ASN cc_start: 0.7658 (t0) cc_final: 0.7044 (t0) REVERT: C 262 LYS cc_start: 0.8779 (tttm) cc_final: 0.8088 (ttpp) REVERT: C 314 LYS cc_start: 0.7239 (ttpt) cc_final: 0.6915 (ttmm) REVERT: C 318 SER cc_start: 0.7619 (t) cc_final: 0.7386 (t) REVERT: C 322 LYS cc_start: 0.7740 (tmmt) cc_final: 0.7369 (mtpm) REVERT: C 332 LEU cc_start: 0.8331 (mt) cc_final: 0.8090 (mt) REVERT: C 410 MET cc_start: 0.6920 (mtp) cc_final: 0.6707 (mtm) REVERT: C 596 GLN cc_start: 0.6766 (mt0) cc_final: 0.5997 (mm-40) REVERT: C 628 ARG cc_start: 0.8112 (mtt-85) cc_final: 0.7418 (mpp-170) REVERT: C 635 ASP cc_start: 0.7066 (t70) cc_final: 0.6638 (p0) REVERT: D 51 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7602 (tt) REVERT: D 174 ASN cc_start: 0.7554 (t0) cc_final: 0.7095 (t0) REVERT: D 262 LYS cc_start: 0.8789 (tttm) cc_final: 0.8100 (ttpp) REVERT: D 303 GLU cc_start: 0.7653 (mp0) cc_final: 0.7227 (mp0) REVERT: D 314 LYS cc_start: 0.7275 (ttpt) cc_final: 0.6962 (ttmm) REVERT: D 322 LYS cc_start: 0.7769 (tmmt) cc_final: 0.7403 (mtpm) REVERT: D 596 GLN cc_start: 0.6583 (mt0) cc_final: 0.5890 (mm-40) REVERT: D 628 ARG cc_start: 0.8152 (mtt-85) cc_final: 0.7476 (mpp-170) REVERT: D 635 ASP cc_start: 0.7075 (t70) cc_final: 0.6654 (p0) outliers start: 43 outliers final: 25 residues processed: 368 average time/residue: 2.4622 time to fit residues: 1059.4646 Evaluate side-chains 350 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 321 time to evaluate : 3.415 ------------------------------------------------------------------------------- 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 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 D residue 49 LEU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 64 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 79 optimal weight: 6.9990 chunk 212 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 138 optimal weight: 9.9990 chunk 58 optimal weight: 8.9990 chunk 236 optimal weight: 2.9990 chunk 195 optimal weight: 7.9990 chunk 109 optimal weight: 1.9990 chunk 19 optimal weight: 7.9990 chunk 78 optimal weight: 3.9990 chunk 123 optimal weight: 7.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 ** B 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 357 ASN ** C 546 ASN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.3807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 21556 Z= 0.347 Angle : 0.646 7.805 29140 Z= 0.319 Chirality : 0.042 0.244 3220 Planarity : 0.005 0.070 3532 Dihedral : 15.042 141.819 4456 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 2.40 % Allowed : 14.69 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.17), residues: 2440 helix: 0.10 (0.14), residues: 1468 sheet: -3.62 (0.48), residues: 84 loop : -1.09 (0.22), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 593 HIS 0.005 0.001 HIS A 522 PHE 0.011 0.002 PHE D 493 TYR 0.017 0.002 TYR A 216 ARG 0.006 0.000 ARG A 621 *********************** 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 387 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 336 time to evaluate : 3.087 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: A 51 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7599 (tt) REVERT: A 174 ASN cc_start: 0.7764 (t0) cc_final: 0.7240 (t0) REVERT: A 262 LYS cc_start: 0.8745 (tttm) cc_final: 0.8264 (ttpt) REVERT: A 300 LYS cc_start: 0.8418 (mttm) cc_final: 0.8216 (mttm) REVERT: A 303 GLU cc_start: 0.7736 (mp0) cc_final: 0.7222 (mp0) REVERT: A 314 LYS cc_start: 0.7373 (ttpt) cc_final: 0.6977 (ttmm) REVERT: A 322 LYS cc_start: 0.7771 (tmmt) cc_final: 0.7392 (mtpm) REVERT: A 596 GLN cc_start: 0.6811 (mt0) cc_final: 0.6006 (mm-40) REVERT: A 628 ARG cc_start: 0.8092 (mtt-85) cc_final: 0.7394 (mpp-170) REVERT: A 635 ASP cc_start: 0.7112 (t70) cc_final: 0.6623 (p0) REVERT: B 31 GLN cc_start: 0.7306 (OUTLIER) cc_final: 0.6383 (tm-30) REVERT: B 51 LEU cc_start: 0.8127 (OUTLIER) cc_final: 0.7618 (tt) REVERT: B 167 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7899 (tp) REVERT: B 174 ASN cc_start: 0.7838 (t0) cc_final: 0.7230 (t0) REVERT: B 262 LYS cc_start: 0.8761 (tttm) cc_final: 0.7966 (ttpp) REVERT: B 303 GLU cc_start: 0.7730 (mp0) cc_final: 0.7310 (mp0) REVERT: B 314 LYS cc_start: 0.7384 (ttpt) cc_final: 0.7043 (ttmm) REVERT: B 322 LYS cc_start: 0.7805 (tmmt) cc_final: 0.7434 (mtpm) REVERT: B 492 ARG cc_start: 0.6546 (OUTLIER) cc_final: 0.5585 (tpp80) REVERT: B 602 VAL cc_start: 0.7907 (t) cc_final: 0.7601 (m) REVERT: B 628 ARG cc_start: 0.8087 (mtt-85) cc_final: 0.7467 (mpp-170) REVERT: B 635 ASP cc_start: 0.7112 (t70) cc_final: 0.6666 (p0) REVERT: C 51 LEU cc_start: 0.8067 (OUTLIER) cc_final: 0.7608 (tt) REVERT: C 167 LEU cc_start: 0.8120 (OUTLIER) cc_final: 0.7828 (tp) REVERT: C 174 ASN cc_start: 0.7783 (t0) cc_final: 0.7163 (t0) REVERT: C 262 LYS cc_start: 0.8764 (tttm) cc_final: 0.7968 (ttpp) REVERT: C 303 GLU cc_start: 0.7717 (mp0) cc_final: 0.7276 (mp0) REVERT: C 314 LYS cc_start: 0.7301 (ttpt) cc_final: 0.6951 (ttmm) REVERT: C 322 LYS cc_start: 0.7736 (tmmt) cc_final: 0.7367 (mtpm) REVERT: C 596 GLN cc_start: 0.6792 (mt0) cc_final: 0.5971 (mm-40) REVERT: C 628 ARG cc_start: 0.8082 (mtt-85) cc_final: 0.7407 (mpp-170) REVERT: C 635 ASP cc_start: 0.7146 (t70) cc_final: 0.6655 (p0) REVERT: D 51 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7608 (tt) REVERT: D 167 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7841 (tp) REVERT: D 174 ASN cc_start: 0.7635 (t0) cc_final: 0.7122 (t0) REVERT: D 262 LYS cc_start: 0.8765 (tttm) cc_final: 0.7982 (ttpp) REVERT: D 303 GLU cc_start: 0.7723 (mp0) cc_final: 0.7252 (mp0) REVERT: D 314 LYS cc_start: 0.7310 (ttpt) cc_final: 0.6962 (ttmm) REVERT: D 322 LYS cc_start: 0.7758 (tmmt) cc_final: 0.7396 (mtpm) REVERT: D 596 GLN cc_start: 0.6684 (mt0) cc_final: 0.5970 (mm-40) REVERT: D 628 ARG cc_start: 0.8094 (mtt-85) cc_final: 0.7456 (mpp-170) REVERT: D 635 ASP cc_start: 0.7097 (t70) cc_final: 0.6639 (p0) outliers start: 51 outliers final: 23 residues processed: 366 average time/residue: 2.5457 time to fit residues: 1083.2746 Evaluate side-chains 358 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 326 time to evaluate : 2.941 ------------------------------------------------------------------------------- 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 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 31 GLN 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 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 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 227 optimal weight: 8.9990 chunk 26 optimal weight: 4.9990 chunk 134 optimal weight: 7.9990 chunk 172 optimal weight: 1.9990 chunk 133 optimal weight: 8.9990 chunk 198 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 235 optimal weight: 2.9990 chunk 147 optimal weight: 4.9990 chunk 143 optimal weight: 0.8980 chunk 108 optimal weight: 0.8980 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 ** B 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 357 ASN ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 357 ASN D 546 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.3920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 21556 Z= 0.235 Angle : 0.605 7.650 29140 Z= 0.302 Chirality : 0.039 0.209 3220 Planarity : 0.004 0.059 3532 Dihedral : 14.434 138.402 4456 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 2.17 % Allowed : 15.49 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.18), residues: 2440 helix: 0.30 (0.14), residues: 1468 sheet: -3.63 (0.47), residues: 84 loop : -1.10 (0.22), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 593 HIS 0.003 0.001 HIS B 201 PHE 0.011 0.001 PHE D 493 TYR 0.012 0.001 TYR A 324 ARG 0.003 0.000 ARG D 621 *********************** 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 383 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 337 time to evaluate : 3.104 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: 0.8055 (OUTLIER) cc_final: 0.7590 (tt) REVERT: A 174 ASN cc_start: 0.7803 (t0) cc_final: 0.7200 (t0) REVERT: A 262 LYS cc_start: 0.8757 (tttm) cc_final: 0.8273 (ttpt) REVERT: A 303 GLU cc_start: 0.7774 (mp0) cc_final: 0.7240 (mp0) REVERT: A 314 LYS cc_start: 0.7357 (ttpt) cc_final: 0.6955 (ttmm) REVERT: A 322 LYS cc_start: 0.7737 (tmmt) cc_final: 0.7368 (mtpm) REVERT: A 596 GLN cc_start: 0.6750 (mt0) cc_final: 0.5961 (mm-40) REVERT: A 628 ARG cc_start: 0.8084 (mtt-85) cc_final: 0.7380 (mpp-170) REVERT: A 635 ASP cc_start: 0.7097 (t70) cc_final: 0.6624 (p0) REVERT: B 31 GLN cc_start: 0.7300 (OUTLIER) cc_final: 0.6375 (tm-30) REVERT: B 51 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7619 (tt) REVERT: B 167 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7939 (tp) REVERT: B 174 ASN cc_start: 0.7808 (t0) cc_final: 0.7192 (t0) REVERT: B 262 LYS cc_start: 0.8750 (tttm) cc_final: 0.7954 (ttpp) REVERT: B 314 LYS cc_start: 0.7368 (ttpt) cc_final: 0.7025 (ttmm) REVERT: B 322 LYS cc_start: 0.7804 (tmmt) cc_final: 0.7419 (mtpm) REVERT: B 492 ARG cc_start: 0.6461 (OUTLIER) cc_final: 0.5479 (tpp80) REVERT: B 602 VAL cc_start: 0.7897 (t) cc_final: 0.7595 (m) REVERT: B 628 ARG cc_start: 0.8085 (mtt-85) cc_final: 0.7439 (mpp-170) REVERT: B 635 ASP cc_start: 0.7102 (t70) cc_final: 0.6639 (p0) REVERT: C 51 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7610 (tt) REVERT: C 167 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7870 (tp) REVERT: C 174 ASN cc_start: 0.7744 (t0) cc_final: 0.7117 (t0) REVERT: C 176 GLU cc_start: 0.7961 (mp0) cc_final: 0.7689 (mp0) REVERT: C 262 LYS cc_start: 0.8752 (tttm) cc_final: 0.7949 (ttpp) REVERT: C 314 LYS cc_start: 0.7295 (ttpt) cc_final: 0.6942 (ttmm) REVERT: C 322 LYS cc_start: 0.7742 (tmmt) cc_final: 0.7354 (mtpm) REVERT: C 596 GLN cc_start: 0.6849 (mt0) cc_final: 0.6000 (mm-40) REVERT: C 628 ARG cc_start: 0.8074 (mtt-85) cc_final: 0.7384 (mpp-170) REVERT: C 635 ASP cc_start: 0.7115 (t70) cc_final: 0.6583 (p0) REVERT: D 51 LEU cc_start: 0.8083 (OUTLIER) cc_final: 0.7609 (tt) REVERT: D 167 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7903 (tp) REVERT: D 174 ASN cc_start: 0.7576 (t0) cc_final: 0.7052 (t0) REVERT: D 262 LYS cc_start: 0.8755 (tttm) cc_final: 0.7966 (ttpp) REVERT: D 303 GLU cc_start: 0.7710 (mp0) cc_final: 0.7224 (mp0) REVERT: D 314 LYS cc_start: 0.7320 (ttpt) cc_final: 0.6969 (ttmm) REVERT: D 322 LYS cc_start: 0.7760 (tmmt) cc_final: 0.7375 (mtpm) REVERT: D 596 GLN cc_start: 0.6620 (mt0) cc_final: 0.5902 (mm-40) REVERT: D 628 ARG cc_start: 0.8094 (mtt-85) cc_final: 0.7447 (mpp-170) REVERT: D 635 ASP cc_start: 0.7138 (t70) cc_final: 0.6634 (p0) outliers start: 46 outliers final: 23 residues processed: 366 average time/residue: 2.5441 time to fit residues: 1079.6985 Evaluate side-chains 363 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 331 time to evaluate : 3.018 ------------------------------------------------------------------------------- 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 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 31 GLN 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 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 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 145 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 140 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 149 optimal weight: 0.4980 chunk 160 optimal weight: 5.9990 chunk 116 optimal weight: 0.0970 chunk 21 optimal weight: 0.9990 chunk 184 optimal weight: 7.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 357 ASN C 546 ASN D 357 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.4007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21556 Z= 0.174 Angle : 0.580 7.440 29140 Z= 0.290 Chirality : 0.038 0.186 3220 Planarity : 0.004 0.059 3532 Dihedral : 13.824 134.728 4456 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.15 % Favored : 93.81 % Rotamer: Outliers : 2.12 % Allowed : 16.67 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.18), residues: 2440 helix: 0.49 (0.14), residues: 1468 sheet: -3.54 (0.48), residues: 84 loop : -1.01 (0.22), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 593 HIS 0.003 0.001 HIS D 201 PHE 0.010 0.001 PHE D 493 TYR 0.012 0.001 TYR D 324 ARG 0.008 0.000 ARG A 621 *********************** 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 388 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 343 time to evaluate : 3.236 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: 0.8054 (OUTLIER) cc_final: 0.7583 (tt) REVERT: A 174 ASN cc_start: 0.7647 (t0) cc_final: 0.7110 (t0) REVERT: A 262 LYS cc_start: 0.8752 (tttm) cc_final: 0.8280 (ttpt) REVERT: A 303 GLU cc_start: 0.7752 (mp0) cc_final: 0.7237 (mp0) REVERT: A 314 LYS cc_start: 0.7340 (ttpt) cc_final: 0.6936 (ttmm) REVERT: A 322 LYS cc_start: 0.7737 (tmmt) cc_final: 0.7353 (mtpm) REVERT: A 596 GLN cc_start: 0.6813 (mt0) cc_final: 0.5975 (mm-40) REVERT: A 628 ARG cc_start: 0.8073 (mtt-85) cc_final: 0.7352 (mpp-170) REVERT: A 635 ASP cc_start: 0.7077 (t70) cc_final: 0.6592 (p0) REVERT: B 51 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7607 (tt) REVERT: B 160 ILE cc_start: 0.8605 (pp) cc_final: 0.8343 (pp) REVERT: B 167 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.7958 (tp) REVERT: B 174 ASN cc_start: 0.7723 (t0) cc_final: 0.7148 (t0) REVERT: B 262 LYS cc_start: 0.8749 (tttm) cc_final: 0.7972 (ttpp) REVERT: B 303 GLU cc_start: 0.7735 (mp0) cc_final: 0.7289 (mp0) REVERT: B 314 LYS cc_start: 0.7364 (ttpt) cc_final: 0.7015 (ttmm) REVERT: B 322 LYS cc_start: 0.7796 (tmmt) cc_final: 0.7405 (mtpm) REVERT: B 492 ARG cc_start: 0.6372 (OUTLIER) cc_final: 0.5370 (tpp80) REVERT: B 602 VAL cc_start: 0.7901 (t) cc_final: 0.7616 (m) REVERT: B 628 ARG cc_start: 0.8069 (mtt-85) cc_final: 0.7409 (mpp-170) REVERT: B 635 ASP cc_start: 0.7051 (t70) cc_final: 0.6637 (p0) REVERT: C 51 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7579 (tt) REVERT: C 167 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7889 (tp) REVERT: C 174 ASN cc_start: 0.7684 (t0) cc_final: 0.7095 (t0) REVERT: C 262 LYS cc_start: 0.8770 (tttm) cc_final: 0.7965 (ttpp) REVERT: C 314 LYS cc_start: 0.7283 (ttpt) cc_final: 0.6929 (ttmm) REVERT: C 322 LYS cc_start: 0.7740 (tmmt) cc_final: 0.7348 (mtpm) REVERT: C 596 GLN cc_start: 0.6897 (mt0) cc_final: 0.5985 (mm-40) REVERT: C 628 ARG cc_start: 0.8064 (mtt-85) cc_final: 0.7372 (mpp-170) REVERT: C 635 ASP cc_start: 0.7096 (t70) cc_final: 0.6573 (p0) REVERT: D 51 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7584 (tt) REVERT: D 160 ILE cc_start: 0.8574 (pp) cc_final: 0.8315 (pp) REVERT: D 167 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7886 (tp) REVERT: D 174 ASN cc_start: 0.7450 (t0) cc_final: 0.7037 (t0) REVERT: D 262 LYS cc_start: 0.8752 (tttm) cc_final: 0.7957 (ttpp) REVERT: D 303 GLU cc_start: 0.7719 (mp0) cc_final: 0.7239 (mp0) REVERT: D 314 LYS cc_start: 0.7308 (ttpt) cc_final: 0.6956 (ttmm) REVERT: D 322 LYS cc_start: 0.7762 (tmmt) cc_final: 0.7369 (mtpm) REVERT: D 596 GLN cc_start: 0.6617 (mt0) cc_final: 0.5903 (mm-40) REVERT: D 628 ARG cc_start: 0.8091 (mtt-85) cc_final: 0.7441 (mpp-170) REVERT: D 635 ASP cc_start: 0.7063 (t70) cc_final: 0.6578 (p0) outliers start: 45 outliers final: 23 residues processed: 373 average time/residue: 2.4997 time to fit residues: 1089.7105 Evaluate side-chains 355 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 324 time to evaluate : 3.478 ------------------------------------------------------------------------------- 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 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 148 THR Chi-restraints excluded: chain B residue 167 LEU 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 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 213 optimal weight: 3.9990 chunk 225 optimal weight: 0.9980 chunk 205 optimal weight: 6.9990 chunk 219 optimal weight: 4.9990 chunk 131 optimal weight: 3.9990 chunk 95 optimal weight: 0.9990 chunk 172 optimal weight: 0.6980 chunk 67 optimal weight: 10.0000 chunk 198 optimal weight: 6.9990 chunk 207 optimal weight: 2.9990 chunk 218 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 357 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.4102 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= 0.192 Angle : 0.581 6.953 29140 Z= 0.292 Chirality : 0.038 0.183 3220 Planarity : 0.004 0.059 3532 Dihedral : 13.517 129.029 4456 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 1.93 % Allowed : 17.66 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.18), residues: 2440 helix: 0.52 (0.14), residues: 1484 sheet: -3.51 (0.47), residues: 84 loop : -0.86 (0.23), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 593 HIS 0.003 0.001 HIS A 201 PHE 0.011 0.001 PHE D 415 TYR 0.011 0.001 TYR D 324 ARG 0.006 0.000 ARG D 621 *********************** 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 376 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 335 time to evaluate : 3.184 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: 0.8077 (OUTLIER) cc_final: 0.7582 (tt) REVERT: A 174 ASN cc_start: 0.7673 (t0) cc_final: 0.7159 (t0) REVERT: A 262 LYS cc_start: 0.8755 (tttm) cc_final: 0.8278 (ttpt) REVERT: A 303 GLU cc_start: 0.7761 (mp0) cc_final: 0.7221 (mp0) REVERT: A 314 LYS cc_start: 0.7317 (ttpt) cc_final: 0.6907 (ttmm) REVERT: A 322 LYS cc_start: 0.7740 (tmmt) cc_final: 0.7352 (mtpm) REVERT: A 596 GLN cc_start: 0.6853 (mt0) cc_final: 0.5991 (mm-40) REVERT: A 628 ARG cc_start: 0.8063 (mtt-85) cc_final: 0.7354 (mpp-170) REVERT: A 635 ASP cc_start: 0.7066 (t70) cc_final: 0.6557 (p0) REVERT: B 51 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7611 (tt) REVERT: B 160 ILE cc_start: 0.8606 (pp) cc_final: 0.8349 (pp) REVERT: B 174 ASN cc_start: 0.7715 (t0) cc_final: 0.7357 (t0) REVERT: B 176 GLU cc_start: 0.7916 (mp0) cc_final: 0.7409 (mt-10) REVERT: B 262 LYS cc_start: 0.8759 (tttm) cc_final: 0.7981 (ttpp) REVERT: B 303 GLU cc_start: 0.7748 (mp0) cc_final: 0.7289 (mp0) REVERT: B 314 LYS cc_start: 0.7360 (ttpt) cc_final: 0.7003 (ttmm) REVERT: B 322 LYS cc_start: 0.7797 (tmmt) cc_final: 0.7404 (mtpm) REVERT: B 602 VAL cc_start: 0.7913 (t) cc_final: 0.7634 (m) REVERT: B 628 ARG cc_start: 0.8067 (mtt-85) cc_final: 0.7404 (mpp-170) REVERT: B 635 ASP cc_start: 0.7072 (t70) cc_final: 0.6648 (p0) REVERT: C 51 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7578 (tt) REVERT: C 153 ARG cc_start: 0.8199 (OUTLIER) cc_final: 0.7909 (mtt90) REVERT: C 174 ASN cc_start: 0.7664 (t0) cc_final: 0.7093 (t0) REVERT: C 262 LYS cc_start: 0.8770 (tttm) cc_final: 0.7969 (ttpp) REVERT: C 303 GLU cc_start: 0.7736 (mp0) cc_final: 0.7256 (mp0) REVERT: C 314 LYS cc_start: 0.7249 (ttpt) cc_final: 0.6888 (ttmm) REVERT: C 322 LYS cc_start: 0.7734 (tmmt) cc_final: 0.7335 (mtpm) REVERT: C 596 GLN cc_start: 0.6881 (mt0) cc_final: 0.5966 (mm-40) REVERT: C 628 ARG cc_start: 0.8062 (mtt-85) cc_final: 0.7366 (mpp-170) REVERT: C 635 ASP cc_start: 0.7078 (t70) cc_final: 0.6571 (p0) REVERT: D 51 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7578 (tt) REVERT: D 160 ILE cc_start: 0.8560 (pp) cc_final: 0.8303 (pp) REVERT: D 174 ASN cc_start: 0.7545 (t0) cc_final: 0.7047 (t0) REVERT: D 262 LYS cc_start: 0.8755 (tttm) cc_final: 0.7957 (ttpp) REVERT: D 303 GLU cc_start: 0.7736 (mp0) cc_final: 0.7251 (mp0) REVERT: D 314 LYS cc_start: 0.7282 (ttpt) cc_final: 0.6922 (ttmm) REVERT: D 322 LYS cc_start: 0.7757 (tmmt) cc_final: 0.7360 (mtpm) REVERT: D 596 GLN cc_start: 0.6633 (mt0) cc_final: 0.5885 (mm-40) REVERT: D 628 ARG cc_start: 0.8074 (mtt-85) cc_final: 0.7439 (mpp-170) REVERT: D 635 ASP cc_start: 0.7022 (t70) cc_final: 0.6581 (p0) outliers start: 41 outliers final: 22 residues processed: 363 average time/residue: 2.5937 time to fit residues: 1091.7310 Evaluate side-chains 351 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 324 time to evaluate : 2.769 ------------------------------------------------------------------------------- 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 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 475 LEU Chi-restraints excluded: chain B residue 479 THR 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 153 ARG 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 143 optimal weight: 1.9990 chunk 231 optimal weight: 2.9990 chunk 141 optimal weight: 5.9990 chunk 109 optimal weight: 1.9990 chunk 161 optimal weight: 4.9990 chunk 243 optimal weight: 3.9990 chunk 223 optimal weight: 2.9990 chunk 193 optimal weight: 5.9990 chunk 20 optimal weight: 0.6980 chunk 149 optimal weight: 0.9990 chunk 118 optimal weight: 5.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- 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 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 357 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.4185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 21556 Z= 0.219 Angle : 0.597 8.122 29140 Z= 0.299 Chirality : 0.038 0.182 3220 Planarity : 0.004 0.076 3532 Dihedral : 13.228 119.506 4456 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.48 % Favored : 93.44 % Rotamer: Outliers : 1.84 % Allowed : 17.98 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.18), residues: 2440 helix: 0.57 (0.14), residues: 1488 sheet: -3.44 (0.48), residues: 84 loop : -0.83 (0.23), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 593 HIS 0.002 0.001 HIS D 201 PHE 0.010 0.001 PHE D 415 TYR 0.012 0.001 TYR B 324 ARG 0.007 0.000 ARG D 621 ********************** 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 371 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 332 time to evaluate : 3.028 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: 0.8075 (OUTLIER) cc_final: 0.7578 (tt) REVERT: A 262 LYS cc_start: 0.8758 (tttm) cc_final: 0.8276 (ttpt) REVERT: A 303 GLU cc_start: 0.7734 (mp0) cc_final: 0.7195 (mp0) REVERT: A 314 LYS cc_start: 0.7292 (ttpt) cc_final: 0.6875 (ttmm) REVERT: A 322 LYS cc_start: 0.7731 (tmmt) cc_final: 0.7338 (mtpm) REVERT: A 596 GLN cc_start: 0.6856 (mt0) cc_final: 0.5988 (mm-40) REVERT: A 628 ARG cc_start: 0.8045 (mtt-85) cc_final: 0.7323 (mpp-170) REVERT: A 635 ASP cc_start: 0.7108 (t70) cc_final: 0.6552 (p0) REVERT: B 31 GLN cc_start: 0.7321 (OUTLIER) cc_final: 0.6370 (tm-30) REVERT: B 51 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7608 (tt) REVERT: B 160 ILE cc_start: 0.8592 (pp) cc_final: 0.8330 (pp) REVERT: B 174 ASN cc_start: 0.7763 (t0) cc_final: 0.7344 (t0) REVERT: B 176 GLU cc_start: 0.7994 (mp0) cc_final: 0.7413 (mt-10) REVERT: B 262 LYS cc_start: 0.8764 (tttm) cc_final: 0.7985 (ttpp) REVERT: B 303 GLU cc_start: 0.7729 (mp0) cc_final: 0.7266 (mp0) REVERT: B 314 LYS cc_start: 0.7330 (ttpt) cc_final: 0.6967 (ttmm) REVERT: B 322 LYS cc_start: 0.7802 (tmmt) cc_final: 0.7398 (mtpm) REVERT: B 602 VAL cc_start: 0.7913 (t) cc_final: 0.7649 (m) REVERT: B 628 ARG cc_start: 0.8061 (mtt-85) cc_final: 0.7397 (mpp-170) REVERT: B 635 ASP cc_start: 0.7089 (t70) cc_final: 0.6591 (p0) REVERT: C 51 LEU cc_start: 0.8071 (OUTLIER) cc_final: 0.7567 (tt) REVERT: C 153 ARG cc_start: 0.8202 (OUTLIER) cc_final: 0.7907 (mtt90) REVERT: C 174 ASN cc_start: 0.7641 (t0) cc_final: 0.7289 (t0) REVERT: C 176 GLU cc_start: 0.7937 (mp0) cc_final: 0.7357 (mt-10) REVERT: C 262 LYS cc_start: 0.8769 (tttm) cc_final: 0.7984 (ttpp) REVERT: C 303 GLU cc_start: 0.7744 (mp0) cc_final: 0.7249 (mp0) REVERT: C 314 LYS cc_start: 0.7235 (ttpt) cc_final: 0.6867 (ttmm) REVERT: C 322 LYS cc_start: 0.7739 (tmmt) cc_final: 0.7332 (mtpm) REVERT: C 596 GLN cc_start: 0.6895 (mt0) cc_final: 0.5967 (mm-40) REVERT: C 628 ARG cc_start: 0.8049 (mtt-85) cc_final: 0.7362 (mpp-170) REVERT: C 635 ASP cc_start: 0.7073 (t70) cc_final: 0.6571 (p0) REVERT: D 51 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7563 (tt) REVERT: D 160 ILE cc_start: 0.8561 (pp) cc_final: 0.8299 (pp) REVERT: D 167 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7790 (tp) REVERT: D 174 ASN cc_start: 0.7540 (t0) cc_final: 0.7025 (t0) REVERT: D 262 LYS cc_start: 0.8749 (tttm) cc_final: 0.7950 (ttpp) REVERT: D 303 GLU cc_start: 0.7727 (mp0) cc_final: 0.7245 (mp0) REVERT: D 314 LYS cc_start: 0.7265 (ttpt) cc_final: 0.6896 (ttmm) REVERT: D 322 LYS cc_start: 0.7756 (tmmt) cc_final: 0.7346 (mtpm) REVERT: D 474 MET cc_start: 0.1701 (mtt) cc_final: 0.1466 (mtt) REVERT: D 596 GLN cc_start: 0.6649 (mt0) cc_final: 0.5895 (mm-40) REVERT: D 628 ARG cc_start: 0.8061 (mtt-85) cc_final: 0.7436 (mpp-170) REVERT: D 635 ASP cc_start: 0.7067 (t70) cc_final: 0.6568 (p0) outliers start: 39 outliers final: 25 residues processed: 359 average time/residue: 2.6560 time to fit residues: 1107.0804 Evaluate side-chains 359 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 327 time to evaluate : 3.166 ------------------------------------------------------------------------------- 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 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 31 GLN 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 233 ASP 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 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 153 ARG 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 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 153 optimal weight: 2.9990 chunk 206 optimal weight: 5.9990 chunk 59 optimal weight: 8.9990 chunk 178 optimal weight: 9.9990 chunk 28 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 193 optimal weight: 5.9990 chunk 81 optimal weight: 0.0770 chunk 199 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 overall best weight: 2.2146 ------------------------------------------------------------------------------- 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 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 = 0.4110 r_free = 0.4110 target = 0.178839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.123690 restraints weight = 66887.368| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 2.14 r_work: 0.3420 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3296 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3181 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3181 r_free = 0.3181 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3177 r_free = 0.3177 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3177 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.4243 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= 0.249 Angle : 0.599 8.028 29140 Z= 0.300 Chirality : 0.039 0.182 3220 Planarity : 0.004 0.059 3532 Dihedral : 13.193 109.864 4456 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 1.88 % Allowed : 18.17 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.18), residues: 2440 helix: 0.57 (0.14), residues: 1488 sheet: -3.48 (0.46), residues: 84 loop : -0.83 (0.22), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 613 HIS 0.003 0.001 HIS B 201 PHE 0.013 0.001 PHE D 415 TYR 0.012 0.001 TYR A 324 ARG 0.007 0.000 ARG D 621 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17165.93 seconds wall clock time: 305 minutes 5.87 seconds (18305.87 seconds total)