Starting phenix.real_space_refine on Tue Jul 7 03:20:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sp8_40676/07_2026/8sp8_40676_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sp8_40676/07_2026/8sp8_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_40676/07_2026/8sp8_40676.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sp8_40676/07_2026/8sp8_40676.map" model { file = "/net/cci-nas-00/data/ceres_data/8sp8_40676/07_2026/8sp8_40676_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sp8_40676/07_2026/8sp8_40676_trim.cif" } resolution = 2.79 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.045 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Ca 1 9.91 5 P 12 5.49 5 S 160 5.16 5 Cl 1 4.86 5 C 13920 2.51 5 N 3336 2.21 5 O 3652 1.98 5 H 19860 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 84 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 40942 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 9877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 9877 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 26, 'TRANS': 585} Chain: "B" Number of atoms: 9877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 9877 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 26, 'TRANS': 585} Chain: "C" Number of atoms: 9877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 9877 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 26, 'TRANS': 585} Chain: "D" Number of atoms: 9877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 9877 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 26, 'TRANS': 585} Chain: "A" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 358 Ad-hoc single atom residues: {' CA': 1, ' CL': 1} Unusual residues: {'I8E': 2, 'POV': 7, 'Y01': 3} Classifications: {'undetermined': 12} Link IDs: {None: 11} Chain breaks: 2 Unresolved non-hydrogen bonds: 153 Unresolved non-hydrogen angles: 187 Unresolved non-hydrogen dihedrals: 136 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'POV:plan-1': 3, 'POV:plan-2': 3, 'POV:plan-3': 3} Unresolved non-hydrogen planarities: 34 Chain: "B" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 358 Unusual residues: {'I8E': 2, 'POV': 7, 'Y01': 3} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 153 Unresolved non-hydrogen angles: 187 Unresolved non-hydrogen dihedrals: 136 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'POV:plan-1': 3, 'POV:plan-2': 3, 'POV:plan-3': 3} Unresolved non-hydrogen planarities: 34 Chain: "C" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 358 Unusual residues: {'I8E': 2, 'POV': 7, 'Y01': 3} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 153 Unresolved non-hydrogen angles: 187 Unresolved non-hydrogen dihedrals: 136 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'POV:plan-1': 3, 'POV:plan-2': 3, 'POV:plan-3': 3} Unresolved non-hydrogen planarities: 34 Chain: "D" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 358 Unusual residues: {'I8E': 2, 'POV': 7, 'Y01': 3} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 153 Unresolved non-hydrogen angles: 187 Unresolved non-hydrogen dihedrals: 136 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'POV:plan-1': 3, 'POV:plan-2': 3, 'POV:plan-3': 3} Unresolved non-hydrogen planarities: 34 Time building chain proxies: 7.62, per 1000 atoms: 0.19 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: 3.92 Conformation dependent library (CDL) restraints added in 1.1 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: 1.07 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: 9.86 Time building geometry restraints manager: 5.33 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: 1.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.220 Extract box with map and model: 0.760 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 39.110 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.176 21556 Z= 0.531 Angle : 1.173 21.550 29140 Z= 0.554 Chirality : 0.065 0.453 3220 Planarity : 0.012 0.259 3532 Dihedral : 16.364 160.443 9180 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.84 (0.14), residues: 2440 helix: -3.54 (0.09), residues: 1384 sheet: -3.59 (0.37), residues: 124 loop : -2.27 (0.20), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 492 TYR 0.022 0.003 TYR C 547 PHE 0.021 0.003 PHE D 537 TRP 0.013 0.003 TRP A 629 HIS 0.010 0.002 HIS A 582 Details of bonding type rmsd/Z covalent geometry : bond 0.01357 / 0.53 (21556) covalent geometry : angle 1.17342 / 0.55 (29140) hydrogen bonds : bond 0.29168 / 19.18 ( 892) hydrogen bonds : angle 9.86009 / 6.87 ( 2508) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 538 time to evaluate : 1.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 ASN cc_start: 0.7348 (t0) cc_final: 0.6874 (t0) REVERT: A 195 LEU cc_start: 0.7827 (mt) cc_final: 0.7620 (mt) REVERT: A 208 ASN cc_start: 0.8227 (t0) cc_final: 0.7993 (t0) REVERT: A 262 LYS cc_start: 0.8602 (tttm) cc_final: 0.7909 (ttpp) REVERT: A 300 LYS cc_start: 0.8439 (mttm) cc_final: 0.8238 (mttm) REVERT: A 306 GLN cc_start: 0.7720 (mm-40) cc_final: 0.7485 (mt0) REVERT: A 318 SER cc_start: 0.8072 (t) cc_final: 0.7780 (m) REVERT: A 322 LYS cc_start: 0.7937 (tmmt) cc_final: 0.7587 (mtpm) REVERT: A 328 TYR cc_start: 0.8453 (m-10) cc_final: 0.8226 (m-80) REVERT: A 554 MET cc_start: 0.8864 (tpt) cc_final: 0.8636 (tpt) REVERT: A 577 MET cc_start: 0.7129 (mtm) cc_final: 0.6832 (mtp) REVERT: A 628 ARG cc_start: 0.8118 (mtt-85) cc_final: 0.7455 (mtp180) REVERT: A 635 ASP cc_start: 0.7232 (t70) cc_final: 0.6802 (p0) REVERT: B 174 ASN cc_start: 0.7367 (t0) cc_final: 0.6988 (t0) REVERT: B 195 LEU cc_start: 0.8019 (mt) cc_final: 0.7801 (mt) REVERT: B 211 PHE cc_start: 0.8731 (m-10) cc_final: 0.8489 (m-10) REVERT: B 262 LYS cc_start: 0.8652 (tttm) cc_final: 0.7961 (ttpp) REVERT: B 306 GLN cc_start: 0.7743 (mm-40) cc_final: 0.7539 (mt0) REVERT: B 318 SER cc_start: 0.8195 (t) cc_final: 0.7834 (m) REVERT: B 322 LYS cc_start: 0.7957 (tmmt) cc_final: 0.7606 (mtpm) REVERT: B 328 TYR cc_start: 0.8498 (m-10) cc_final: 0.8255 (m-10) REVERT: B 602 VAL cc_start: 0.7695 (t) cc_final: 0.7492 (m) REVERT: B 628 ARG cc_start: 0.8179 (mtt-85) cc_final: 0.7545 (mpp-170) REVERT: B 635 ASP cc_start: 0.7102 (t70) cc_final: 0.6789 (p0) REVERT: C 113 GLU cc_start: 0.8239 (tt0) cc_final: 0.8017 (tt0) REVERT: C 174 ASN cc_start: 0.7331 (t0) cc_final: 0.6922 (t0) REVERT: C 195 LEU cc_start: 0.7936 (mt) cc_final: 0.7720 (mt) REVERT: C 208 ASN cc_start: 0.8305 (t0) cc_final: 0.8083 (t0) REVERT: C 262 LYS cc_start: 0.8629 (tttm) cc_final: 0.7921 (ttpp) REVERT: C 300 LYS cc_start: 0.8434 (mttm) cc_final: 0.8226 (mttm) REVERT: C 306 GLN cc_start: 0.7718 (mm-40) cc_final: 0.7489 (mt0) REVERT: C 318 SER cc_start: 0.8140 (t) cc_final: 0.7787 (m) REVERT: C 322 LYS cc_start: 0.7962 (tmmt) cc_final: 0.7552 (mtpm) REVERT: C 328 TYR cc_start: 0.8512 (m-10) cc_final: 0.8251 (m-10) REVERT: C 577 MET cc_start: 0.7178 (mtm) cc_final: 0.6948 (mtp) REVERT: C 602 VAL cc_start: 0.7633 (t) cc_final: 0.7424 (m) REVERT: C 628 ARG cc_start: 0.8162 (mtt-85) cc_final: 0.7479 (mpp-170) REVERT: C 635 ASP cc_start: 0.7110 (t70) cc_final: 0.6750 (p0) REVERT: D 113 GLU cc_start: 0.8287 (tt0) cc_final: 0.7984 (tt0) REVERT: D 174 ASN cc_start: 0.7364 (t0) cc_final: 0.6958 (t0) REVERT: D 195 LEU cc_start: 0.7979 (mt) cc_final: 0.7745 (mt) REVERT: D 211 PHE cc_start: 0.8723 (m-10) cc_final: 0.8455 (m-10) REVERT: D 262 LYS cc_start: 0.8664 (tttm) cc_final: 0.7950 (ttpp) REVERT: D 300 LYS cc_start: 0.8412 (mttm) cc_final: 0.8209 (mttm) REVERT: D 303 GLU cc_start: 0.7602 (mp0) cc_final: 0.7138 (mp0) REVERT: D 306 GLN cc_start: 0.7722 (mm-40) cc_final: 0.7492 (mt0) REVERT: D 318 SER cc_start: 0.8182 (t) cc_final: 0.7826 (m) REVERT: D 322 LYS cc_start: 0.7989 (tmmt) cc_final: 0.7591 (mtpm) REVERT: D 328 TYR cc_start: 0.8482 (m-10) cc_final: 0.8184 (m-10) REVERT: D 577 MET cc_start: 0.7162 (mtm) cc_final: 0.6943 (mtp) REVERT: D 602 VAL cc_start: 0.7595 (t) cc_final: 0.7389 (m) REVERT: D 628 ARG cc_start: 0.8185 (mtt-85) cc_final: 0.7506 (mpp-170) REVERT: D 635 ASP cc_start: 0.7099 (t70) cc_final: 0.6735 (p0) outliers start: 0 outliers final: 0 residues processed: 538 average time/residue: 1.4352 time to fit residues: 877.7554 Evaluate side-chains 374 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 374 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 216 optimal weight: 0.8980 chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 8.9990 chunk 227 optimal weight: 0.8980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.7980 chunk 235 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 118 GLN A 197 ASN A 357 ASN A 582 HIS B 118 GLN B 197 ASN ** B 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 357 ASN B 582 HIS C 118 GLN C 197 ASN ** C 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 357 ASN C 582 HIS D 31 GLN D 118 GLN D 197 ASN D 357 ASN D 582 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.186124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.132469 restraints weight = 66220.095| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 2.21 r_work: 0.3501 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3368 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3304 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3304 r_free = 0.3304 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3301 r_free = 0.3301 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (10 function evaluations) r_final: 0.3301 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 21556 Z= 0.165 Angle : 0.735 11.904 29140 Z= 0.371 Chirality : 0.040 0.229 3220 Planarity : 0.006 0.077 3532 Dihedral : 18.017 159.477 4456 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.07 % Favored : 93.77 % Rotamer: Outliers : 1.41 % Allowed : 11.91 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.85 (0.16), residues: 2440 helix: -1.69 (0.12), residues: 1420 sheet: -3.27 (0.36), residues: 124 loop : -1.71 (0.23), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 492 TYR 0.016 0.002 TYR C 377 PHE 0.016 0.001 PHE B 493 TRP 0.008 0.001 TRP A 593 HIS 0.005 0.001 HIS B 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 (21556) covalent geometry : angle 0.73464 / 0.37 (29140) hydrogen bonds : bond 0.06652 / 4.26 ( 892) hydrogen bonds : angle 5.64515 / 3.94 ( 2508) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 369 time to evaluate : 1.111 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: A 104 GLU cc_start: 0.6966 (tm-30) cc_final: 0.6721 (tm-30) REVERT: A 174 ASN cc_start: 0.7586 (t0) cc_final: 0.7095 (t0) REVERT: A 208 ASN cc_start: 0.8233 (t0) cc_final: 0.7875 (t0) REVERT: A 262 LYS cc_start: 0.8715 (tttm) cc_final: 0.8033 (ttpp) REVERT: A 270 TYR cc_start: 0.7918 (t80) cc_final: 0.7716 (t80) REVERT: A 300 LYS cc_start: 0.8502 (mttm) cc_final: 0.8200 (mttm) REVERT: A 303 GLU cc_start: 0.7571 (mp0) cc_final: 0.7166 (mp0) REVERT: A 318 SER cc_start: 0.7902 (t) cc_final: 0.7393 (m) REVERT: A 322 LYS cc_start: 0.7960 (tmmt) cc_final: 0.7606 (mtpm) REVERT: A 554 MET cc_start: 0.8960 (tpt) cc_final: 0.8387 (tpt) REVERT: A 596 GLN cc_start: 0.6776 (mt0) cc_final: 0.6019 (mm-40) REVERT: A 628 ARG cc_start: 0.8158 (mtt-85) cc_final: 0.7311 (mpp-170) REVERT: A 635 ASP cc_start: 0.7488 (t70) cc_final: 0.6770 (p0) REVERT: B 174 ASN cc_start: 0.7581 (t0) cc_final: 0.7007 (t0) REVERT: B 262 LYS cc_start: 0.8743 (tttm) cc_final: 0.8068 (ttpp) REVERT: B 314 LYS cc_start: 0.7461 (ttpt) cc_final: 0.7164 (ttmm) REVERT: B 318 SER cc_start: 0.7922 (t) cc_final: 0.7697 (t) REVERT: B 322 LYS cc_start: 0.7953 (tmmt) cc_final: 0.7588 (mtpm) REVERT: B 328 TYR cc_start: 0.8803 (m-10) cc_final: 0.8592 (m-80) REVERT: B 410 MET cc_start: 0.6769 (mtp) cc_final: 0.6559 (mtm) REVERT: B 554 MET cc_start: 0.8972 (tpt) cc_final: 0.8626 (tpt) REVERT: B 596 GLN cc_start: 0.6761 (mt0) cc_final: 0.6498 (pt0) REVERT: B 602 VAL cc_start: 0.7526 (t) cc_final: 0.7277 (m) REVERT: B 628 ARG cc_start: 0.8191 (mtt-85) cc_final: 0.7308 (mpp-170) REVERT: B 635 ASP cc_start: 0.7404 (t70) cc_final: 0.6684 (p0) REVERT: C 113 GLU cc_start: 0.8417 (tt0) cc_final: 0.8215 (tt0) REVERT: C 174 ASN cc_start: 0.7553 (t0) cc_final: 0.6966 (t0) REVERT: C 208 ASN cc_start: 0.8298 (t0) cc_final: 0.7958 (t0) REVERT: C 211 PHE cc_start: 0.8799 (m-10) cc_final: 0.8487 (m-10) REVERT: C 262 LYS cc_start: 0.8747 (tttm) cc_final: 0.8073 (ttpp) REVERT: C 300 LYS cc_start: 0.8501 (mttm) cc_final: 0.8230 (mttm) REVERT: C 306 GLN cc_start: 0.7732 (mm-40) cc_final: 0.7520 (mt0) REVERT: C 314 LYS cc_start: 0.7459 (ttpt) cc_final: 0.6920 (ttmm) REVERT: C 318 SER cc_start: 0.7871 (t) cc_final: 0.7312 (m) REVERT: C 322 LYS cc_start: 0.7921 (tmmt) cc_final: 0.7578 (mtpm) REVERT: C 596 GLN cc_start: 0.6700 (mt0) cc_final: 0.5942 (mm-40) REVERT: C 602 VAL cc_start: 0.7526 (t) cc_final: 0.7285 (m) REVERT: C 622 GLU cc_start: 0.7299 (pm20) cc_final: 0.7079 (pm20) REVERT: C 628 ARG cc_start: 0.8163 (mtt-85) cc_final: 0.7283 (mpp-170) REVERT: C 635 ASP cc_start: 0.7447 (t70) cc_final: 0.6674 (p0) REVERT: D 113 GLU cc_start: 0.8384 (tt0) cc_final: 0.8160 (tt0) REVERT: D 174 ASN cc_start: 0.7463 (t0) cc_final: 0.6977 (t0) REVERT: D 262 LYS cc_start: 0.8768 (tttm) cc_final: 0.8070 (ttpp) REVERT: D 300 LYS cc_start: 0.8472 (mttm) cc_final: 0.8235 (mttm) REVERT: D 303 GLU cc_start: 0.7629 (mp0) cc_final: 0.7215 (mp0) REVERT: D 314 LYS cc_start: 0.7480 (ttpt) cc_final: 0.7101 (ttmm) REVERT: D 315 GLU cc_start: 0.8294 (mp0) cc_final: 0.7380 (mp0) REVERT: D 318 SER cc_start: 0.7914 (t) cc_final: 0.7695 (t) REVERT: D 322 LYS cc_start: 0.7946 (tmmt) cc_final: 0.7596 (mtpm) REVERT: D 328 TYR cc_start: 0.8785 (m-10) cc_final: 0.8563 (m-80) REVERT: D 410 MET cc_start: 0.7319 (ttp) cc_final: 0.7041 (mtm) REVERT: D 554 MET cc_start: 0.8996 (tpt) cc_final: 0.8625 (tpt) REVERT: D 596 GLN cc_start: 0.6749 (mt0) cc_final: 0.6470 (pt0) REVERT: D 602 VAL cc_start: 0.7467 (t) cc_final: 0.7237 (m) REVERT: D 628 ARG cc_start: 0.8183 (mtt-85) cc_final: 0.7329 (mpp-170) REVERT: D 635 ASP cc_start: 0.7444 (t70) cc_final: 0.6685 (p0) outliers start: 30 outliers final: 12 residues processed: 391 average time/residue: 1.2403 time to fit residues: 562.6991 Evaluate side-chains 355 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 343 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 379 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 61 optimal weight: 10.0000 chunk 159 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 196 optimal weight: 6.9990 chunk 81 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 88 optimal weight: 0.2980 chunk 27 optimal weight: 0.0050 chunk 224 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 overall best weight: 1.8600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 31 GLN A 91 ASN ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 ASN B 546 ASN C 91 ASN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 546 ASN D 91 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.182284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.126059 restraints weight = 66828.551| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 2.25 r_work: 0.3427 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3296 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3233 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3233 r_free = 0.3233 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3233 r_free = 0.3233 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3233 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 21556 Z= 0.166 Angle : 0.673 9.591 29140 Z= 0.330 Chirality : 0.039 0.199 3220 Planarity : 0.005 0.064 3532 Dihedral : 16.169 158.049 4456 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 1.88 % Allowed : 12.90 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.17), residues: 2440 helix: -0.64 (0.13), residues: 1448 sheet: -2.95 (0.40), residues: 124 loop : -1.45 (0.23), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 492 TYR 0.011 0.001 TYR A 222 PHE 0.014 0.001 PHE A 478 TRP 0.007 0.001 TRP A 593 HIS 0.003 0.001 HIS B 426 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.17 (21556) covalent geometry : angle 0.67274 / 0.33 (29140) hydrogen bonds : bond 0.05109 / 3.28 ( 892) hydrogen bonds : angle 5.00468 / 3.51 ( 2508) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 376 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7570 (tt) REVERT: A 104 GLU cc_start: 0.7072 (tm-30) cc_final: 0.6849 (tm-30) REVERT: A 174 ASN cc_start: 0.7605 (t0) cc_final: 0.7120 (t0) REVERT: A 262 LYS cc_start: 0.8867 (tttm) cc_final: 0.8073 (ttpp) REVERT: A 300 LYS cc_start: 0.8502 (mttm) cc_final: 0.8217 (mttm) REVERT: A 303 GLU cc_start: 0.7702 (mp0) cc_final: 0.7201 (mp0) REVERT: A 314 LYS cc_start: 0.7424 (ttpt) cc_final: 0.7112 (ttmm) REVERT: A 318 SER cc_start: 0.7882 (t) cc_final: 0.7670 (t) REVERT: A 322 LYS cc_start: 0.7975 (tmmt) cc_final: 0.7634 (mtpm) REVERT: A 596 GLN cc_start: 0.6846 (mt0) cc_final: 0.6043 (mm-40) REVERT: A 628 ARG cc_start: 0.8130 (mtt-85) cc_final: 0.7245 (mpp-170) REVERT: A 635 ASP cc_start: 0.7597 (t70) cc_final: 0.6848 (p0) REVERT: B 51 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.7546 (tt) REVERT: B 174 ASN cc_start: 0.7621 (t0) cc_final: 0.7070 (t0) REVERT: B 262 LYS cc_start: 0.8790 (tttm) cc_final: 0.8115 (ttpp) REVERT: B 314 LYS cc_start: 0.7434 (ttpt) cc_final: 0.7145 (ttmm) REVERT: B 318 SER cc_start: 0.7961 (t) cc_final: 0.7743 (t) REVERT: B 322 LYS cc_start: 0.7925 (tmmt) cc_final: 0.7535 (mtpm) REVERT: B 596 GLN cc_start: 0.6718 (mt0) cc_final: 0.5940 (mm-40) REVERT: B 602 VAL cc_start: 0.7611 (t) cc_final: 0.7303 (m) REVERT: B 628 ARG cc_start: 0.8154 (mtt-85) cc_final: 0.7272 (mpp-170) REVERT: B 635 ASP cc_start: 0.7537 (t70) cc_final: 0.6806 (p0) REVERT: C 51 LEU cc_start: 0.7945 (OUTLIER) cc_final: 0.7542 (tt) REVERT: C 113 GLU cc_start: 0.8485 (tt0) cc_final: 0.8273 (tt0) REVERT: C 174 ASN cc_start: 0.7717 (t0) cc_final: 0.7097 (t0) REVERT: C 208 ASN cc_start: 0.8119 (t0) cc_final: 0.7764 (t0) REVERT: C 211 PHE cc_start: 0.8778 (m-10) cc_final: 0.8402 (m-10) REVERT: C 262 LYS cc_start: 0.8778 (tttm) cc_final: 0.8095 (ttpp) REVERT: C 300 LYS cc_start: 0.8497 (mttm) cc_final: 0.8236 (mttm) REVERT: C 306 GLN cc_start: 0.7751 (mm-40) cc_final: 0.7524 (mt0) REVERT: C 314 LYS cc_start: 0.7406 (ttpt) cc_final: 0.7114 (ttmm) REVERT: C 318 SER cc_start: 0.7958 (t) cc_final: 0.7737 (t) REVERT: C 322 LYS cc_start: 0.7995 (tmmt) cc_final: 0.7614 (mtpm) REVERT: C 332 LEU cc_start: 0.8281 (mt) cc_final: 0.8067 (mt) REVERT: C 596 GLN cc_start: 0.6795 (mt0) cc_final: 0.6005 (mm-40) REVERT: C 602 VAL cc_start: 0.7646 (t) cc_final: 0.7352 (m) REVERT: C 622 GLU cc_start: 0.7505 (pm20) cc_final: 0.7266 (pm20) REVERT: C 628 ARG cc_start: 0.8132 (mtt-85) cc_final: 0.7240 (mpp-170) REVERT: C 635 ASP cc_start: 0.7575 (t70) cc_final: 0.6807 (p0) REVERT: D 51 LEU cc_start: 0.7969 (OUTLIER) cc_final: 0.7556 (tt) REVERT: D 113 GLU cc_start: 0.8422 (tt0) cc_final: 0.8183 (tt0) REVERT: D 174 ASN cc_start: 0.7382 (t0) cc_final: 0.7051 (t0) REVERT: D 262 LYS cc_start: 0.8888 (tttm) cc_final: 0.8182 (ttpp) REVERT: D 300 LYS cc_start: 0.8486 (mttm) cc_final: 0.8220 (mttm) REVERT: D 301 LYS cc_start: 0.8427 (OUTLIER) cc_final: 0.7913 (mtpm) REVERT: D 303 GLU cc_start: 0.7713 (mp0) cc_final: 0.7143 (mp0) REVERT: D 314 LYS cc_start: 0.7441 (ttpt) cc_final: 0.7150 (ttmm) REVERT: D 318 SER cc_start: 0.7974 (t) cc_final: 0.7759 (t) REVERT: D 322 LYS cc_start: 0.8017 (tmmt) cc_final: 0.7635 (mtpm) REVERT: D 374 GLN cc_start: 0.8515 (mp-120) cc_final: 0.8309 (mm-40) REVERT: D 474 MET cc_start: 0.2083 (OUTLIER) cc_final: 0.1820 (mtt) REVERT: D 490 LEU cc_start: 0.6031 (OUTLIER) cc_final: 0.5808 (tt) REVERT: D 596 GLN cc_start: 0.6702 (mt0) cc_final: 0.5934 (mm-40) REVERT: D 602 VAL cc_start: 0.7594 (t) cc_final: 0.7304 (m) REVERT: D 628 ARG cc_start: 0.8175 (mtt-85) cc_final: 0.7308 (mpp-170) REVERT: D 635 ASP cc_start: 0.7579 (t70) cc_final: 0.6824 (p0) outliers start: 40 outliers final: 25 residues processed: 401 average time/residue: 1.0727 time to fit residues: 505.1929 Evaluate side-chains 372 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 340 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain 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 255 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 301 LYS Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 490 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 55 optimal weight: 10.0000 chunk 117 optimal weight: 7.9990 chunk 232 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 229 optimal weight: 8.9990 chunk 183 optimal weight: 9.9990 chunk 114 optimal weight: 1.9990 chunk 6 optimal weight: 10.0000 chunk 65 optimal weight: 10.0000 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 91 ASN A 118 GLN ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 ASN A 546 ASN ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 357 ASN C 118 GLN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 357 ASN D 91 ASN D 118 GLN ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 357 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.179969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.123436 restraints weight = 67476.889| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 2.24 r_work: 0.3403 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3202 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3202 r_free = 0.3202 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3202 r_free = 0.3202 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3202 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.3387 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= 0.180 Angle : 0.644 8.606 29140 Z= 0.316 Chirality : 0.040 0.212 3220 Planarity : 0.005 0.056 3532 Dihedral : 15.622 153.578 4456 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.19 % Favored : 93.77 % Rotamer: Outliers : 2.21 % Allowed : 13.84 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.17), residues: 2440 helix: -0.19 (0.14), residues: 1456 sheet: -3.67 (0.48), residues: 84 loop : -1.30 (0.22), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 492 TYR 0.012 0.002 TYR C 216 PHE 0.011 0.001 PHE C 478 TRP 0.007 0.001 TRP B 593 HIS 0.003 0.001 HIS B 426 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.18 (21556) covalent geometry : angle 0.64367 / 0.32 (29140) hydrogen bonds : bond 0.04419 / 2.84 ( 892) hydrogen bonds : angle 4.74632 / 3.34 ( 2508) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 345 time to evaluate : 1.074 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: 0.8002 (OUTLIER) cc_final: 0.7586 (tt) REVERT: A 174 ASN cc_start: 0.7736 (t0) cc_final: 0.7247 (t0) REVERT: A 262 LYS cc_start: 0.8927 (tttm) cc_final: 0.8169 (ttpt) REVERT: A 300 LYS cc_start: 0.8505 (mttm) cc_final: 0.8235 (mttm) REVERT: A 303 GLU cc_start: 0.7856 (mp0) cc_final: 0.7391 (mp0) REVERT: A 314 LYS cc_start: 0.7493 (ttpt) cc_final: 0.7191 (ttmm) REVERT: A 322 LYS cc_start: 0.8009 (tmmt) cc_final: 0.7655 (mtpm) REVERT: A 378 MET cc_start: 0.8376 (mtp) cc_final: 0.8169 (mtm) REVERT: A 490 LEU cc_start: 0.6056 (OUTLIER) cc_final: 0.5854 (tt) REVERT: A 492 ARG cc_start: 0.5808 (tpp80) cc_final: 0.5283 (tpp80) REVERT: A 596 GLN cc_start: 0.6897 (mt0) cc_final: 0.6079 (mm-40) REVERT: A 628 ARG cc_start: 0.8126 (mtt-85) cc_final: 0.7262 (mpp-170) REVERT: A 635 ASP cc_start: 0.7655 (t70) cc_final: 0.6892 (p0) REVERT: B 51 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7557 (tt) REVERT: B 174 ASN cc_start: 0.7763 (t0) cc_final: 0.7161 (t0) REVERT: B 262 LYS cc_start: 0.8915 (tttm) cc_final: 0.8155 (ttpp) REVERT: B 314 LYS cc_start: 0.7472 (ttpt) cc_final: 0.7189 (ttmm) REVERT: B 318 SER cc_start: 0.7980 (t) cc_final: 0.7740 (t) REVERT: B 322 LYS cc_start: 0.7944 (tmmt) cc_final: 0.7580 (mtpm) REVERT: B 378 MET cc_start: 0.8418 (mtm) cc_final: 0.8122 (mtm) REVERT: B 474 MET cc_start: 0.2231 (OUTLIER) cc_final: 0.1977 (mtt) REVERT: B 596 GLN cc_start: 0.6806 (mt0) cc_final: 0.5995 (mm-40) REVERT: B 602 VAL cc_start: 0.7765 (t) cc_final: 0.7448 (m) REVERT: B 628 ARG cc_start: 0.8152 (mtt-85) cc_final: 0.7302 (mpp-170) REVERT: B 635 ASP cc_start: 0.7632 (t70) cc_final: 0.6860 (p0) REVERT: C 51 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7552 (tt) REVERT: C 174 ASN cc_start: 0.7731 (t0) cc_final: 0.7156 (t0) REVERT: C 211 PHE cc_start: 0.8773 (m-10) cc_final: 0.8545 (m-10) REVERT: C 262 LYS cc_start: 0.8925 (tttm) cc_final: 0.8174 (ttpp) REVERT: C 300 LYS cc_start: 0.8495 (mttm) cc_final: 0.8247 (mttm) REVERT: C 303 GLU cc_start: 0.7717 (mp0) cc_final: 0.7390 (mp0) REVERT: C 306 GLN cc_start: 0.7780 (mm-40) cc_final: 0.7568 (mt0) REVERT: C 314 LYS cc_start: 0.7461 (ttpt) cc_final: 0.7177 (ttmm) REVERT: C 318 SER cc_start: 0.7958 (t) cc_final: 0.7725 (t) REVERT: C 322 LYS cc_start: 0.7953 (tmmt) cc_final: 0.7597 (mtpm) REVERT: C 378 MET cc_start: 0.8406 (mtm) cc_final: 0.8108 (mtm) REVERT: C 596 GLN cc_start: 0.6906 (mt0) cc_final: 0.6063 (mm-40) REVERT: C 602 VAL cc_start: 0.7835 (t) cc_final: 0.7522 (m) REVERT: C 622 GLU cc_start: 0.7679 (pm20) cc_final: 0.7366 (pm20) REVERT: C 628 ARG cc_start: 0.8165 (mtt-85) cc_final: 0.7305 (mpp-170) REVERT: C 635 ASP cc_start: 0.7668 (t70) cc_final: 0.6908 (p0) REVERT: D 51 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7555 (tt) REVERT: D 113 GLU cc_start: 0.8473 (tt0) cc_final: 0.8208 (tt0) REVERT: D 174 ASN cc_start: 0.7705 (t0) cc_final: 0.7241 (t0) REVERT: D 262 LYS cc_start: 0.8920 (tttm) cc_final: 0.8151 (ttpp) REVERT: D 300 LYS cc_start: 0.8485 (mttm) cc_final: 0.8234 (mttm) REVERT: D 303 GLU cc_start: 0.7887 (mp0) cc_final: 0.7407 (mp0) REVERT: D 314 LYS cc_start: 0.7474 (ttpt) cc_final: 0.7192 (ttmm) REVERT: D 322 LYS cc_start: 0.8006 (tmmt) cc_final: 0.7629 (mtpm) REVERT: D 374 GLN cc_start: 0.8528 (mp-120) cc_final: 0.8248 (mm-40) REVERT: D 378 MET cc_start: 0.8404 (mtm) cc_final: 0.8115 (mtm) REVERT: D 596 GLN cc_start: 0.6761 (mt0) cc_final: 0.5959 (mm-40) REVERT: D 602 VAL cc_start: 0.7713 (t) cc_final: 0.7414 (m) REVERT: D 628 ARG cc_start: 0.8150 (mtt-85) cc_final: 0.7321 (mpp-170) REVERT: D 635 ASP cc_start: 0.7618 (t70) cc_final: 0.6856 (p0) outliers start: 47 outliers final: 21 residues processed: 373 average time/residue: 1.1096 time to fit residues: 483.3143 Evaluate side-chains 347 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 320 time to evaluate : 0.965 ------------------------------------------------------------------------------- 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 479 THR Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain C residue 492 ARG Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 490 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 66 optimal weight: 6.9990 chunk 163 optimal weight: 3.9990 chunk 139 optimal weight: 3.9990 chunk 122 optimal weight: 10.0000 chunk 44 optimal weight: 0.9980 chunk 206 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 108 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 144 optimal weight: 1.9990 chunk 115 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 118 GLN ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 ASN B 357 ASN ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 357 ASN ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 357 ASN D 546 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.181023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.126338 restraints weight = 66460.879| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 2.15 r_work: 0.3460 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3334 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3230 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3230 r_free = 0.3230 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3230 r_free = 0.3230 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3230 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.3599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21556 Z= 0.128 Angle : 0.600 8.015 29140 Z= 0.297 Chirality : 0.038 0.209 3220 Planarity : 0.004 0.057 3532 Dihedral : 14.590 150.151 4456 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.35 % Favored : 93.57 % Rotamer: Outliers : 2.26 % Allowed : 14.74 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.18), residues: 2440 helix: 0.14 (0.14), residues: 1452 sheet: -3.68 (0.48), residues: 84 loop : -1.17 (0.22), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 75 TYR 0.013 0.001 TYR C 216 PHE 0.010 0.001 PHE D 493 TRP 0.007 0.001 TRP C 593 HIS 0.003 0.001 HIS B 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (21556) covalent geometry : angle 0.59967 / 0.30 (29140) hydrogen bonds : bond 0.04110 / 2.64 ( 892) hydrogen bonds : angle 4.59783 / 3.24 ( 2508) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 344 time to evaluate : 1.033 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: 0.7952 (OUTLIER) cc_final: 0.7520 (tt) REVERT: A 174 ASN cc_start: 0.7668 (t0) cc_final: 0.7214 (t0) REVERT: A 262 LYS cc_start: 0.8903 (tttm) cc_final: 0.8453 (ttpt) REVERT: A 300 LYS cc_start: 0.8491 (mttm) cc_final: 0.8218 (mttm) REVERT: A 303 GLU cc_start: 0.7876 (mp0) cc_final: 0.7385 (mp0) REVERT: A 314 LYS cc_start: 0.7427 (ttpt) cc_final: 0.7119 (ttmm) REVERT: A 322 LYS cc_start: 0.7926 (tmmt) cc_final: 0.7553 (mtpm) REVERT: A 378 MET cc_start: 0.8343 (mtp) cc_final: 0.8001 (mtm) REVERT: A 596 GLN cc_start: 0.6820 (mt0) cc_final: 0.5960 (mm-40) REVERT: A 628 ARG cc_start: 0.8122 (mtt-85) cc_final: 0.7258 (mpp-170) REVERT: A 635 ASP cc_start: 0.7611 (t70) cc_final: 0.6875 (p0) REVERT: B 51 LEU cc_start: 0.7956 (OUTLIER) cc_final: 0.7513 (tt) REVERT: B 174 ASN cc_start: 0.7716 (t0) cc_final: 0.7127 (t0) REVERT: B 262 LYS cc_start: 0.8921 (tttm) cc_final: 0.8163 (ttpp) REVERT: B 314 LYS cc_start: 0.7365 (ttpt) cc_final: 0.7071 (ttmm) REVERT: B 318 SER cc_start: 0.7863 (t) cc_final: 0.7630 (t) REVERT: B 322 LYS cc_start: 0.7901 (tmmt) cc_final: 0.7514 (mtpm) REVERT: B 378 MET cc_start: 0.8388 (mtm) cc_final: 0.7979 (mtm) REVERT: B 410 MET cc_start: 0.6618 (mtp) cc_final: 0.6397 (mtm) REVERT: B 596 GLN cc_start: 0.6871 (mt0) cc_final: 0.5994 (mm-40) REVERT: B 602 VAL cc_start: 0.7790 (t) cc_final: 0.7469 (m) REVERT: B 628 ARG cc_start: 0.8127 (mtt-85) cc_final: 0.7264 (mpp-170) REVERT: B 635 ASP cc_start: 0.7543 (t70) cc_final: 0.6801 (p0) REVERT: C 51 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7516 (tt) REVERT: C 174 ASN cc_start: 0.7709 (t0) cc_final: 0.7102 (t0) REVERT: C 262 LYS cc_start: 0.8901 (tttm) cc_final: 0.8130 (ttpp) REVERT: C 300 LYS cc_start: 0.8516 (mttm) cc_final: 0.8282 (mttm) REVERT: C 303 GLU cc_start: 0.7674 (mp0) cc_final: 0.7342 (mp0) REVERT: C 306 GLN cc_start: 0.7763 (mm-40) cc_final: 0.7525 (mt0) REVERT: C 314 LYS cc_start: 0.7375 (ttpt) cc_final: 0.7083 (ttmm) REVERT: C 318 SER cc_start: 0.7874 (t) cc_final: 0.7632 (t) REVERT: C 322 LYS cc_start: 0.7903 (tmmt) cc_final: 0.7529 (mtpm) REVERT: C 378 MET cc_start: 0.8403 (mtm) cc_final: 0.7994 (mtm) REVERT: C 490 LEU cc_start: 0.5897 (OUTLIER) cc_final: 0.5670 (tt) REVERT: C 596 GLN cc_start: 0.6863 (mt0) cc_final: 0.5980 (mm-40) REVERT: C 602 VAL cc_start: 0.7798 (t) cc_final: 0.7491 (m) REVERT: C 622 GLU cc_start: 0.7729 (pm20) cc_final: 0.7403 (pm20) REVERT: C 628 ARG cc_start: 0.8115 (mtt-85) cc_final: 0.7239 (mpp-170) REVERT: C 635 ASP cc_start: 0.7577 (t70) cc_final: 0.6830 (p0) REVERT: D 51 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7522 (tt) REVERT: D 113 GLU cc_start: 0.8447 (tt0) cc_final: 0.8179 (tt0) REVERT: D 167 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7837 (tp) REVERT: D 174 ASN cc_start: 0.7585 (t0) cc_final: 0.7181 (t0) REVERT: D 262 LYS cc_start: 0.8907 (tttm) cc_final: 0.8140 (ttpp) REVERT: D 300 LYS cc_start: 0.8477 (mttm) cc_final: 0.8231 (mttm) REVERT: D 303 GLU cc_start: 0.7860 (mp0) cc_final: 0.7249 (mp0) REVERT: D 314 LYS cc_start: 0.7372 (ttpt) cc_final: 0.7076 (ttmm) REVERT: D 318 SER cc_start: 0.7884 (t) cc_final: 0.7639 (t) REVERT: D 322 LYS cc_start: 0.7929 (tmmt) cc_final: 0.7565 (mtpm) REVERT: D 374 GLN cc_start: 0.8494 (mp-120) cc_final: 0.8175 (mm-40) REVERT: D 378 MET cc_start: 0.8364 (mtm) cc_final: 0.7963 (mtm) REVERT: D 490 LEU cc_start: 0.5889 (OUTLIER) cc_final: 0.5681 (tt) REVERT: D 596 GLN cc_start: 0.6689 (mt0) cc_final: 0.5874 (mm-40) REVERT: D 602 VAL cc_start: 0.7700 (t) cc_final: 0.7422 (m) REVERT: D 621 ARG cc_start: 0.7595 (ttm110) cc_final: 0.7372 (ttp-110) REVERT: D 628 ARG cc_start: 0.8149 (mtt-85) cc_final: 0.7313 (mpp-170) REVERT: D 635 ASP cc_start: 0.7542 (t70) cc_final: 0.6806 (p0) outliers start: 48 outliers final: 27 residues processed: 380 average time/residue: 1.0773 time to fit residues: 480.2988 Evaluate side-chains 363 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 329 time to evaluate : 1.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 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 490 LEU Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 490 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 206 optimal weight: 0.8980 chunk 209 optimal weight: 6.9990 chunk 75 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 13 optimal weight: 6.9990 chunk 219 optimal weight: 3.9990 chunk 55 optimal weight: 10.0000 chunk 76 optimal weight: 0.6980 chunk 4 optimal weight: 20.0000 chunk 80 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 ASN B 357 ASN ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 357 ASN ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 357 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.181818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.125308 restraints weight = 67327.947| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 2.25 r_work: 0.3427 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3226 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3226 r_free = 0.3226 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3226 r_free = 0.3226 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3226 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.3679 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= 0.116 Angle : 0.583 8.146 29140 Z= 0.289 Chirality : 0.037 0.193 3220 Planarity : 0.004 0.057 3532 Dihedral : 14.102 146.348 4456 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.66 % Favored : 94.22 % Rotamer: Outliers : 2.40 % Allowed : 14.97 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.18), residues: 2440 helix: 0.35 (0.14), residues: 1452 sheet: -3.65 (0.47), residues: 84 loop : -1.09 (0.22), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 621 TYR 0.021 0.001 TYR C 216 PHE 0.009 0.001 PHE D 493 TRP 0.007 0.001 TRP C 593 HIS 0.003 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (21556) covalent geometry : angle 0.58254 / 0.29 (29140) hydrogen bonds : bond 0.03896 / 2.50 ( 892) hydrogen bonds : angle 4.49633 / 3.16 ( 2508) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 345 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LEU cc_start: 0.7978 (OUTLIER) cc_final: 0.7541 (tt) REVERT: A 174 ASN cc_start: 0.7667 (t0) cc_final: 0.7205 (t0) REVERT: A 262 LYS cc_start: 0.8930 (tttm) cc_final: 0.8464 (ttpt) REVERT: A 300 LYS cc_start: 0.8485 (mttm) cc_final: 0.8216 (mttm) REVERT: A 303 GLU cc_start: 0.7894 (mp0) cc_final: 0.7386 (mp0) REVERT: A 314 LYS cc_start: 0.7433 (ttpt) cc_final: 0.7120 (ttmm) REVERT: A 318 SER cc_start: 0.7885 (t) cc_final: 0.7638 (t) REVERT: A 322 LYS cc_start: 0.7917 (tmmt) cc_final: 0.7574 (mtpm) REVERT: A 378 MET cc_start: 0.8363 (mtp) cc_final: 0.8027 (mtm) REVERT: A 596 GLN cc_start: 0.6892 (mt0) cc_final: 0.5977 (mm-40) REVERT: A 628 ARG cc_start: 0.8118 (mtt-85) cc_final: 0.7257 (mpp-170) REVERT: A 635 ASP cc_start: 0.7587 (t70) cc_final: 0.6866 (p0) REVERT: B 51 LEU cc_start: 0.7958 (OUTLIER) cc_final: 0.7511 (tt) REVERT: B 167 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7831 (tp) REVERT: B 174 ASN cc_start: 0.7713 (t0) cc_final: 0.7148 (t0) REVERT: B 262 LYS cc_start: 0.8938 (tttm) cc_final: 0.8225 (ttpp) REVERT: B 303 GLU cc_start: 0.7871 (mp0) cc_final: 0.7383 (mp0) REVERT: B 314 LYS cc_start: 0.7376 (ttpt) cc_final: 0.7083 (ttmm) REVERT: B 318 SER cc_start: 0.7891 (t) cc_final: 0.7656 (t) REVERT: B 322 LYS cc_start: 0.7928 (tmmt) cc_final: 0.7536 (mtpm) REVERT: B 378 MET cc_start: 0.8425 (mtm) cc_final: 0.8063 (mtm) REVERT: B 492 ARG cc_start: 0.5937 (OUTLIER) cc_final: 0.4900 (tpp80) REVERT: B 596 GLN cc_start: 0.6910 (mt0) cc_final: 0.6543 (pt0) REVERT: B 602 VAL cc_start: 0.7795 (t) cc_final: 0.7476 (m) REVERT: B 621 ARG cc_start: 0.7618 (ttm110) cc_final: 0.7416 (ttp-110) REVERT: B 628 ARG cc_start: 0.8077 (mtt-85) cc_final: 0.7235 (mpp-170) REVERT: B 635 ASP cc_start: 0.7542 (t70) cc_final: 0.6795 (p0) REVERT: C 51 LEU cc_start: 0.7947 (OUTLIER) cc_final: 0.7508 (tt) REVERT: C 167 LEU cc_start: 0.8080 (OUTLIER) cc_final: 0.7792 (tp) REVERT: C 174 ASN cc_start: 0.7701 (t0) cc_final: 0.7131 (t0) REVERT: C 262 LYS cc_start: 0.8929 (tttm) cc_final: 0.8205 (ttpp) REVERT: C 300 LYS cc_start: 0.8473 (mttm) cc_final: 0.8238 (mttm) REVERT: C 303 GLU cc_start: 0.7722 (mp0) cc_final: 0.7386 (mp0) REVERT: C 306 GLN cc_start: 0.7784 (mm-40) cc_final: 0.7561 (mt0) REVERT: C 314 LYS cc_start: 0.7399 (ttpt) cc_final: 0.7102 (ttmm) REVERT: C 318 SER cc_start: 0.7906 (t) cc_final: 0.7664 (t) REVERT: C 322 LYS cc_start: 0.7934 (tmmt) cc_final: 0.7556 (mtpm) REVERT: C 378 MET cc_start: 0.8443 (mtm) cc_final: 0.8079 (mtm) REVERT: C 596 GLN cc_start: 0.6943 (mt0) cc_final: 0.6031 (mm-40) REVERT: C 602 VAL cc_start: 0.7803 (t) cc_final: 0.7499 (m) REVERT: C 628 ARG cc_start: 0.8093 (mtt-85) cc_final: 0.7234 (mpp-170) REVERT: C 635 ASP cc_start: 0.7590 (t70) cc_final: 0.6837 (p0) REVERT: D 51 LEU cc_start: 0.7940 (OUTLIER) cc_final: 0.7500 (tt) REVERT: D 113 GLU cc_start: 0.8466 (tt0) cc_final: 0.8234 (tt0) REVERT: D 167 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7826 (tp) REVERT: D 174 ASN cc_start: 0.7594 (t0) cc_final: 0.7167 (t0) REVERT: D 262 LYS cc_start: 0.8941 (tttm) cc_final: 0.8173 (ttpp) REVERT: D 300 LYS cc_start: 0.8488 (mttm) cc_final: 0.8250 (mttm) REVERT: D 303 GLU cc_start: 0.7867 (mp0) cc_final: 0.7280 (mp0) REVERT: D 314 LYS cc_start: 0.7408 (ttpt) cc_final: 0.7113 (ttmm) REVERT: D 318 SER cc_start: 0.7903 (t) cc_final: 0.7660 (t) REVERT: D 322 LYS cc_start: 0.7945 (tmmt) cc_final: 0.7578 (mtpm) REVERT: D 374 GLN cc_start: 0.8497 (mp-120) cc_final: 0.8227 (mm-40) REVERT: D 378 MET cc_start: 0.8425 (mtm) cc_final: 0.8071 (mtm) REVERT: D 406 ASP cc_start: 0.6430 (OUTLIER) cc_final: 0.6163 (t70) REVERT: D 596 GLN cc_start: 0.6690 (mt0) cc_final: 0.5892 (mm-40) REVERT: D 602 VAL cc_start: 0.7728 (t) cc_final: 0.7451 (m) REVERT: D 621 ARG cc_start: 0.7581 (ttm110) cc_final: 0.7357 (ttp-110) REVERT: D 628 ARG cc_start: 0.8138 (mtt-85) cc_final: 0.7301 (mpp-170) REVERT: D 635 ASP cc_start: 0.7547 (t70) cc_final: 0.6802 (p0) outliers start: 51 outliers final: 28 residues processed: 380 average time/residue: 1.0600 time to fit residues: 471.5724 Evaluate side-chains 363 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 326 time to evaluate : 1.299 ------------------------------------------------------------------------------- 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 345 MET Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 492 ARG Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 406 ASP Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 490 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 82 optimal weight: 1.9990 chunk 211 optimal weight: 3.9990 chunk 172 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 236 optimal weight: 1.9990 chunk 161 optimal weight: 8.9990 chunk 227 optimal weight: 8.9990 chunk 132 optimal weight: 0.7980 chunk 108 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 ASN B 357 ASN ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 357 ASN D 118 GLN D 357 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.181196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.126358 restraints weight = 66686.059| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 2.16 r_work: 0.3430 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3303 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3230 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3230 r_free = 0.3230 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3230 r_free = 0.3230 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3230 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.3820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21556 Z= 0.126 Angle : 0.584 8.111 29140 Z= 0.291 Chirality : 0.038 0.195 3220 Planarity : 0.004 0.059 3532 Dihedral : 13.650 140.913 4456 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 2.45 % Allowed : 15.07 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.18), residues: 2440 helix: 0.42 (0.14), residues: 1484 sheet: -3.63 (0.47), residues: 84 loop : -0.88 (0.23), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 492 TYR 0.014 0.001 TYR D 324 PHE 0.009 0.001 PHE D 493 TRP 0.006 0.001 TRP A 593 HIS 0.003 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (21556) covalent geometry : angle 0.58430 / 0.29 (29140) hydrogen bonds : bond 0.03812 / 2.45 ( 892) hydrogen bonds : angle 4.42046 / 3.11 ( 2508) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 346 time to evaluate : 1.114 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: 0.7990 (OUTLIER) cc_final: 0.7544 (tt) REVERT: A 174 ASN cc_start: 0.7735 (t0) cc_final: 0.7264 (t0) REVERT: A 262 LYS cc_start: 0.8904 (tttm) cc_final: 0.8066 (ttpp) REVERT: A 300 LYS cc_start: 0.8485 (mttm) cc_final: 0.8221 (mttm) REVERT: A 303 GLU cc_start: 0.7920 (mp0) cc_final: 0.7403 (mp0) REVERT: A 314 LYS cc_start: 0.7411 (ttpt) cc_final: 0.7085 (ttmm) REVERT: A 318 SER cc_start: 0.7901 (t) cc_final: 0.7659 (t) REVERT: A 322 LYS cc_start: 0.7926 (tmmt) cc_final: 0.7573 (mtpm) REVERT: A 378 MET cc_start: 0.8322 (mtp) cc_final: 0.7982 (mtm) REVERT: A 596 GLN cc_start: 0.6915 (mt0) cc_final: 0.5964 (mm-40) REVERT: A 628 ARG cc_start: 0.8126 (mtt-85) cc_final: 0.7277 (mpp-170) REVERT: A 635 ASP cc_start: 0.7564 (t70) cc_final: 0.6862 (p0) REVERT: B 51 LEU cc_start: 0.7968 (OUTLIER) cc_final: 0.7491 (tt) REVERT: B 153 ARG cc_start: 0.8321 (OUTLIER) cc_final: 0.8064 (mtt90) REVERT: B 167 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7840 (tp) REVERT: B 174 ASN cc_start: 0.7733 (t0) cc_final: 0.7162 (t0) REVERT: B 262 LYS cc_start: 0.8926 (tttm) cc_final: 0.8227 (ttpp) REVERT: B 303 GLU cc_start: 0.7911 (mp0) cc_final: 0.7417 (mp0) REVERT: B 314 LYS cc_start: 0.7395 (ttpt) cc_final: 0.7093 (ttmm) REVERT: B 318 SER cc_start: 0.7870 (t) cc_final: 0.7636 (t) REVERT: B 322 LYS cc_start: 0.7931 (tmmt) cc_final: 0.7541 (mtpm) REVERT: B 474 MET cc_start: 0.1968 (mtt) cc_final: 0.1759 (mtt) REVERT: B 492 ARG cc_start: 0.5917 (OUTLIER) cc_final: 0.4842 (tpp80) REVERT: B 596 GLN cc_start: 0.6955 (mt0) cc_final: 0.6023 (mm-40) REVERT: B 602 VAL cc_start: 0.7842 (t) cc_final: 0.7532 (m) REVERT: B 621 ARG cc_start: 0.7580 (ttm110) cc_final: 0.7330 (ttp-110) REVERT: B 628 ARG cc_start: 0.8052 (mtt-85) cc_final: 0.7228 (mpp-170) REVERT: B 635 ASP cc_start: 0.7499 (t70) cc_final: 0.6782 (p0) REVERT: C 51 LEU cc_start: 0.7952 (OUTLIER) cc_final: 0.7487 (tt) REVERT: C 167 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7860 (tp) REVERT: C 174 ASN cc_start: 0.7737 (t0) cc_final: 0.7158 (t0) REVERT: C 262 LYS cc_start: 0.8930 (tttm) cc_final: 0.8174 (ttpp) REVERT: C 300 LYS cc_start: 0.8469 (mttm) cc_final: 0.8241 (mttm) REVERT: C 303 GLU cc_start: 0.7775 (mp0) cc_final: 0.7433 (mp0) REVERT: C 306 GLN cc_start: 0.7783 (mm-40) cc_final: 0.7578 (mt0) REVERT: C 314 LYS cc_start: 0.7425 (ttpt) cc_final: 0.7121 (ttmm) REVERT: C 318 SER cc_start: 0.7883 (t) cc_final: 0.7646 (t) REVERT: C 322 LYS cc_start: 0.7942 (tmmt) cc_final: 0.7559 (mtpm) REVERT: C 490 LEU cc_start: 0.5941 (OUTLIER) cc_final: 0.5719 (tt) REVERT: C 596 GLN cc_start: 0.6982 (mt0) cc_final: 0.6045 (mm-40) REVERT: C 602 VAL cc_start: 0.7836 (t) cc_final: 0.7531 (m) REVERT: C 628 ARG cc_start: 0.8060 (mtt-85) cc_final: 0.7216 (mpp-170) REVERT: C 635 ASP cc_start: 0.7575 (t70) cc_final: 0.6834 (p0) REVERT: D 51 LEU cc_start: 0.7947 (OUTLIER) cc_final: 0.7502 (tt) REVERT: D 113 GLU cc_start: 0.8446 (tt0) cc_final: 0.8221 (tt0) REVERT: D 167 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7873 (tp) REVERT: D 174 ASN cc_start: 0.7615 (t0) cc_final: 0.7200 (t0) REVERT: D 262 LYS cc_start: 0.8932 (tttm) cc_final: 0.8172 (ttpp) REVERT: D 300 LYS cc_start: 0.8494 (mttm) cc_final: 0.8261 (mttm) REVERT: D 303 GLU cc_start: 0.7901 (mp0) cc_final: 0.7314 (mp0) REVERT: D 314 LYS cc_start: 0.7422 (ttpt) cc_final: 0.7117 (ttmm) REVERT: D 318 SER cc_start: 0.7904 (t) cc_final: 0.7662 (t) REVERT: D 322 LYS cc_start: 0.7958 (tmmt) cc_final: 0.7580 (mtpm) REVERT: D 596 GLN cc_start: 0.6722 (mt0) cc_final: 0.5920 (mm-40) REVERT: D 602 VAL cc_start: 0.7776 (t) cc_final: 0.7487 (m) REVERT: D 621 ARG cc_start: 0.7601 (ttm110) cc_final: 0.7367 (ttp-110) REVERT: D 628 ARG cc_start: 0.8119 (mtt-85) cc_final: 0.7300 (mpp-170) REVERT: D 635 ASP cc_start: 0.7566 (t70) cc_final: 0.6819 (p0) outliers start: 52 outliers final: 25 residues processed: 382 average time/residue: 1.0889 time to fit residues: 485.6145 Evaluate side-chains 363 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 328 time to evaluate : 1.025 ------------------------------------------------------------------------------- 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 345 MET 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 153 ARG 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 490 LEU Chi-restraints excluded: chain B residue 492 ARG Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 479 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 99 optimal weight: 6.9990 chunk 198 optimal weight: 3.9990 chunk 121 optimal weight: 7.9990 chunk 68 optimal weight: 10.0000 chunk 147 optimal weight: 6.9990 chunk 179 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 39 optimal weight: 9.9990 chunk 50 optimal weight: 1.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 357 ASN C 118 GLN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 357 ASN D 118 GLN ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 357 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.176656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.121125 restraints weight = 67482.016| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 2.17 r_work: 0.3387 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3147 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3147 r_free = 0.3147 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3147 r_free = 0.3147 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3147 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.3941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.095 21556 Z= 0.260 Angle : 0.659 7.832 29140 Z= 0.325 Chirality : 0.043 0.219 3220 Planarity : 0.005 0.060 3532 Dihedral : 14.603 133.415 4456 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 2.59 % Allowed : 15.87 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.17), residues: 2440 helix: 0.24 (0.14), residues: 1484 sheet: -3.62 (0.47), residues: 84 loop : -1.04 (0.22), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 350 TYR 0.021 0.002 TYR A 216 PHE 0.011 0.002 PHE B 553 TRP 0.005 0.001 TRP B 593 HIS 0.006 0.001 HIS A 522 Details of bonding type rmsd/Z covalent geometry : bond 0.00634 / 0.26 (21556) covalent geometry : angle 0.65944 / 0.32 (29140) hydrogen bonds : bond 0.04258 / 2.74 ( 892) hydrogen bonds : angle 4.56237 / 3.21 ( 2508) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 338 time to evaluate : 1.107 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: 0.7998 (OUTLIER) cc_final: 0.7519 (tt) REVERT: A 174 ASN cc_start: 0.7767 (t0) cc_final: 0.7276 (t0) REVERT: A 262 LYS cc_start: 0.8928 (tttm) cc_final: 0.8481 (ttpt) REVERT: A 300 LYS cc_start: 0.8503 (mttm) cc_final: 0.8248 (mttm) REVERT: A 303 GLU cc_start: 0.7980 (mp0) cc_final: 0.7413 (mp0) REVERT: A 314 LYS cc_start: 0.7528 (ttpt) cc_final: 0.7157 (ttmm) REVERT: A 322 LYS cc_start: 0.7979 (tmmt) cc_final: 0.7615 (mtpm) REVERT: A 378 MET cc_start: 0.8406 (mtp) cc_final: 0.8065 (mtm) REVERT: A 596 GLN cc_start: 0.7032 (mt0) cc_final: 0.6072 (mm-40) REVERT: A 628 ARG cc_start: 0.8117 (mtt-85) cc_final: 0.7262 (mpp-170) REVERT: A 635 ASP cc_start: 0.7667 (t70) cc_final: 0.6894 (p0) REVERT: B 51 LEU cc_start: 0.7987 (OUTLIER) cc_final: 0.7512 (tt) REVERT: B 167 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7900 (tp) REVERT: B 174 ASN cc_start: 0.7793 (t0) cc_final: 0.7283 (t0) REVERT: B 262 LYS cc_start: 0.8908 (tttm) cc_final: 0.8115 (ttpp) REVERT: B 303 GLU cc_start: 0.7974 (mp0) cc_final: 0.7436 (mp0) REVERT: B 314 LYS cc_start: 0.7455 (ttpt) cc_final: 0.7127 (ttmm) REVERT: B 322 LYS cc_start: 0.7950 (tmmt) cc_final: 0.7557 (mtpm) REVERT: B 378 MET cc_start: 0.8542 (mtm) cc_final: 0.8199 (mtm) REVERT: B 492 ARG cc_start: 0.6109 (OUTLIER) cc_final: 0.4974 (tpp80) REVERT: B 596 GLN cc_start: 0.6965 (mt0) cc_final: 0.6034 (mm-40) REVERT: B 602 VAL cc_start: 0.7882 (t) cc_final: 0.7563 (m) REVERT: B 628 ARG cc_start: 0.8070 (mtt-85) cc_final: 0.7250 (mpp-170) REVERT: B 635 ASP cc_start: 0.7610 (t70) cc_final: 0.6840 (p0) REVERT: C 51 LEU cc_start: 0.7985 (OUTLIER) cc_final: 0.7515 (tt) REVERT: C 167 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7934 (tp) REVERT: C 174 ASN cc_start: 0.7815 (t0) cc_final: 0.7299 (t0) REVERT: C 262 LYS cc_start: 0.8900 (tttm) cc_final: 0.8105 (ttpp) REVERT: C 300 LYS cc_start: 0.8476 (mttm) cc_final: 0.8251 (mttm) REVERT: C 303 GLU cc_start: 0.7838 (mp0) cc_final: 0.7414 (mp0) REVERT: C 306 GLN cc_start: 0.7839 (mm-40) cc_final: 0.7632 (mt0) REVERT: C 314 LYS cc_start: 0.7496 (ttpt) cc_final: 0.7168 (ttmm) REVERT: C 322 LYS cc_start: 0.7960 (tmmt) cc_final: 0.7573 (mtpm) REVERT: C 378 MET cc_start: 0.8534 (mtm) cc_final: 0.8199 (mtm) REVERT: C 596 GLN cc_start: 0.7050 (mt0) cc_final: 0.6120 (mm-40) REVERT: C 602 VAL cc_start: 0.7885 (t) cc_final: 0.7581 (m) REVERT: C 628 ARG cc_start: 0.8090 (mtt-85) cc_final: 0.7254 (mpp-170) REVERT: C 635 ASP cc_start: 0.7658 (t70) cc_final: 0.6862 (p0) REVERT: D 51 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7532 (tt) REVERT: D 113 GLU cc_start: 0.8459 (tt0) cc_final: 0.8230 (tt0) REVERT: D 167 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7933 (tp) REVERT: D 174 ASN cc_start: 0.7752 (t0) cc_final: 0.7293 (t0) REVERT: D 262 LYS cc_start: 0.8926 (tttm) cc_final: 0.8119 (ttpp) REVERT: D 300 LYS cc_start: 0.8499 (mttm) cc_final: 0.8271 (mttm) REVERT: D 303 GLU cc_start: 0.7931 (mp0) cc_final: 0.7331 (mp0) REVERT: D 314 LYS cc_start: 0.7473 (ttpt) cc_final: 0.7144 (ttmm) REVERT: D 322 LYS cc_start: 0.7973 (tmmt) cc_final: 0.7591 (mtpm) REVERT: D 378 MET cc_start: 0.8514 (mtm) cc_final: 0.8180 (mtm) REVERT: D 474 MET cc_start: 0.2313 (mtt) cc_final: 0.2034 (mtt) REVERT: D 492 ARG cc_start: 0.6282 (tpp-160) cc_final: 0.5337 (tpp80) REVERT: D 596 GLN cc_start: 0.6880 (mt0) cc_final: 0.6035 (mm-40) REVERT: D 602 VAL cc_start: 0.7838 (t) cc_final: 0.7551 (m) REVERT: D 628 ARG cc_start: 0.8091 (mtt-85) cc_final: 0.7276 (mpp-170) REVERT: D 635 ASP cc_start: 0.7626 (t70) cc_final: 0.6824 (p0) outliers start: 55 outliers final: 26 residues processed: 375 average time/residue: 1.0728 time to fit residues: 471.8791 Evaluate side-chains 359 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 325 time to evaluate : 0.826 ------------------------------------------------------------------------------- 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 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 490 LEU Chi-restraints excluded: chain B residue 492 ARG Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 118 GLN Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 118 GLN 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 228 optimal weight: 0.9980 chunk 118 optimal weight: 4.9990 chunk 40 optimal weight: 0.6980 chunk 231 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 229 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 chunk 36 optimal weight: 3.9990 chunk 236 optimal weight: 1.9990 chunk 86 optimal weight: 5.9990 chunk 78 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 357 ASN C 357 ASN ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 357 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.179081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.123894 restraints weight = 67085.614| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 2.16 r_work: 0.3435 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3312 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3201 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3201 r_free = 0.3201 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3201 r_free = 0.3201 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3201 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.4025 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= 0.129 Angle : 0.595 7.799 29140 Z= 0.298 Chirality : 0.038 0.194 3220 Planarity : 0.004 0.060 3532 Dihedral : 13.940 130.934 4456 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 1.98 % Allowed : 17.23 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.18), residues: 2440 helix: 0.51 (0.14), residues: 1468 sheet: -3.61 (0.46), residues: 84 loop : -1.09 (0.22), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 621 TYR 0.011 0.001 TYR D 324 PHE 0.012 0.001 PHE D 493 TRP 0.007 0.001 TRP B 462 HIS 0.003 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 (21556) covalent geometry : angle 0.59523 / 0.30 (29140) hydrogen bonds : bond 0.03851 / 2.47 ( 892) hydrogen bonds : angle 4.42557 / 3.11 ( 2508) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 339 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LEU cc_start: 0.7968 (OUTLIER) cc_final: 0.7498 (tt) REVERT: A 174 ASN cc_start: 0.7672 (t0) cc_final: 0.7212 (t0) REVERT: A 262 LYS cc_start: 0.8885 (tttm) cc_final: 0.8418 (ttpt) REVERT: A 300 LYS cc_start: 0.8490 (mttm) cc_final: 0.8244 (mttm) REVERT: A 303 GLU cc_start: 0.7970 (mp0) cc_final: 0.7398 (mp0) REVERT: A 314 LYS cc_start: 0.7471 (ttpt) cc_final: 0.7103 (ttmm) REVERT: A 322 LYS cc_start: 0.7920 (tmmt) cc_final: 0.7543 (mtpm) REVERT: A 378 MET cc_start: 0.8399 (mtp) cc_final: 0.8044 (mtm) REVERT: A 596 GLN cc_start: 0.6970 (mt0) cc_final: 0.5987 (mm-40) REVERT: A 628 ARG cc_start: 0.8088 (mtt-85) cc_final: 0.7203 (mpp-170) REVERT: A 635 ASP cc_start: 0.7595 (t70) cc_final: 0.6780 (p0) REVERT: B 51 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.7488 (tt) REVERT: B 167 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7861 (tp) REVERT: B 174 ASN cc_start: 0.7713 (t0) cc_final: 0.7395 (t0) REVERT: B 176 GLU cc_start: 0.7936 (mp0) cc_final: 0.7348 (mt-10) REVERT: B 262 LYS cc_start: 0.8903 (tttm) cc_final: 0.8104 (ttpp) REVERT: B 303 GLU cc_start: 0.7951 (mp0) cc_final: 0.7398 (mp0) REVERT: B 314 LYS cc_start: 0.7395 (ttpt) cc_final: 0.7070 (ttmm) REVERT: B 322 LYS cc_start: 0.7896 (tmmt) cc_final: 0.7488 (mtpm) REVERT: B 378 MET cc_start: 0.8587 (mtm) cc_final: 0.8191 (mtm) REVERT: B 596 GLN cc_start: 0.6872 (mt0) cc_final: 0.5972 (mm-40) REVERT: B 602 VAL cc_start: 0.7826 (t) cc_final: 0.7516 (m) REVERT: B 628 ARG cc_start: 0.8042 (mtt-85) cc_final: 0.7196 (mpp-170) REVERT: B 635 ASP cc_start: 0.7587 (t70) cc_final: 0.6752 (p0) REVERT: C 51 LEU cc_start: 0.7957 (OUTLIER) cc_final: 0.7490 (tt) REVERT: C 167 LEU cc_start: 0.8127 (OUTLIER) cc_final: 0.7868 (tp) REVERT: C 174 ASN cc_start: 0.7739 (t0) cc_final: 0.7410 (t0) REVERT: C 176 GLU cc_start: 0.7917 (mp0) cc_final: 0.7305 (mt-10) REVERT: C 262 LYS cc_start: 0.8869 (tttm) cc_final: 0.8061 (ttpp) REVERT: C 300 LYS cc_start: 0.8444 (mttm) cc_final: 0.8216 (mttm) REVERT: C 303 GLU cc_start: 0.7854 (mp0) cc_final: 0.7415 (mp0) REVERT: C 306 GLN cc_start: 0.7763 (mm-40) cc_final: 0.7508 (mt0) REVERT: C 314 LYS cc_start: 0.7418 (ttpt) cc_final: 0.7091 (ttmm) REVERT: C 322 LYS cc_start: 0.7916 (tmmt) cc_final: 0.7516 (mtpm) REVERT: C 378 MET cc_start: 0.8595 (mtm) cc_final: 0.8199 (mtm) REVERT: C 490 LEU cc_start: 0.5816 (OUTLIER) cc_final: 0.5559 (tt) REVERT: C 596 GLN cc_start: 0.6967 (mt0) cc_final: 0.6008 (mm-40) REVERT: C 602 VAL cc_start: 0.7826 (t) cc_final: 0.7525 (m) REVERT: C 628 ARG cc_start: 0.8043 (mtt-85) cc_final: 0.7187 (mpp-170) REVERT: C 635 ASP cc_start: 0.7624 (t70) cc_final: 0.6799 (p0) REVERT: D 51 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7489 (tt) REVERT: D 113 GLU cc_start: 0.8438 (tt0) cc_final: 0.8213 (tt0) REVERT: D 167 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7880 (tp) REVERT: D 174 ASN cc_start: 0.7658 (t0) cc_final: 0.7168 (t0) REVERT: D 176 GLU cc_start: 0.7931 (mp0) cc_final: 0.7680 (mp0) REVERT: D 262 LYS cc_start: 0.8882 (tttm) cc_final: 0.8076 (ttpp) REVERT: D 300 LYS cc_start: 0.8484 (mttm) cc_final: 0.8251 (mttm) REVERT: D 303 GLU cc_start: 0.7932 (mp0) cc_final: 0.7331 (mp0) REVERT: D 314 LYS cc_start: 0.7421 (ttpt) cc_final: 0.7090 (ttmm) REVERT: D 322 LYS cc_start: 0.7922 (tmmt) cc_final: 0.7525 (mtpm) REVERT: D 378 MET cc_start: 0.8593 (mtm) cc_final: 0.8203 (mtm) REVERT: D 474 MET cc_start: 0.2428 (mtt) cc_final: 0.2198 (mtt) REVERT: D 596 GLN cc_start: 0.6713 (mt0) cc_final: 0.5893 (mm-40) REVERT: D 602 VAL cc_start: 0.7754 (t) cc_final: 0.7474 (m) REVERT: D 621 ARG cc_start: 0.7581 (ttm110) cc_final: 0.7352 (ttp-110) REVERT: D 628 ARG cc_start: 0.8074 (mtt-85) cc_final: 0.7239 (mpp-170) REVERT: D 635 ASP cc_start: 0.7563 (t70) cc_final: 0.6741 (p0) outliers start: 42 outliers final: 26 residues processed: 367 average time/residue: 1.1505 time to fit residues: 492.5248 Evaluate side-chains 360 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 326 time to evaluate : 1.041 ------------------------------------------------------------------------------- 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 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 490 LEU Chi-restraints excluded: chain B residue 492 ARG Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 280 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 81 optimal weight: 0.0670 chunk 167 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 144 optimal weight: 3.9990 chunk 121 optimal weight: 8.9990 chunk 123 optimal weight: 6.9990 chunk 8 optimal weight: 6.9990 chunk 152 optimal weight: 0.6980 chunk 117 optimal weight: 9.9990 chunk 109 optimal weight: 1.9990 overall best weight: 1.7524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 357 ASN C 118 GLN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 357 ASN D 118 GLN ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 357 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.179084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.124027 restraints weight = 66834.309| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 2.14 r_work: 0.3434 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3311 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3187 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3187 r_free = 0.3187 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3187 r_free = 0.3187 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3187 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.4103 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= 0.144 Angle : 0.593 7.473 29140 Z= 0.296 Chirality : 0.038 0.195 3220 Planarity : 0.005 0.072 3532 Dihedral : 13.413 123.094 4456 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 1.98 % Allowed : 17.37 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.18), residues: 2440 helix: 0.60 (0.14), residues: 1472 sheet: -3.56 (0.47), residues: 84 loop : -0.97 (0.22), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 621 TYR 0.012 0.001 TYR B 324 PHE 0.009 0.001 PHE D 493 TRP 0.007 0.001 TRP B 613 HIS 0.003 0.001 HIS B 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.14 (21556) covalent geometry : angle 0.59321 / 0.30 (29140) hydrogen bonds : bond 0.03771 / 2.43 ( 892) hydrogen bonds : angle 4.39065 / 3.10 ( 2508) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 334 time to evaluate : 1.003 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: A 51 LEU cc_start: 0.7974 (OUTLIER) cc_final: 0.7492 (tt) REVERT: A 174 ASN cc_start: 0.7701 (t0) cc_final: 0.7228 (t0) REVERT: A 262 LYS cc_start: 0.8892 (tttm) cc_final: 0.8340 (mttm) REVERT: A 300 LYS cc_start: 0.8470 (mttm) cc_final: 0.8206 (mttm) REVERT: A 303 GLU cc_start: 0.7950 (mp0) cc_final: 0.7361 (mp0) REVERT: A 314 LYS cc_start: 0.7473 (ttpt) cc_final: 0.7104 (ttmm) REVERT: A 322 LYS cc_start: 0.7927 (tmmt) cc_final: 0.7548 (mtpm) REVERT: A 378 MET cc_start: 0.8408 (mtp) cc_final: 0.7928 (mmm) REVERT: A 596 GLN cc_start: 0.6987 (mt0) cc_final: 0.6005 (mm-40) REVERT: A 628 ARG cc_start: 0.8074 (mtt-85) cc_final: 0.7179 (mpp-170) REVERT: A 635 ASP cc_start: 0.7603 (t70) cc_final: 0.6808 (p0) REVERT: B 51 LEU cc_start: 0.7966 (OUTLIER) cc_final: 0.7493 (tt) REVERT: B 174 ASN cc_start: 0.7755 (t0) cc_final: 0.7397 (t0) REVERT: B 176 GLU cc_start: 0.7944 (mp0) cc_final: 0.7356 (mt-10) REVERT: B 262 LYS cc_start: 0.8900 (tttm) cc_final: 0.8097 (ttpp) REVERT: B 314 LYS cc_start: 0.7377 (ttpt) cc_final: 0.7047 (ttmm) REVERT: B 322 LYS cc_start: 0.7905 (tmmt) cc_final: 0.7493 (mtpm) REVERT: B 378 MET cc_start: 0.8604 (mtm) cc_final: 0.8226 (mtm) REVERT: B 596 GLN cc_start: 0.6912 (mt0) cc_final: 0.5961 (mm-40) REVERT: B 602 VAL cc_start: 0.7843 (t) cc_final: 0.7534 (m) REVERT: B 628 ARG cc_start: 0.8041 (mtt-85) cc_final: 0.7186 (mpp-170) REVERT: B 635 ASP cc_start: 0.7562 (t70) cc_final: 0.6737 (p0) REVERT: C 51 LEU cc_start: 0.7968 (OUTLIER) cc_final: 0.7494 (tt) REVERT: C 174 ASN cc_start: 0.7742 (t0) cc_final: 0.7377 (t0) REVERT: C 176 GLU cc_start: 0.7905 (mp0) cc_final: 0.7319 (mt-10) REVERT: C 262 LYS cc_start: 0.8870 (tttm) cc_final: 0.8062 (ttpp) REVERT: C 300 LYS cc_start: 0.8453 (mttm) cc_final: 0.8210 (mttm) REVERT: C 303 GLU cc_start: 0.7860 (mp0) cc_final: 0.7421 (mp0) REVERT: C 306 GLN cc_start: 0.7766 (mm-40) cc_final: 0.7515 (mt0) REVERT: C 314 LYS cc_start: 0.7417 (ttpt) cc_final: 0.7087 (ttmm) REVERT: C 322 LYS cc_start: 0.7923 (tmmt) cc_final: 0.7517 (mtpm) REVERT: C 378 MET cc_start: 0.8608 (mtm) cc_final: 0.8219 (mtm) REVERT: C 596 GLN cc_start: 0.6991 (mt0) cc_final: 0.6031 (mm-40) REVERT: C 602 VAL cc_start: 0.7817 (t) cc_final: 0.7520 (m) REVERT: C 628 ARG cc_start: 0.8048 (mtt-85) cc_final: 0.7175 (mpp-170) REVERT: C 635 ASP cc_start: 0.7597 (t70) cc_final: 0.6790 (p0) REVERT: D 51 LEU cc_start: 0.7945 (OUTLIER) cc_final: 0.7498 (tt) REVERT: D 113 GLU cc_start: 0.8403 (tt0) cc_final: 0.8184 (tt0) REVERT: D 167 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7872 (tp) REVERT: D 174 ASN cc_start: 0.7676 (t0) cc_final: 0.7180 (t0) REVERT: D 176 GLU cc_start: 0.7930 (mp0) cc_final: 0.7721 (mp0) REVERT: D 262 LYS cc_start: 0.8871 (tttm) cc_final: 0.8063 (ttpp) REVERT: D 300 LYS cc_start: 0.8479 (mttm) cc_final: 0.8238 (mttm) REVERT: D 303 GLU cc_start: 0.7912 (mp0) cc_final: 0.7316 (mp0) REVERT: D 314 LYS cc_start: 0.7407 (ttpt) cc_final: 0.7077 (ttmm) REVERT: D 322 LYS cc_start: 0.7932 (tmmt) cc_final: 0.7532 (mtpm) REVERT: D 378 MET cc_start: 0.8612 (mtm) cc_final: 0.8242 (mtm) REVERT: D 474 MET cc_start: 0.2434 (mtt) cc_final: 0.2200 (mtt) REVERT: D 492 ARG cc_start: 0.6064 (OUTLIER) cc_final: 0.4998 (tpp80) REVERT: D 596 GLN cc_start: 0.6736 (mt0) cc_final: 0.5911 (mm-40) REVERT: D 602 VAL cc_start: 0.7796 (t) cc_final: 0.7497 (m) REVERT: D 621 ARG cc_start: 0.7591 (ttm110) cc_final: 0.7376 (ttp-110) REVERT: D 628 ARG cc_start: 0.8057 (mtt-85) cc_final: 0.7193 (mpp-170) REVERT: D 635 ASP cc_start: 0.7554 (t70) cc_final: 0.6757 (p0) outliers start: 42 outliers final: 26 residues processed: 365 average time/residue: 1.2021 time to fit residues: 511.1840 Evaluate side-chains 356 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 324 time to evaluate : 1.102 ------------------------------------------------------------------------------- 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 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 490 LEU Chi-restraints excluded: chain B residue 492 ARG Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 118 GLN Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 118 GLN 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 Chi-restraints excluded: chain D residue 492 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 187 optimal weight: 20.0000 chunk 234 optimal weight: 1.9990 chunk 129 optimal weight: 10.0000 chunk 228 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 61 optimal weight: 10.0000 chunk 3 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 76 optimal weight: 0.9990 chunk 150 optimal weight: 2.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 357 ASN C 118 GLN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 357 ASN D 118 GLN ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 357 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.178948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.123827 restraints weight = 67357.106| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 2.15 r_work: 0.3436 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3312 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3197 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3197 r_free = 0.3197 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3197 r_free = 0.3197 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3197 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.4108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.244 21556 Z= 0.227 Angle : 0.864 59.198 29140 Z= 0.503 Chirality : 0.042 0.701 3220 Planarity : 0.005 0.071 3532 Dihedral : 13.414 123.055 4456 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 1.51 % Allowed : 17.84 % Favored : 80.65 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.18), residues: 2440 helix: 0.61 (0.14), residues: 1472 sheet: -3.55 (0.47), residues: 84 loop : -0.99 (0.22), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 621 TYR 0.009 0.001 TYR A 324 PHE 0.009 0.001 PHE D 493 TRP 0.006 0.001 TRP D 593 HIS 0.003 0.001 HIS B 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.23 (21556) covalent geometry : angle 0.86373 / 0.50 (29140) hydrogen bonds : bond 0.03770 / 2.42 ( 892) hydrogen bonds : angle 4.39124 / 3.10 ( 2508) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16437.77 seconds wall clock time: 278 minutes 9.42 seconds (16689.42 seconds total)