Starting phenix.real_space_refine on Fri Aug 7 13:24:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/13lp_77140/08_2026/13lp_77140.cif Found real_map, /net/cci-nas-00/data/ceres_data/13lp_77140/08_2026/13lp_77140.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/13lp_77140/08_2026/13lp_77140.cif" } default_model = "/net/cci-nas-00/data/ceres_data/13lp_77140/08_2026/13lp_77140.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/13lp_77140/08_2026/13lp_77140.map" default_real_map = "/net/cci-nas-00/data/ceres_data/13lp_77140/08_2026/13lp_77140.map" } resolution = 3.02 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.025 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: 6 Type Number sf(0) Gaussians P 24 5.49 5 S 116 5.16 5 Na 4 4.78 5 C 14108 2.51 5 N 3304 2.21 5 O 3736 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21292 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4978 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 14, 'TRANS': 597} Chain breaks: 2 Chain: "B" Number of atoms: 4978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4978 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 14, 'TRANS': 597} Chain breaks: 2 Chain: "C" Number of atoms: 4978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4978 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 14, 'TRANS': 597} Chain breaks: 2 Chain: "D" Number of atoms: 4978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4978 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 14, 'TRANS': 597} Chain breaks: 2 Chain: "A" Number of atoms: 346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 346 Unusual residues: {' NA': 2, 'POV': 8} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'POV:plan-2': 2, 'POV:plan-3': 2} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 344 Unusual residues: {'POV': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'POV:plan-2': 2, 'POV:plan-3': 2} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 346 Unusual residues: {' NA': 2, 'POV': 8} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'POV:plan-2': 2, 'POV:plan-3': 2} Unresolved non-hydrogen planarities: 14 Chain: "D" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 344 Unusual residues: {'POV': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'POV:plan-2': 2, 'POV:plan-3': 2} Unresolved non-hydrogen planarities: 14 Time building chain proxies: 4.99, per 1000 atoms: 0.23 Number of scatterers: 21292 At special positions: 0 Unit cell: (148.291, 148.291, 122.366, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 116 16.00 P 24 15.00 Na 4 11.00 O 3736 8.00 N 3304 7.00 C 14108 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.47 Conformation dependent library (CDL) restraints added in 894.6 milliseconds 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4672 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 4 sheets defined 61.6% alpha, 3.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 119 through 129 removed outlier: 3.589A pdb=" N ALA A 125 " --> pdb=" O LYS A 121 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL A 127 " --> pdb=" O ILE A 123 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU A 129 " --> pdb=" O ALA A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 144 removed outlier: 3.640A pdb=" N GLU A 141 " --> pdb=" O GLU A 137 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU A 144 " --> pdb=" O VAL A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 149 removed outlier: 3.808A pdb=" N ARG A 148 " --> pdb=" O LEU A 145 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ARG A 149 " --> pdb=" O CYS A 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 145 through 149' Processing helix chain 'A' and resid 153 through 162 removed outlier: 3.814A pdb=" N MET A 159 " --> pdb=" O PRO A 155 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N HIS A 160 " --> pdb=" O ASP A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 178 removed outlier: 3.518A pdb=" N LEU A 176 " --> pdb=" O LEU A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 197 removed outlier: 3.563A pdb=" N VAL A 187 " --> pdb=" O THR A 183 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG A 188 " --> pdb=" O LYS A 184 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASN A 197 " --> pdb=" O PHE A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 204 removed outlier: 3.581A pdb=" N ILE A 204 " --> pdb=" O LEU A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 225 removed outlier: 3.768A pdb=" N ILE A 221 " --> pdb=" O THR A 217 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA A 222 " --> pdb=" O ALA A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 237 Processing helix chain 'A' and resid 264 through 272 Processing helix chain 'A' and resid 274 through 283 removed outlier: 3.694A pdb=" N GLU A 283 " --> pdb=" O GLN A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 306 removed outlier: 3.533A pdb=" N ALA A 302 " --> pdb=" O ASN A 298 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU A 303 " --> pdb=" O ILE A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 329 Processing helix chain 'A' and resid 343 through 352 removed outlier: 3.528A pdb=" N ALA A 348 " --> pdb=" O PRO A 344 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA A 349 " --> pdb=" O LEU A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 362 removed outlier: 3.696A pdb=" N TYR A 359 " --> pdb=" O GLU A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 374 Processing helix chain 'A' and resid 402 through 409 Processing helix chain 'A' and resid 415 through 420 Processing helix chain 'A' and resid 422 through 434 removed outlier: 3.640A pdb=" N THR A 427 " --> pdb=" O GLU A 423 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU A 428 " --> pdb=" O PRO A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 458 removed outlier: 3.548A pdb=" N CYS A 446 " --> pdb=" O PHE A 442 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N TYR A 451 " --> pdb=" O PHE A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 507 Processing helix chain 'A' and resid 518 through 542 removed outlier: 4.041A pdb=" N PHE A 522 " --> pdb=" O SER A 518 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N HIS A 523 " --> pdb=" O ASP A 519 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N PHE A 524 " --> pdb=" O ALA A 520 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE A 526 " --> pdb=" O PHE A 522 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE A 527 " --> pdb=" O HIS A 523 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN A 529 " --> pdb=" O VAL A 525 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL A 533 " --> pdb=" O GLN A 529 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE A 534 " --> pdb=" O ALA A 530 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N TYR A 540 " --> pdb=" O SER A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 561 removed outlier: 3.762A pdb=" N LEU A 553 " --> pdb=" O ALA A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 567 removed outlier: 3.547A pdb=" N THR A 566 " --> pdb=" O LEU A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 586 removed outlier: 4.154A pdb=" N VAL A 582 " --> pdb=" O MET A 578 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ASP A 586 " --> pdb=" O VAL A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 607 removed outlier: 4.200A pdb=" N VAL A 593 " --> pdb=" O LYS A 589 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL A 596 " --> pdb=" O PHE A 592 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA A 604 " --> pdb=" O GLY A 600 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER A 607 " --> pdb=" O VAL A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 637 removed outlier: 3.540A pdb=" N ALA A 628 " --> pdb=" O SER A 624 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A 635 " --> pdb=" O GLU A 631 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR A 636 " --> pdb=" O LEU A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 676 removed outlier: 4.231A pdb=" N VAL A 662 " --> pdb=" O LEU A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 707 removed outlier: 3.586A pdb=" N ARG A 696 " --> pdb=" O GLY A 692 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU A 701 " --> pdb=" O ALA A 697 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS A 705 " --> pdb=" O LEU A 701 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N MET A 706 " --> pdb=" O GLU A 702 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU A 707 " --> pdb=" O PHE A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 713 removed outlier: 3.888A pdb=" N SER A 713 " --> pdb=" O GLU A 709 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 129 removed outlier: 3.590A pdb=" N ALA B 125 " --> pdb=" O LYS B 121 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL B 127 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU B 129 " --> pdb=" O ALA B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 144 removed outlier: 3.641A pdb=" N GLU B 141 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU B 144 " --> pdb=" O VAL B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 149 removed outlier: 3.809A pdb=" N ARG B 148 " --> pdb=" O LEU B 145 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ARG B 149 " --> pdb=" O CYS B 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 145 through 149' Processing helix chain 'B' and resid 153 through 162 removed outlier: 3.814A pdb=" N MET B 159 " --> pdb=" O PRO B 155 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N HIS B 160 " --> pdb=" O ASP B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 178 removed outlier: 3.518A pdb=" N LEU B 176 " --> pdb=" O LEU B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 197 removed outlier: 3.563A pdb=" N VAL B 187 " --> pdb=" O THR B 183 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG B 188 " --> pdb=" O LYS B 184 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASN B 197 " --> pdb=" O PHE B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 204 removed outlier: 3.581A pdb=" N ILE B 204 " --> pdb=" O LEU B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 225 removed outlier: 3.768A pdb=" N ILE B 221 " --> pdb=" O THR B 217 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA B 222 " --> pdb=" O ALA B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 237 Processing helix chain 'B' and resid 264 through 272 Processing helix chain 'B' and resid 274 through 283 removed outlier: 3.695A pdb=" N GLU B 283 " --> pdb=" O GLN B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 306 removed outlier: 3.533A pdb=" N ALA B 302 " --> pdb=" O ASN B 298 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU B 303 " --> pdb=" O ILE B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 329 Processing helix chain 'B' and resid 343 through 352 removed outlier: 3.529A pdb=" N ALA B 348 " --> pdb=" O PRO B 344 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA B 349 " --> pdb=" O LEU B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 362 removed outlier: 3.696A pdb=" N TYR B 359 " --> pdb=" O GLU B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 374 Processing helix chain 'B' and resid 402 through 409 Processing helix chain 'B' and resid 415 through 420 Processing helix chain 'B' and resid 422 through 434 removed outlier: 3.641A pdb=" N THR B 427 " --> pdb=" O GLU B 423 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU B 428 " --> pdb=" O PRO B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 458 removed outlier: 3.548A pdb=" N CYS B 446 " --> pdb=" O PHE B 442 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N TYR B 451 " --> pdb=" O PHE B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 507 Processing helix chain 'B' and resid 518 through 542 removed outlier: 4.041A pdb=" N PHE B 522 " --> pdb=" O SER B 518 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N HIS B 523 " --> pdb=" O ASP B 519 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N PHE B 524 " --> pdb=" O ALA B 520 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE B 526 " --> pdb=" O PHE B 522 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE B 527 " --> pdb=" O HIS B 523 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN B 529 " --> pdb=" O VAL B 525 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL B 533 " --> pdb=" O GLN B 529 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE B 534 " --> pdb=" O ALA B 530 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N TYR B 540 " --> pdb=" O SER B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 561 removed outlier: 3.762A pdb=" N LEU B 553 " --> pdb=" O ALA B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 567 removed outlier: 3.548A pdb=" N THR B 566 " --> pdb=" O LEU B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 586 removed outlier: 4.153A pdb=" N VAL B 582 " --> pdb=" O MET B 578 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ASP B 586 " --> pdb=" O VAL B 582 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 607 removed outlier: 4.199A pdb=" N VAL B 593 " --> pdb=" O LYS B 589 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL B 596 " --> pdb=" O PHE B 592 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA B 604 " --> pdb=" O GLY B 600 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER B 607 " --> pdb=" O VAL B 603 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 637 removed outlier: 3.540A pdb=" N ALA B 628 " --> pdb=" O SER B 624 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU B 635 " --> pdb=" O GLU B 631 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR B 636 " --> pdb=" O LEU B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 676 removed outlier: 4.231A pdb=" N VAL B 662 " --> pdb=" O LEU B 658 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 707 removed outlier: 3.585A pdb=" N ARG B 696 " --> pdb=" O GLY B 692 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU B 701 " --> pdb=" O ALA B 697 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS B 705 " --> pdb=" O LEU B 701 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N MET B 706 " --> pdb=" O GLU B 702 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU B 707 " --> pdb=" O PHE B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 713 removed outlier: 3.887A pdb=" N SER B 713 " --> pdb=" O GLU B 709 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 129 removed outlier: 3.589A pdb=" N ALA C 125 " --> pdb=" O LYS C 121 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL C 127 " --> pdb=" O ILE C 123 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU C 129 " --> pdb=" O ALA C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 144 removed outlier: 3.640A pdb=" N GLU C 141 " --> pdb=" O GLU C 137 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU C 144 " --> pdb=" O VAL C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 149 removed outlier: 3.808A pdb=" N ARG C 148 " --> pdb=" O LEU C 145 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ARG C 149 " --> pdb=" O CYS C 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 145 through 149' Processing helix chain 'C' and resid 153 through 162 removed outlier: 3.815A pdb=" N MET C 159 " --> pdb=" O PRO C 155 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N HIS C 160 " --> pdb=" O ASP C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 178 removed outlier: 3.518A pdb=" N LEU C 176 " --> pdb=" O LEU C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 197 removed outlier: 3.563A pdb=" N VAL C 187 " --> pdb=" O THR C 183 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG C 188 " --> pdb=" O LYS C 184 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASN C 197 " --> pdb=" O PHE C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 204 removed outlier: 3.581A pdb=" N ILE C 204 " --> pdb=" O LEU C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 225 removed outlier: 3.768A pdb=" N ILE C 221 " --> pdb=" O THR C 217 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA C 222 " --> pdb=" O ALA C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 237 Processing helix chain 'C' and resid 264 through 272 Processing helix chain 'C' and resid 274 through 283 removed outlier: 3.695A pdb=" N GLU C 283 " --> pdb=" O GLN C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 306 removed outlier: 3.534A pdb=" N ALA C 302 " --> pdb=" O ASN C 298 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU C 303 " --> pdb=" O ILE C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 329 Processing helix chain 'C' and resid 343 through 352 removed outlier: 3.529A pdb=" N ALA C 348 " --> pdb=" O PRO C 344 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA C 349 " --> pdb=" O LEU C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 362 removed outlier: 3.696A pdb=" N TYR C 359 " --> pdb=" O GLU C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 374 Processing helix chain 'C' and resid 402 through 409 Processing helix chain 'C' and resid 415 through 420 Processing helix chain 'C' and resid 422 through 434 removed outlier: 3.639A pdb=" N THR C 427 " --> pdb=" O GLU C 423 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU C 428 " --> pdb=" O PRO C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 458 removed outlier: 3.547A pdb=" N CYS C 446 " --> pdb=" O PHE C 442 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N TYR C 451 " --> pdb=" O PHE C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 507 Processing helix chain 'C' and resid 518 through 542 removed outlier: 4.041A pdb=" N PHE C 522 " --> pdb=" O SER C 518 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N HIS C 523 " --> pdb=" O ASP C 519 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N PHE C 524 " --> pdb=" O ALA C 520 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE C 526 " --> pdb=" O PHE C 522 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE C 527 " --> pdb=" O HIS C 523 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN C 529 " --> pdb=" O VAL C 525 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL C 533 " --> pdb=" O GLN C 529 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE C 534 " --> pdb=" O ALA C 530 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N TYR C 540 " --> pdb=" O SER C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 561 removed outlier: 3.762A pdb=" N LEU C 553 " --> pdb=" O ALA C 549 " (cutoff:3.500A) Processing helix chain 'C' and resid 562 through 567 removed outlier: 3.547A pdb=" N THR C 566 " --> pdb=" O LEU C 563 " (cutoff:3.500A) Processing helix chain 'C' and resid 576 through 586 removed outlier: 4.153A pdb=" N VAL C 582 " --> pdb=" O MET C 578 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ASP C 586 " --> pdb=" O VAL C 582 " (cutoff:3.500A) Processing helix chain 'C' and resid 587 through 607 removed outlier: 4.200A pdb=" N VAL C 593 " --> pdb=" O LYS C 589 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL C 596 " --> pdb=" O PHE C 592 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA C 604 " --> pdb=" O GLY C 600 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER C 607 " --> pdb=" O VAL C 603 " (cutoff:3.500A) Processing helix chain 'C' and resid 623 through 637 removed outlier: 3.539A pdb=" N ALA C 628 " --> pdb=" O SER C 624 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU C 635 " --> pdb=" O GLU C 631 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR C 636 " --> pdb=" O LEU C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 650 through 676 removed outlier: 4.231A pdb=" N VAL C 662 " --> pdb=" O LEU C 658 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 707 removed outlier: 3.586A pdb=" N ARG C 696 " --> pdb=" O GLY C 692 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU C 701 " --> pdb=" O ALA C 697 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS C 705 " --> pdb=" O LEU C 701 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N MET C 706 " --> pdb=" O GLU C 702 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU C 707 " --> pdb=" O PHE C 703 " (cutoff:3.500A) Processing helix chain 'C' and resid 708 through 713 removed outlier: 3.887A pdb=" N SER C 713 " --> pdb=" O GLU C 709 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 129 removed outlier: 3.590A pdb=" N ALA D 125 " --> pdb=" O LYS D 121 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL D 127 " --> pdb=" O ILE D 123 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU D 129 " --> pdb=" O ALA D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 144 removed outlier: 3.640A pdb=" N GLU D 141 " --> pdb=" O GLU D 137 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU D 144 " --> pdb=" O VAL D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 149 removed outlier: 3.809A pdb=" N ARG D 148 " --> pdb=" O LEU D 145 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ARG D 149 " --> pdb=" O CYS D 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 145 through 149' Processing helix chain 'D' and resid 153 through 162 removed outlier: 3.815A pdb=" N MET D 159 " --> pdb=" O PRO D 155 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N HIS D 160 " --> pdb=" O ASP D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 178 removed outlier: 3.519A pdb=" N LEU D 176 " --> pdb=" O LEU D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 197 removed outlier: 3.563A pdb=" N VAL D 187 " --> pdb=" O THR D 183 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG D 188 " --> pdb=" O LYS D 184 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASN D 197 " --> pdb=" O PHE D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 204 removed outlier: 3.581A pdb=" N ILE D 204 " --> pdb=" O LEU D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 225 removed outlier: 3.768A pdb=" N ILE D 221 " --> pdb=" O THR D 217 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA D 222 " --> pdb=" O ALA D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 237 Processing helix chain 'D' and resid 264 through 272 Processing helix chain 'D' and resid 274 through 283 removed outlier: 3.695A pdb=" N GLU D 283 " --> pdb=" O GLN D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 306 removed outlier: 3.534A pdb=" N ALA D 302 " --> pdb=" O ASN D 298 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU D 303 " --> pdb=" O ILE D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 329 Processing helix chain 'D' and resid 343 through 352 removed outlier: 3.529A pdb=" N ALA D 348 " --> pdb=" O PRO D 344 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA D 349 " --> pdb=" O LEU D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 362 removed outlier: 3.696A pdb=" N TYR D 359 " --> pdb=" O GLU D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 374 Processing helix chain 'D' and resid 402 through 409 Processing helix chain 'D' and resid 415 through 420 Processing helix chain 'D' and resid 422 through 434 removed outlier: 3.640A pdb=" N THR D 427 " --> pdb=" O GLU D 423 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU D 428 " --> pdb=" O PRO D 424 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 458 removed outlier: 3.547A pdb=" N CYS D 446 " --> pdb=" O PHE D 442 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N TYR D 451 " --> pdb=" O PHE D 447 " (cutoff:3.500A) Processing helix chain 'D' and resid 482 through 507 Processing helix chain 'D' and resid 518 through 542 removed outlier: 4.041A pdb=" N PHE D 522 " --> pdb=" O SER D 518 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N HIS D 523 " --> pdb=" O ASP D 519 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N PHE D 524 " --> pdb=" O ALA D 520 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE D 526 " --> pdb=" O PHE D 522 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE D 527 " --> pdb=" O HIS D 523 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN D 529 " --> pdb=" O VAL D 525 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL D 533 " --> pdb=" O GLN D 529 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE D 534 " --> pdb=" O ALA D 530 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N TYR D 540 " --> pdb=" O SER D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 561 removed outlier: 3.761A pdb=" N LEU D 553 " --> pdb=" O ALA D 549 " (cutoff:3.500A) Processing helix chain 'D' and resid 562 through 567 removed outlier: 3.547A pdb=" N THR D 566 " --> pdb=" O LEU D 563 " (cutoff:3.500A) Processing helix chain 'D' and resid 576 through 586 removed outlier: 4.153A pdb=" N VAL D 582 " --> pdb=" O MET D 578 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ASP D 586 " --> pdb=" O VAL D 582 " (cutoff:3.500A) Processing helix chain 'D' and resid 587 through 607 removed outlier: 4.200A pdb=" N VAL D 593 " --> pdb=" O LYS D 589 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL D 596 " --> pdb=" O PHE D 592 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA D 604 " --> pdb=" O GLY D 600 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER D 607 " --> pdb=" O VAL D 603 " (cutoff:3.500A) Processing helix chain 'D' and resid 623 through 637 removed outlier: 3.540A pdb=" N ALA D 628 " --> pdb=" O SER D 624 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU D 635 " --> pdb=" O GLU D 631 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR D 636 " --> pdb=" O LEU D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 676 removed outlier: 4.231A pdb=" N VAL D 662 " --> pdb=" O LEU D 658 " (cutoff:3.500A) Processing helix chain 'D' and resid 687 through 707 removed outlier: 3.586A pdb=" N ARG D 696 " --> pdb=" O GLY D 692 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU D 701 " --> pdb=" O ALA D 697 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS D 705 " --> pdb=" O LEU D 701 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N MET D 706 " --> pdb=" O GLU D 702 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU D 707 " --> pdb=" O PHE D 703 " (cutoff:3.500A) Processing helix chain 'D' and resid 708 through 713 removed outlier: 3.887A pdb=" N SER D 713 " --> pdb=" O GLU D 709 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 376 through 381 removed outlier: 6.730A pdb=" N SER A 387 " --> pdb=" O ASP A 379 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N ASP A 727 " --> pdb=" O VAL A 723 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 376 through 381 removed outlier: 6.729A pdb=" N SER B 387 " --> pdb=" O ASP B 379 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N ASP B 727 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 376 through 381 removed outlier: 6.730A pdb=" N SER C 387 " --> pdb=" O ASP C 379 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N ASP C 727 " --> pdb=" O VAL C 723 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 376 through 381 removed outlier: 6.730A pdb=" N SER D 387 " --> pdb=" O ASP D 379 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N ASP D 727 " --> pdb=" O VAL D 723 " (cutoff:3.500A) 884 hydrogen bonds defined for protein. 2580 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: 2.84 Time building geometry restraints manager: 2.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3407 1.32 - 1.44: 5474 1.44 - 1.56: 12559 1.56 - 1.69: 48 1.69 - 1.81: 196 Bond restraints: 21684 Sorted by residual: bond pdb=" O12 POV A1102 " pdb=" P POV A1102 " ideal model delta sigma weight residual 1.657 1.594 0.063 2.00e-02 2.50e+03 1.00e+01 bond pdb=" O12 POV D1106 " pdb=" P POV D1106 " ideal model delta sigma weight residual 1.657 1.594 0.063 2.00e-02 2.50e+03 1.00e+01 bond pdb=" O12 POV B1103 " pdb=" P POV B1103 " ideal model delta sigma weight residual 1.657 1.594 0.063 2.00e-02 2.50e+03 1.00e+01 bond pdb=" O12 POV C1103 " pdb=" P POV C1103 " ideal model delta sigma weight residual 1.657 1.594 0.063 2.00e-02 2.50e+03 9.96e+00 bond pdb=" O12 POV B1101 " pdb=" P POV B1101 " ideal model delta sigma weight residual 1.657 1.594 0.063 2.00e-02 2.50e+03 9.94e+00 ... (remaining 21679 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.46: 28009 2.46 - 4.92: 824 4.92 - 7.38: 159 7.38 - 9.84: 42 9.84 - 12.29: 10 Bond angle restraints: 29044 Sorted by residual: angle pdb=" N ILE D 659 " pdb=" CA ILE D 659 " pdb=" C ILE D 659 " ideal model delta sigma weight residual 111.90 106.93 4.97 8.10e-01 1.52e+00 3.77e+01 angle pdb=" N ILE C 659 " pdb=" CA ILE C 659 " pdb=" C ILE C 659 " ideal model delta sigma weight residual 111.90 106.94 4.96 8.10e-01 1.52e+00 3.75e+01 angle pdb=" N ILE B 659 " pdb=" CA ILE B 659 " pdb=" C ILE B 659 " ideal model delta sigma weight residual 111.90 106.97 4.93 8.10e-01 1.52e+00 3.71e+01 angle pdb=" N ILE A 659 " pdb=" CA ILE A 659 " pdb=" C ILE A 659 " ideal model delta sigma weight residual 111.90 106.99 4.91 8.10e-01 1.52e+00 3.68e+01 angle pdb=" C SER A 685 " pdb=" N LYS A 686 " pdb=" CA LYS A 686 " ideal model delta sigma weight residual 121.54 131.41 -9.87 1.91e+00 2.74e-01 2.67e+01 ... (remaining 29039 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.68: 12796 34.68 - 69.36: 345 69.36 - 104.04: 23 104.04 - 138.72: 28 138.72 - 173.40: 36 Dihedral angle restraints: 13228 sinusoidal: 6028 harmonic: 7200 Sorted by residual: dihedral pdb=" CA HIS A 284 " pdb=" C HIS A 284 " pdb=" N GLU A 285 " pdb=" CA GLU A 285 " ideal model delta harmonic sigma weight residual 180.00 151.46 28.54 0 5.00e+00 4.00e-02 3.26e+01 dihedral pdb=" CA HIS C 284 " pdb=" C HIS C 284 " pdb=" N GLU C 285 " pdb=" CA GLU C 285 " ideal model delta harmonic sigma weight residual 180.00 151.48 28.52 0 5.00e+00 4.00e-02 3.25e+01 dihedral pdb=" CA HIS D 284 " pdb=" C HIS D 284 " pdb=" N GLU D 285 " pdb=" CA GLU D 285 " ideal model delta harmonic sigma weight residual 180.00 151.48 28.52 0 5.00e+00 4.00e-02 3.25e+01 ... (remaining 13225 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 2650 0.064 - 0.127: 429 0.127 - 0.191: 77 0.191 - 0.255: 4 0.255 - 0.319: 12 Chirality restraints: 3172 Sorted by residual: chirality pdb=" C2 POV C1102 " pdb=" C1 POV C1102 " pdb=" C3 POV C1102 " pdb=" O21 POV C1102 " both_signs ideal model delta sigma weight residual False 2.43 2.11 0.32 2.00e-01 2.50e+01 2.54e+00 chirality pdb=" C2 POV B1102 " pdb=" C1 POV B1102 " pdb=" C3 POV B1102 " pdb=" O21 POV B1102 " both_signs ideal model delta sigma weight residual False 2.43 2.11 0.32 2.00e-01 2.50e+01 2.48e+00 chirality pdb=" C2 POV A1101 " pdb=" C1 POV A1101 " pdb=" C3 POV A1101 " pdb=" O21 POV A1101 " both_signs ideal model delta sigma weight residual False 2.43 2.12 0.31 2.00e-01 2.50e+01 2.46e+00 ... (remaining 3169 not shown) Planarity restraints: 3508 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B 637 " -0.012 2.00e-02 2.50e+03 2.43e-02 5.90e+00 pdb=" C ILE B 637 " 0.042 2.00e-02 2.50e+03 pdb=" O ILE B 637 " -0.016 2.00e-02 2.50e+03 pdb=" N GLY B 638 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 637 " -0.012 2.00e-02 2.50e+03 2.42e-02 5.87e+00 pdb=" C ILE A 637 " 0.042 2.00e-02 2.50e+03 pdb=" O ILE A 637 " -0.016 2.00e-02 2.50e+03 pdb=" N GLY A 638 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 637 " 0.012 2.00e-02 2.50e+03 2.42e-02 5.84e+00 pdb=" C ILE C 637 " -0.042 2.00e-02 2.50e+03 pdb=" O ILE C 637 " 0.016 2.00e-02 2.50e+03 pdb=" N GLY C 638 " 0.014 2.00e-02 2.50e+03 ... (remaining 3505 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 3801 2.76 - 3.30: 17767 3.30 - 3.83: 32106 3.83 - 4.37: 40788 4.37 - 4.90: 69922 Nonbonded interactions: 164384 Sorted by model distance: nonbonded pdb=" O PRO B 753 " pdb=" OH TYR C 213 " model vdw 2.231 3.040 nonbonded pdb=" O PRO C 753 " pdb=" OH TYR D 213 " model vdw 2.245 3.040 nonbonded pdb=" OH TYR A 213 " pdb=" O PRO D 753 " model vdw 2.270 3.040 nonbonded pdb=" O PRO A 753 " pdb=" OH TYR B 213 " model vdw 2.271 3.040 nonbonded pdb=" O LEU A 281 " pdb=" OG1 THR A 287 " model vdw 2.319 3.040 ... (remaining 164379 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: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 118 through 1103 or (resid 1104 through 1105 and (name C21 \ or name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name \ C28 or name C29 or name C210 or name C211 or name C212 or name C213 or name C21 \ 4 or name C215 or name C216 or name C217 or name C218)) or (resid 1106 through 1 \ 108 and (name C25 or name C26 or name C27 or name C28 or name C29 or name C210 o \ r name C211 or name C212 or name C213 or name C214 or name C215 or name C216 or \ name C217 or name C218)))) selection = (chain 'B' and (resid 118 through 1102 or (resid 1103 through 1105 and (name C21 \ or name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name \ C28 or name C29 or name C210 or name C211 or name C212 or name C213 or name C21 \ 4 or name C215 or name C216 or name C217 or name C218)) or (resid 1106 through 1 \ 108 and (name C25 or name C26 or name C27 or name C28 or name C29 or name C210 o \ r name C211 or name C212 or name C213 or name C214 or name C215 or name C216 or \ name C217 or name C218)))) selection = (chain 'C' and (resid 118 through 1102 or (resid 1103 through 1105 and (name C21 \ or name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name \ C28 or name C29 or name C210 or name C211 or name C212 or name C213 or name C21 \ 4 or name C215 or name C216 or name C217 or name C218)) or (resid 1106 through 1 \ 108 and (name C25 or name C26 or name C27 or name C28 or name C29 or name C210 o \ r name C211 or name C212 or name C213 or name C214 or name C215 or name C216 or \ name C217 or name C218)))) selection = (chain 'D' and (resid 118 through 1102 or (resid 1103 through 1105 and (name C21 \ or name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name \ C28 or name C29 or name C210 or name C211 or name C212 or name C213 or name C21 \ 4 or name C215 or name C216 or name C217 or name C218)) or (resid 1106 through 1 \ 108 and (name C25 or name C26 or name C27 or name C28 or name C29 or name C210 o \ r name C211 or name C212 or name C213 or name C214 or name C215 or name C216 or \ name C217 or name C218)))) } 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: 1.080 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: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 18.010 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 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 : 0.007 0.063 21684 Z= 0.338 Angle : 1.067 12.294 29044 Z= 0.534 Chirality : 0.054 0.319 3172 Planarity : 0.006 0.059 3508 Dihedral : 18.770 173.396 8556 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.83 % Allowed : 7.88 % Favored : 91.30 % Rotamer: Outliers : 0.92 % Allowed : 2.82 % Favored : 96.26 % 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: -6.69 (0.09), residues: 2424 helix: -4.62 (0.05), residues: 1596 sheet: -2.28 (0.39), residues: 92 loop : -3.63 (0.17), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 698 TYR 0.026 0.003 TYR B 575 PHE 0.026 0.003 PHE D 526 TRP 0.009 0.001 TRP B 521 HIS 0.009 0.002 HIS C 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00746 / 0.34 (21684) covalent geometry : angle 1.06669 / 0.53 (29044) hydrogen bonds : bond 0.33540 / 22.11 ( 884) hydrogen bonds : angle 10.04529 / 6.87 ( 2580) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 522 time to evaluate : 0.768 Fit side-chains REVERT: A 214 GLU cc_start: 0.7518 (tt0) cc_final: 0.6879 (tp30) REVERT: A 220 ASN cc_start: 0.7479 (m110) cc_final: 0.7071 (t0) REVERT: A 227 GLN cc_start: 0.8178 (mm-40) cc_final: 0.7975 (mm-40) REVERT: A 308 GLU cc_start: 0.8011 (mm-30) cc_final: 0.7752 (mm-30) REVERT: A 358 LYS cc_start: 0.8637 (tttt) cc_final: 0.8404 (tttm) REVERT: A 412 ASN cc_start: 0.8112 (m110) cc_final: 0.7884 (t0) REVERT: A 429 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8223 (mt) REVERT: A 431 MET cc_start: 0.7513 (mtp) cc_final: 0.7304 (mtt) REVERT: A 447 PHE cc_start: 0.8001 (m-10) cc_final: 0.7790 (m-80) REVERT: A 553 LEU cc_start: 0.8240 (mt) cc_final: 0.8039 (mt) REVERT: A 647 ASN cc_start: 0.8645 (m-40) cc_final: 0.8141 (m-40) REVERT: A 650 TYR cc_start: 0.8151 (m-80) cc_final: 0.7861 (m-10) REVERT: A 716 ARG cc_start: 0.7695 (ttp-170) cc_final: 0.7367 (tpm170) REVERT: B 214 GLU cc_start: 0.7544 (tt0) cc_final: 0.6928 (tp30) REVERT: B 220 ASN cc_start: 0.7494 (m110) cc_final: 0.7055 (t0) REVERT: B 308 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7745 (mm-30) REVERT: B 358 LYS cc_start: 0.8636 (tttt) cc_final: 0.8435 (tttm) REVERT: B 412 ASN cc_start: 0.8096 (m110) cc_final: 0.7838 (t0) REVERT: B 429 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8199 (mt) REVERT: B 447 PHE cc_start: 0.8090 (m-10) cc_final: 0.7866 (m-80) REVERT: B 553 LEU cc_start: 0.8275 (mt) cc_final: 0.8069 (mt) REVERT: B 650 TYR cc_start: 0.8174 (m-80) cc_final: 0.7881 (m-10) REVERT: B 716 ARG cc_start: 0.7700 (ttp-170) cc_final: 0.7370 (tpm170) REVERT: B 721 CYS cc_start: 0.8386 (m) cc_final: 0.8079 (m) REVERT: C 214 GLU cc_start: 0.7538 (tt0) cc_final: 0.6904 (tp30) REVERT: C 251 ASN cc_start: 0.8105 (t0) cc_final: 0.7896 (t0) REVERT: C 308 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7618 (mm-30) REVERT: C 312 THR cc_start: 0.8635 (m) cc_final: 0.8430 (m) REVERT: C 358 LYS cc_start: 0.8628 (tttt) cc_final: 0.8409 (tttm) REVERT: C 412 ASN cc_start: 0.8170 (m110) cc_final: 0.7896 (t0) REVERT: C 429 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8200 (mt) REVERT: C 524 PHE cc_start: 0.7752 (t80) cc_final: 0.7550 (t80) REVERT: C 553 LEU cc_start: 0.8376 (mt) cc_final: 0.8173 (mt) REVERT: C 716 ARG cc_start: 0.7713 (ttp-170) cc_final: 0.7389 (tpm170) REVERT: C 721 CYS cc_start: 0.8397 (m) cc_final: 0.8073 (m) REVERT: D 214 GLU cc_start: 0.7521 (tt0) cc_final: 0.6925 (tp30) REVERT: D 220 ASN cc_start: 0.7505 (m110) cc_final: 0.7036 (t0) REVERT: D 227 GLN cc_start: 0.8165 (mm-40) cc_final: 0.7947 (mm-40) REVERT: D 308 GLU cc_start: 0.7985 (mm-30) cc_final: 0.7731 (mm-30) REVERT: D 412 ASN cc_start: 0.8131 (m110) cc_final: 0.7896 (t0) REVERT: D 429 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8204 (mt) REVERT: D 431 MET cc_start: 0.7512 (mtp) cc_final: 0.7293 (mtt) REVERT: D 553 LEU cc_start: 0.8245 (mt) cc_final: 0.8040 (mt) REVERT: D 643 ASN cc_start: 0.7962 (t0) cc_final: 0.7718 (m-40) REVERT: D 647 ASN cc_start: 0.8619 (m-40) cc_final: 0.8151 (m-40) REVERT: D 650 TYR cc_start: 0.8155 (m-80) cc_final: 0.7862 (m-10) REVERT: D 716 ARG cc_start: 0.7708 (ttp-170) cc_final: 0.7369 (tpm170) outliers start: 20 outliers final: 0 residues processed: 538 average time/residue: 0.1625 time to fit residues: 130.7619 Evaluate side-chains 365 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 361 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain D residue 429 LEU 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: 20.0000 chunk 194 optimal weight: 7.9990 chunk 227 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 1.9990 chunk 235 optimal weight: 0.7980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 570 GLN A 671 ASN A 683 ASN B 570 GLN B 671 ASN B 683 ASN C 256 HIS C 570 GLN C 671 ASN C 683 ASN D 570 GLN D 671 ASN D 683 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.162662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.113913 restraints weight = 24317.744| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.51 r_work: 0.3025 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3016 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3016 r_free = 0.3016 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3011 r_free = 0.3011 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.3011 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 21684 Z= 0.138 Angle : 0.670 10.462 29044 Z= 0.338 Chirality : 0.039 0.199 3172 Planarity : 0.005 0.041 3508 Dihedral : 21.816 159.819 3792 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.33 % Allowed : 7.18 % Favored : 92.49 % Rotamer: Outliers : 1.52 % Allowed : 7.95 % Favored : 90.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -4.00 (0.14), residues: 2424 helix: -2.27 (0.11), residues: 1620 sheet: -1.20 (0.41), residues: 92 loop : -3.36 (0.19), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 226 TYR 0.011 0.002 TYR C 254 PHE 0.018 0.002 PHE C 524 TRP 0.012 0.001 TRP D 493 HIS 0.010 0.001 HIS C 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (21684) covalent geometry : angle 0.67022 / 0.34 (29044) hydrogen bonds : bond 0.03944 / 2.56 ( 884) hydrogen bonds : angle 4.00265 / 2.75 ( 2580) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 353 time to evaluate : 0.846 Fit side-chains REVERT: A 214 GLU cc_start: 0.7988 (tt0) cc_final: 0.7302 (tp30) REVERT: A 308 GLU cc_start: 0.8435 (mm-30) cc_final: 0.8095 (mm-30) REVERT: A 412 ASN cc_start: 0.8346 (m110) cc_final: 0.7956 (t0) REVERT: A 429 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8498 (mt) REVERT: A 447 PHE cc_start: 0.8423 (m-10) cc_final: 0.8200 (m-80) REVERT: A 639 LEU cc_start: 0.7765 (pt) cc_final: 0.7339 (pp) REVERT: A 716 ARG cc_start: 0.7988 (ttp-170) cc_final: 0.7423 (tpm170) REVERT: A 726 ASP cc_start: 0.8084 (OUTLIER) cc_final: 0.7883 (t0) REVERT: B 214 GLU cc_start: 0.7988 (tt0) cc_final: 0.7318 (tp30) REVERT: B 286 GLN cc_start: 0.8195 (mm110) cc_final: 0.7978 (mm110) REVERT: B 308 GLU cc_start: 0.8445 (mm-30) cc_final: 0.8087 (mm-30) REVERT: B 412 ASN cc_start: 0.8348 (m110) cc_final: 0.7967 (t0) REVERT: B 429 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8490 (mt) REVERT: B 431 MET cc_start: 0.8525 (mtt) cc_final: 0.8291 (mtp) REVERT: B 447 PHE cc_start: 0.8436 (m-10) cc_final: 0.8224 (m-80) REVERT: B 716 ARG cc_start: 0.8022 (ttp-170) cc_final: 0.7439 (tpm170) REVERT: C 214 GLU cc_start: 0.7999 (tt0) cc_final: 0.7360 (tp30) REVERT: C 251 ASN cc_start: 0.8205 (t0) cc_final: 0.7950 (t0) REVERT: C 308 GLU cc_start: 0.8442 (mm-30) cc_final: 0.8080 (mm-30) REVERT: C 412 ASN cc_start: 0.8366 (m110) cc_final: 0.8002 (t0) REVERT: C 429 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8474 (mt) REVERT: C 431 MET cc_start: 0.8558 (mtt) cc_final: 0.8330 (mtp) REVERT: C 564 TYR cc_start: 0.8745 (t80) cc_final: 0.8517 (t80) REVERT: C 639 LEU cc_start: 0.7629 (pt) cc_final: 0.7250 (pp) REVERT: C 681 VAL cc_start: 0.8232 (m) cc_final: 0.8030 (t) REVERT: C 716 ARG cc_start: 0.8001 (ttp-170) cc_final: 0.7427 (tpm170) REVERT: D 210 GLU cc_start: 0.7714 (tt0) cc_final: 0.7190 (tt0) REVERT: D 214 GLU cc_start: 0.7975 (tt0) cc_final: 0.7309 (tp30) REVERT: D 286 GLN cc_start: 0.8153 (mm110) cc_final: 0.7946 (mm110) REVERT: D 308 GLU cc_start: 0.8447 (mm-30) cc_final: 0.8106 (mm-30) REVERT: D 412 ASN cc_start: 0.8346 (m110) cc_final: 0.7965 (t0) REVERT: D 429 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8501 (mt) REVERT: D 639 LEU cc_start: 0.7739 (pt) cc_final: 0.7311 (pp) REVERT: D 716 ARG cc_start: 0.7930 (ttp-170) cc_final: 0.7408 (tpm170) REVERT: D 726 ASP cc_start: 0.8077 (OUTLIER) cc_final: 0.7876 (t0) outliers start: 33 outliers final: 11 residues processed: 366 average time/residue: 0.1411 time to fit residues: 80.7780 Evaluate side-chains 340 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 323 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 550 CYS Chi-restraints excluded: chain A residue 726 ASP Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 550 CYS Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain D residue 550 CYS Chi-restraints excluded: chain D residue 726 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 122 optimal weight: 10.0000 chunk 192 optimal weight: 7.9990 chunk 82 optimal weight: 6.9990 chunk 61 optimal weight: 10.0000 chunk 203 optimal weight: 3.9990 chunk 237 optimal weight: 0.8980 chunk 167 optimal weight: 1.9990 chunk 90 optimal weight: 6.9990 chunk 191 optimal weight: 2.9990 chunk 7 optimal weight: 10.0000 chunk 128 optimal weight: 0.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 150 HIS A 570 GLN A 735 ASN B 150 HIS B 570 GLN B 735 ASN C 570 GLN C 735 ASN D 570 GLN D 735 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.156448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.108368 restraints weight = 24638.211| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 2.48 r_work: 0.2996 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2988 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2988 r_free = 0.2988 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2988 r_free = 0.2988 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2988 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 21684 Z= 0.191 Angle : 0.683 10.461 29044 Z= 0.337 Chirality : 0.041 0.178 3172 Planarity : 0.004 0.043 3508 Dihedral : 21.506 163.330 3792 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.55 % Favored : 92.29 % Rotamer: Outliers : 2.36 % Allowed : 9.61 % Favored : 88.03 % 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: -2.60 (0.16), residues: 2424 helix: -1.06 (0.13), residues: 1620 sheet: -0.33 (0.43), residues: 92 loop : -3.28 (0.20), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 225 TYR 0.017 0.002 TYR B 565 PHE 0.021 0.002 PHE C 526 TRP 0.011 0.001 TRP C 493 HIS 0.006 0.001 HIS A 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.19 (21684) covalent geometry : angle 0.68264 / 0.34 (29044) hydrogen bonds : bond 0.04147 / 2.71 ( 884) hydrogen bonds : angle 3.69381 / 2.53 ( 2580) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 329 time to evaluate : 0.787 Fit side-chains REVERT: A 171 CYS cc_start: 0.8815 (p) cc_final: 0.8571 (p) REVERT: A 184 LYS cc_start: 0.7918 (mmmm) cc_final: 0.7483 (mmmt) REVERT: A 210 GLU cc_start: 0.7859 (tt0) cc_final: 0.7257 (tt0) REVERT: A 214 GLU cc_start: 0.8025 (tt0) cc_final: 0.7385 (tp30) REVERT: A 308 GLU cc_start: 0.8450 (mm-30) cc_final: 0.8205 (mm-30) REVERT: A 412 ASN cc_start: 0.8338 (m110) cc_final: 0.8034 (t0) REVERT: A 447 PHE cc_start: 0.8489 (m-10) cc_final: 0.8250 (m-80) REVERT: A 716 ARG cc_start: 0.7984 (ttp-170) cc_final: 0.7533 (tpm170) REVERT: B 171 CYS cc_start: 0.8816 (p) cc_final: 0.8567 (p) REVERT: B 184 LYS cc_start: 0.7913 (mmmm) cc_final: 0.7479 (mmmt) REVERT: B 210 GLU cc_start: 0.7884 (tt0) cc_final: 0.7273 (tt0) REVERT: B 214 GLU cc_start: 0.8077 (tt0) cc_final: 0.7420 (tp30) REVERT: B 308 GLU cc_start: 0.8447 (mm-30) cc_final: 0.8205 (mm-30) REVERT: B 412 ASN cc_start: 0.8386 (m110) cc_final: 0.8057 (t0) REVERT: B 447 PHE cc_start: 0.8513 (m-10) cc_final: 0.8281 (m-80) REVERT: B 716 ARG cc_start: 0.7976 (ttp-170) cc_final: 0.7562 (tpm170) REVERT: C 171 CYS cc_start: 0.8602 (m) cc_final: 0.8319 (p) REVERT: C 184 LYS cc_start: 0.7927 (mmmm) cc_final: 0.7462 (mmmt) REVERT: C 210 GLU cc_start: 0.7857 (tt0) cc_final: 0.7268 (tt0) REVERT: C 214 GLU cc_start: 0.8052 (tt0) cc_final: 0.7387 (tp30) REVERT: C 308 GLU cc_start: 0.8413 (mm-30) cc_final: 0.8151 (mm-30) REVERT: C 412 ASN cc_start: 0.8379 (m110) cc_final: 0.8094 (t0) REVERT: C 429 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8679 (mt) REVERT: C 491 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7921 (mm) REVERT: C 716 ARG cc_start: 0.7998 (ttp-170) cc_final: 0.7543 (tpm170) REVERT: D 171 CYS cc_start: 0.8536 (m) cc_final: 0.8314 (p) REVERT: D 184 LYS cc_start: 0.7974 (mmmm) cc_final: 0.7518 (mmmt) REVERT: D 210 GLU cc_start: 0.7908 (tt0) cc_final: 0.7309 (tt0) REVERT: D 214 GLU cc_start: 0.8061 (tt0) cc_final: 0.7441 (tp30) REVERT: D 308 GLU cc_start: 0.8475 (mm-30) cc_final: 0.8238 (mm-30) REVERT: D 412 ASN cc_start: 0.8385 (m110) cc_final: 0.8065 (t0) REVERT: D 716 ARG cc_start: 0.7967 (ttp-170) cc_final: 0.7529 (tpm170) outliers start: 51 outliers final: 24 residues processed: 361 average time/residue: 0.1384 time to fit residues: 78.3980 Evaluate side-chains 334 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 308 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 550 CYS Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 550 CYS Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 732 LEU Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 550 CYS Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 732 LEU Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain D residue 550 CYS Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 732 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 185 optimal weight: 5.9990 chunk 190 optimal weight: 2.9990 chunk 134 optimal weight: 10.0000 chunk 93 optimal weight: 0.8980 chunk 76 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 87 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 240 optimal weight: 0.6980 chunk 5 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 570 GLN B 570 GLN C 570 GLN D 570 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.162847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.114814 restraints weight = 24227.561| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 2.41 r_work: 0.3036 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3006 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3006 r_free = 0.3006 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3006 r_free = 0.3006 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3006 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 21684 Z= 0.127 Angle : 0.611 10.384 29044 Z= 0.303 Chirality : 0.038 0.180 3172 Planarity : 0.003 0.044 3508 Dihedral : 20.654 157.630 3786 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.22 % Favored : 92.74 % Rotamer: Outliers : 1.76 % Allowed : 10.44 % Favored : 87.80 % 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: -1.76 (0.17), residues: 2424 helix: -0.40 (0.13), residues: 1592 sheet: 0.30 (0.46), residues: 92 loop : -2.95 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 363 TYR 0.014 0.001 TYR C 564 PHE 0.017 0.001 PHE C 524 TRP 0.014 0.001 TRP D 493 HIS 0.005 0.001 HIS B 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (21684) covalent geometry : angle 0.61081 / 0.30 (29044) hydrogen bonds : bond 0.03070 / 2.00 ( 884) hydrogen bonds : angle 3.46555 / 2.39 ( 2580) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 323 time to evaluate : 0.787 Fit side-chains revert: symmetry clash REVERT: A 141 GLU cc_start: 0.7747 (tt0) cc_final: 0.7396 (mt-10) REVERT: A 210 GLU cc_start: 0.7768 (tt0) cc_final: 0.7105 (tt0) REVERT: A 214 GLU cc_start: 0.7813 (tt0) cc_final: 0.7054 (tp30) REVERT: A 412 ASN cc_start: 0.8261 (m110) cc_final: 0.7850 (t0) REVERT: A 447 PHE cc_start: 0.8173 (m-10) cc_final: 0.7915 (m-80) REVERT: A 489 PHE cc_start: 0.7005 (t80) cc_final: 0.6651 (t80) REVERT: A 639 LEU cc_start: 0.7473 (pt) cc_final: 0.7167 (pp) REVERT: A 716 ARG cc_start: 0.7917 (ttp-170) cc_final: 0.7290 (tpm170) REVERT: A 734 ILE cc_start: 0.8106 (OUTLIER) cc_final: 0.7840 (mt) REVERT: B 141 GLU cc_start: 0.7731 (tt0) cc_final: 0.7411 (mt-10) REVERT: B 210 GLU cc_start: 0.7685 (tt0) cc_final: 0.7054 (tt0) REVERT: B 214 GLU cc_start: 0.7826 (tt0) cc_final: 0.7061 (tp30) REVERT: B 412 ASN cc_start: 0.8267 (m110) cc_final: 0.7890 (t0) REVERT: B 447 PHE cc_start: 0.8179 (m-10) cc_final: 0.7925 (m-80) REVERT: B 489 PHE cc_start: 0.7017 (t80) cc_final: 0.6642 (t80) REVERT: B 639 LEU cc_start: 0.7627 (pt) cc_final: 0.7299 (pp) REVERT: B 716 ARG cc_start: 0.7916 (ttp-170) cc_final: 0.7277 (tpm170) REVERT: B 734 ILE cc_start: 0.8106 (OUTLIER) cc_final: 0.7844 (mt) REVERT: C 141 GLU cc_start: 0.7739 (tt0) cc_final: 0.7405 (mt-10) REVERT: C 210 GLU cc_start: 0.7720 (tt0) cc_final: 0.7055 (tt0) REVERT: C 214 GLU cc_start: 0.7774 (tt0) cc_final: 0.7030 (tp30) REVERT: C 412 ASN cc_start: 0.8338 (m110) cc_final: 0.7935 (t0) REVERT: C 429 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8230 (mt) REVERT: C 639 LEU cc_start: 0.7465 (pt) cc_final: 0.7155 (pp) REVERT: C 683 ASN cc_start: 0.7539 (m-40) cc_final: 0.7328 (m-40) REVERT: C 716 ARG cc_start: 0.7970 (ttp-170) cc_final: 0.7292 (tpm170) REVERT: C 734 ILE cc_start: 0.8093 (OUTLIER) cc_final: 0.7831 (mt) REVERT: D 141 GLU cc_start: 0.7758 (tt0) cc_final: 0.7395 (mt-10) REVERT: D 185 GLU cc_start: 0.8014 (mp0) cc_final: 0.7801 (mp0) REVERT: D 210 GLU cc_start: 0.7725 (tt0) cc_final: 0.7077 (tt0) REVERT: D 214 GLU cc_start: 0.7826 (tt0) cc_final: 0.7061 (tp30) REVERT: D 412 ASN cc_start: 0.8254 (m110) cc_final: 0.7842 (t0) REVERT: D 639 LEU cc_start: 0.7470 (pt) cc_final: 0.7168 (pp) REVERT: D 676 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7873 (mt) REVERT: D 716 ARG cc_start: 0.7917 (ttp-170) cc_final: 0.7276 (tpm170) REVERT: D 734 ILE cc_start: 0.8106 (OUTLIER) cc_final: 0.7842 (mt) outliers start: 38 outliers final: 15 residues processed: 341 average time/residue: 0.1483 time to fit residues: 79.4810 Evaluate side-chains 321 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 300 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 550 CYS Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 496 CYS Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain D residue 734 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 158 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 chunk 221 optimal weight: 9.9990 chunk 32 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 21 optimal weight: 7.9990 chunk 120 optimal weight: 3.9990 chunk 211 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 chunk 124 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 570 GLN B 570 GLN C 570 GLN C 585 HIS D 570 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.157125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.108635 restraints weight = 24347.110| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 2.41 r_work: 0.2926 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2899 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2899 r_free = 0.2899 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2899 r_free = 0.2899 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2899 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.3384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 21684 Z= 0.220 Angle : 0.699 12.897 29044 Z= 0.341 Chirality : 0.042 0.178 3172 Planarity : 0.004 0.045 3508 Dihedral : 20.924 163.732 3786 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.43 % Favored : 92.41 % Rotamer: Outliers : 2.63 % Allowed : 10.12 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.46 (0.17), residues: 2424 helix: -0.19 (0.13), residues: 1604 sheet: 0.77 (0.49), residues: 92 loop : -2.90 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 225 TYR 0.016 0.002 TYR B 565 PHE 0.019 0.002 PHE C 524 TRP 0.011 0.001 TRP D 493 HIS 0.007 0.001 HIS A 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00536 / 0.22 (21684) covalent geometry : angle 0.69860 / 0.34 (29044) hydrogen bonds : bond 0.03889 / 2.54 ( 884) hydrogen bonds : angle 3.59515 / 2.45 ( 2580) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 320 time to evaluate : 0.802 Fit side-chains REVERT: A 141 GLU cc_start: 0.7675 (tt0) cc_final: 0.7357 (mt-10) REVERT: A 171 CYS cc_start: 0.8661 (p) cc_final: 0.8408 (p) REVERT: A 184 LYS cc_start: 0.7738 (mmmm) cc_final: 0.7333 (mmmt) REVERT: A 210 GLU cc_start: 0.7690 (tt0) cc_final: 0.7017 (tt0) REVERT: A 214 GLU cc_start: 0.7967 (tt0) cc_final: 0.7203 (tp30) REVERT: A 358 LYS cc_start: 0.8420 (tttt) cc_final: 0.8150 (tttm) REVERT: A 412 ASN cc_start: 0.8276 (m110) cc_final: 0.7885 (t0) REVERT: A 447 PHE cc_start: 0.8299 (m-10) cc_final: 0.8005 (m-80) REVERT: A 564 TYR cc_start: 0.8521 (t80) cc_final: 0.8304 (t80) REVERT: A 716 ARG cc_start: 0.7993 (ttp-170) cc_final: 0.7373 (tpm170) REVERT: B 141 GLU cc_start: 0.7620 (tt0) cc_final: 0.7359 (mt-10) REVERT: B 184 LYS cc_start: 0.7738 (mmmm) cc_final: 0.7340 (mmmt) REVERT: B 210 GLU cc_start: 0.7712 (tt0) cc_final: 0.7061 (tt0) REVERT: B 214 GLU cc_start: 0.7974 (tt0) cc_final: 0.7209 (tp30) REVERT: B 358 LYS cc_start: 0.8430 (tttt) cc_final: 0.8161 (tttm) REVERT: B 412 ASN cc_start: 0.8278 (m110) cc_final: 0.7898 (t0) REVERT: B 447 PHE cc_start: 0.8301 (m-10) cc_final: 0.8007 (m-80) REVERT: B 564 TYR cc_start: 0.8522 (t80) cc_final: 0.8310 (t80) REVERT: B 716 ARG cc_start: 0.7997 (ttp-170) cc_final: 0.7375 (tpm170) REVERT: C 118 ARG cc_start: 0.6601 (ptt90) cc_final: 0.5581 (ptm160) REVERT: C 138 LEU cc_start: 0.7715 (mp) cc_final: 0.7472 (mp) REVERT: C 141 GLU cc_start: 0.7728 (tt0) cc_final: 0.7211 (mt-10) REVERT: C 171 CYS cc_start: 0.8425 (m) cc_final: 0.8150 (p) REVERT: C 184 LYS cc_start: 0.7747 (mmmm) cc_final: 0.7525 (mmmt) REVERT: C 210 GLU cc_start: 0.7731 (tt0) cc_final: 0.7082 (tt0) REVERT: C 214 GLU cc_start: 0.7967 (tt0) cc_final: 0.7188 (tp30) REVERT: C 358 LYS cc_start: 0.8440 (tttt) cc_final: 0.8175 (tttm) REVERT: C 412 ASN cc_start: 0.8330 (m110) cc_final: 0.7927 (t0) REVERT: C 429 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8286 (mt) REVERT: C 564 TYR cc_start: 0.8542 (t80) cc_final: 0.8318 (t80) REVERT: C 716 ARG cc_start: 0.8010 (ttp-170) cc_final: 0.7365 (tpm170) REVERT: D 141 GLU cc_start: 0.7694 (tt0) cc_final: 0.7359 (mt-10) REVERT: D 171 CYS cc_start: 0.8401 (m) cc_final: 0.8160 (p) REVERT: D 184 LYS cc_start: 0.7777 (mmmm) cc_final: 0.7358 (mmmt) REVERT: D 210 GLU cc_start: 0.7731 (tt0) cc_final: 0.7083 (tt0) REVERT: D 214 GLU cc_start: 0.7978 (tt0) cc_final: 0.7210 (tp30) REVERT: D 412 ASN cc_start: 0.8272 (m110) cc_final: 0.7876 (t0) REVERT: D 564 TYR cc_start: 0.8534 (t80) cc_final: 0.8311 (t80) REVERT: D 716 ARG cc_start: 0.7985 (ttp-170) cc_final: 0.7358 (tpm170) outliers start: 57 outliers final: 37 residues processed: 344 average time/residue: 0.1576 time to fit residues: 84.3133 Evaluate side-chains 343 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 305 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 550 CYS Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 550 CYS Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain B residue 732 LEU Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 550 CYS Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain C residue 732 LEU Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 285 GLU Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain D residue 550 CYS Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 670 LEU Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain D residue 732 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 30 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 chunk 106 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 165 optimal weight: 0.6980 chunk 107 optimal weight: 0.7980 chunk 123 optimal weight: 0.7980 chunk 192 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 570 GLN B 570 GLN C 430 HIS C 570 GLN D 570 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.162876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.116114 restraints weight = 24069.403| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 2.30 r_work: 0.3015 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3023 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3023 r_free = 0.3023 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3023 r_free = 0.3023 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.3023 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.3578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 21684 Z= 0.106 Angle : 0.588 10.419 29044 Z= 0.291 Chirality : 0.037 0.175 3172 Planarity : 0.003 0.047 3508 Dihedral : 19.963 157.075 3786 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 1.29 % Allowed : 11.88 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.17), residues: 2424 helix: 0.26 (0.13), residues: 1588 sheet: 1.23 (0.53), residues: 92 loop : -2.72 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 202 TYR 0.011 0.001 TYR B 208 PHE 0.017 0.001 PHE C 524 TRP 0.014 0.001 TRP D 493 HIS 0.005 0.001 HIS B 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (21684) covalent geometry : angle 0.58782 / 0.29 (29044) hydrogen bonds : bond 0.02707 / 1.75 ( 884) hydrogen bonds : angle 3.41601 / 2.35 ( 2580) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 314 time to evaluate : 0.807 Fit side-chains REVERT: A 141 GLU cc_start: 0.7643 (tt0) cc_final: 0.7263 (mt-10) REVERT: A 184 LYS cc_start: 0.7629 (mmmm) cc_final: 0.7360 (mmmt) REVERT: A 210 GLU cc_start: 0.7653 (tt0) cc_final: 0.7003 (tt0) REVERT: A 214 GLU cc_start: 0.7753 (tt0) cc_final: 0.6997 (tp30) REVERT: A 412 ASN cc_start: 0.8343 (m110) cc_final: 0.7921 (t0) REVERT: A 447 PHE cc_start: 0.8130 (m-10) cc_final: 0.7857 (m-80) REVERT: A 639 LEU cc_start: 0.7390 (pt) cc_final: 0.7098 (pp) REVERT: A 716 ARG cc_start: 0.7928 (ttp-170) cc_final: 0.7284 (tpm170) REVERT: A 734 ILE cc_start: 0.8078 (pt) cc_final: 0.7857 (mt) REVERT: B 141 GLU cc_start: 0.7617 (tt0) cc_final: 0.7289 (mt-10) REVERT: B 184 LYS cc_start: 0.7627 (mmmm) cc_final: 0.7365 (mmmt) REVERT: B 210 GLU cc_start: 0.7616 (tt0) cc_final: 0.6979 (tt0) REVERT: B 214 GLU cc_start: 0.7757 (tt0) cc_final: 0.7009 (tp30) REVERT: B 412 ASN cc_start: 0.8278 (m110) cc_final: 0.7837 (t0) REVERT: B 447 PHE cc_start: 0.8117 (m-10) cc_final: 0.7838 (m-80) REVERT: B 639 LEU cc_start: 0.7556 (pt) cc_final: 0.7269 (pp) REVERT: B 716 ARG cc_start: 0.7921 (ttp-170) cc_final: 0.7278 (tpm170) REVERT: B 734 ILE cc_start: 0.8076 (pt) cc_final: 0.7852 (mt) REVERT: C 118 ARG cc_start: 0.6566 (ptt90) cc_final: 0.5583 (ptp-110) REVERT: C 138 LEU cc_start: 0.7695 (mp) cc_final: 0.7445 (mp) REVERT: C 141 GLU cc_start: 0.7721 (tt0) cc_final: 0.7254 (mt-10) REVERT: C 184 LYS cc_start: 0.7703 (mmmm) cc_final: 0.7310 (mmmt) REVERT: C 185 GLU cc_start: 0.7923 (mp0) cc_final: 0.7715 (mp0) REVERT: C 199 ILE cc_start: 0.6299 (OUTLIER) cc_final: 0.6026 (tp) REVERT: C 210 GLU cc_start: 0.7667 (tt0) cc_final: 0.7004 (tt0) REVERT: C 214 GLU cc_start: 0.7725 (tt0) cc_final: 0.6963 (tp30) REVERT: C 322 ASP cc_start: 0.8113 (t0) cc_final: 0.7770 (t70) REVERT: C 412 ASN cc_start: 0.8297 (m110) cc_final: 0.7862 (t0) REVERT: C 639 LEU cc_start: 0.7384 (pt) cc_final: 0.7089 (pp) REVERT: C 716 ARG cc_start: 0.7931 (ttp-170) cc_final: 0.7273 (tpm170) REVERT: C 734 ILE cc_start: 0.8076 (pt) cc_final: 0.7855 (mt) REVERT: D 141 GLU cc_start: 0.7637 (tt0) cc_final: 0.7249 (mt-10) REVERT: D 184 LYS cc_start: 0.7646 (mmmm) cc_final: 0.7371 (mmmt) REVERT: D 210 GLU cc_start: 0.7675 (tt0) cc_final: 0.7004 (tt0) REVERT: D 214 GLU cc_start: 0.7759 (tt0) cc_final: 0.7009 (tp30) REVERT: D 412 ASN cc_start: 0.8261 (m110) cc_final: 0.7822 (t0) REVERT: D 639 LEU cc_start: 0.7380 (pt) cc_final: 0.7080 (pp) REVERT: D 716 ARG cc_start: 0.7920 (ttp-170) cc_final: 0.7273 (tpm170) REVERT: D 734 ILE cc_start: 0.8084 (pt) cc_final: 0.7860 (mt) outliers start: 28 outliers final: 21 residues processed: 327 average time/residue: 0.1587 time to fit residues: 80.7260 Evaluate side-chains 320 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 298 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 HIS Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 550 CYS Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain B residue 256 HIS Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 550 CYS Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 550 CYS Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain D residue 256 HIS Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 588 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 109 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 236 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 62 optimal weight: 0.0770 chunk 113 optimal weight: 1.9990 chunk 154 optimal weight: 4.9990 chunk 175 optimal weight: 3.9990 chunk 164 optimal weight: 3.9990 chunk 94 optimal weight: 0.7980 chunk 202 optimal weight: 0.5980 overall best weight: 0.8540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 570 GLN B 570 GLN C 570 GLN D 570 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.161367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.113848 restraints weight = 24407.830| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 2.36 r_work: 0.3004 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3016 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3016 r_free = 0.3016 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3016 r_free = 0.3016 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3016 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.3743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 21684 Z= 0.105 Angle : 0.578 11.519 29044 Z= 0.284 Chirality : 0.037 0.167 3172 Planarity : 0.003 0.046 3508 Dihedral : 19.151 157.586 3784 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.26 % Favored : 92.57 % Rotamer: Outliers : 1.94 % Allowed : 10.72 % Favored : 87.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.18), residues: 2424 helix: 0.48 (0.14), residues: 1612 sheet: 1.47 (0.53), residues: 92 loop : -2.69 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 225 TYR 0.011 0.001 TYR D 208 PHE 0.018 0.001 PHE B 524 TRP 0.012 0.001 TRP D 493 HIS 0.006 0.001 HIS D 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (21684) covalent geometry : angle 0.57826 / 0.28 (29044) hydrogen bonds : bond 0.02642 / 1.71 ( 884) hydrogen bonds : angle 3.33207 / 2.29 ( 2580) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 326 time to evaluate : 0.790 Fit side-chains REVERT: A 141 GLU cc_start: 0.7635 (tt0) cc_final: 0.7345 (mt-10) REVERT: A 184 LYS cc_start: 0.7619 (mmmm) cc_final: 0.7406 (mmmt) REVERT: A 210 GLU cc_start: 0.7651 (tt0) cc_final: 0.7082 (tt0) REVERT: A 214 GLU cc_start: 0.7761 (tt0) cc_final: 0.6978 (tp30) REVERT: A 332 GLU cc_start: 0.7577 (mm-30) cc_final: 0.7145 (mm-30) REVERT: A 412 ASN cc_start: 0.8278 (m110) cc_final: 0.7883 (t0) REVERT: A 447 PHE cc_start: 0.8134 (m-10) cc_final: 0.7871 (m-80) REVERT: A 716 ARG cc_start: 0.7926 (ttp-170) cc_final: 0.7262 (tpm170) REVERT: B 141 GLU cc_start: 0.7638 (tt0) cc_final: 0.7340 (mt-10) REVERT: B 184 LYS cc_start: 0.7632 (mmmm) cc_final: 0.7421 (mmmt) REVERT: B 210 GLU cc_start: 0.7629 (tt0) cc_final: 0.7089 (tt0) REVERT: B 214 GLU cc_start: 0.7766 (tt0) cc_final: 0.7018 (tp30) REVERT: B 322 ASP cc_start: 0.8104 (t0) cc_final: 0.7772 (t70) REVERT: B 332 GLU cc_start: 0.7569 (mm-30) cc_final: 0.7192 (mm-30) REVERT: B 412 ASN cc_start: 0.8246 (m110) cc_final: 0.7627 (t0) REVERT: B 447 PHE cc_start: 0.8124 (m-10) cc_final: 0.7861 (m-80) REVERT: B 716 ARG cc_start: 0.7924 (ttp-170) cc_final: 0.7263 (tpm170) REVERT: C 118 ARG cc_start: 0.6557 (ptt90) cc_final: 0.5591 (ptp-110) REVERT: C 138 LEU cc_start: 0.7779 (OUTLIER) cc_final: 0.7540 (mp) REVERT: C 141 GLU cc_start: 0.7738 (tt0) cc_final: 0.7315 (mt-10) REVERT: C 184 LYS cc_start: 0.7692 (mmmm) cc_final: 0.7296 (mmmt) REVERT: C 185 GLU cc_start: 0.7886 (mp0) cc_final: 0.7579 (mp0) REVERT: C 210 GLU cc_start: 0.7677 (tt0) cc_final: 0.7078 (tt0) REVERT: C 214 GLU cc_start: 0.7782 (tt0) cc_final: 0.6975 (tp30) REVERT: C 322 ASP cc_start: 0.8104 (t0) cc_final: 0.7769 (t70) REVERT: C 332 GLU cc_start: 0.7555 (mm-30) cc_final: 0.7120 (mm-30) REVERT: C 412 ASN cc_start: 0.8354 (m110) cc_final: 0.7910 (t0) REVERT: C 683 ASN cc_start: 0.7527 (m-40) cc_final: 0.7228 (m-40) REVERT: C 716 ARG cc_start: 0.7953 (ttp-170) cc_final: 0.7259 (tpm170) REVERT: D 141 GLU cc_start: 0.7637 (tt0) cc_final: 0.7336 (mt-10) REVERT: D 184 LYS cc_start: 0.7692 (mmmm) cc_final: 0.7423 (mmmt) REVERT: D 210 GLU cc_start: 0.7689 (tt0) cc_final: 0.7115 (tt0) REVERT: D 214 GLU cc_start: 0.7763 (tt0) cc_final: 0.6981 (tp30) REVERT: D 332 GLU cc_start: 0.7565 (mm-30) cc_final: 0.7129 (mm-30) REVERT: D 412 ASN cc_start: 0.8233 (m110) cc_final: 0.7614 (t0) REVERT: D 716 ARG cc_start: 0.7911 (ttp-170) cc_final: 0.7248 (tpm170) outliers start: 42 outliers final: 33 residues processed: 348 average time/residue: 0.1536 time to fit residues: 83.4277 Evaluate side-chains 334 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 300 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 256 HIS Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 550 CYS Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 256 HIS Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 550 CYS Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain B residue 732 LEU Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 256 HIS Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 550 CYS Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain C residue 732 LEU Chi-restraints excluded: chain D residue 256 HIS Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain D residue 550 CYS Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 670 LEU Chi-restraints excluded: chain D residue 732 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 158 optimal weight: 5.9990 chunk 128 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 124 optimal weight: 8.9990 chunk 187 optimal weight: 8.9990 chunk 143 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 213 optimal weight: 1.9990 chunk 194 optimal weight: 1.9990 chunk 142 optimal weight: 0.8980 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 570 GLN A 585 HIS B 570 GLN B 585 HIS C 570 GLN D 570 GLN D 585 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.158829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.111159 restraints weight = 24234.049| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 2.35 r_work: 0.2976 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3018 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3018 r_free = 0.3018 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3018 r_free = 0.3018 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3018 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.3762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 21684 Z= 0.171 Angle : 0.646 13.141 29044 Z= 0.318 Chirality : 0.040 0.152 3172 Planarity : 0.003 0.043 3508 Dihedral : 19.384 158.554 3784 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.43 % Favored : 92.41 % Rotamer: Outliers : 1.57 % Allowed : 11.69 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.59 (0.18), residues: 2424 helix: 0.45 (0.13), residues: 1624 sheet: 1.52 (0.52), residues: 92 loop : -2.63 (0.22), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 202 TYR 0.014 0.002 TYR B 565 PHE 0.018 0.001 PHE C 524 TRP 0.008 0.001 TRP D 493 HIS 0.007 0.001 HIS B 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.17 (21684) covalent geometry : angle 0.64607 / 0.32 (29044) hydrogen bonds : bond 0.03302 / 2.15 ( 884) hydrogen bonds : angle 3.50247 / 2.40 ( 2580) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 313 time to evaluate : 0.739 Fit side-chains REVERT: A 141 GLU cc_start: 0.7690 (tt0) cc_final: 0.7366 (mt-10) REVERT: A 210 GLU cc_start: 0.7689 (tt0) cc_final: 0.7070 (tt0) REVERT: A 214 GLU cc_start: 0.7939 (tt0) cc_final: 0.7148 (tp30) REVERT: A 412 ASN cc_start: 0.8331 (m110) cc_final: 0.7944 (t0) REVERT: A 447 PHE cc_start: 0.8180 (m-10) cc_final: 0.7920 (m-80) REVERT: A 639 LEU cc_start: 0.7590 (pt) cc_final: 0.7269 (pp) REVERT: A 716 ARG cc_start: 0.7986 (ttp-170) cc_final: 0.7340 (tpm170) REVERT: B 141 GLU cc_start: 0.7660 (tt0) cc_final: 0.7386 (mt-10) REVERT: B 210 GLU cc_start: 0.7676 (tt0) cc_final: 0.7030 (tt0) REVERT: B 214 GLU cc_start: 0.7933 (tt0) cc_final: 0.7167 (tp30) REVERT: B 322 ASP cc_start: 0.8255 (t0) cc_final: 0.7899 (t70) REVERT: B 412 ASN cc_start: 0.8353 (m110) cc_final: 0.7932 (t0) REVERT: B 447 PHE cc_start: 0.8174 (m-10) cc_final: 0.7915 (m-80) REVERT: B 716 ARG cc_start: 0.7972 (ttp-170) cc_final: 0.7337 (tpm170) REVERT: C 118 ARG cc_start: 0.6581 (ptt90) cc_final: 0.5602 (ptp-110) REVERT: C 138 LEU cc_start: 0.7816 (OUTLIER) cc_final: 0.7583 (mp) REVERT: C 141 GLU cc_start: 0.7757 (tt0) cc_final: 0.7339 (mt-10) REVERT: C 184 LYS cc_start: 0.7738 (mmmm) cc_final: 0.7306 (mmmt) REVERT: C 185 GLU cc_start: 0.7982 (mp0) cc_final: 0.7636 (mp0) REVERT: C 200 LEU cc_start: 0.7151 (tp) cc_final: 0.6898 (tp) REVERT: C 210 GLU cc_start: 0.7709 (tt0) cc_final: 0.7073 (tt0) REVERT: C 214 GLU cc_start: 0.7946 (tt0) cc_final: 0.7144 (tp30) REVERT: C 322 ASP cc_start: 0.8250 (t0) cc_final: 0.7893 (t70) REVERT: C 412 ASN cc_start: 0.8337 (m110) cc_final: 0.7930 (t0) REVERT: C 443 LEU cc_start: 0.7315 (OUTLIER) cc_final: 0.6819 (mp) REVERT: C 716 ARG cc_start: 0.7988 (ttp-170) cc_final: 0.7345 (tpm170) REVERT: D 141 GLU cc_start: 0.7663 (tt0) cc_final: 0.7387 (mt-10) REVERT: D 184 LYS cc_start: 0.7692 (mmmm) cc_final: 0.7458 (mmmt) REVERT: D 210 GLU cc_start: 0.7717 (tt0) cc_final: 0.7104 (tt0) REVERT: D 214 GLU cc_start: 0.7942 (tt0) cc_final: 0.7168 (tp30) REVERT: D 412 ASN cc_start: 0.8348 (m110) cc_final: 0.7927 (t0) REVERT: D 443 LEU cc_start: 0.7286 (OUTLIER) cc_final: 0.6803 (mp) REVERT: D 639 LEU cc_start: 0.7583 (pt) cc_final: 0.7264 (pp) REVERT: D 716 ARG cc_start: 0.7960 (ttp-170) cc_final: 0.7317 (tpm170) outliers start: 34 outliers final: 30 residues processed: 328 average time/residue: 0.1469 time to fit residues: 75.0552 Evaluate side-chains 340 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 307 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 550 CYS Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 256 HIS Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 550 CYS Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain B residue 732 LEU Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 550 CYS Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain D residue 256 HIS Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain D residue 550 CYS Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 670 LEU Chi-restraints excluded: chain D residue 732 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 51 optimal weight: 0.9990 chunk 2 optimal weight: 5.9990 chunk 124 optimal weight: 8.9990 chunk 137 optimal weight: 0.4980 chunk 238 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 192 optimal weight: 1.9990 chunk 121 optimal weight: 5.9990 chunk 227 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 95 optimal weight: 0.9980 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 570 GLN B 570 GLN C 570 GLN D 570 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.162989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.116183 restraints weight = 24131.990| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 2.30 r_work: 0.3024 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3030 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3030 r_free = 0.3030 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3030 r_free = 0.3030 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3030 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.3900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 21684 Z= 0.108 Angle : 0.585 13.703 29044 Z= 0.287 Chirality : 0.038 0.164 3172 Planarity : 0.003 0.043 3508 Dihedral : 18.708 156.737 3784 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 1.52 % Allowed : 11.37 % Favored : 87.11 % 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: -0.36 (0.18), residues: 2424 helix: 0.70 (0.14), residues: 1608 sheet: 0.81 (0.50), residues: 112 loop : -2.62 (0.23), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 202 TYR 0.012 0.001 TYR B 208 PHE 0.016 0.001 PHE C 524 TRP 0.011 0.001 TRP D 493 HIS 0.006 0.001 HIS B 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (21684) covalent geometry : angle 0.58529 / 0.29 (29044) hydrogen bonds : bond 0.02575 / 1.66 ( 884) hydrogen bonds : angle 3.37431 / 2.32 ( 2580) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 314 time to evaluate : 0.756 Fit side-chains REVERT: A 118 ARG cc_start: 0.6625 (ptt90) cc_final: 0.5631 (ptp-110) REVERT: A 141 GLU cc_start: 0.7731 (tt0) cc_final: 0.7327 (mt-10) REVERT: A 210 GLU cc_start: 0.7639 (tt0) cc_final: 0.6965 (tt0) REVERT: A 214 GLU cc_start: 0.7801 (tt0) cc_final: 0.7033 (tp30) REVERT: A 322 ASP cc_start: 0.8173 (t0) cc_final: 0.7830 (t70) REVERT: A 412 ASN cc_start: 0.8314 (m110) cc_final: 0.7687 (t0) REVERT: A 639 LEU cc_start: 0.7646 (pt) cc_final: 0.7349 (pp) REVERT: A 716 ARG cc_start: 0.7946 (ttp-170) cc_final: 0.7291 (tpm170) REVERT: B 141 GLU cc_start: 0.7728 (tt0) cc_final: 0.7428 (mt-10) REVERT: B 210 GLU cc_start: 0.7603 (tt0) cc_final: 0.6977 (tt0) REVERT: B 214 GLU cc_start: 0.7802 (tt0) cc_final: 0.7031 (tp30) REVERT: B 322 ASP cc_start: 0.8171 (t0) cc_final: 0.7823 (t70) REVERT: B 412 ASN cc_start: 0.8301 (m110) cc_final: 0.7664 (t0) REVERT: B 716 ARG cc_start: 0.7934 (ttp-170) cc_final: 0.7289 (tpm170) REVERT: C 118 ARG cc_start: 0.6543 (ptt90) cc_final: 0.5502 (ptp-110) REVERT: C 138 LEU cc_start: 0.7790 (OUTLIER) cc_final: 0.7558 (mp) REVERT: C 141 GLU cc_start: 0.7778 (tt0) cc_final: 0.7368 (mt-10) REVERT: C 184 LYS cc_start: 0.7738 (mmmm) cc_final: 0.7317 (mmmt) REVERT: C 185 GLU cc_start: 0.8079 (mp0) cc_final: 0.7716 (mp0) REVERT: C 200 LEU cc_start: 0.7154 (tp) cc_final: 0.6895 (tp) REVERT: C 210 GLU cc_start: 0.7660 (tt0) cc_final: 0.6975 (tt0) REVERT: C 214 GLU cc_start: 0.7800 (tt0) cc_final: 0.7020 (tp30) REVERT: C 322 ASP cc_start: 0.8175 (t0) cc_final: 0.7824 (t70) REVERT: C 412 ASN cc_start: 0.8306 (m110) cc_final: 0.7674 (t0) REVERT: C 639 LEU cc_start: 0.7618 (pt) cc_final: 0.7333 (pp) REVERT: C 683 ASN cc_start: 0.7508 (m-40) cc_final: 0.7246 (m-40) REVERT: C 716 ARG cc_start: 0.7945 (ttp-170) cc_final: 0.7302 (tpm170) REVERT: D 141 GLU cc_start: 0.7703 (tt0) cc_final: 0.7419 (mt-10) REVERT: D 184 LYS cc_start: 0.7688 (mmmm) cc_final: 0.7468 (mmmt) REVERT: D 210 GLU cc_start: 0.7688 (tt0) cc_final: 0.7010 (tt0) REVERT: D 214 GLU cc_start: 0.7823 (tt0) cc_final: 0.7029 (tp30) REVERT: D 322 ASP cc_start: 0.8174 (t0) cc_final: 0.7826 (t70) REVERT: D 412 ASN cc_start: 0.8285 (m110) cc_final: 0.7658 (t0) REVERT: D 639 LEU cc_start: 0.7646 (pt) cc_final: 0.7352 (pp) REVERT: D 716 ARG cc_start: 0.7937 (ttp-170) cc_final: 0.7284 (tpm170) outliers start: 33 outliers final: 32 residues processed: 330 average time/residue: 0.1399 time to fit residues: 71.9792 Evaluate side-chains 334 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 301 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 256 HIS Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 550 CYS Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 256 HIS Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 550 CYS Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain B residue 732 LEU Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 550 CYS Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain C residue 732 LEU Chi-restraints excluded: chain D residue 256 HIS Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain D residue 550 CYS Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 670 LEU Chi-restraints excluded: chain D residue 732 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 127 optimal weight: 2.9990 chunk 197 optimal weight: 0.9980 chunk 234 optimal weight: 0.9980 chunk 46 optimal weight: 0.5980 chunk 119 optimal weight: 0.8980 chunk 173 optimal weight: 0.7980 chunk 235 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 79 optimal weight: 0.9990 chunk 178 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 570 GLN B 570 GLN C 570 GLN D 570 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.163550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.116692 restraints weight = 24050.030| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 2.31 r_work: 0.3021 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3028 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3028 r_free = 0.3028 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3028 r_free = 0.3028 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3028 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.3971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 21684 Z= 0.107 Angle : 0.590 13.750 29044 Z= 0.289 Chirality : 0.038 0.253 3172 Planarity : 0.003 0.042 3508 Dihedral : 18.272 150.652 3784 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.72 % Favored : 93.11 % Rotamer: Outliers : 1.57 % Allowed : 11.74 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.18), residues: 2424 helix: 0.82 (0.14), residues: 1604 sheet: 0.94 (0.49), residues: 112 loop : -2.55 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 202 TYR 0.011 0.001 TYR C 208 PHE 0.023 0.001 PHE C 489 TRP 0.012 0.001 TRP D 493 HIS 0.006 0.001 HIS B 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (21684) covalent geometry : angle 0.58980 / 0.29 (29044) hydrogen bonds : bond 0.02588 / 1.67 ( 884) hydrogen bonds : angle 3.35446 / 2.31 ( 2580) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 310 time to evaluate : 0.744 Fit side-chains REVERT: A 118 ARG cc_start: 0.6619 (ptt90) cc_final: 0.5625 (ptp-110) REVERT: A 141 GLU cc_start: 0.7748 (tt0) cc_final: 0.7353 (mt-10) REVERT: A 210 GLU cc_start: 0.7618 (tt0) cc_final: 0.7098 (tt0) REVERT: A 213 TYR cc_start: 0.8043 (m-80) cc_final: 0.7710 (m-80) REVERT: A 214 GLU cc_start: 0.7819 (tt0) cc_final: 0.7011 (tp30) REVERT: A 322 ASP cc_start: 0.8159 (t0) cc_final: 0.7813 (t70) REVERT: A 412 ASN cc_start: 0.8298 (m110) cc_final: 0.7667 (t0) REVERT: A 639 LEU cc_start: 0.7401 (pt) cc_final: 0.7130 (pp) REVERT: A 716 ARG cc_start: 0.7933 (ttp-170) cc_final: 0.7270 (tpm170) REVERT: B 141 GLU cc_start: 0.7748 (tt0) cc_final: 0.7454 (mt-10) REVERT: B 210 GLU cc_start: 0.7636 (tt0) cc_final: 0.6987 (tt0) REVERT: B 214 GLU cc_start: 0.7802 (tt0) cc_final: 0.7022 (tp30) REVERT: B 322 ASP cc_start: 0.8155 (t0) cc_final: 0.7803 (t70) REVERT: B 412 ASN cc_start: 0.8281 (m110) cc_final: 0.7660 (t0) REVERT: B 716 ARG cc_start: 0.7920 (ttp-170) cc_final: 0.7271 (tpm170) REVERT: C 118 ARG cc_start: 0.6449 (ptt90) cc_final: 0.5382 (ptp-110) REVERT: C 138 LEU cc_start: 0.7781 (OUTLIER) cc_final: 0.7550 (mp) REVERT: C 141 GLU cc_start: 0.7809 (tt0) cc_final: 0.7408 (mt-10) REVERT: C 184 LYS cc_start: 0.7683 (mmmm) cc_final: 0.7263 (mmmt) REVERT: C 185 GLU cc_start: 0.8070 (mp0) cc_final: 0.7704 (mp0) REVERT: C 200 LEU cc_start: 0.7177 (tp) cc_final: 0.6942 (tp) REVERT: C 210 GLU cc_start: 0.7665 (tt0) cc_final: 0.7031 (tt0) REVERT: C 214 GLU cc_start: 0.7793 (tt0) cc_final: 0.7002 (tp30) REVERT: C 322 ASP cc_start: 0.8161 (t0) cc_final: 0.7812 (t70) REVERT: C 412 ASN cc_start: 0.8302 (m110) cc_final: 0.7665 (t0) REVERT: C 639 LEU cc_start: 0.7395 (pt) cc_final: 0.7139 (pp) REVERT: C 683 ASN cc_start: 0.7481 (m-40) cc_final: 0.7206 (m-40) REVERT: C 716 ARG cc_start: 0.7937 (ttp-170) cc_final: 0.7281 (tpm170) REVERT: D 118 ARG cc_start: 0.6603 (ptt90) cc_final: 0.5606 (ptp-110) REVERT: D 141 GLU cc_start: 0.7757 (tt0) cc_final: 0.7345 (mt-10) REVERT: D 184 LYS cc_start: 0.7635 (mmmm) cc_final: 0.7423 (mmmt) REVERT: D 210 GLU cc_start: 0.7681 (tt0) cc_final: 0.7045 (tt0) REVERT: D 214 GLU cc_start: 0.7803 (tt0) cc_final: 0.7020 (tp30) REVERT: D 322 ASP cc_start: 0.8162 (t0) cc_final: 0.7814 (t70) REVERT: D 412 ASN cc_start: 0.8270 (m110) cc_final: 0.7647 (t0) REVERT: D 639 LEU cc_start: 0.7417 (pt) cc_final: 0.7153 (pp) REVERT: D 716 ARG cc_start: 0.7932 (ttp-170) cc_final: 0.7263 (tpm170) outliers start: 34 outliers final: 33 residues processed: 327 average time/residue: 0.1353 time to fit residues: 68.5204 Evaluate side-chains 334 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 300 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 256 HIS Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 550 CYS Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 256 HIS Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 550 CYS Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain B residue 732 LEU Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 256 HIS Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 550 CYS Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain C residue 732 LEU Chi-restraints excluded: chain D residue 256 HIS Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain D residue 550 CYS Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 670 LEU Chi-restraints excluded: chain D residue 732 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 151 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 227 optimal weight: 4.9990 chunk 230 optimal weight: 3.9990 chunk 8 optimal weight: 7.9990 chunk 235 optimal weight: 2.9990 chunk 237 optimal weight: 5.9990 chunk 109 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 194 optimal weight: 0.9990 chunk 123 optimal weight: 0.9980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 570 GLN B 286 GLN B 570 GLN C 570 GLN D 570 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.161204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.113192 restraints weight = 24236.984| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.40 r_work: 0.3084 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3012 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3012 r_free = 0.3012 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3012 r_free = 0.3012 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (5 function evaluations) r_final: 0.3012 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.3958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 21684 Z= 0.145 Angle : 0.626 13.785 29044 Z= 0.305 Chirality : 0.040 0.251 3172 Planarity : 0.003 0.041 3508 Dihedral : 18.443 151.362 3784 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.38 % Favored : 92.45 % Rotamer: Outliers : 1.66 % Allowed : 11.92 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2424 helix: 0.76 (0.14), residues: 1596 sheet: 0.90 (0.50), residues: 112 loop : -2.47 (0.22), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 202 TYR 0.011 0.001 TYR C 565 PHE 0.024 0.001 PHE D 489 TRP 0.016 0.001 TRP B 493 HIS 0.006 0.001 HIS A 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (21684) covalent geometry : angle 0.62557 / 0.31 (29044) hydrogen bonds : bond 0.03033 / 1.97 ( 884) hydrogen bonds : angle 3.47546 / 2.38 ( 2580) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4872.42 seconds wall clock time: 84 minutes 5.68 seconds (5045.68 seconds total)