Starting phenix.real_space_refine on Sat Jul 4 12:22:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cuh_45933/07_2026/9cuh_45933.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cuh_45933/07_2026/9cuh_45933.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cuh_45933/07_2026/9cuh_45933.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cuh_45933/07_2026/9cuh_45933.map" model { file = "/net/cci-nas-00/data/ceres_data/9cuh_45933/07_2026/9cuh_45933.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cuh_45933/07_2026/9cuh_45933.cif" } resolution = 3.03 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.155 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 Ca 1 9.91 5 P 20 5.49 5 S 148 5.16 5 C 13776 2.51 5 N 3256 2.21 5 O 3676 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 68 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20877 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 4770 Classifications: {'peptide': 594} Link IDs: {'PTRANS': 26, 'TRANS': 567} Chain breaks: 1 Chain: "B" Number of atoms: 4770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 4770 Classifications: {'peptide': 594} Link IDs: {'PTRANS': 26, 'TRANS': 567} Chain breaks: 1 Chain: "C" Number of atoms: 4770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 4770 Classifications: {'peptide': 594} Link IDs: {'PTRANS': 26, 'TRANS': 567} Chain breaks: 1 Chain: "D" Number of atoms: 4770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 4770 Classifications: {'peptide': 594} Link IDs: {'PTRANS': 26, 'TRANS': 567} Chain breaks: 1 Chain: "A" Number of atoms: 432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 431 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'PCW': 1, 'POV': 8, 'Y01': 3} Classifications: {'undetermined': 12} Link IDs: {None: 11} Chain breaks: 1 Unresolved non-hydrogen bonds: 144 Unresolved non-hydrogen angles: 177 Unresolved non-hydrogen dihedrals: 128 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PCW:plan-1': 1, 'PCW:plan-3': 1, 'PCW:plan-4': 1, 'POV:plan-3': 2, 'POV:plan-1': 1, 'POV:plan-2': 1} Unresolved non-hydrogen planarities: 28 Chain: "B" Number of atoms: 431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 431 Unusual residues: {'PCW': 1, 'POV': 8, 'Y01': 3} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 144 Unresolved non-hydrogen angles: 177 Unresolved non-hydrogen dihedrals: 128 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PCW:plan-1': 1, 'PCW:plan-3': 1, 'PCW:plan-4': 1, 'POV:plan-3': 2, 'POV:plan-1': 1, 'POV:plan-2': 1} Unresolved non-hydrogen planarities: 28 Chain: "C" Number of atoms: 431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 431 Unusual residues: {'PCW': 1, 'POV': 8, 'Y01': 3} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 144 Unresolved non-hydrogen angles: 177 Unresolved non-hydrogen dihedrals: 128 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PCW:plan-1': 1, 'PCW:plan-3': 1, 'PCW:plan-4': 1, 'POV:plan-3': 2, 'POV:plan-1': 1, 'POV:plan-2': 1} Unresolved non-hydrogen planarities: 28 Chain: "D" Number of atoms: 431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 431 Unusual residues: {'PCW': 1, 'POV': 8, 'Y01': 3} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 144 Unresolved non-hydrogen angles: 177 Unresolved non-hydrogen dihedrals: 128 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PCW:plan-1': 1, 'PCW:plan-3': 1, 'PCW:plan-4': 1, 'POV:plan-3': 2, 'POV:plan-1': 1, 'POV:plan-2': 1} Unresolved non-hydrogen planarities: 28 Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "B" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "C" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "D" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Time building chain proxies: 5.18, per 1000 atoms: 0.25 Number of scatterers: 20877 At special positions: 0 Unit cell: (139.777, 139.777, 121.638, 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) Ca 1 19.99 S 148 16.00 P 20 15.00 O 3676 8.00 N 3256 7.00 C 13776 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: 1.72 Conformation dependent library (CDL) restraints added in 845.0 milliseconds 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4504 Finding SS restraints... Secondary structure from input PDB file: 128 helices and 8 sheets defined 64.9% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 28 through 47 removed outlier: 3.548A pdb=" N GLN A 36 " --> pdb=" O SER A 32 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLN A 41 " --> pdb=" O ASN A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 55 Processing helix chain 'A' and resid 57 through 66 removed outlier: 3.510A pdb=" N LEU A 61 " --> pdb=" O ASP A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 89 removed outlier: 3.617A pdb=" N ILE A 85 " --> pdb=" O THR A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 102 removed outlier: 3.820A pdb=" N VAL A 97 " --> pdb=" O GLU A 93 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU A 98 " --> pdb=" O ALA A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 106 removed outlier: 3.724A pdb=" N VAL A 106 " --> pdb=" O PRO A 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 103 through 106' Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.649A pdb=" N ILE A 123 " --> pdb=" O THR A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 139 removed outlier: 3.731A pdb=" N ARG A 134 " --> pdb=" O MET A 130 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA A 135 " --> pdb=" O ASN A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 173 Processing helix chain 'A' and resid 175 through 185 removed outlier: 3.733A pdb=" N GLU A 184 " --> pdb=" O ARG A 180 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N HIS A 185 " --> pdb=" O LEU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 removed outlier: 3.544A pdb=" N LEU A 203 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE A 204 " --> pdb=" O LEU A 200 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU A 205 " --> pdb=" O HIS A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 219 removed outlier: 3.540A pdb=" N ALA A 212 " --> pdb=" O ASN A 208 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N CYS A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLN A 214 " --> pdb=" O THR A 210 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN A 217 " --> pdb=" O CYS A 213 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU A 218 " --> pdb=" O GLN A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 235 removed outlier: 3.685A pdb=" N VAL A 235 " --> pdb=" O LEU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 250 removed outlier: 3.669A pdb=" N GLY A 248 " --> pdb=" O PHE A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 261 removed outlier: 3.619A pdb=" N GLN A 261 " --> pdb=" O GLN A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 298 removed outlier: 3.657A pdb=" N ILE A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR A 298 " --> pdb=" O GLU A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 310 removed outlier: 3.531A pdb=" N ARG A 305 " --> pdb=" O ARG A 302 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU A 308 " --> pdb=" O ARG A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 324 removed outlier: 3.653A pdb=" N SER A 318 " --> pdb=" O LYS A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 349 removed outlier: 3.676A pdb=" N LEU A 332 " --> pdb=" O TYR A 328 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA A 334 " --> pdb=" O CYS A 330 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU A 337 " --> pdb=" O GLY A 333 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N CYS A 346 " --> pdb=" O CYS A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 377 removed outlier: 4.364A pdb=" N TYR A 377 " --> pdb=" O LEU A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 403 removed outlier: 3.690A pdb=" N THR A 392 " --> pdb=" O GLY A 388 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA A 396 " --> pdb=" O THR A 392 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU A 400 " --> pdb=" O ALA A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 445 removed outlier: 3.612A pdb=" N ILE A 429 " --> pdb=" O PHE A 425 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU A 437 " --> pdb=" O ALA A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 463 removed outlier: 3.523A pdb=" N PHE A 456 " --> pdb=" O VAL A 452 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL A 459 " --> pdb=" O SER A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 470 removed outlier: 3.520A pdb=" N ALA A 469 " --> pdb=" O MET A 466 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG A 470 " --> pdb=" O TYR A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 487 Processing helix chain 'A' and resid 489 through 492 removed outlier: 3.573A pdb=" N ARG A 492 " --> pdb=" O ASP A 489 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 489 through 492' Processing helix chain 'A' and resid 493 through 512 removed outlier: 3.911A pdb=" N VAL A 499 " --> pdb=" O TRP A 495 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL A 500 " --> pdb=" O LEU A 496 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER A 506 " --> pdb=" O LEU A 502 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE A 512 " --> pdb=" O PHE A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 538 Processing helix chain 'A' and resid 552 through 566 removed outlier: 4.173A pdb=" N SER A 556 " --> pdb=" O PRO A 552 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ILE A 557 " --> pdb=" O PHE A 553 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE A 564 " --> pdb=" O ALA A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 588 removed outlier: 3.520A pdb=" N ASN A 572 " --> pdb=" O LEU A 568 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU A 574 " --> pdb=" O MET A 570 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP A 580 " --> pdb=" O ALA A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 608 removed outlier: 3.542A pdb=" N ALA A 595 " --> pdb=" O GLU A 591 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN A 596 " --> pdb=" O LEU A 592 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS A 607 " --> pdb=" O MET A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 613 Processing helix chain 'B' and resid 29 through 47 removed outlier: 3.548A pdb=" N GLN B 36 " --> pdb=" O SER B 32 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLN B 41 " --> pdb=" O ASN B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 55 Processing helix chain 'B' and resid 57 through 66 removed outlier: 3.511A pdb=" N LEU B 61 " --> pdb=" O ASP B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 89 removed outlier: 3.617A pdb=" N ILE B 85 " --> pdb=" O THR B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 102 removed outlier: 3.819A pdb=" N VAL B 97 " --> pdb=" O GLU B 93 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU B 98 " --> pdb=" O ALA B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 106 removed outlier: 3.724A pdb=" N VAL B 106 " --> pdb=" O PRO B 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 103 through 106' Processing helix chain 'B' and resid 119 through 127 removed outlier: 3.650A pdb=" N ILE B 123 " --> pdb=" O THR B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 139 removed outlier: 3.731A pdb=" N ARG B 134 " --> pdb=" O MET B 130 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA B 135 " --> pdb=" O ASN B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 173 Processing helix chain 'B' and resid 175 through 185 removed outlier: 3.733A pdb=" N GLU B 184 " --> pdb=" O ARG B 180 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N HIS B 185 " --> pdb=" O LEU B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 205 removed outlier: 3.544A pdb=" N LEU B 203 " --> pdb=" O VAL B 199 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE B 204 " --> pdb=" O LEU B 200 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU B 205 " --> pdb=" O HIS B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 219 removed outlier: 3.540A pdb=" N ALA B 212 " --> pdb=" O ASN B 208 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N CYS B 213 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLN B 214 " --> pdb=" O THR B 210 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASN B 217 " --> pdb=" O CYS B 213 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU B 218 " --> pdb=" O GLN B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 235 removed outlier: 3.685A pdb=" N VAL B 235 " --> pdb=" O LEU B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 250 removed outlier: 3.670A pdb=" N GLY B 248 " --> pdb=" O PHE B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 261 removed outlier: 3.618A pdb=" N GLN B 261 " --> pdb=" O GLN B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 298 removed outlier: 3.657A pdb=" N ILE B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR B 298 " --> pdb=" O GLU B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 310 removed outlier: 3.532A pdb=" N ARG B 305 " --> pdb=" O ARG B 302 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU B 308 " --> pdb=" O ARG B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 324 removed outlier: 3.654A pdb=" N SER B 318 " --> pdb=" O LYS B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 349 removed outlier: 3.676A pdb=" N LEU B 332 " --> pdb=" O TYR B 328 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA B 334 " --> pdb=" O CYS B 330 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU B 337 " --> pdb=" O GLY B 333 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N CYS B 346 " --> pdb=" O CYS B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 377 removed outlier: 4.364A pdb=" N TYR B 377 " --> pdb=" O LEU B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 403 removed outlier: 3.690A pdb=" N THR B 392 " --> pdb=" O GLY B 388 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA B 396 " --> pdb=" O THR B 392 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU B 400 " --> pdb=" O ALA B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 445 removed outlier: 3.612A pdb=" N ILE B 429 " --> pdb=" O PHE B 425 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU B 437 " --> pdb=" O ALA B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 463 removed outlier: 3.523A pdb=" N PHE B 456 " --> pdb=" O VAL B 452 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL B 459 " --> pdb=" O SER B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 470 removed outlier: 3.520A pdb=" N ALA B 469 " --> pdb=" O MET B 466 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG B 470 " --> pdb=" O TYR B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 487 Processing helix chain 'B' and resid 489 through 492 removed outlier: 3.572A pdb=" N ARG B 492 " --> pdb=" O ASP B 489 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 489 through 492' Processing helix chain 'B' and resid 493 through 512 removed outlier: 3.913A pdb=" N VAL B 499 " --> pdb=" O TRP B 495 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL B 500 " --> pdb=" O LEU B 496 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER B 506 " --> pdb=" O LEU B 502 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE B 512 " --> pdb=" O PHE B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 538 Processing helix chain 'B' and resid 552 through 566 removed outlier: 4.174A pdb=" N SER B 556 " --> pdb=" O PRO B 552 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ILE B 557 " --> pdb=" O PHE B 553 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE B 564 " --> pdb=" O ALA B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 588 removed outlier: 3.519A pdb=" N ASN B 572 " --> pdb=" O LEU B 568 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU B 574 " --> pdb=" O MET B 570 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP B 580 " --> pdb=" O ALA B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 608 removed outlier: 3.542A pdb=" N ALA B 595 " --> pdb=" O GLU B 591 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS B 607 " --> pdb=" O MET B 603 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 613 Processing helix chain 'C' and resid 29 through 47 removed outlier: 3.548A pdb=" N GLN C 36 " --> pdb=" O SER C 32 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLN C 41 " --> pdb=" O ASN C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 55 Processing helix chain 'C' and resid 57 through 66 removed outlier: 3.510A pdb=" N LEU C 61 " --> pdb=" O ASP C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 removed outlier: 3.618A pdb=" N ILE C 85 " --> pdb=" O THR C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 102 removed outlier: 3.819A pdb=" N VAL C 97 " --> pdb=" O GLU C 93 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU C 98 " --> pdb=" O ALA C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 106 removed outlier: 3.724A pdb=" N VAL C 106 " --> pdb=" O PRO C 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 103 through 106' Processing helix chain 'C' and resid 119 through 127 removed outlier: 3.650A pdb=" N ILE C 123 " --> pdb=" O THR C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 139 removed outlier: 3.732A pdb=" N ARG C 134 " --> pdb=" O MET C 130 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA C 135 " --> pdb=" O ASN C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 173 Processing helix chain 'C' and resid 175 through 185 removed outlier: 3.733A pdb=" N GLU C 184 " --> pdb=" O ARG C 180 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N HIS C 185 " --> pdb=" O LEU C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 205 removed outlier: 3.544A pdb=" N LEU C 203 " --> pdb=" O VAL C 199 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE C 204 " --> pdb=" O LEU C 200 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU C 205 " --> pdb=" O HIS C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 219 removed outlier: 3.541A pdb=" N ALA C 212 " --> pdb=" O ASN C 208 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N CYS C 213 " --> pdb=" O LYS C 209 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLN C 214 " --> pdb=" O THR C 210 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN C 217 " --> pdb=" O CYS C 213 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU C 218 " --> pdb=" O GLN C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 235 removed outlier: 3.684A pdb=" N VAL C 235 " --> pdb=" O LEU C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 250 removed outlier: 3.669A pdb=" N GLY C 248 " --> pdb=" O PHE C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 261 removed outlier: 3.618A pdb=" N GLN C 261 " --> pdb=" O GLN C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 298 removed outlier: 3.656A pdb=" N ILE C 297 " --> pdb=" O LEU C 293 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR C 298 " --> pdb=" O GLU C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 310 removed outlier: 3.532A pdb=" N ARG C 305 " --> pdb=" O ARG C 302 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU C 308 " --> pdb=" O ARG C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 324 removed outlier: 3.654A pdb=" N SER C 318 " --> pdb=" O LYS C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 349 removed outlier: 3.676A pdb=" N LEU C 332 " --> pdb=" O TYR C 328 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA C 334 " --> pdb=" O CYS C 330 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU C 337 " --> pdb=" O GLY C 333 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N CYS C 346 " --> pdb=" O CYS C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 377 removed outlier: 4.365A pdb=" N TYR C 377 " --> pdb=" O LEU C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 403 removed outlier: 3.690A pdb=" N THR C 392 " --> pdb=" O GLY C 388 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA C 396 " --> pdb=" O THR C 392 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU C 400 " --> pdb=" O ALA C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 445 removed outlier: 3.611A pdb=" N ILE C 429 " --> pdb=" O PHE C 425 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU C 437 " --> pdb=" O ALA C 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 463 removed outlier: 3.523A pdb=" N PHE C 456 " --> pdb=" O VAL C 452 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL C 459 " --> pdb=" O SER C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 464 through 470 removed outlier: 3.520A pdb=" N ALA C 469 " --> pdb=" O MET C 466 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG C 470 " --> pdb=" O TYR C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 487 Processing helix chain 'C' and resid 489 through 492 removed outlier: 3.573A pdb=" N ARG C 492 " --> pdb=" O ASP C 489 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 489 through 492' Processing helix chain 'C' and resid 493 through 512 removed outlier: 3.912A pdb=" N VAL C 499 " --> pdb=" O TRP C 495 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL C 500 " --> pdb=" O LEU C 496 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER C 506 " --> pdb=" O LEU C 502 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE C 512 " --> pdb=" O PHE C 508 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 538 Processing helix chain 'C' and resid 552 through 566 removed outlier: 4.174A pdb=" N SER C 556 " --> pdb=" O PRO C 552 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ILE C 557 " --> pdb=" O PHE C 553 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE C 564 " --> pdb=" O ALA C 560 " (cutoff:3.500A) Processing helix chain 'C' and resid 568 through 588 removed outlier: 3.519A pdb=" N ASN C 572 " --> pdb=" O LEU C 568 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU C 574 " --> pdb=" O MET C 570 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP C 580 " --> pdb=" O ALA C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 588 through 608 removed outlier: 3.543A pdb=" N ALA C 595 " --> pdb=" O GLU C 591 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN C 596 " --> pdb=" O LEU C 592 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS C 607 " --> pdb=" O MET C 603 " (cutoff:3.500A) Processing helix chain 'C' and resid 609 through 613 Processing helix chain 'D' and resid 29 through 47 removed outlier: 3.549A pdb=" N GLN D 36 " --> pdb=" O SER D 32 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLN D 41 " --> pdb=" O ASN D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 55 Processing helix chain 'D' and resid 57 through 66 removed outlier: 3.511A pdb=" N LEU D 61 " --> pdb=" O ASP D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 89 removed outlier: 3.617A pdb=" N ILE D 85 " --> pdb=" O THR D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 102 removed outlier: 3.819A pdb=" N VAL D 97 " --> pdb=" O GLU D 93 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU D 98 " --> pdb=" O ALA D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 106 removed outlier: 3.724A pdb=" N VAL D 106 " --> pdb=" O PRO D 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 103 through 106' Processing helix chain 'D' and resid 119 through 127 removed outlier: 3.650A pdb=" N ILE D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 139 removed outlier: 3.731A pdb=" N ARG D 134 " --> pdb=" O MET D 130 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA D 135 " --> pdb=" O ASN D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 173 Processing helix chain 'D' and resid 175 through 185 removed outlier: 3.733A pdb=" N GLU D 184 " --> pdb=" O ARG D 180 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N HIS D 185 " --> pdb=" O LEU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 removed outlier: 3.544A pdb=" N LEU D 203 " --> pdb=" O VAL D 199 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE D 204 " --> pdb=" O LEU D 200 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU D 205 " --> pdb=" O HIS D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 219 removed outlier: 3.540A pdb=" N ALA D 212 " --> pdb=" O ASN D 208 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N CYS D 213 " --> pdb=" O LYS D 209 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLN D 214 " --> pdb=" O THR D 210 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN D 217 " --> pdb=" O CYS D 213 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU D 218 " --> pdb=" O GLN D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 235 removed outlier: 3.684A pdb=" N VAL D 235 " --> pdb=" O LEU D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 250 removed outlier: 3.670A pdb=" N GLY D 248 " --> pdb=" O PHE D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 261 removed outlier: 3.618A pdb=" N GLN D 261 " --> pdb=" O GLN D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 298 removed outlier: 3.656A pdb=" N ILE D 297 " --> pdb=" O LEU D 293 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR D 298 " --> pdb=" O GLU D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 310 removed outlier: 3.531A pdb=" N ARG D 305 " --> pdb=" O ARG D 302 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU D 308 " --> pdb=" O ARG D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 324 removed outlier: 3.653A pdb=" N SER D 318 " --> pdb=" O LYS D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 349 removed outlier: 3.675A pdb=" N LEU D 332 " --> pdb=" O TYR D 328 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA D 334 " --> pdb=" O CYS D 330 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU D 337 " --> pdb=" O GLY D 333 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N CYS D 346 " --> pdb=" O CYS D 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 377 removed outlier: 4.365A pdb=" N TYR D 377 " --> pdb=" O LEU D 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 379 through 403 removed outlier: 3.690A pdb=" N THR D 392 " --> pdb=" O GLY D 388 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA D 396 " --> pdb=" O THR D 392 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU D 400 " --> pdb=" O ALA D 396 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 445 removed outlier: 3.612A pdb=" N ILE D 429 " --> pdb=" O PHE D 425 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU D 437 " --> pdb=" O ALA D 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 463 removed outlier: 3.522A pdb=" N PHE D 456 " --> pdb=" O VAL D 452 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL D 459 " --> pdb=" O SER D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 464 through 470 removed outlier: 3.520A pdb=" N ALA D 469 " --> pdb=" O MET D 466 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG D 470 " --> pdb=" O TYR D 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 477 through 487 Processing helix chain 'D' and resid 489 through 492 removed outlier: 3.573A pdb=" N ARG D 492 " --> pdb=" O ASP D 489 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 489 through 492' Processing helix chain 'D' and resid 493 through 512 removed outlier: 3.912A pdb=" N VAL D 499 " --> pdb=" O TRP D 495 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL D 500 " --> pdb=" O LEU D 496 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER D 506 " --> pdb=" O LEU D 502 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE D 512 " --> pdb=" O PHE D 508 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 538 Processing helix chain 'D' and resid 552 through 566 removed outlier: 4.173A pdb=" N SER D 556 " --> pdb=" O PRO D 552 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ILE D 557 " --> pdb=" O PHE D 553 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE D 564 " --> pdb=" O ALA D 560 " (cutoff:3.500A) Processing helix chain 'D' and resid 568 through 588 removed outlier: 3.520A pdb=" N ASN D 572 " --> pdb=" O LEU D 568 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU D 574 " --> pdb=" O MET D 570 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP D 580 " --> pdb=" O ALA D 576 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 608 removed outlier: 3.542A pdb=" N ALA D 595 " --> pdb=" O GLU D 591 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN D 596 " --> pdb=" O LEU D 592 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS D 607 " --> pdb=" O MET D 603 " (cutoff:3.500A) Processing helix chain 'D' and resid 609 through 613 Processing sheet with id=AA1, first strand: chain 'A' and resid 266 through 269 removed outlier: 6.835A pdb=" N SER A 275 " --> pdb=" O GLN A 267 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N THR A 269 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LEU A 273 " --> pdb=" O THR A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 352 through 354 Processing sheet with id=AA3, first strand: chain 'B' and resid 266 through 269 removed outlier: 6.835A pdb=" N SER B 275 " --> pdb=" O GLN B 267 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N THR B 269 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LEU B 273 " --> pdb=" O THR B 269 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 352 through 354 Processing sheet with id=AA5, first strand: chain 'C' and resid 266 through 269 removed outlier: 6.834A pdb=" N SER C 275 " --> pdb=" O GLN C 267 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N THR C 269 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N LEU C 273 " --> pdb=" O THR C 269 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 352 through 354 Processing sheet with id=AA7, first strand: chain 'D' and resid 266 through 269 removed outlier: 6.834A pdb=" N SER D 275 " --> pdb=" O GLN D 267 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N THR D 269 " --> pdb=" O LEU D 273 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LEU D 273 " --> pdb=" O THR D 269 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 352 through 354 873 hydrogen bonds defined for protein. 2499 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.34 Time building geometry restraints manager: 2.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3144 1.31 - 1.44: 5428 1.44 - 1.56: 12372 1.56 - 1.69: 44 1.69 - 1.82: 252 Bond restraints: 21240 Sorted by residual: bond pdb=" C29 POV A 807 " pdb="C210 POV A 807 " ideal model delta sigma weight residual 1.333 1.548 -0.215 2.00e-02 2.50e+03 1.15e+02 bond pdb=" C29 POV C 809 " pdb="C210 POV C 809 " ideal model delta sigma weight residual 1.333 1.545 -0.212 2.00e-02 2.50e+03 1.12e+02 bond pdb=" C29 POV B 809 " pdb="C210 POV B 809 " ideal model delta sigma weight residual 1.333 1.544 -0.211 2.00e-02 2.50e+03 1.12e+02 bond pdb=" C29 POV D 811 " pdb="C210 POV D 811 " ideal model delta sigma weight residual 1.333 1.544 -0.211 2.00e-02 2.50e+03 1.12e+02 bond pdb=" C29 POV A 804 " pdb="C210 POV A 804 " ideal model delta sigma weight residual 1.333 1.544 -0.211 2.00e-02 2.50e+03 1.12e+02 ... (remaining 21235 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.90: 27818 3.90 - 7.81: 595 7.81 - 11.71: 142 11.71 - 15.62: 29 15.62 - 19.52: 12 Bond angle restraints: 28596 Sorted by residual: angle pdb=" C29 POV D 808 " pdb="C210 POV D 808 " pdb="C211 POV D 808 " ideal model delta sigma weight residual 127.67 108.15 19.52 3.00e+00 1.11e-01 4.23e+01 angle pdb=" C29 POV C 806 " pdb="C210 POV C 806 " pdb="C211 POV C 806 " ideal model delta sigma weight residual 127.67 108.39 19.28 3.00e+00 1.11e-01 4.13e+01 angle pdb=" C29 POV B 806 " pdb="C210 POV B 806 " pdb="C211 POV B 806 " ideal model delta sigma weight residual 127.67 108.75 18.92 3.00e+00 1.11e-01 3.98e+01 angle pdb=" C29 POV A 804 " pdb="C210 POV A 804 " pdb="C211 POV A 804 " ideal model delta sigma weight residual 127.67 109.97 17.70 3.00e+00 1.11e-01 3.48e+01 angle pdb=" C28 POV D 811 " pdb=" C29 POV D 811 " pdb="C210 POV D 811 " ideal model delta sigma weight residual 127.79 110.22 17.57 3.00e+00 1.11e-01 3.43e+01 ... (remaining 28591 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.96: 12944 32.96 - 65.91: 563 65.91 - 98.87: 80 98.87 - 131.83: 5 131.83 - 164.78: 12 Dihedral angle restraints: 13604 sinusoidal: 6640 harmonic: 6964 Sorted by residual: dihedral pdb=" CA ASP B 69 " pdb=" C ASP B 69 " pdb=" N CYS B 70 " pdb=" CA CYS B 70 " ideal model delta harmonic sigma weight residual 180.00 153.36 26.64 0 5.00e+00 4.00e-02 2.84e+01 dihedral pdb=" CA ASP A 69 " pdb=" C ASP A 69 " pdb=" N CYS A 70 " pdb=" CA CYS A 70 " ideal model delta harmonic sigma weight residual 180.00 153.37 26.63 0 5.00e+00 4.00e-02 2.84e+01 dihedral pdb=" CA ASP D 69 " pdb=" C ASP D 69 " pdb=" N CYS D 70 " pdb=" CA CYS D 70 " ideal model delta harmonic sigma weight residual 180.00 153.38 26.62 0 5.00e+00 4.00e-02 2.83e+01 ... (remaining 13601 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 2447 0.065 - 0.129: 586 0.129 - 0.193: 83 0.193 - 0.258: 12 0.258 - 0.322: 4 Chirality restraints: 3132 Sorted by residual: chirality pdb=" CA THR A 311 " pdb=" N THR A 311 " pdb=" C THR A 311 " pdb=" CB THR A 311 " both_signs ideal model delta sigma weight residual False 2.53 2.20 0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" CA THR B 311 " pdb=" N THR B 311 " pdb=" C THR B 311 " pdb=" CB THR B 311 " both_signs ideal model delta sigma weight residual False 2.53 2.20 0.32 2.00e-01 2.50e+01 2.59e+00 chirality pdb=" CA THR D 311 " pdb=" N THR D 311 " pdb=" C THR D 311 " pdb=" CB THR D 311 " both_signs ideal model delta sigma weight residual False 2.53 2.20 0.32 2.00e-01 2.50e+01 2.58e+00 ... (remaining 3129 not shown) Planarity restraints: 3456 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C28 POV A 804 " -0.149 2.00e-02 2.50e+03 2.48e-01 6.16e+02 pdb=" C29 POV A 804 " 0.319 2.00e-02 2.50e+03 pdb="C210 POV A 804 " -0.317 2.00e-02 2.50e+03 pdb="C211 POV A 804 " 0.148 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV D 808 " -0.153 2.00e-02 2.50e+03 2.47e-01 6.11e+02 pdb=" C29 POV D 808 " 0.318 2.00e-02 2.50e+03 pdb="C210 POV D 808 " -0.313 2.00e-02 2.50e+03 pdb="C211 POV D 808 " 0.148 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV C 806 " 0.148 2.00e-02 2.50e+03 2.36e-01 5.59e+02 pdb=" C29 POV C 806 " -0.303 2.00e-02 2.50e+03 pdb="C210 POV C 806 " 0.298 2.00e-02 2.50e+03 pdb="C211 POV C 806 " -0.143 2.00e-02 2.50e+03 ... (remaining 3453 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 5856 2.82 - 3.34: 17419 3.34 - 3.86: 32341 3.86 - 4.38: 41394 4.38 - 4.90: 70722 Nonbonded interactions: 167732 Sorted by model distance: nonbonded pdb=" O ALA C 563 " pdb=" OG1 THR C 567 " model vdw 2.295 3.040 nonbonded pdb=" O ALA A 563 " pdb=" OG1 THR A 567 " model vdw 2.295 3.040 nonbonded pdb=" O ALA D 563 " pdb=" OG1 THR D 567 " model vdw 2.295 3.040 nonbonded pdb=" O ALA B 563 " pdb=" OG1 THR B 567 " model vdw 2.296 3.040 nonbonded pdb=" O ILE C 541 " pdb=" O HOH C 901 " model vdw 2.332 3.040 ... (remaining 167727 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 28 through 637 or (resid 809 and (name C2 or name C21 or n \ ame C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C28 \ or name C29 or name O21 or name O22 or name C210 or name C211 or name C212 or na \ me C213 or name C214 or name C215 or name C216)) or (resid 810 and (name C3 or n \ ame C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 \ or name C38 or name C39 or name O31 or name O32 or name C310 or name C311)) or ( \ resid 812 and (name C3 or name C31 or name C32 or name C33 or name C34 or name C \ 35 or name C36 or name C37 or name C38 or name C39 or name O31 or name O32 or na \ me C310 or name C311)))) selection = (chain 'B' and (resid 28 through 637 or resid 809 through 810 or (resid 812 and \ (name C3 or name C31 or name C32 or name C33 or name C34 or name C35 or name C36 \ or name C37 or name C38 or name C39 or name O31 or name O32 or name C310 or nam \ e C311)))) selection = (chain 'C' and (resid 28 through 637 or resid 809 through 810 or (resid 812 and \ (name C3 or name C31 or name C32 or name C33 or name C34 or name C35 or name C36 \ or name C37 or name C38 or name C39 or name O31 or name O32 or name C310 or nam \ e C311)))) selection = (chain 'D' and (resid 28 through 637 or (resid 809 and (name C2 or name C21 or n \ ame C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C28 \ or name C29 or name O21 or name O22 or name C210 or name C211 or name C212 or na \ me C213 or name C214 or name C215 or name C216)) or (resid 810 and (name C3 or n \ ame C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 \ or name C38 or name C39 or name O31 or name O32 or name C310 or name C311)) or r \ esid 812)) } 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: 1.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.030 Process input model: 19.050 Find NCS groups from input model: 0.530 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.215 21240 Z= 0.617 Angle : 1.534 19.521 28596 Z= 0.730 Chirality : 0.058 0.322 3132 Planarity : 0.012 0.248 3456 Dihedral : 17.811 164.782 9100 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.31 % Favored : 93.52 % Rotamer: Outliers : 1.16 % Allowed : 3.10 % Favored : 95.74 % 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: -5.89 (0.11), residues: 2360 helix: -4.49 (0.06), residues: 1344 sheet: -3.49 (0.37), residues: 124 loop : -2.61 (0.17), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 632 TYR 0.023 0.003 TYR A 270 PHE 0.029 0.004 PHE B 169 TRP 0.025 0.003 TRP C 583 HIS 0.013 0.003 HIS A 238 Details of bonding type rmsd/Z covalent geometry : bond 0.01386 / 0.62 (21240) covalent geometry : angle 1.53360 / 0.73 (28596) hydrogen bonds : bond 0.32968 / 21.75 ( 873) hydrogen bonds : angle 10.30914 / 7.24 ( 2499) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 418 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 LYS cc_start: 0.8721 (mptt) cc_final: 0.8380 (tttm) REVERT: A 262 LYS cc_start: 0.8685 (tmmt) cc_final: 0.8163 (ttmt) REVERT: A 440 MET cc_start: 0.8420 (ttp) cc_final: 0.8135 (ttp) REVERT: A 555 TYR cc_start: 0.8936 (t80) cc_final: 0.8614 (t80) REVERT: A 565 ILE cc_start: 0.8644 (tt) cc_final: 0.8242 (pt) REVERT: B 63 LYS cc_start: 0.8741 (mptt) cc_final: 0.8391 (tttm) REVERT: B 262 LYS cc_start: 0.8684 (tmmt) cc_final: 0.8148 (ttmt) REVERT: B 440 MET cc_start: 0.8420 (ttp) cc_final: 0.8125 (ttp) REVERT: B 448 SER cc_start: 0.9199 (m) cc_final: 0.8733 (p) REVERT: B 555 TYR cc_start: 0.8886 (t80) cc_final: 0.8584 (t80) REVERT: B 565 ILE cc_start: 0.8685 (tt) cc_final: 0.8295 (pt) REVERT: C 63 LYS cc_start: 0.8733 (mptt) cc_final: 0.8383 (tttm) REVERT: C 262 LYS cc_start: 0.8693 (tmmt) cc_final: 0.8164 (ttmt) REVERT: C 440 MET cc_start: 0.8410 (ttp) cc_final: 0.8133 (ttp) REVERT: C 448 SER cc_start: 0.9202 (m) cc_final: 0.8699 (p) REVERT: C 555 TYR cc_start: 0.8900 (t80) cc_final: 0.8594 (t80) REVERT: C 565 ILE cc_start: 0.8656 (tt) cc_final: 0.8267 (pt) REVERT: C 583 TRP cc_start: 0.7940 (t60) cc_final: 0.7667 (t60) REVERT: D 63 LYS cc_start: 0.8728 (mptt) cc_final: 0.8371 (tttm) REVERT: D 233 ASP cc_start: 0.7488 (p0) cc_final: 0.7146 (t0) REVERT: D 279 ASP cc_start: 0.7920 (t0) cc_final: 0.7714 (t0) REVERT: D 435 MET cc_start: 0.8626 (mmt) cc_final: 0.8420 (mmp) REVERT: D 440 MET cc_start: 0.8396 (ttp) cc_final: 0.8122 (ttp) REVERT: D 583 TRP cc_start: 0.7933 (t60) cc_final: 0.7641 (t60) outliers start: 24 outliers final: 11 residues processed: 438 average time/residue: 0.1846 time to fit residues: 118.0064 Evaluate side-chains 289 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 278 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 452 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 216 optimal weight: 0.9980 chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 0.8980 chunk 227 optimal weight: 0.4980 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 2.9990 chunk 235 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 37 ASN A 174 ASN A 267 GLN ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 ASN B 174 ASN ** B 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 ASN C 174 ASN ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 ASN D 62 ASN D 174 ASN D 238 HIS D 426 HIS ** D 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.154183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.115519 restraints weight = 22942.616| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 1.68 r_work: 0.3005 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2789 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2789 r_free = 0.2789 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2782 r_free = 0.2782 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (11 function evaluations) r_final: 0.2782 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 21240 Z= 0.135 Angle : 0.655 11.855 28596 Z= 0.325 Chirality : 0.040 0.167 3132 Planarity : 0.006 0.048 3456 Dihedral : 19.470 149.552 4526 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.66 % Allowed : 9.30 % 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: -3.58 (0.15), residues: 2360 helix: -2.23 (0.11), residues: 1384 sheet: -3.48 (0.34), residues: 124 loop : -2.11 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 43 TYR 0.020 0.001 TYR D 555 PHE 0.012 0.001 PHE C 531 TRP 0.010 0.001 TRP D 462 HIS 0.006 0.001 HIS D 265 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (21240) covalent geometry : angle 0.65522 / 0.33 (28596) hydrogen bonds : bond 0.05693 / 3.83 ( 873) hydrogen bonds : angle 4.74488 / 3.33 ( 2499) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 341 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 435 MET cc_start: 0.8982 (mmt) cc_final: 0.8612 (mmp) REVERT: A 440 MET cc_start: 0.9023 (ttp) cc_final: 0.8799 (ttp) REVERT: A 448 SER cc_start: 0.9144 (m) cc_final: 0.8694 (p) REVERT: B 435 MET cc_start: 0.9005 (mmt) cc_final: 0.8624 (mmp) REVERT: B 440 MET cc_start: 0.9034 (ttp) cc_final: 0.8816 (ttp) REVERT: B 448 SER cc_start: 0.9162 (m) cc_final: 0.8718 (p) REVERT: C 116 GLU cc_start: 0.7515 (tp30) cc_final: 0.7218 (tp30) REVERT: C 435 MET cc_start: 0.8974 (mmt) cc_final: 0.8576 (mmp) REVERT: C 440 MET cc_start: 0.9047 (ttp) cc_final: 0.8841 (ttp) REVERT: C 448 SER cc_start: 0.9149 (m) cc_final: 0.8681 (p) REVERT: C 583 TRP cc_start: 0.8616 (t60) cc_final: 0.8398 (t60) REVERT: D 233 ASP cc_start: 0.7925 (p0) cc_final: 0.7559 (t0) REVERT: D 255 MET cc_start: 0.8984 (mmm) cc_final: 0.8769 (mmm) REVERT: D 434 PHE cc_start: 0.7592 (m-80) cc_final: 0.7247 (t80) REVERT: D 435 MET cc_start: 0.9016 (mmt) cc_final: 0.8798 (mmt) REVERT: D 452 VAL cc_start: 0.8984 (OUTLIER) cc_final: 0.8765 (t) REVERT: D 583 TRP cc_start: 0.8592 (t60) cc_final: 0.8349 (t60) outliers start: 55 outliers final: 19 residues processed: 362 average time/residue: 0.1436 time to fit residues: 82.2106 Evaluate side-chains 290 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 270 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 357 ASN Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 357 ASN Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 539 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 70 optimal weight: 9.9990 chunk 234 optimal weight: 3.9990 chunk 87 optimal weight: 0.8980 chunk 218 optimal weight: 0.8980 chunk 34 optimal weight: 0.5980 chunk 100 optimal weight: 0.5980 chunk 178 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 116 optimal weight: 10.0000 chunk 235 optimal weight: 4.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 257 GLN ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 257 GLN ** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 257 GLN ** C 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 257 GLN ** D 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.151074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.111592 restraints weight = 23051.045| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 1.80 r_work: 0.2953 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2952 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2952 r_free = 0.2952 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2951 r_free = 0.2951 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (10 function evaluations) r_final: 0.2951 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 21240 Z= 0.138 Angle : 0.590 8.383 28596 Z= 0.295 Chirality : 0.040 0.186 3132 Planarity : 0.005 0.047 3456 Dihedral : 17.831 144.415 4515 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 1.50 % Allowed : 10.47 % 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: -1.92 (0.16), residues: 2360 helix: -0.72 (0.13), residues: 1392 sheet: -3.24 (0.47), residues: 84 loop : -1.81 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 153 TYR 0.015 0.001 TYR B 555 PHE 0.013 0.001 PHE C 537 TRP 0.008 0.001 TRP A 462 HIS 0.005 0.001 HIS D 265 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (21240) covalent geometry : angle 0.59015 / 0.30 (28596) hydrogen bonds : bond 0.04968 / 3.36 ( 873) hydrogen bonds : angle 4.15068 / 2.91 ( 2499) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 285 time to evaluate : 0.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 GLU cc_start: 0.7430 (tp30) cc_final: 0.7176 (tp30) REVERT: B 116 GLU cc_start: 0.7467 (tp30) cc_final: 0.7168 (tp30) REVERT: B 435 MET cc_start: 0.8865 (mmt) cc_final: 0.8619 (mmp) REVERT: C 116 GLU cc_start: 0.7449 (tp30) cc_final: 0.7151 (tp30) REVERT: D 40 GLN cc_start: 0.8405 (tt0) cc_final: 0.8026 (tt0) REVERT: D 116 GLU cc_start: 0.7440 (tp30) cc_final: 0.7217 (tp30) REVERT: D 434 PHE cc_start: 0.7498 (m-80) cc_final: 0.7070 (t80) REVERT: D 435 MET cc_start: 0.8843 (mmt) cc_final: 0.8592 (mmt) REVERT: D 452 VAL cc_start: 0.8974 (OUTLIER) cc_final: 0.8757 (t) outliers start: 31 outliers final: 19 residues processed: 309 average time/residue: 0.1426 time to fit residues: 69.8365 Evaluate side-chains 283 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 263 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 554 MET Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 357 ASN Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 357 ASN Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 458 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 170 optimal weight: 0.9990 chunk 140 optimal weight: 6.9990 chunk 234 optimal weight: 20.0000 chunk 206 optimal weight: 0.7980 chunk 59 optimal weight: 5.9990 chunk 152 optimal weight: 0.9990 chunk 233 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 176 optimal weight: 5.9990 chunk 14 optimal weight: 0.6980 chunk 232 optimal weight: 0.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 257 GLN A 290 GLN ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 257 GLN B 290 GLN ** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 257 GLN C 290 GLN ** C 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 257 GLN ** D 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.152084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.112616 restraints weight = 22943.989| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 1.78 r_work: 0.2904 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2881 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2881 r_free = 0.2881 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2881 r_free = 0.2881 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2881 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 21240 Z= 0.113 Angle : 0.541 6.858 28596 Z= 0.269 Chirality : 0.039 0.170 3132 Planarity : 0.004 0.038 3456 Dihedral : 16.436 143.561 4515 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.31 % Allowed : 10.13 % Favored : 88.57 % 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: -1.05 (0.17), residues: 2360 helix: 0.12 (0.14), residues: 1384 sheet: -3.13 (0.47), residues: 84 loop : -1.67 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 153 TYR 0.016 0.001 TYR D 555 PHE 0.010 0.001 PHE A 537 TRP 0.007 0.001 TRP B 462 HIS 0.004 0.001 HIS D 265 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 (21240) covalent geometry : angle 0.54110 / 0.27 (28596) hydrogen bonds : bond 0.04116 / 2.79 ( 873) hydrogen bonds : angle 3.87785 / 2.73 ( 2499) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 302 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 GLU cc_start: 0.7446 (tp30) cc_final: 0.7134 (tp30) REVERT: A 229 LEU cc_start: 0.6241 (OUTLIER) cc_final: 0.6023 (mt) REVERT: A 605 GLU cc_start: 0.7884 (tt0) cc_final: 0.7656 (tt0) REVERT: B 116 GLU cc_start: 0.7455 (tp30) cc_final: 0.7142 (tp30) REVERT: B 229 LEU cc_start: 0.6239 (OUTLIER) cc_final: 0.6032 (mt) REVERT: B 435 MET cc_start: 0.8866 (mmt) cc_final: 0.8411 (mmp) REVERT: C 116 GLU cc_start: 0.7443 (tp30) cc_final: 0.7133 (tp30) REVERT: C 229 LEU cc_start: 0.6218 (OUTLIER) cc_final: 0.6005 (mt) REVERT: C 435 MET cc_start: 0.8814 (mmt) cc_final: 0.8497 (mmp) REVERT: D 116 GLU cc_start: 0.7405 (tp30) cc_final: 0.7154 (tp30) REVERT: D 229 LEU cc_start: 0.6195 (OUTLIER) cc_final: 0.5923 (mt) REVERT: D 434 PHE cc_start: 0.7510 (m-80) cc_final: 0.7061 (t80) REVERT: D 435 MET cc_start: 0.8852 (mmt) cc_final: 0.8617 (mmt) REVERT: D 452 VAL cc_start: 0.8941 (OUTLIER) cc_final: 0.8697 (t) REVERT: D 605 GLU cc_start: 0.7923 (tt0) cc_final: 0.7666 (tt0) REVERT: D 612 LEU cc_start: 0.8241 (pp) cc_final: 0.7551 (tp) outliers start: 27 outliers final: 18 residues processed: 323 average time/residue: 0.1401 time to fit residues: 70.7928 Evaluate side-chains 300 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 277 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 554 MET Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 357 ASN Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 357 ASN Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 346 CYS Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 458 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 178 optimal weight: 1.9990 chunk 100 optimal weight: 0.5980 chunk 127 optimal weight: 0.6980 chunk 134 optimal weight: 8.9990 chunk 138 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 187 optimal weight: 0.4980 chunk 227 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 2 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 257 GLN ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 572 ASN B 257 GLN ** B 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 572 ASN C 257 GLN ** C 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 257 GLN D 290 GLN ** D 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.158153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.120139 restraints weight = 22538.059| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 1.60 r_work: 0.3030 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2798 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2798 r_free = 0.2798 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2798 r_free = 0.2798 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2798 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 21240 Z= 0.116 Angle : 0.537 6.802 28596 Z= 0.266 Chirality : 0.040 0.178 3132 Planarity : 0.004 0.036 3456 Dihedral : 15.652 135.739 4515 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.79 % Allowed : 11.14 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.65 (0.17), residues: 2360 helix: 0.46 (0.14), residues: 1384 sheet: -2.93 (0.48), residues: 84 loop : -1.54 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 153 TYR 0.019 0.001 TYR B 555 PHE 0.011 0.001 PHE C 537 TRP 0.006 0.001 TRP C 462 HIS 0.004 0.001 HIS D 265 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (21240) covalent geometry : angle 0.53734 / 0.27 (28596) hydrogen bonds : bond 0.04052 / 2.75 ( 873) hydrogen bonds : angle 3.80172 / 2.66 ( 2499) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 297 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 GLU cc_start: 0.7582 (tp30) cc_final: 0.7279 (tp30) REVERT: A 628 ARG cc_start: 0.7635 (mtp85) cc_final: 0.7402 (mtm180) REVERT: B 116 GLU cc_start: 0.7584 (tp30) cc_final: 0.7258 (tp30) REVERT: B 605 GLU cc_start: 0.7959 (tt0) cc_final: 0.7720 (tt0) REVERT: B 628 ARG cc_start: 0.7619 (mtp85) cc_final: 0.7372 (mtm180) REVERT: C 116 GLU cc_start: 0.7573 (tp30) cc_final: 0.7245 (tp30) REVERT: C 450 GLU cc_start: 0.8585 (mt-10) cc_final: 0.8278 (mt-10) REVERT: C 628 ARG cc_start: 0.7627 (mtp85) cc_final: 0.7390 (mtm180) REVERT: D 116 GLU cc_start: 0.7538 (tp30) cc_final: 0.7270 (tp30) REVERT: D 229 LEU cc_start: 0.6336 (OUTLIER) cc_final: 0.6109 (mt) REVERT: D 434 PHE cc_start: 0.7672 (m-80) cc_final: 0.7172 (t80) REVERT: D 435 MET cc_start: 0.8926 (mmt) cc_final: 0.8525 (mmp) REVERT: D 442 MET cc_start: 0.8922 (mtp) cc_final: 0.8396 (mtp) REVERT: D 452 VAL cc_start: 0.8980 (OUTLIER) cc_final: 0.8747 (t) REVERT: D 605 GLU cc_start: 0.8065 (tt0) cc_final: 0.7789 (tt0) REVERT: D 612 LEU cc_start: 0.8270 (pp) cc_final: 0.7542 (tp) REVERT: D 628 ARG cc_start: 0.7622 (mtp85) cc_final: 0.7370 (mtm180) outliers start: 37 outliers final: 23 residues processed: 326 average time/residue: 0.1323 time to fit residues: 68.1787 Evaluate side-chains 308 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 283 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 554 MET Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 346 CYS Chi-restraints excluded: chain B residue 357 ASN Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 346 CYS Chi-restraints excluded: chain C residue 357 ASN Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 346 CYS Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 458 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 31 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 chunk 206 optimal weight: 4.9990 chunk 89 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 22 optimal weight: 6.9990 chunk 131 optimal weight: 2.9990 chunk 212 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 193 optimal weight: 0.1980 chunk 57 optimal weight: 10.0000 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 74 GLN A 257 GLN A 290 GLN ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 257 GLN B 261 GLN B 290 GLN ** B 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 GLN C 257 GLN C 261 GLN C 290 GLN ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 572 ASN D 261 GLN D 290 GLN ** D 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 572 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.152183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.112506 restraints weight = 22711.612| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 1.67 r_work: 0.2934 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2720 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2720 r_free = 0.2720 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2720 r_free = 0.2720 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2720 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 21240 Z= 0.152 Angle : 0.573 7.611 28596 Z= 0.281 Chirality : 0.041 0.181 3132 Planarity : 0.004 0.036 3456 Dihedral : 15.434 135.991 4515 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 1.50 % Allowed : 11.97 % Favored : 86.53 % 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: -0.49 (0.17), residues: 2360 helix: 0.59 (0.14), residues: 1384 sheet: -2.77 (0.49), residues: 84 loop : -1.49 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 153 TYR 0.016 0.001 TYR D 555 PHE 0.013 0.001 PHE A 537 TRP 0.006 0.001 TRP A 495 HIS 0.003 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.15 (21240) covalent geometry : angle 0.57300 / 0.28 (28596) hydrogen bonds : bond 0.04432 / 3.00 ( 873) hydrogen bonds : angle 3.85456 / 2.70 ( 2499) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 290 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 GLU cc_start: 0.7497 (tp30) cc_final: 0.7240 (tp30) REVERT: A 605 GLU cc_start: 0.8070 (tt0) cc_final: 0.7808 (tt0) REVERT: A 628 ARG cc_start: 0.7562 (mtp85) cc_final: 0.7190 (mtm180) REVERT: B 116 GLU cc_start: 0.7516 (tp30) cc_final: 0.7245 (tp30) REVERT: B 218 LEU cc_start: 0.8605 (tt) cc_final: 0.8400 (tp) REVERT: B 435 MET cc_start: 0.8791 (mmt) cc_final: 0.8550 (mmp) REVERT: B 605 GLU cc_start: 0.8057 (tt0) cc_final: 0.7792 (tt0) REVERT: B 628 ARG cc_start: 0.7543 (mtp85) cc_final: 0.7245 (mtm180) REVERT: C 116 GLU cc_start: 0.7504 (tp30) cc_final: 0.7235 (tp30) REVERT: C 218 LEU cc_start: 0.8611 (tt) cc_final: 0.8408 (tp) REVERT: C 450 GLU cc_start: 0.8606 (mt-10) cc_final: 0.8256 (mt-10) REVERT: C 628 ARG cc_start: 0.7562 (mtp85) cc_final: 0.7190 (mtm180) REVERT: D 116 GLU cc_start: 0.7459 (tp30) cc_final: 0.7253 (tp30) REVERT: D 434 PHE cc_start: 0.7608 (m-80) cc_final: 0.6979 (t80) REVERT: D 435 MET cc_start: 0.8820 (mmt) cc_final: 0.8613 (mmt) REVERT: D 605 GLU cc_start: 0.8101 (tt0) cc_final: 0.7783 (tt0) REVERT: D 628 ARG cc_start: 0.7551 (mtp85) cc_final: 0.7261 (mtm180) outliers start: 31 outliers final: 24 residues processed: 311 average time/residue: 0.1390 time to fit residues: 68.0952 Evaluate side-chains 302 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 278 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 554 MET Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 346 CYS Chi-restraints excluded: chain B residue 357 ASN Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 346 CYS Chi-restraints excluded: chain C residue 357 ASN Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 346 CYS Chi-restraints excluded: chain D residue 357 ASN Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 458 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 151 optimal weight: 7.9990 chunk 28 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 154 optimal weight: 1.9990 chunk 56 optimal weight: 7.9990 chunk 235 optimal weight: 4.9990 chunk 169 optimal weight: 3.9990 chunk 234 optimal weight: 8.9990 chunk 76 optimal weight: 9.9990 chunk 55 optimal weight: 0.8980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 257 GLN ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 74 GLN B 257 GLN B 261 GLN ** B 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 257 GLN C 261 GLN ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 GLN D 261 GLN ** D 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.150931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.111924 restraints weight = 22790.660| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 1.67 r_work: 0.2975 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2822 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2722 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2722 r_free = 0.2722 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2722 r_free = 0.2722 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2722 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 21240 Z= 0.164 Angle : 0.579 8.763 28596 Z= 0.284 Chirality : 0.041 0.184 3132 Planarity : 0.004 0.043 3456 Dihedral : 15.178 139.238 4514 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.74 % Allowed : 12.45 % Favored : 85.80 % 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: -0.37 (0.17), residues: 2360 helix: 0.68 (0.14), residues: 1384 sheet: -2.63 (0.50), residues: 84 loop : -1.43 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 153 TYR 0.016 0.001 TYR B 555 PHE 0.013 0.001 PHE D 537 TRP 0.007 0.001 TRP B 45 HIS 0.004 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.16 (21240) covalent geometry : angle 0.57941 / 0.28 (28596) hydrogen bonds : bond 0.04528 / 3.06 ( 873) hydrogen bonds : angle 3.89532 / 2.73 ( 2499) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 291 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 GLU cc_start: 0.7661 (tp30) cc_final: 0.7405 (tp30) REVERT: A 280 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8072 (mp) REVERT: A 442 MET cc_start: 0.8883 (mtm) cc_final: 0.8525 (mtp) REVERT: A 605 GLU cc_start: 0.8126 (tt0) cc_final: 0.7872 (tt0) REVERT: A 628 ARG cc_start: 0.7796 (mtp85) cc_final: 0.7456 (mtm180) REVERT: B 116 GLU cc_start: 0.7675 (tp30) cc_final: 0.7411 (tp30) REVERT: B 218 LEU cc_start: 0.8764 (tt) cc_final: 0.8553 (tp) REVERT: B 280 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8073 (mp) REVERT: B 442 MET cc_start: 0.8848 (mtm) cc_final: 0.8527 (mtp) REVERT: B 605 GLU cc_start: 0.8117 (tt0) cc_final: 0.7868 (tt0) REVERT: B 628 ARG cc_start: 0.7769 (mtp85) cc_final: 0.7439 (mtm180) REVERT: C 116 GLU cc_start: 0.7667 (tp30) cc_final: 0.7399 (tp30) REVERT: C 218 LEU cc_start: 0.8773 (tt) cc_final: 0.8559 (tp) REVERT: C 280 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8062 (mp) REVERT: C 450 GLU cc_start: 0.8648 (mt-10) cc_final: 0.8381 (mt-10) REVERT: C 605 GLU cc_start: 0.8105 (tt0) cc_final: 0.7857 (tt0) REVERT: C 628 ARG cc_start: 0.7773 (mtp85) cc_final: 0.7450 (mtm180) REVERT: D 116 GLU cc_start: 0.7661 (tp30) cc_final: 0.7388 (tp30) REVERT: D 280 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8113 (mp) REVERT: D 300 LYS cc_start: 0.8215 (mmtm) cc_final: 0.7762 (mtmt) REVERT: D 450 GLU cc_start: 0.8696 (mt-10) cc_final: 0.8442 (mt-10) REVERT: D 605 GLU cc_start: 0.8151 (tt0) cc_final: 0.7893 (tt0) REVERT: D 628 ARG cc_start: 0.7790 (mtp85) cc_final: 0.7454 (mtm180) outliers start: 36 outliers final: 25 residues processed: 318 average time/residue: 0.1406 time to fit residues: 69.9246 Evaluate side-chains 319 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 290 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 554 MET Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 346 CYS Chi-restraints excluded: chain B residue 357 ASN Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 346 CYS Chi-restraints excluded: chain C residue 357 ASN Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 346 CYS Chi-restraints excluded: chain D residue 357 ASN Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 591 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 96 optimal weight: 0.9980 chunk 57 optimal weight: 10.0000 chunk 192 optimal weight: 5.9990 chunk 165 optimal weight: 3.9990 chunk 144 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 135 optimal weight: 10.0000 chunk 123 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 132 optimal weight: 0.9990 chunk 42 optimal weight: 0.5980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 257 GLN ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 257 GLN ** B 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 257 GLN ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 261 GLN ** D 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.153224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.114364 restraints weight = 22769.311| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 1.64 r_work: 0.2966 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2746 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2746 r_free = 0.2746 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2746 r_free = 0.2746 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (31 function evaluations) r_final: 0.2746 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.3322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 21240 Z= 0.111 Angle : 0.527 7.497 28596 Z= 0.260 Chirality : 0.039 0.171 3132 Planarity : 0.004 0.039 3456 Dihedral : 14.542 142.466 4514 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.45 % Allowed : 13.03 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.08 (0.17), residues: 2360 helix: 0.89 (0.14), residues: 1384 sheet: -2.59 (0.51), residues: 84 loop : -1.26 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 153 TYR 0.016 0.001 TYR D 555 PHE 0.009 0.001 PHE A 537 TRP 0.006 0.001 TRP A 462 HIS 0.003 0.001 HIS B 265 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.11 (21240) covalent geometry : angle 0.52699 / 0.26 (28596) hydrogen bonds : bond 0.03959 / 2.69 ( 873) hydrogen bonds : angle 3.76232 / 2.63 ( 2499) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 308 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 GLU cc_start: 0.7542 (tp30) cc_final: 0.7196 (tp30) REVERT: A 280 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.7976 (mp) REVERT: A 450 GLU cc_start: 0.8572 (mt-10) cc_final: 0.8273 (mt-10) REVERT: A 605 GLU cc_start: 0.8074 (tt0) cc_final: 0.7783 (tt0) REVERT: A 628 ARG cc_start: 0.7599 (mtp85) cc_final: 0.7312 (mtm180) REVERT: B 78 MET cc_start: 0.7820 (mmp) cc_final: 0.7613 (mmp) REVERT: B 116 GLU cc_start: 0.7533 (tp30) cc_final: 0.7280 (tp30) REVERT: B 280 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.7981 (mp) REVERT: B 426 HIS cc_start: 0.8073 (m170) cc_final: 0.7693 (m90) REVERT: B 450 GLU cc_start: 0.8603 (mt-10) cc_final: 0.8302 (mt-10) REVERT: B 605 GLU cc_start: 0.8040 (tt0) cc_final: 0.7748 (tt0) REVERT: B 621 ARG cc_start: 0.7415 (ttm-80) cc_final: 0.6791 (mtm-85) REVERT: B 628 ARG cc_start: 0.7624 (mtp85) cc_final: 0.7268 (mtm180) REVERT: C 116 GLU cc_start: 0.7526 (tp30) cc_final: 0.7268 (tp30) REVERT: C 280 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.7977 (mp) REVERT: C 435 MET cc_start: 0.8724 (mmt) cc_final: 0.8349 (mmp) REVERT: C 450 GLU cc_start: 0.8598 (mt-10) cc_final: 0.8324 (mt-10) REVERT: C 605 GLU cc_start: 0.8036 (tt0) cc_final: 0.7744 (tt0) REVERT: C 621 ARG cc_start: 0.7430 (ttm-80) cc_final: 0.6798 (mtm-85) REVERT: C 628 ARG cc_start: 0.7624 (mtp85) cc_final: 0.7252 (mtm180) REVERT: D 116 GLU cc_start: 0.7515 (tp30) cc_final: 0.7236 (tp30) REVERT: D 300 LYS cc_start: 0.8197 (mmtm) cc_final: 0.7696 (mtmt) REVERT: D 435 MET cc_start: 0.8837 (mmt) cc_final: 0.8612 (mmp) REVERT: D 450 GLU cc_start: 0.8587 (mt-10) cc_final: 0.8323 (mt-10) REVERT: D 605 GLU cc_start: 0.8088 (tt0) cc_final: 0.7798 (tt0) REVERT: D 612 LEU cc_start: 0.8182 (pp) cc_final: 0.7509 (tp) REVERT: D 621 ARG cc_start: 0.7419 (ttm-80) cc_final: 0.6811 (ttm-80) REVERT: D 628 ARG cc_start: 0.7628 (mtp85) cc_final: 0.7264 (mtm180) outliers start: 30 outliers final: 25 residues processed: 329 average time/residue: 0.1345 time to fit residues: 69.4750 Evaluate side-chains 317 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 289 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 554 MET Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 346 CYS Chi-restraints excluded: chain B residue 357 ASN Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 346 CYS Chi-restraints excluded: chain C residue 357 ASN Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 346 CYS Chi-restraints excluded: chain D residue 357 ASN Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 591 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 113 optimal weight: 2.9990 chunk 219 optimal weight: 0.7980 chunk 187 optimal weight: 0.3980 chunk 115 optimal weight: 4.9990 chunk 205 optimal weight: 0.9990 chunk 208 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 226 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 62 optimal weight: 10.0000 chunk 5 optimal weight: 1.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 257 GLN ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 257 GLN B 261 GLN ** B 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 257 GLN ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 257 GLN D 261 GLN ** D 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.154208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.115041 restraints weight = 22723.250| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 1.66 r_work: 0.3029 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2845 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2845 r_free = 0.2845 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2845 r_free = 0.2845 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2845 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.3420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21240 Z= 0.108 Angle : 0.547 13.140 28596 Z= 0.265 Chirality : 0.040 0.168 3132 Planarity : 0.004 0.037 3456 Dihedral : 14.023 142.949 4514 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.50 % Allowed : 12.98 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.07 (0.18), residues: 2360 helix: 0.97 (0.14), residues: 1384 sheet: -2.53 (0.52), residues: 84 loop : -1.12 (0.21), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 153 TYR 0.013 0.001 TYR C 555 PHE 0.009 0.001 PHE A 537 TRP 0.006 0.001 TRP A 462 HIS 0.003 0.001 HIS D 265 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (21240) covalent geometry : angle 0.54676 / 0.26 (28596) hydrogen bonds : bond 0.03882 / 2.63 ( 873) hydrogen bonds : angle 3.77203 / 2.64 ( 2499) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 290 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 GLU cc_start: 0.7648 (tp30) cc_final: 0.7286 (tp30) REVERT: A 450 GLU cc_start: 0.8563 (mt-10) cc_final: 0.8272 (mt-10) REVERT: A 605 GLU cc_start: 0.8072 (tt0) cc_final: 0.7814 (tt0) REVERT: A 628 ARG cc_start: 0.7696 (mtp85) cc_final: 0.7401 (mtm180) REVERT: B 116 GLU cc_start: 0.7646 (tp30) cc_final: 0.7393 (tp30) REVERT: B 450 GLU cc_start: 0.8612 (mt-10) cc_final: 0.8318 (mt-10) REVERT: B 605 GLU cc_start: 0.8055 (tt0) cc_final: 0.7796 (tt0) REVERT: B 628 ARG cc_start: 0.7689 (mtp85) cc_final: 0.7397 (mtm180) REVERT: C 116 GLU cc_start: 0.7645 (tp30) cc_final: 0.7396 (tp30) REVERT: C 435 MET cc_start: 0.8776 (mmt) cc_final: 0.8418 (mmp) REVERT: C 450 GLU cc_start: 0.8611 (mt-10) cc_final: 0.8364 (mt-10) REVERT: C 605 GLU cc_start: 0.8065 (tt0) cc_final: 0.7813 (tt0) REVERT: C 612 LEU cc_start: 0.8239 (pp) cc_final: 0.7450 (tt) REVERT: D 300 LYS cc_start: 0.8161 (mmtm) cc_final: 0.7767 (mtmt) REVERT: D 426 HIS cc_start: 0.8073 (m170) cc_final: 0.7670 (m-70) REVERT: D 450 GLU cc_start: 0.8623 (mt-10) cc_final: 0.8382 (mt-10) REVERT: D 591 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.8067 (tm-30) REVERT: D 605 GLU cc_start: 0.8085 (tt0) cc_final: 0.7818 (tt0) REVERT: D 612 LEU cc_start: 0.8239 (pp) cc_final: 0.7556 (tp) outliers start: 31 outliers final: 23 residues processed: 312 average time/residue: 0.1325 time to fit residues: 65.9958 Evaluate side-chains 303 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 279 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 554 MET Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 346 CYS Chi-restraints excluded: chain B residue 357 ASN Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 346 CYS Chi-restraints excluded: chain C residue 357 ASN Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 346 CYS Chi-restraints excluded: chain D residue 357 ASN Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 591 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 4 optimal weight: 0.7980 chunk 68 optimal weight: 0.9990 chunk 91 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 81 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 189 optimal weight: 0.8980 chunk 8 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 82 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 257 GLN A 261 GLN ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 257 GLN B 261 GLN ** B 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 257 GLN ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 261 GLN ** D 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.154005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.114823 restraints weight = 22974.509| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 1.68 r_work: 0.2971 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2748 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2748 r_free = 0.2748 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2748 r_free = 0.2748 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (11 function evaluations) r_final: 0.2748 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.3465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21240 Z= 0.115 Angle : 0.552 15.879 28596 Z= 0.267 Chirality : 0.040 0.169 3132 Planarity : 0.004 0.037 3456 Dihedral : 13.685 143.342 4514 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.26 % Allowed : 13.42 % Favored : 85.32 % 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: 0.18 (0.18), residues: 2360 helix: 1.03 (0.14), residues: 1384 sheet: -2.56 (0.52), residues: 84 loop : -0.99 (0.21), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 180 TYR 0.007 0.001 TYR A 89 PHE 0.010 0.001 PHE D 537 TRP 0.005 0.001 TRP D 462 HIS 0.004 0.001 HIS D 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.11 (21240) covalent geometry : angle 0.55158 / 0.27 (28596) hydrogen bonds : bond 0.03921 / 2.66 ( 873) hydrogen bonds : angle 3.79895 / 2.65 ( 2499) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 285 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 GLU cc_start: 0.7535 (tp30) cc_final: 0.7278 (tp30) REVERT: A 175 SER cc_start: 0.8101 (t) cc_final: 0.7788 (p) REVERT: A 435 MET cc_start: 0.8794 (mmp) cc_final: 0.8553 (mmp) REVERT: A 450 GLU cc_start: 0.8547 (mt-10) cc_final: 0.8233 (mt-10) REVERT: A 605 GLU cc_start: 0.8096 (tt0) cc_final: 0.7792 (tt0) REVERT: B 116 GLU cc_start: 0.7546 (tp30) cc_final: 0.7270 (tp30) REVERT: B 450 GLU cc_start: 0.8577 (mt-10) cc_final: 0.8264 (mt-10) REVERT: B 605 GLU cc_start: 0.8069 (tt0) cc_final: 0.7770 (tt0) REVERT: C 116 GLU cc_start: 0.7557 (tp30) cc_final: 0.7297 (tp30) REVERT: C 357 ASN cc_start: 0.7405 (OUTLIER) cc_final: 0.7157 (p0) REVERT: C 435 MET cc_start: 0.8727 (mmt) cc_final: 0.8366 (mmp) REVERT: C 450 GLU cc_start: 0.8598 (mt-10) cc_final: 0.8323 (mt-10) REVERT: C 605 GLU cc_start: 0.8084 (tt0) cc_final: 0.7792 (tt0) REVERT: C 612 LEU cc_start: 0.8138 (pp) cc_final: 0.7381 (tt) REVERT: D 300 LYS cc_start: 0.8213 (mmtm) cc_final: 0.7738 (mtmt) REVERT: D 426 HIS cc_start: 0.8059 (m170) cc_final: 0.7663 (m-70) REVERT: D 435 MET cc_start: 0.8757 (mmt) cc_final: 0.8542 (mmp) REVERT: D 450 GLU cc_start: 0.8609 (mt-10) cc_final: 0.8338 (mt-10) REVERT: D 605 GLU cc_start: 0.8069 (tt0) cc_final: 0.7762 (tt0) REVERT: D 612 LEU cc_start: 0.8229 (pp) cc_final: 0.7509 (tp) outliers start: 26 outliers final: 22 residues processed: 302 average time/residue: 0.1305 time to fit residues: 63.0824 Evaluate side-chains 304 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 281 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 554 MET Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 346 CYS Chi-restraints excluded: chain B residue 357 ASN Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain C residue 346 CYS Chi-restraints excluded: chain C residue 357 ASN Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 346 CYS Chi-restraints excluded: chain D residue 357 ASN Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 591 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 168 optimal weight: 0.5980 chunk 53 optimal weight: 4.9990 chunk 29 optimal weight: 0.5980 chunk 6 optimal weight: 10.0000 chunk 174 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 196 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 140 optimal weight: 4.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 257 GLN A 261 GLN ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 257 GLN B 261 GLN ** B 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 257 GLN C 261 GLN ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 257 GLN ** D 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.151956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.113645 restraints weight = 22855.611| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 1.67 r_work: 0.3000 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2828 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2828 r_free = 0.2828 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2828 r_free = 0.2828 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (21 function evaluations) r_final: 0.2828 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.3415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 21240 Z= 0.145 Angle : 0.582 16.483 28596 Z= 0.281 Chirality : 0.041 0.177 3132 Planarity : 0.004 0.036 3456 Dihedral : 13.676 145.930 4514 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 1.16 % Allowed : 13.57 % Favored : 85.27 % 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: 0.13 (0.17), residues: 2360 helix: 0.97 (0.14), residues: 1384 sheet: -2.57 (0.52), residues: 84 loop : -0.99 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 153 TYR 0.009 0.001 TYR A 222 PHE 0.012 0.001 PHE A 537 TRP 0.006 0.001 TRP B 495 HIS 0.003 0.001 HIS B 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.14 (21240) covalent geometry : angle 0.58239 / 0.28 (28596) hydrogen bonds : bond 0.04296 / 2.91 ( 873) hydrogen bonds : angle 3.88146 / 2.71 ( 2499) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5624.28 seconds wall clock time: 96 minutes 40.75 seconds (5800.75 seconds total)