Starting phenix.real_space_refine on Thu Sep 18 22:34:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cuh_45933/09_2025/9cuh_45933.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cuh_45933/09_2025/9cuh_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 { model { file = "/net/cci-nas-00/data/ceres_data/9cuh_45933/09_2025/9cuh_45933.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cuh_45933/09_2025/9cuh_45933.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9cuh_45933/09_2025/9cuh_45933.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cuh_45933/09_2025/9cuh_45933.map" } 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-2.0-5805/lib/python3.9/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, 432 Unusual residues: {' CA': 1, 'PCW': 1, 'POV': 8, 'Y01': 3} Classifications: {'undetermined': 13} Link IDs: {None: 12} 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: 4.72, per 1000 atoms: 0.23 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: 1.77 Conformation dependent library (CDL) restraints added in 799.3 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.72 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: 3.25 Time building geometry restraints manager: 2.36 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: 1.070 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: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 18.810 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 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 aren 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 covalent geometry : bond 0.01386 (21240) covalent geometry : angle 1.53360 (28596) hydrogen bonds : bond 0.32968 ( 873) hydrogen bonds : angle 10.30914 ( 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 : 0.605 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: 0.8421 (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: 0.8390 (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: 0.8885 (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: 0.8692 (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: 0.1858 time to fit residues: 118.0862 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 : 0.786 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 174 ASN D 238 HIS D 426 HIS ** D 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.154496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.115863 restraints weight = 22869.508| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 1.68 r_work: 0.2989 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2836 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2836 r_free = 0.2836 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2828 r_free = 0.2828 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.2828 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 21240 Z= 0.137 Angle : 0.657 12.057 28596 Z= 0.327 Chirality : 0.040 0.163 3132 Planarity : 0.006 0.047 3456 Dihedral : 19.525 150.216 4526 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.66 % Allowed : 9.25 % Favored : 88.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.50 (0.15), residues: 2360 helix: -2.15 (0.11), residues: 1384 sheet: -3.48 (0.34), residues: 124 loop : -2.12 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 621 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 covalent geometry : bond 0.00278 (21240) covalent geometry : angle 0.65664 (28596) hydrogen bonds : bond 0.05459 ( 873) hydrogen bonds : angle 4.68898 ( 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 397 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 342 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 435 MET cc_start: 0.8846 (mmt) cc_final: 0.8507 (mmp) REVERT: A 440 MET cc_start: 0.8939 (ttp) cc_final: 0.8699 (ttp) REVERT: A 448 SER cc_start: 0.9140 (m) cc_final: 0.8642 (p) REVERT: B 435 MET cc_start: 0.8873 (mmt) cc_final: 0.8498 (mmp) REVERT: B 440 MET cc_start: 0.8955 (ttp) cc_final: 0.8723 (ttp) REVERT: B 448 SER cc_start: 0.9157 (m) cc_final: 0.8670 (p) REVERT: C 116 GLU cc_start: 0.7349 (tp30) cc_final: 0.7055 (tp30) REVERT: C 255 MET cc_start: 0.8970 (mmm) cc_final: 0.8761 (mmm) REVERT: C 435 MET cc_start: 0.8848 (mmt) cc_final: 0.8454 (mmp) REVERT: C 440 MET cc_start: 0.8973 (ttp) cc_final: 0.8752 (ttp) REVERT: C 448 SER cc_start: 0.9144 (m) cc_final: 0.8630 (p) REVERT: C 583 TRP cc_start: 0.8452 (t60) cc_final: 0.8218 (t60) REVERT: D 233 ASP cc_start: 0.7853 (p0) cc_final: 0.7496 (t0) REVERT: D 255 MET cc_start: 0.8833 (mmm) cc_final: 0.8607 (mmm) REVERT: D 434 PHE cc_start: 0.7399 (m-80) cc_final: 0.6997 (t80) REVERT: D 435 MET cc_start: 0.8855 (mmt) cc_final: 0.8627 (mmt) REVERT: D 452 VAL cc_start: 0.8926 (OUTLIER) cc_final: 0.8706 (t) REVERT: D 583 TRP cc_start: 0.8436 (t60) cc_final: 0.8176 (t60) outliers start: 55 outliers final: 19 residues processed: 363 average time/residue: 0.1462 time to fit residues: 83.2510 Evaluate side-chains 294 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 274 time to evaluate : 0.864 ------------------------------------------------------------------------------- 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: 2.9990 chunk 87 optimal weight: 2.9990 chunk 218 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 100 optimal weight: 0.6980 chunk 178 optimal weight: 7.9990 chunk 47 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 116 optimal weight: 0.8980 chunk 235 optimal weight: 2.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 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 = 0.3619 r_free = 0.3619 target = 0.149620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.109409 restraints weight = 23076.180| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 1.90 r_work: 0.2876 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2707 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2664 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2664 r_free = 0.2664 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2664 r_free = 0.2664 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.2664 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.2531 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= 0.159 Angle : 0.608 8.227 28596 Z= 0.304 Chirality : 0.041 0.199 3132 Planarity : 0.005 0.047 3456 Dihedral : 18.015 144.479 4515 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 1.41 % Allowed : 10.66 % Favored : 87.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.93 (0.16), residues: 2360 helix: -0.71 (0.13), residues: 1392 sheet: -3.23 (0.47), residues: 84 loop : -1.84 (0.19), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 153 TYR 0.015 0.002 TYR B 555 PHE 0.014 0.001 PHE B 537 TRP 0.008 0.001 TRP C 462 HIS 0.005 0.001 HIS D 265 Details of bonding type rmsd covalent geometry : bond 0.00371 (21240) covalent geometry : angle 0.60790 (28596) hydrogen bonds : bond 0.05128 ( 873) hydrogen bonds : angle 4.18339 ( 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 309 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 280 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 GLU cc_start: 0.7551 (tp30) cc_final: 0.7237 (tp30) REVERT: A 569 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8726 (tt) REVERT: B 116 GLU cc_start: 0.7557 (tp30) cc_final: 0.7246 (tp30) REVERT: B 435 MET cc_start: 0.8967 (mmt) cc_final: 0.8736 (mmp) REVERT: B 569 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8700 (tt) REVERT: C 40 GLN cc_start: 0.8386 (tt0) cc_final: 0.8048 (tt0) REVERT: C 45 TRP cc_start: 0.7460 (m-90) cc_final: 0.7226 (m-90) REVERT: C 116 GLU cc_start: 0.7548 (tp30) cc_final: 0.7244 (tp30) REVERT: C 569 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8696 (tt) REVERT: D 40 GLN cc_start: 0.8380 (tt0) cc_final: 0.8007 (tt0) REVERT: D 116 GLU cc_start: 0.7529 (tp30) cc_final: 0.7282 (tp30) REVERT: D 233 ASP cc_start: 0.7966 (p0) cc_final: 0.7619 (t0) REVERT: D 434 PHE cc_start: 0.7682 (m-80) cc_final: 0.7082 (t80) REVERT: D 435 MET cc_start: 0.8943 (mmt) cc_final: 0.8721 (mmt) outliers start: 29 outliers final: 19 residues processed: 302 average time/residue: 0.1428 time to fit residues: 68.2348 Evaluate side-chains 279 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 257 time to evaluate : 0.732 ------------------------------------------------------------------------------- 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 A residue 569 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 B residue 569 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 C residue 569 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 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: 7.9990 chunk 234 optimal weight: 20.0000 chunk 206 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 152 optimal weight: 3.9990 chunk 233 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 176 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 chunk 232 optimal weight: 0.8980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** D 572 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.155356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.117045 restraints weight = 22736.257| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 1.60 r_work: 0.3014 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2832 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2832 r_free = 0.2832 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2832 r_free = 0.2832 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.2832 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2818 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= 0.127 Angle : 0.551 6.677 28596 Z= 0.275 Chirality : 0.040 0.171 3132 Planarity : 0.004 0.044 3456 Dihedral : 16.637 144.518 4514 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.60 % Allowed : 10.51 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.08 (0.17), residues: 2360 helix: 0.12 (0.14), residues: 1384 sheet: -3.14 (0.47), residues: 84 loop : -1.72 (0.19), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 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 D 462 HIS 0.004 0.001 HIS D 265 Details of bonding type rmsd covalent geometry : bond 0.00301 (21240) covalent geometry : angle 0.55105 (28596) hydrogen bonds : bond 0.04296 ( 873) hydrogen bonds : angle 3.90998 ( 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 328 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 295 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 GLU cc_start: 0.7591 (tp30) cc_final: 0.7260 (tp30) REVERT: A 229 LEU cc_start: 0.6203 (OUTLIER) cc_final: 0.5979 (mt) REVERT: A 450 GLU cc_start: 0.8598 (mt-10) cc_final: 0.8287 (mt-10) REVERT: A 569 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8639 (tt) REVERT: B 116 GLU cc_start: 0.7586 (tp30) cc_final: 0.7248 (tp30) REVERT: B 229 LEU cc_start: 0.6259 (OUTLIER) cc_final: 0.6034 (mt) REVERT: C 45 TRP cc_start: 0.7470 (m-90) cc_final: 0.7189 (m-90) REVERT: C 116 GLU cc_start: 0.7572 (tp30) cc_final: 0.7245 (tp30) REVERT: C 229 LEU cc_start: 0.6224 (OUTLIER) cc_final: 0.6000 (mt) REVERT: C 435 MET cc_start: 0.8861 (mmt) cc_final: 0.8543 (mmp) REVERT: C 569 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8657 (tt) REVERT: D 116 GLU cc_start: 0.7563 (tp30) cc_final: 0.7223 (tp30) REVERT: D 229 LEU cc_start: 0.6039 (OUTLIER) cc_final: 0.5720 (mt) REVERT: D 233 ASP cc_start: 0.7804 (p0) cc_final: 0.7564 (t0) REVERT: D 255 MET cc_start: 0.8937 (mmm) cc_final: 0.8629 (mmm) REVERT: D 378 VAL cc_start: 0.8607 (t) cc_final: 0.8384 (m) REVERT: D 434 PHE cc_start: 0.7643 (m-80) cc_final: 0.7160 (t80) REVERT: D 435 MET cc_start: 0.8922 (mmt) cc_final: 0.8687 (mmt) outliers start: 33 outliers final: 20 residues processed: 319 average time/residue: 0.1567 time to fit residues: 77.2605 Evaluate side-chains 297 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 271 time to evaluate : 0.824 ------------------------------------------------------------------------------- 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 A residue 569 LEU Chi-restraints excluded: chain B residue 183 ILE 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 183 ILE 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 C residue 569 LEU Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 229 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 178 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 127 optimal weight: 0.9980 chunk 134 optimal weight: 10.0000 chunk 138 optimal weight: 7.9990 chunk 10 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 187 optimal weight: 0.0020 chunk 227 optimal weight: 5.9990 chunk 68 optimal weight: 0.8980 chunk 2 optimal weight: 5.9990 overall best weight: 0.9390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.151887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.112551 restraints weight = 22893.621| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 1.82 r_work: 0.2943 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2756 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2756 r_free = 0.2756 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 = 0.2756 r_free = 0.2756 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.2756 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 21240 Z= 0.115 Angle : 0.535 6.799 28596 Z= 0.266 Chirality : 0.039 0.174 3132 Planarity : 0.004 0.045 3456 Dihedral : 15.614 136.654 4514 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.08 % Allowed : 10.71 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.68 (0.17), residues: 2360 helix: 0.45 (0.14), residues: 1384 sheet: -2.92 (0.48), residues: 84 loop : -1.58 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 153 TYR 0.014 0.001 TYR B 555 PHE 0.010 0.001 PHE D 537 TRP 0.006 0.001 TRP C 462 HIS 0.004 0.001 HIS D 265 Details of bonding type rmsd covalent geometry : bond 0.00269 (21240) covalent geometry : angle 0.53528 (28596) hydrogen bonds : bond 0.04064 ( 873) hydrogen bonds : angle 3.78672 ( 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 332 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 289 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 GLU cc_start: 0.7538 (tp30) cc_final: 0.7274 (tp30) REVERT: A 182 LEU cc_start: 0.7987 (pp) cc_final: 0.7652 (mp) REVERT: A 450 GLU cc_start: 0.8614 (mt-10) cc_final: 0.8291 (mt-10) REVERT: A 569 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8605 (tt) REVERT: A 605 GLU cc_start: 0.8069 (tt0) cc_final: 0.7825 (tt0) REVERT: A 628 ARG cc_start: 0.7603 (mtp85) cc_final: 0.7310 (mtm180) REVERT: B 116 GLU cc_start: 0.7548 (tp30) cc_final: 0.7275 (tp30) REVERT: B 435 MET cc_start: 0.8816 (mmt) cc_final: 0.8526 (mmp) REVERT: B 450 GLU cc_start: 0.8638 (mt-10) cc_final: 0.8318 (mt-10) REVERT: B 628 ARG cc_start: 0.7586 (mtp85) cc_final: 0.7303 (mtm180) REVERT: C 45 TRP cc_start: 0.7456 (OUTLIER) cc_final: 0.7210 (m-90) REVERT: C 116 GLU cc_start: 0.7528 (tp30) cc_final: 0.7253 (tp30) REVERT: C 182 LEU cc_start: 0.8021 (pp) cc_final: 0.7666 (mp) REVERT: C 569 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8608 (tt) REVERT: C 628 ARG cc_start: 0.7608 (mtp85) cc_final: 0.7308 (mtm180) REVERT: D 116 GLU cc_start: 0.7512 (tp30) cc_final: 0.7237 (tp30) REVERT: D 218 LEU cc_start: 0.8666 (tt) cc_final: 0.8456 (tp) REVERT: D 229 LEU cc_start: 0.6304 (OUTLIER) cc_final: 0.6051 (mt) REVERT: D 233 ASP cc_start: 0.7817 (p0) cc_final: 0.7556 (t0) REVERT: D 378 VAL cc_start: 0.8574 (t) cc_final: 0.8367 (m) REVERT: D 434 PHE cc_start: 0.7651 (m-80) cc_final: 0.7051 (t80) REVERT: D 435 MET cc_start: 0.8886 (mmt) cc_final: 0.8496 (mmp) REVERT: D 450 GLU cc_start: 0.8618 (mt-10) cc_final: 0.8290 (mt-10) REVERT: D 605 GLU cc_start: 0.8071 (tt0) cc_final: 0.7821 (tt0) REVERT: D 628 ARG cc_start: 0.7595 (mtp85) cc_final: 0.7286 (mtm180) outliers start: 43 outliers final: 24 residues processed: 322 average time/residue: 0.1521 time to fit residues: 76.8731 Evaluate side-chains 314 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 286 time to evaluate : 0.762 ------------------------------------------------------------------------------- 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 A residue 569 LEU 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 45 TRP 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 C residue 569 LEU Chi-restraints excluded: chain D residue 39 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 458 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 31 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 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: 6.9990 chunk 212 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 193 optimal weight: 0.0470 chunk 57 optimal weight: 9.9990 overall best weight: 1.9484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN 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 74 GLN C 257 GLN C 261 GLN ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 GLN ** D 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.150723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.112153 restraints weight = 22737.694| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 1.68 r_work: 0.2938 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2660 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2660 r_free = 0.2660 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2660 r_free = 0.2660 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.2660 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 21240 Z= 0.180 Angle : 0.602 6.944 28596 Z= 0.295 Chirality : 0.042 0.187 3132 Planarity : 0.004 0.043 3456 Dihedral : 15.585 139.328 4514 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.89 % Allowed : 11.48 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.60 (0.17), residues: 2360 helix: 0.53 (0.14), residues: 1380 sheet: -2.78 (0.49), residues: 84 loop : -1.58 (0.20), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 153 TYR 0.021 0.001 TYR D 555 PHE 0.015 0.001 PHE A 537 TRP 0.006 0.001 TRP B 495 HIS 0.004 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00441 (21240) covalent geometry : angle 0.60201 (28596) hydrogen bonds : bond 0.04760 ( 873) hydrogen bonds : angle 3.93101 ( 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 325 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 286 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 GLU cc_start: 0.7746 (tp30) cc_final: 0.7497 (tp30) REVERT: A 218 LEU cc_start: 0.8786 (tt) cc_final: 0.8558 (tp) REVERT: A 280 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8090 (mp) REVERT: A 450 GLU cc_start: 0.8707 (mt-10) cc_final: 0.8399 (mt-10) REVERT: A 605 GLU cc_start: 0.8221 (tt0) cc_final: 0.7936 (tt0) REVERT: A 628 ARG cc_start: 0.7730 (mtp85) cc_final: 0.7472 (mtm180) REVERT: B 116 GLU cc_start: 0.7743 (tp30) cc_final: 0.7485 (tp30) REVERT: B 218 LEU cc_start: 0.8782 (tt) cc_final: 0.8558 (tp) REVERT: B 280 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8053 (mp) REVERT: B 628 ARG cc_start: 0.7748 (mtp85) cc_final: 0.7441 (mtm180) REVERT: C 45 TRP cc_start: 0.7533 (OUTLIER) cc_final: 0.7111 (m-90) REVERT: C 116 GLU cc_start: 0.7736 (tp30) cc_final: 0.7479 (tp30) REVERT: C 218 LEU cc_start: 0.8810 (tt) cc_final: 0.8582 (tp) REVERT: C 280 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8046 (mp) REVERT: C 435 MET cc_start: 0.8922 (mmt) cc_final: 0.8718 (mmp) REVERT: C 628 ARG cc_start: 0.7740 (mtp85) cc_final: 0.7405 (mtm180) REVERT: D 116 GLU cc_start: 0.7737 (tp30) cc_final: 0.7481 (tp30) REVERT: D 218 LEU cc_start: 0.8786 (tt) cc_final: 0.8550 (tp) REVERT: D 233 ASP cc_start: 0.7945 (p0) cc_final: 0.7679 (t0) REVERT: D 280 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8065 (mp) REVERT: D 378 VAL cc_start: 0.8594 (t) cc_final: 0.8385 (m) REVERT: D 450 GLU cc_start: 0.8710 (mt-10) cc_final: 0.8411 (mt-10) REVERT: D 605 GLU cc_start: 0.8221 (tt0) cc_final: 0.7940 (tt0) REVERT: D 628 ARG cc_start: 0.7736 (mtp85) cc_final: 0.7392 (mtm180) outliers start: 39 outliers final: 24 residues processed: 314 average time/residue: 0.1529 time to fit residues: 75.4408 Evaluate side-chains 306 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 277 time to evaluate : 0.754 ------------------------------------------------------------------------------- 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 45 TRP 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 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: 0.7980 chunk 24 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 154 optimal weight: 0.9990 chunk 56 optimal weight: 4.9990 chunk 235 optimal weight: 0.8980 chunk 169 optimal weight: 2.9990 chunk 234 optimal weight: 7.9990 chunk 76 optimal weight: 10.0000 chunk 55 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 261 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 = 0.3689 r_free = 0.3689 target = 0.154932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.116718 restraints weight = 22786.899| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 1.62 r_work: 0.2954 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2772 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2772 r_free = 0.2772 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2772 r_free = 0.2772 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.2772 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.3238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 21240 Z= 0.108 Angle : 0.520 6.558 28596 Z= 0.259 Chirality : 0.039 0.167 3132 Planarity : 0.004 0.046 3456 Dihedral : 14.859 142.748 4514 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.31 % Allowed : 12.50 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.17), residues: 2360 helix: 0.84 (0.14), residues: 1380 sheet: -2.69 (0.50), residues: 84 loop : -1.40 (0.20), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 153 TYR 0.015 0.001 TYR B 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 covalent geometry : bond 0.00250 (21240) covalent geometry : angle 0.51970 (28596) hydrogen bonds : bond 0.03918 ( 873) hydrogen bonds : angle 3.76337 ( 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 335 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 308 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 GLU cc_start: 0.7553 (tp30) cc_final: 0.7249 (tp30) REVERT: A 426 HIS cc_start: 0.8101 (m170) cc_final: 0.7711 (m90) REVERT: A 435 MET cc_start: 0.8815 (mmt) cc_final: 0.8584 (mmp) REVERT: A 450 GLU cc_start: 0.8574 (mt-10) cc_final: 0.8260 (mt-10) REVERT: A 535 GLU cc_start: 0.8477 (mt-10) cc_final: 0.8175 (mt-10) REVERT: A 605 GLU cc_start: 0.8122 (tt0) cc_final: 0.7820 (tt0) REVERT: A 628 ARG cc_start: 0.7596 (mtp85) cc_final: 0.7311 (mtm180) REVERT: B 116 GLU cc_start: 0.7540 (tp30) cc_final: 0.7194 (tp30) REVERT: B 435 MET cc_start: 0.8778 (mmt) cc_final: 0.8572 (mmp) REVERT: B 450 GLU cc_start: 0.8613 (mt-10) cc_final: 0.8305 (mt-10) REVERT: B 628 ARG cc_start: 0.7614 (mtp85) cc_final: 0.7282 (mtm180) REVERT: C 45 TRP cc_start: 0.7391 (OUTLIER) cc_final: 0.7093 (m-90) REVERT: C 116 GLU cc_start: 0.7543 (tp30) cc_final: 0.7196 (tp30) REVERT: C 435 MET cc_start: 0.8801 (mmt) cc_final: 0.8559 (mmp) REVERT: C 450 GLU cc_start: 0.8608 (mt-10) cc_final: 0.8303 (mt-10) REVERT: C 628 ARG cc_start: 0.7583 (mtp85) cc_final: 0.7298 (mtm180) REVERT: D 116 GLU cc_start: 0.7521 (tp30) cc_final: 0.7230 (tp30) REVERT: D 233 ASP cc_start: 0.7836 (p0) cc_final: 0.7618 (t0) REVERT: D 426 HIS cc_start: 0.8078 (m170) cc_final: 0.7726 (m90) REVERT: D 435 MET cc_start: 0.8830 (mmt) cc_final: 0.8577 (mmp) REVERT: D 450 GLU cc_start: 0.8590 (mt-10) cc_final: 0.8310 (mt-10) REVERT: D 605 GLU cc_start: 0.8102 (tt0) cc_final: 0.7824 (tt0) REVERT: D 612 LEU cc_start: 0.8226 (pp) cc_final: 0.7555 (tp) REVERT: D 628 ARG cc_start: 0.7609 (mtp85) cc_final: 0.7294 (mtm180) outliers start: 27 outliers final: 22 residues processed: 327 average time/residue: 0.1517 time to fit residues: 78.0490 Evaluate side-chains 311 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 288 time to evaluate : 0.743 ------------------------------------------------------------------------------- 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 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 45 TRP 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 C residue 591 GLU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 96 optimal weight: 4.9990 chunk 57 optimal weight: 0.0000 chunk 192 optimal weight: 0.6980 chunk 165 optimal weight: 4.9990 chunk 144 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 135 optimal weight: 10.0000 chunk 123 optimal weight: 7.9990 chunk 35 optimal weight: 3.9990 chunk 132 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.3390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3643 r_free = 0.3643 target = 0.151643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.112605 restraints weight = 22839.916| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 1.66 r_work: 0.2938 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2686 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2686 r_free = 0.2686 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2686 r_free = 0.2686 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.2686 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.3279 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= 0.140 Angle : 0.578 13.238 28596 Z= 0.279 Chirality : 0.041 0.173 3132 Planarity : 0.004 0.045 3456 Dihedral : 14.632 146.374 4514 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.50 % Allowed : 12.60 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.18 (0.17), residues: 2360 helix: 0.82 (0.14), residues: 1384 sheet: -2.59 (0.51), residues: 84 loop : -1.33 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 153 TYR 0.014 0.001 TYR D 555 PHE 0.011 0.001 PHE C 537 TRP 0.005 0.001 TRP D 462 HIS 0.003 0.001 HIS D 265 Details of bonding type rmsd covalent geometry : bond 0.00341 (21240) covalent geometry : angle 0.57829 (28596) hydrogen bonds : bond 0.04273 ( 873) hydrogen bonds : angle 3.86225 ( 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 308 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 277 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 GLU cc_start: 0.7739 (tp30) cc_final: 0.7487 (tp30) REVERT: A 280 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8085 (mp) REVERT: A 435 MET cc_start: 0.8980 (mmt) cc_final: 0.8769 (mmp) REVERT: A 450 GLU cc_start: 0.8669 (mt-10) cc_final: 0.8366 (mt-10) REVERT: A 605 GLU cc_start: 0.8198 (tt0) cc_final: 0.7934 (tt0) REVERT: A 628 ARG cc_start: 0.7737 (mtp85) cc_final: 0.7479 (mtm180) REVERT: B 116 GLU cc_start: 0.7761 (tp30) cc_final: 0.7483 (tp30) REVERT: B 450 GLU cc_start: 0.8697 (mt-10) cc_final: 0.8380 (mt-10) REVERT: B 605 GLU cc_start: 0.8185 (tt0) cc_final: 0.7922 (tt0) REVERT: B 628 ARG cc_start: 0.7727 (mtp85) cc_final: 0.7417 (mtm180) REVERT: C 45 TRP cc_start: 0.7525 (OUTLIER) cc_final: 0.7186 (m-90) REVERT: C 116 GLU cc_start: 0.7745 (tp30) cc_final: 0.7495 (tp30) REVERT: C 280 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8120 (mp) REVERT: C 357 ASN cc_start: 0.7596 (OUTLIER) cc_final: 0.7340 (p0) REVERT: C 450 GLU cc_start: 0.8673 (mt-10) cc_final: 0.8356 (mt-10) REVERT: C 628 ARG cc_start: 0.7736 (mtp85) cc_final: 0.7469 (mtm180) REVERT: D 116 GLU cc_start: 0.7729 (tp30) cc_final: 0.7503 (tp30) REVERT: D 233 ASP cc_start: 0.7891 (p0) cc_final: 0.7676 (t0) REVERT: D 450 GLU cc_start: 0.8699 (mt-10) cc_final: 0.8430 (mt-10) REVERT: D 605 GLU cc_start: 0.8216 (tt0) cc_final: 0.7960 (tt0) REVERT: D 612 LEU cc_start: 0.8269 (pp) cc_final: 0.7564 (tp) REVERT: D 628 ARG cc_start: 0.7732 (mtp85) cc_final: 0.7461 (mtm180) outliers start: 31 outliers final: 25 residues processed: 298 average time/residue: 0.1552 time to fit residues: 72.0834 Evaluate side-chains 305 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 276 time to evaluate : 0.983 ------------------------------------------------------------------------------- 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 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 45 TRP 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 C residue 591 GLU 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: 0.6980 chunk 187 optimal weight: 6.9990 chunk 115 optimal weight: 0.0870 chunk 205 optimal weight: 2.9990 chunk 208 optimal weight: 0.9990 chunk 8 optimal weight: 7.9990 chunk 226 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 62 optimal weight: 10.0000 chunk 5 optimal weight: 0.9980 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.154215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.115106 restraints weight = 22743.045| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 1.67 r_work: 0.3039 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2781 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2781 r_free = 0.2781 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2781 r_free = 0.2781 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.2781 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 21240 Z= 0.105 Angle : 0.537 10.810 28596 Z= 0.261 Chirality : 0.039 0.165 3132 Planarity : 0.004 0.046 3456 Dihedral : 14.007 148.634 4514 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.36 % Allowed : 12.98 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.05 (0.18), residues: 2360 helix: 1.01 (0.14), residues: 1384 sheet: -2.63 (0.40), residues: 124 loop : -1.11 (0.21), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 153 TYR 0.007 0.001 TYR D 524 PHE 0.008 0.001 PHE A 537 TRP 0.005 0.001 TRP D 462 HIS 0.003 0.001 HIS D 265 Details of bonding type rmsd covalent geometry : bond 0.00244 (21240) covalent geometry : angle 0.53703 (28596) hydrogen bonds : bond 0.03778 ( 873) hydrogen bonds : angle 3.76958 ( 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 319 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 291 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 GLU cc_start: 0.7630 (tp30) cc_final: 0.7377 (tp30) REVERT: A 435 MET cc_start: 0.8901 (mmt) cc_final: 0.8650 (mmp) REVERT: A 450 GLU cc_start: 0.8575 (mt-10) cc_final: 0.8299 (mt-10) REVERT: A 605 GLU cc_start: 0.8100 (tt0) cc_final: 0.7845 (tt0) REVERT: A 628 ARG cc_start: 0.7623 (mtp85) cc_final: 0.7340 (mtm180) REVERT: B 116 GLU cc_start: 0.7636 (tp30) cc_final: 0.7358 (tp30) REVERT: B 426 HIS cc_start: 0.8031 (m170) cc_final: 0.7696 (m90) REVERT: B 450 GLU cc_start: 0.8608 (mt-10) cc_final: 0.8326 (mt-10) REVERT: B 605 GLU cc_start: 0.8070 (tt0) cc_final: 0.7815 (tt0) REVERT: B 621 ARG cc_start: 0.7419 (ttm-80) cc_final: 0.6854 (ttm-80) REVERT: C 45 TRP cc_start: 0.7475 (OUTLIER) cc_final: 0.7251 (m-90) REVERT: C 116 GLU cc_start: 0.7636 (tp30) cc_final: 0.7381 (tp30) REVERT: C 176 GLU cc_start: 0.7759 (pm20) cc_final: 0.7544 (mp0) REVERT: C 357 ASN cc_start: 0.7490 (OUTLIER) cc_final: 0.7288 (p0) REVERT: C 426 HIS cc_start: 0.8035 (m170) cc_final: 0.7700 (m90) REVERT: C 435 MET cc_start: 0.8832 (mmt) cc_final: 0.8585 (mmp) REVERT: C 450 GLU cc_start: 0.8575 (mt-10) cc_final: 0.8293 (mt-10) REVERT: C 605 GLU cc_start: 0.8053 (tt0) cc_final: 0.7805 (tt0) REVERT: D 78 MET cc_start: 0.7783 (mmp) cc_final: 0.7274 (mmt) REVERT: D 359 ARG cc_start: 0.7925 (mtm180) cc_final: 0.7688 (mtm180) REVERT: D 426 HIS cc_start: 0.8027 (m170) cc_final: 0.7634 (m-70) REVERT: D 450 GLU cc_start: 0.8600 (mt-10) cc_final: 0.8343 (mt-10) REVERT: D 605 GLU cc_start: 0.8088 (tt0) cc_final: 0.7831 (tt0) REVERT: D 612 LEU cc_start: 0.8243 (pp) cc_final: 0.7570 (tp) REVERT: D 628 ARG cc_start: 0.7655 (mtp85) cc_final: 0.7417 (mtm180) outliers start: 28 outliers final: 21 residues processed: 310 average time/residue: 0.1516 time to fit residues: 73.9960 Evaluate side-chains 302 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 279 time to evaluate : 0.758 ------------------------------------------------------------------------------- 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 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 45 TRP 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 C residue 591 GLU 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: 0.9980 chunk 91 optimal weight: 0.7980 chunk 55 optimal weight: 0.6980 chunk 81 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 189 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 103 optimal weight: 0.7980 chunk 33 optimal weight: 9.9990 chunk 82 optimal weight: 0.1980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3678 r_free = 0.3678 target = 0.154587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.115951 restraints weight = 22943.072| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 1.66 r_work: 0.2952 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2840 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2840 r_free = 0.2840 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2840 r_free = 0.2840 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.2840 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.3532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 21240 Z= 0.102 Angle : 0.539 10.572 28596 Z= 0.262 Chirality : 0.039 0.163 3132 Planarity : 0.004 0.046 3456 Dihedral : 13.580 149.525 4514 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.21 % Allowed : 13.18 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.19 (0.18), residues: 2360 helix: 1.08 (0.14), residues: 1384 sheet: -2.61 (0.40), residues: 124 loop : -0.96 (0.21), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 153 TYR 0.018 0.001 TYR A 555 PHE 0.008 0.001 PHE B 537 TRP 0.006 0.001 TRP A 462 HIS 0.003 0.001 HIS D 265 Details of bonding type rmsd covalent geometry : bond 0.00233 (21240) covalent geometry : angle 0.53870 (28596) hydrogen bonds : bond 0.03690 ( 873) hydrogen bonds : angle 3.72878 ( 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 317 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 292 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 GLU cc_start: 0.7527 (tp30) cc_final: 0.7253 (tp30) REVERT: A 357 ASN cc_start: 0.7377 (OUTLIER) cc_final: 0.7136 (p0) REVERT: A 435 MET cc_start: 0.8820 (mmt) cc_final: 0.8578 (mmp) REVERT: A 450 GLU cc_start: 0.8557 (mt-10) cc_final: 0.8248 (mt-10) REVERT: A 605 GLU cc_start: 0.8129 (tt0) cc_final: 0.7846 (tt0) REVERT: A 628 ARG cc_start: 0.7562 (mtp85) cc_final: 0.7221 (mtm180) REVERT: B 78 MET cc_start: 0.7649 (mmp) cc_final: 0.7129 (mmt) REVERT: B 116 GLU cc_start: 0.7503 (tp30) cc_final: 0.7148 (tp30) REVERT: B 357 ASN cc_start: 0.7334 (OUTLIER) cc_final: 0.7086 (p0) REVERT: B 450 GLU cc_start: 0.8587 (mt-10) cc_final: 0.8271 (mt-10) REVERT: B 605 GLU cc_start: 0.8134 (tt0) cc_final: 0.7849 (tt0) REVERT: B 628 ARG cc_start: 0.7538 (mtp85) cc_final: 0.7186 (mtm180) REVERT: C 116 GLU cc_start: 0.7520 (tp30) cc_final: 0.7236 (tp30) REVERT: C 357 ASN cc_start: 0.7364 (OUTLIER) cc_final: 0.7132 (p0) REVERT: C 450 GLU cc_start: 0.8569 (mt-10) cc_final: 0.8258 (mt-10) REVERT: C 605 GLU cc_start: 0.8114 (tt0) cc_final: 0.7827 (tt0) REVERT: C 628 ARG cc_start: 0.7560 (mtp85) cc_final: 0.7204 (mtm180) REVERT: D 78 MET cc_start: 0.7644 (mmp) cc_final: 0.7437 (mmm) REVERT: D 357 ASN cc_start: 0.7370 (OUTLIER) cc_final: 0.7116 (p0) REVERT: D 359 ARG cc_start: 0.7851 (mtm180) cc_final: 0.7598 (mtm180) REVERT: D 426 HIS cc_start: 0.8049 (m170) cc_final: 0.7668 (m-70) REVERT: D 435 MET cc_start: 0.8815 (mmp) cc_final: 0.8607 (mmp) REVERT: D 450 GLU cc_start: 0.8585 (mt-10) cc_final: 0.8296 (mt-10) REVERT: D 605 GLU cc_start: 0.8062 (tt0) cc_final: 0.7786 (tt0) REVERT: D 612 LEU cc_start: 0.8176 (pp) cc_final: 0.7580 (tp) outliers start: 25 outliers final: 18 residues processed: 311 average time/residue: 0.1502 time to fit residues: 74.5100 Evaluate side-chains 301 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 279 time to evaluate : 0.803 ------------------------------------------------------------------------------- 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 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 C residue 591 GLU 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: 0.8980 chunk 53 optimal weight: 4.9990 chunk 29 optimal weight: 0.0770 chunk 6 optimal weight: 9.9990 chunk 174 optimal weight: 0.7980 chunk 104 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 196 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 140 optimal weight: 5.9990 overall best weight: 1.9542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 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 = 0.3701 r_free = 0.3701 target = 0.155631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.117875 restraints weight = 22597.277| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 1.66 r_work: 0.2983 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2804 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2804 r_free = 0.2804 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 = 0.2804 r_free = 0.2804 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.2804 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 21240 Z= 0.180 Angle : 0.613 11.326 28596 Z= 0.296 Chirality : 0.043 0.185 3132 Planarity : 0.004 0.045 3456 Dihedral : 13.990 155.078 4514 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 1.21 % Allowed : 13.37 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.17), residues: 2360 helix: 0.93 (0.14), residues: 1384 sheet: -2.52 (0.52), residues: 84 loop : -1.06 (0.21), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 153 TYR 0.009 0.001 TYR B 89 PHE 0.014 0.001 PHE B 537 TRP 0.007 0.001 TRP C 45 HIS 0.004 0.001 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00443 (21240) covalent geometry : angle 0.61271 (28596) hydrogen bonds : bond 0.04638 ( 873) hydrogen bonds : angle 3.92609 ( 2499) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6282.10 seconds wall clock time: 108 minutes 0.35 seconds (6480.35 seconds total)