Starting phenix.real_space_refine on Wed Jun 18 05:10:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cuh_45933/06_2025/9cuh_45933.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cuh_45933/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9cuh_45933/06_2025/9cuh_45933.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cuh_45933/06_2025/9cuh_45933.map" model { file = "/net/cci-nas-00/data/ceres_data/9cuh_45933/06_2025/9cuh_45933.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cuh_45933/06_2025/9cuh_45933.cif" } resolution = 3.03 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.155 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'POV:plan-3': 2, 'POV:plan-2': 1, 'POV:plan-1': 1, 'PCW:plan-1': 1, 'PCW:plan-3': 1, 'PCW:plan-4': 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: {'POV:plan-3': 2, 'POV:plan-2': 1, 'POV:plan-1': 1, 'PCW:plan-1': 1, 'PCW:plan-3': 1, 'PCW:plan-4': 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: {'POV:plan-3': 2, 'POV:plan-2': 1, 'POV:plan-1': 1, 'PCW:plan-1': 1, 'PCW:plan-3': 1, 'PCW:plan-4': 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: {'POV:plan-3': 2, 'POV:plan-2': 1, 'POV:plan-1': 1, 'PCW:plan-1': 1, 'PCW:plan-3': 1, 'PCW:plan-4': 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: 12.71, per 1000 atoms: 0.61 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: 5.26 Conformation dependent library (CDL) restraints added in 2.4 seconds 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: 2.53 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: 5.61 Time building geometry restraints manager: 6.13 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: 1.160 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: 0.810 Check model and map are aligned: 0.140 Set scattering table: 0.200 Process input model: 45.460 Find NCS groups from input model: 1.270 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.720 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.025 0.003 TRP C 583 HIS 0.013 0.003 HIS A 238 PHE 0.029 0.004 PHE B 169 TYR 0.023 0.003 TYR A 270 ARG 0.013 0.001 ARG D 632 Details of bonding type rmsd hydrogen bonds : bond 0.32968 ( 873) hydrogen bonds : angle 10.30914 ( 2499) covalent geometry : bond 0.01386 (21240) covalent geometry : angle 1.53360 (28596) *********************** 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 : 2.212 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: 0.4044 time to fit residues: 258.6072 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 : 2.249 ------------------------------------------------------------------------------- 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 199 optimal weight: 1.9990 chunk 178 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 120 optimal weight: 5.9990 chunk 95 optimal weight: 0.9990 chunk 184 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 112 optimal weight: 0.8980 chunk 137 optimal weight: 0.1980 chunk 214 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 426 HIS ** 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.155270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.116822 restraints weight = 22722.968| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 1.67 r_work: 0.2970 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2751 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2751 r_free = 0.2751 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2744 r_free = 0.2744 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.2744 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 21240 Z= 0.131 Angle : 0.657 11.797 28596 Z= 0.327 Chirality : 0.040 0.165 3132 Planarity : 0.006 0.047 3456 Dihedral : 19.507 150.045 4526 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.51 (0.15), residues: 2360 helix: -2.16 (0.11), residues: 1384 sheet: -3.47 (0.34), residues: 124 loop : -2.11 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 462 HIS 0.006 0.001 HIS D 265 PHE 0.012 0.001 PHE C 531 TYR 0.020 0.001 TYR D 555 ARG 0.004 0.001 ARG B 621 Details of bonding type rmsd hydrogen bonds : bond 0.05422 ( 873) hydrogen bonds : angle 4.70369 ( 2499) covalent geometry : bond 0.00281 (21240) covalent geometry : angle 0.65731 (28596) *********************** 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 393 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 338 time to evaluate : 2.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 435 MET cc_start: 0.8983 (mmt) cc_final: 0.8614 (mmp) REVERT: A 448 SER cc_start: 0.9147 (m) cc_final: 0.8691 (p) REVERT: B 435 MET cc_start: 0.8987 (mmt) cc_final: 0.8604 (mmp) REVERT: B 440 MET cc_start: 0.9032 (ttp) cc_final: 0.8779 (ttp) REVERT: B 448 SER cc_start: 0.9164 (m) cc_final: 0.8711 (p) REVERT: C 116 GLU cc_start: 0.7512 (tp30) cc_final: 0.7225 (tp30) REVERT: C 435 MET cc_start: 0.8976 (mmt) cc_final: 0.8581 (mmp) REVERT: C 440 MET cc_start: 0.9048 (ttp) cc_final: 0.8832 (ttp) REVERT: C 448 SER cc_start: 0.9152 (m) cc_final: 0.8675 (p) REVERT: C 583 TRP cc_start: 0.8611 (t60) cc_final: 0.8391 (t60) REVERT: D 233 ASP cc_start: 0.7945 (p0) cc_final: 0.7557 (t0) REVERT: D 255 MET cc_start: 0.8972 (mmm) cc_final: 0.8761 (mmm) REVERT: D 434 PHE cc_start: 0.7607 (m-80) cc_final: 0.7252 (t80) REVERT: D 435 MET cc_start: 0.8990 (mmt) cc_final: 0.8766 (mmt) REVERT: D 452 VAL cc_start: 0.9006 (OUTLIER) cc_final: 0.8776 (t) REVERT: D 583 TRP cc_start: 0.8607 (t60) cc_final: 0.8364 (t60) outliers start: 55 outliers final: 19 residues processed: 360 average time/residue: 0.3099 time to fit residues: 174.5582 Evaluate side-chains 289 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 269 time to evaluate : 2.038 ------------------------------------------------------------------------------- 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 217 optimal weight: 0.7980 chunk 92 optimal weight: 0.0030 chunk 183 optimal weight: 7.9990 chunk 14 optimal weight: 0.7980 chunk 119 optimal weight: 7.9990 chunk 5 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 49 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 11 optimal weight: 9.9990 overall best weight: 0.6392 ------------------------------------------------------------------------------- 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 206 GLN B 257 GLN ** B 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 257 GLN ** C 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 257 GLN ** D 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.152803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.113692 restraints weight = 22934.119| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.78 r_work: 0.2952 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2886 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2886 r_free = 0.2886 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2885 r_free = 0.2885 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.2885 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 21240 Z= 0.118 Angle : 0.558 8.036 28596 Z= 0.281 Chirality : 0.040 0.202 3132 Planarity : 0.005 0.046 3456 Dihedral : 17.649 145.362 4515 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.60 % Allowed : 10.08 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.16), residues: 2360 helix: -0.66 (0.13), residues: 1392 sheet: -3.20 (0.49), residues: 84 loop : -1.79 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 462 HIS 0.004 0.001 HIS D 265 PHE 0.010 0.001 PHE A 537 TYR 0.015 0.001 TYR B 555 ARG 0.007 0.000 ARG B 153 Details of bonding type rmsd hydrogen bonds : bond 0.04578 ( 873) hydrogen bonds : angle 4.08361 ( 2499) covalent geometry : bond 0.00248 (21240) covalent geometry : angle 0.55825 (28596) *********************** 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 324 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 291 time to evaluate : 2.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 GLU cc_start: 0.7381 (tp30) cc_final: 0.7107 (tp30) REVERT: B 116 GLU cc_start: 0.7413 (tp30) cc_final: 0.7127 (tp30) REVERT: B 435 MET cc_start: 0.8846 (mmt) cc_final: 0.8605 (mmp) REVERT: C 116 GLU cc_start: 0.7397 (tp30) cc_final: 0.7112 (tp30) REVERT: C 435 MET cc_start: 0.8811 (mmt) cc_final: 0.8596 (mmp) REVERT: D 40 GLN cc_start: 0.8369 (tt0) cc_final: 0.7978 (tt0) REVERT: D 434 PHE cc_start: 0.7407 (m-80) cc_final: 0.7020 (t80) REVERT: D 435 MET cc_start: 0.8847 (mmt) cc_final: 0.8602 (mmt) REVERT: D 452 VAL cc_start: 0.8892 (OUTLIER) cc_final: 0.8623 (t) outliers start: 33 outliers final: 19 residues processed: 314 average time/residue: 0.3091 time to fit residues: 153.3489 Evaluate side-chains 283 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 263 time to evaluate : 2.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 554 MET Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 357 ASN Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 357 ASN Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 458 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 17 optimal weight: 0.5980 chunk 193 optimal weight: 10.0000 chunk 221 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 226 optimal weight: 0.8980 chunk 38 optimal weight: 4.9990 chunk 1 optimal weight: 7.9990 chunk 164 optimal weight: 0.0980 chunk 88 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.159093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.121275 restraints weight = 22762.237| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 1.61 r_work: 0.2967 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2790 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2790 r_free = 0.2790 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 = 0.2790 r_free = 0.2790 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.2790 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 21240 Z= 0.104 Angle : 0.532 6.638 28596 Z= 0.265 Chirality : 0.039 0.155 3132 Planarity : 0.004 0.044 3456 Dihedral : 16.284 136.650 4515 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.26 % Allowed : 10.51 % Favored : 88.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.17), residues: 2360 helix: 0.15 (0.14), residues: 1384 sheet: -3.00 (0.50), residues: 84 loop : -1.60 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 462 HIS 0.004 0.001 HIS D 265 PHE 0.010 0.001 PHE C 537 TYR 0.016 0.001 TYR D 555 ARG 0.006 0.000 ARG A 153 Details of bonding type rmsd hydrogen bonds : bond 0.03962 ( 873) hydrogen bonds : angle 3.86060 ( 2499) covalent geometry : bond 0.00234 (21240) covalent geometry : angle 0.53218 (28596) *********************** 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 319 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 293 time to evaluate : 2.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 GLU cc_start: 0.7431 (tp30) cc_final: 0.7114 (tp30) REVERT: A 229 LEU cc_start: 0.6343 (OUTLIER) cc_final: 0.6133 (mt) REVERT: B 116 GLU cc_start: 0.7436 (tp30) cc_final: 0.7104 (tp30) REVERT: B 229 LEU cc_start: 0.6332 (OUTLIER) cc_final: 0.6126 (mt) REVERT: B 435 MET cc_start: 0.8859 (mmt) cc_final: 0.8639 (mmp) REVERT: C 116 GLU cc_start: 0.7423 (tp30) cc_final: 0.7105 (tp30) REVERT: C 229 LEU cc_start: 0.6330 (OUTLIER) cc_final: 0.6123 (mt) REVERT: C 303 GLU cc_start: 0.8270 (mp0) cc_final: 0.8033 (mp0) REVERT: D 255 MET cc_start: 0.8830 (mmm) cc_final: 0.8488 (mmm) REVERT: D 378 VAL cc_start: 0.8570 (t) cc_final: 0.8330 (m) REVERT: D 434 PHE cc_start: 0.7550 (m-80) cc_final: 0.7004 (t80) REVERT: D 435 MET cc_start: 0.8857 (mmt) cc_final: 0.8631 (mmp) outliers start: 26 outliers final: 18 residues processed: 314 average time/residue: 0.3093 time to fit residues: 151.4758 Evaluate side-chains 292 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 271 time to evaluate : 2.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 554 MET Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 357 ASN Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 357 ASN Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 458 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 124 optimal weight: 1.9990 chunk 99 optimal weight: 7.9990 chunk 175 optimal weight: 9.9990 chunk 14 optimal weight: 0.7980 chunk 92 optimal weight: 6.9990 chunk 215 optimal weight: 3.9990 chunk 231 optimal weight: 0.9980 chunk 112 optimal weight: 0.6980 chunk 39 optimal weight: 0.6980 chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 GLN ** B 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 257 GLN ** C 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 257 GLN D 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.153528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.114742 restraints weight = 23011.925| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 1.68 r_work: 0.2957 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2732 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2732 r_free = 0.2732 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2732 r_free = 0.2732 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.2732 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.3077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 21240 Z= 0.104 Angle : 0.521 6.730 28596 Z= 0.259 Chirality : 0.039 0.173 3132 Planarity : 0.004 0.045 3456 Dihedral : 15.314 126.109 4515 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.50 % Allowed : 10.85 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.17), residues: 2360 helix: 0.56 (0.14), residues: 1380 sheet: -2.91 (0.50), residues: 84 loop : -1.45 (0.20), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 321 HIS 0.003 0.001 HIS D 265 PHE 0.010 0.001 PHE B 537 TYR 0.019 0.001 TYR C 555 ARG 0.006 0.000 ARG D 153 Details of bonding type rmsd hydrogen bonds : bond 0.03874 ( 873) hydrogen bonds : angle 3.72631 ( 2499) covalent geometry : bond 0.00239 (21240) covalent geometry : angle 0.52148 (28596) *********************** 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 331 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 300 time to evaluate : 2.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 GLU cc_start: 0.7620 (tp30) cc_final: 0.7304 (tp30) REVERT: A 176 GLU cc_start: 0.7719 (pm20) cc_final: 0.7518 (mp0) REVERT: A 605 GLU cc_start: 0.8104 (tt0) cc_final: 0.7858 (tt0) REVERT: A 628 ARG cc_start: 0.7658 (mtp85) cc_final: 0.7404 (mtm180) REVERT: B 116 GLU cc_start: 0.7634 (tp30) cc_final: 0.7313 (tp30) REVERT: B 176 GLU cc_start: 0.7710 (pm20) cc_final: 0.7490 (mp0) REVERT: B 182 LEU cc_start: 0.8015 (pp) cc_final: 0.7794 (mp) REVERT: B 605 GLU cc_start: 0.8064 (tt0) cc_final: 0.7820 (tt0) REVERT: B 628 ARG cc_start: 0.7644 (mtp85) cc_final: 0.7383 (mtm180) REVERT: C 116 GLU cc_start: 0.7611 (tp30) cc_final: 0.7299 (tp30) REVERT: C 176 GLU cc_start: 0.7645 (pm20) cc_final: 0.7439 (mp0) REVERT: C 182 LEU cc_start: 0.8046 (pp) cc_final: 0.7784 (mp) REVERT: C 435 MET cc_start: 0.8910 (mmt) cc_final: 0.8659 (mmp) REVERT: C 605 GLU cc_start: 0.8227 (tt0) cc_final: 0.7997 (tt0) REVERT: C 612 LEU cc_start: 0.8135 (pp) cc_final: 0.7586 (tp) REVERT: C 628 ARG cc_start: 0.7674 (mtp85) cc_final: 0.7408 (mtm180) REVERT: D 176 GLU cc_start: 0.7682 (pm20) cc_final: 0.7446 (mp0) REVERT: D 378 VAL cc_start: 0.8609 (t) cc_final: 0.8403 (m) REVERT: D 434 PHE cc_start: 0.7768 (m-80) cc_final: 0.7239 (t80) REVERT: D 435 MET cc_start: 0.8972 (mmt) cc_final: 0.8772 (mmp) REVERT: D 628 ARG cc_start: 0.7651 (mtp85) cc_final: 0.7384 (mtm180) outliers start: 31 outliers final: 25 residues processed: 321 average time/residue: 0.3238 time to fit residues: 162.6410 Evaluate side-chains 311 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 286 time to evaluate : 2.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 554 MET Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 346 CYS Chi-restraints excluded: chain B residue 357 ASN Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 346 CYS Chi-restraints excluded: chain C residue 357 ASN Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 346 CYS Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 458 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 78 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 26 optimal weight: 0.0170 chunk 35 optimal weight: 3.9990 chunk 147 optimal weight: 0.0470 chunk 69 optimal weight: 0.0000 chunk 89 optimal weight: 0.6980 chunk 177 optimal weight: 0.9990 chunk 88 optimal weight: 0.6980 chunk 229 optimal weight: 0.5980 chunk 124 optimal weight: 2.9990 overall best weight: 0.2720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 GLN ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 257 GLN B 261 GLN B 290 GLN ** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 GLN C 290 GLN ** C 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 546 ASN D 261 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.162344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.124869 restraints weight = 22650.515| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.65 r_work: 0.3139 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2854 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2854 r_free = 0.2854 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2854 r_free = 0.2854 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.2854 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.3362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 21240 Z= 0.086 Angle : 0.487 7.219 28596 Z= 0.242 Chirality : 0.038 0.160 3132 Planarity : 0.004 0.046 3456 Dihedral : 14.480 122.668 4515 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.70 % Allowed : 11.77 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.18), residues: 2360 helix: 0.83 (0.14), residues: 1388 sheet: -2.70 (0.39), residues: 124 loop : -1.13 (0.21), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 462 HIS 0.003 0.001 HIS D 265 PHE 0.006 0.001 PHE A 537 TYR 0.017 0.001 TYR D 555 ARG 0.006 0.000 ARG D 153 Details of bonding type rmsd hydrogen bonds : bond 0.03281 ( 873) hydrogen bonds : angle 3.59422 ( 2499) covalent geometry : bond 0.00181 (21240) covalent geometry : angle 0.48686 (28596) *********************** 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 360 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 325 time to evaluate : 2.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 435 MET cc_start: 0.8867 (mmt) cc_final: 0.8617 (mmp) REVERT: A 450 GLU cc_start: 0.8600 (mt-10) cc_final: 0.8290 (mt-10) REVERT: A 591 GLU cc_start: 0.8298 (pt0) cc_final: 0.8068 (tm-30) REVERT: A 605 GLU cc_start: 0.8062 (tt0) cc_final: 0.7849 (tt0) REVERT: A 612 LEU cc_start: 0.8257 (pp) cc_final: 0.7432 (tt) REVERT: A 628 ARG cc_start: 0.7611 (mtp85) cc_final: 0.7358 (mtm180) REVERT: B 116 GLU cc_start: 0.7574 (tp30) cc_final: 0.7271 (tp30) REVERT: B 435 MET cc_start: 0.8846 (mmt) cc_final: 0.8595 (mmp) REVERT: B 450 GLU cc_start: 0.8610 (mt-10) cc_final: 0.8345 (mt-10) REVERT: B 591 GLU cc_start: 0.8321 (pt0) cc_final: 0.8075 (tm-30) REVERT: B 612 LEU cc_start: 0.8246 (pp) cc_final: 0.7473 (tt) REVERT: B 628 ARG cc_start: 0.7608 (mtp85) cc_final: 0.7373 (mtm180) REVERT: C 116 GLU cc_start: 0.7586 (tp30) cc_final: 0.7301 (tp30) REVERT: C 450 GLU cc_start: 0.8579 (mt-10) cc_final: 0.8311 (mt-10) REVERT: C 591 GLU cc_start: 0.8299 (pt0) cc_final: 0.8056 (tm-30) REVERT: C 605 GLU cc_start: 0.8127 (tt0) cc_final: 0.7899 (tt0) REVERT: C 612 LEU cc_start: 0.8187 (pp) cc_final: 0.7693 (tp) REVERT: C 628 ARG cc_start: 0.7628 (mtp85) cc_final: 0.7357 (mtm180) REVERT: D 300 LYS cc_start: 0.8144 (mmtm) cc_final: 0.7702 (mtmt) REVERT: D 434 PHE cc_start: 0.7764 (m-80) cc_final: 0.7288 (t80) REVERT: D 435 MET cc_start: 0.8916 (mmt) cc_final: 0.8709 (mmt) REVERT: D 591 GLU cc_start: 0.8312 (pt0) cc_final: 0.8102 (tm-30) REVERT: D 612 LEU cc_start: 0.8241 (pp) cc_final: 0.7532 (tp) outliers start: 35 outliers final: 21 residues processed: 353 average time/residue: 0.3113 time to fit residues: 172.5521 Evaluate side-chains 310 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 289 time to evaluate : 2.201 ------------------------------------------------------------------------------- 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 554 MET Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 346 CYS Chi-restraints excluded: chain B residue 357 ASN Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 346 CYS Chi-restraints excluded: chain C residue 357 ASN Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 346 CYS Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 452 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 117 optimal weight: 0.8980 chunk 134 optimal weight: 0.6980 chunk 233 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 199 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 210 optimal weight: 4.9990 chunk 137 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 114 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- 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 74 GLN B 257 GLN B 261 GLN ** B 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 572 ASN C 74 GLN C 257 GLN C 261 GLN ** C 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 572 ASN D 74 GLN D 257 GLN D 261 GLN ** D 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 572 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.153356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.114455 restraints weight = 22866.057| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 1.68 r_work: 0.2986 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- 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: 0.8352 moved from start: 0.3245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 21240 Z= 0.160 Angle : 0.597 13.276 28596 Z= 0.287 Chirality : 0.041 0.176 3132 Planarity : 0.004 0.046 3456 Dihedral : 14.643 120.923 4513 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.11 % Allowed : 13.18 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.18), residues: 2360 helix: 0.82 (0.14), residues: 1380 sheet: -2.61 (0.51), residues: 84 loop : -1.19 (0.20), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 495 HIS 0.003 0.001 HIS C 201 PHE 0.015 0.001 PHE B 537 TYR 0.008 0.001 TYR D 89 ARG 0.004 0.000 ARG D 153 Details of bonding type rmsd hydrogen bonds : bond 0.04394 ( 873) hydrogen bonds : angle 3.81858 ( 2499) covalent geometry : bond 0.00391 (21240) covalent geometry : angle 0.59673 (28596) *********************** 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 304 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 281 time to evaluate : 2.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 GLU cc_start: 0.7648 (tp30) cc_final: 0.7391 (tp30) REVERT: A 435 MET cc_start: 0.8923 (mmt) cc_final: 0.8687 (mmp) REVERT: A 605 GLU cc_start: 0.8151 (tt0) cc_final: 0.7925 (tt0) REVERT: A 612 LEU cc_start: 0.8217 (pp) cc_final: 0.7523 (tp) REVERT: A 628 ARG cc_start: 0.7710 (mtp85) cc_final: 0.7410 (mtm180) REVERT: B 116 GLU cc_start: 0.7639 (tp30) cc_final: 0.7371 (tp30) REVERT: B 450 GLU cc_start: 0.8675 (mt-10) cc_final: 0.8397 (mt-10) REVERT: B 628 ARG cc_start: 0.7677 (mtp85) cc_final: 0.7372 (mtm180) REVERT: C 116 GLU cc_start: 0.7636 (tp30) cc_final: 0.7363 (tp30) REVERT: C 605 GLU cc_start: 0.8185 (tt0) cc_final: 0.7936 (tt0) REVERT: C 612 LEU cc_start: 0.8158 (pp) cc_final: 0.7607 (tp) REVERT: C 628 ARG cc_start: 0.7700 (mtp85) cc_final: 0.7390 (mtm180) REVERT: D 78 MET cc_start: 0.7829 (mmp) cc_final: 0.7626 (mmm) REVERT: D 434 PHE cc_start: 0.7745 (m-80) cc_final: 0.7200 (t80) outliers start: 23 outliers final: 18 residues processed: 297 average time/residue: 0.3361 time to fit residues: 155.2789 Evaluate side-chains 286 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 268 time to evaluate : 2.196 ------------------------------------------------------------------------------- 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 554 MET Chi-restraints excluded: chain B residue 183 ILE 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 346 CYS Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 452 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 90 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 85 optimal weight: 0.0870 chunk 24 optimal weight: 1.9990 chunk 33 optimal weight: 7.9990 chunk 154 optimal weight: 2.9990 chunk 202 optimal weight: 5.9990 chunk 159 optimal weight: 0.9980 chunk 179 optimal weight: 5.9990 chunk 64 optimal weight: 0.9980 chunk 106 optimal weight: 0.7980 overall best weight: 0.6958 ------------------------------------------------------------------------------- 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 D 257 GLN ** D 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.154635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.115386 restraints weight = 22998.554| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 1.67 r_work: 0.2953 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2789 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2789 r_free = 0.2789 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2789 r_free = 0.2789 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.2789 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.3421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 21240 Z= 0.102 Angle : 0.536 12.397 28596 Z= 0.260 Chirality : 0.039 0.171 3132 Planarity : 0.004 0.047 3456 Dihedral : 13.982 115.152 4513 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.45 % Allowed : 12.98 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.18), residues: 2360 helix: 1.01 (0.14), residues: 1388 sheet: -2.60 (0.40), residues: 124 loop : -0.98 (0.21), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 495 HIS 0.003 0.001 HIS A 426 PHE 0.008 0.001 PHE A 537 TYR 0.007 0.001 TYR A 524 ARG 0.004 0.000 ARG D 153 Details of bonding type rmsd hydrogen bonds : bond 0.03699 ( 873) hydrogen bonds : angle 3.72409 ( 2499) covalent geometry : bond 0.00235 (21240) covalent geometry : angle 0.53615 (28596) *********************** 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 304 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 274 time to evaluate : 2.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 GLU cc_start: 0.7511 (tp30) cc_final: 0.7182 (tp30) REVERT: A 426 HIS cc_start: 0.8049 (m170) cc_final: 0.7665 (m90) REVERT: A 435 MET cc_start: 0.8839 (mmt) cc_final: 0.8556 (mmp) REVERT: A 450 GLU cc_start: 0.8564 (mt-10) cc_final: 0.8269 (mt-10) REVERT: A 605 GLU cc_start: 0.8095 (tt0) cc_final: 0.7842 (tt0) REVERT: A 612 LEU cc_start: 0.8089 (pp) cc_final: 0.7562 (tp) REVERT: A 628 ARG cc_start: 0.7563 (mtp85) cc_final: 0.7223 (mtm180) REVERT: B 116 GLU cc_start: 0.7500 (tp30) cc_final: 0.7151 (tp30) REVERT: B 426 HIS cc_start: 0.8065 (m170) cc_final: 0.7689 (m90) REVERT: B 450 GLU cc_start: 0.8613 (mt-10) cc_final: 0.8354 (mt-10) REVERT: B 612 LEU cc_start: 0.8099 (pp) cc_final: 0.7633 (tp) REVERT: B 628 ARG cc_start: 0.7542 (mtp85) cc_final: 0.7277 (mtm180) REVERT: C 116 GLU cc_start: 0.7495 (tp30) cc_final: 0.7158 (tp30) REVERT: C 426 HIS cc_start: 0.8051 (m170) cc_final: 0.7646 (m90) REVERT: C 450 GLU cc_start: 0.8564 (mt-10) cc_final: 0.8294 (mt-10) REVERT: C 605 GLU cc_start: 0.8094 (tt0) cc_final: 0.7829 (tt0) REVERT: C 612 LEU cc_start: 0.8013 (pp) cc_final: 0.7558 (tp) REVERT: C 628 ARG cc_start: 0.7551 (mtp85) cc_final: 0.7202 (mtm180) REVERT: D 300 LYS cc_start: 0.8227 (mmtm) cc_final: 0.7687 (mtmt) REVERT: D 434 PHE cc_start: 0.7671 (m-80) cc_final: 0.7059 (t80) REVERT: D 435 MET cc_start: 0.8814 (mmt) cc_final: 0.8568 (mmp) REVERT: D 452 VAL cc_start: 0.8934 (OUTLIER) cc_final: 0.8695 (t) REVERT: D 612 LEU cc_start: 0.8121 (pp) cc_final: 0.7425 (tp) REVERT: D 628 ARG cc_start: 0.7296 (mtm180) cc_final: 0.7011 (mtm180) outliers start: 30 outliers final: 25 residues processed: 295 average time/residue: 0.3158 time to fit residues: 146.2726 Evaluate side-chains 292 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 266 time to evaluate : 2.303 ------------------------------------------------------------------------------- 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 554 MET Chi-restraints excluded: chain A residue 591 GLU Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 346 CYS 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 591 GLU 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 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 452 VAL 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 133 optimal weight: 0.5980 chunk 138 optimal weight: 0.0770 chunk 113 optimal weight: 3.9990 chunk 182 optimal weight: 7.9990 chunk 130 optimal weight: 0.0370 chunk 93 optimal weight: 6.9990 chunk 131 optimal weight: 0.9980 chunk 134 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 chunk 143 optimal weight: 0.0270 chunk 12 optimal weight: 8.9990 overall best weight: 0.3474 ------------------------------------------------------------------------------- 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 257 GLN B 261 GLN ** B 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 257 GLN C 546 ASN 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 = 0.3773 r_free = 0.3773 target = 0.162365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.124643 restraints weight = 22418.531| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 1.64 r_work: 0.3106 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2833 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2833 r_free = 0.2833 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2833 r_free = 0.2833 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| r_final: 0.2833 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.3690 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= 0.089 Angle : 0.513 11.973 28596 Z= 0.248 Chirality : 0.038 0.153 3132 Planarity : 0.004 0.048 3456 Dihedral : 12.986 95.204 4513 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.45 % Allowed : 13.08 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.18), residues: 2360 helix: 1.19 (0.14), residues: 1392 sheet: -2.47 (0.41), residues: 124 loop : -0.62 (0.22), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 321 HIS 0.003 0.001 HIS B 426 PHE 0.007 0.001 PHE C 537 TYR 0.007 0.001 TYR D 524 ARG 0.003 0.000 ARG D 153 Details of bonding type rmsd hydrogen bonds : bond 0.03214 ( 873) hydrogen bonds : angle 3.59008 ( 2499) covalent geometry : bond 0.00194 (21240) covalent geometry : angle 0.51283 (28596) *********************** 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 327 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 297 time to evaluate : 2.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 GLU cc_start: 0.7594 (tp30) cc_final: 0.7333 (tp30) REVERT: A 175 SER cc_start: 0.8269 (t) cc_final: 0.7999 (p) REVERT: A 426 HIS cc_start: 0.7966 (m170) cc_final: 0.7644 (m90) REVERT: A 435 MET cc_start: 0.8880 (mmt) cc_final: 0.8592 (mmp) REVERT: A 450 GLU cc_start: 0.8571 (mt-10) cc_final: 0.8326 (mt-10) REVERT: A 591 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7911 (tm-30) REVERT: A 605 GLU cc_start: 0.8136 (tt0) cc_final: 0.7915 (tt0) REVERT: A 612 LEU cc_start: 0.8147 (pp) cc_final: 0.7696 (tp) REVERT: A 628 ARG cc_start: 0.7597 (mtp85) cc_final: 0.7320 (mtm180) REVERT: B 116 GLU cc_start: 0.7594 (tp30) cc_final: 0.7293 (tp30) REVERT: B 175 SER cc_start: 0.8367 (t) cc_final: 0.8096 (p) REVERT: B 426 HIS cc_start: 0.7960 (m170) cc_final: 0.7624 (m90) REVERT: B 450 GLU cc_start: 0.8605 (mt-10) cc_final: 0.8383 (mt-10) REVERT: B 591 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7949 (tm-30) REVERT: B 612 LEU cc_start: 0.8141 (pp) cc_final: 0.7742 (tp) REVERT: B 628 ARG cc_start: 0.7603 (mtp85) cc_final: 0.7332 (mtm180) REVERT: C 116 GLU cc_start: 0.7606 (tp30) cc_final: 0.7291 (tp30) REVERT: C 426 HIS cc_start: 0.7947 (m170) cc_final: 0.7585 (m90) REVERT: C 450 GLU cc_start: 0.8588 (mt-10) cc_final: 0.8364 (mt-10) REVERT: C 605 GLU cc_start: 0.8163 (tt0) cc_final: 0.7933 (tt0) REVERT: C 612 LEU cc_start: 0.8114 (pp) cc_final: 0.7658 (tp) REVERT: C 628 ARG cc_start: 0.7623 (mtp85) cc_final: 0.7322 (mtm180) REVERT: D 175 SER cc_start: 0.8247 (t) cc_final: 0.8002 (p) REVERT: D 300 LYS cc_start: 0.8196 (mmtm) cc_final: 0.7727 (mtmt) REVERT: D 357 ASN cc_start: 0.7366 (m-40) cc_final: 0.7153 (p0) REVERT: D 434 PHE cc_start: 0.7737 (m-80) cc_final: 0.7226 (t80) REVERT: D 591 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7994 (tm-30) REVERT: D 612 LEU cc_start: 0.8154 (pp) cc_final: 0.7496 (tp) outliers start: 30 outliers final: 22 residues processed: 317 average time/residue: 0.3070 time to fit residues: 155.2197 Evaluate side-chains 314 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 289 time to evaluate : 2.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 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 554 MET Chi-restraints excluded: chain A residue 591 GLU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 346 CYS 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 591 GLU Chi-restraints excluded: chain C residue 182 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 379 THR Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 452 VAL 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 59 optimal weight: 7.9990 chunk 56 optimal weight: 0.3980 chunk 26 optimal weight: 0.8980 chunk 5 optimal weight: 0.4980 chunk 73 optimal weight: 0.9990 chunk 8 optimal weight: 0.1980 chunk 12 optimal weight: 0.9980 chunk 181 optimal weight: 0.0570 chunk 209 optimal weight: 0.3980 chunk 1 optimal weight: 5.9990 chunk 120 optimal weight: 3.9990 overall best weight: 0.3098 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 257 GLN B 261 GLN ** B 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 257 GLN C 261 GLN ** C 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 257 GLN D 261 GLN ** D 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 572 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 = 0.3774 r_free = 0.3774 target = 0.162471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.124703 restraints weight = 22516.819| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 1.66 r_work: 0.3046 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2890 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2890 r_free = 0.2890 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2890 r_free = 0.2890 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| r_final: 0.2890 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.3782 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= 0.088 Angle : 0.513 12.243 28596 Z= 0.247 Chirality : 0.038 0.154 3132 Planarity : 0.004 0.048 3456 Dihedral : 12.497 88.654 4513 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.26 % Allowed : 13.42 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.18), residues: 2360 helix: 1.30 (0.14), residues: 1392 sheet: -2.47 (0.41), residues: 124 loop : -0.49 (0.22), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 462 HIS 0.003 0.000 HIS D 265 PHE 0.007 0.001 PHE D 537 TYR 0.007 0.001 TYR D 524 ARG 0.004 0.000 ARG D 153 Details of bonding type rmsd hydrogen bonds : bond 0.03191 ( 873) hydrogen bonds : angle 3.56201 ( 2499) covalent geometry : bond 0.00190 (21240) covalent geometry : angle 0.51263 (28596) ********************** 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 318 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 292 time to evaluate : 2.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 SER cc_start: 0.8127 (t) cc_final: 0.7879 (p) REVERT: A 426 HIS cc_start: 0.7926 (m170) cc_final: 0.7639 (m90) REVERT: A 435 MET cc_start: 0.8893 (mmt) cc_final: 0.8604 (mmp) REVERT: A 450 GLU cc_start: 0.8592 (mt-10) cc_final: 0.8317 (mt-10) REVERT: A 591 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7925 (tm-30) REVERT: A 605 GLU cc_start: 0.8134 (tt0) cc_final: 0.7917 (tt0) REVERT: A 612 LEU cc_start: 0.8136 (pp) cc_final: 0.7691 (tp) REVERT: A 628 ARG cc_start: 0.7581 (mtp85) cc_final: 0.7323 (mtm180) REVERT: B 78 MET cc_start: 0.7762 (mmm) cc_final: 0.7553 (mtm) REVERT: B 175 SER cc_start: 0.8165 (t) cc_final: 0.7923 (p) REVERT: B 426 HIS cc_start: 0.7912 (m170) cc_final: 0.7613 (m90) REVERT: B 450 GLU cc_start: 0.8650 (mt-10) cc_final: 0.8411 (mt-10) REVERT: B 591 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7950 (tm-30) REVERT: B 612 LEU cc_start: 0.8055 (pp) cc_final: 0.7687 (tp) REVERT: B 628 ARG cc_start: 0.7565 (mtp85) cc_final: 0.7307 (mtm180) REVERT: C 78 MET cc_start: 0.7728 (mmm) cc_final: 0.7454 (mtm) REVERT: C 136 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7587 (mp) REVERT: C 426 HIS cc_start: 0.7898 (m170) cc_final: 0.7573 (m90) REVERT: C 450 GLU cc_start: 0.8631 (mt-10) cc_final: 0.8381 (mt-10) REVERT: C 591 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7911 (tm-30) REVERT: C 605 GLU cc_start: 0.8167 (tt0) cc_final: 0.7940 (tt0) REVERT: C 612 LEU cc_start: 0.8057 (pp) cc_final: 0.7639 (tp) REVERT: C 628 ARG cc_start: 0.7584 (mtp85) cc_final: 0.7309 (mtm180) REVERT: D 175 SER cc_start: 0.8107 (t) cc_final: 0.7878 (p) REVERT: D 300 LYS cc_start: 0.8215 (mmtm) cc_final: 0.7723 (mtmt) REVERT: D 357 ASN cc_start: 0.7339 (m-40) cc_final: 0.7111 (p0) REVERT: D 591 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7948 (tm-30) REVERT: D 612 LEU cc_start: 0.8080 (pp) cc_final: 0.7436 (tp) REVERT: D 628 ARG cc_start: 0.7312 (mtm180) cc_final: 0.7069 (mtm180) outliers start: 26 outliers final: 19 residues processed: 311 average time/residue: 0.2955 time to fit residues: 146.4921 Evaluate side-chains 312 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 288 time to evaluate : 2.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 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 554 MET Chi-restraints excluded: chain A residue 591 GLU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 346 CYS Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 591 GLU Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 182 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 591 GLU Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 346 CYS Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 591 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 50 optimal weight: 2.9990 chunk 173 optimal weight: 0.8980 chunk 115 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 197 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 106 optimal weight: 0.9980 chunk 159 optimal weight: 2.9990 chunk 200 optimal weight: 5.9990 chunk 10 optimal weight: 0.0970 chunk 127 optimal weight: 0.4980 overall best weight: 0.6378 ------------------------------------------------------------------------------- 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 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 = 0.3764 r_free = 0.3764 target = 0.161407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.123056 restraints weight = 22489.379| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 1.67 r_work: 0.3048 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2898 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2898 r_free = 0.2898 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2898 r_free = 0.2898 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| r_final: 0.2898 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.3758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 21240 Z= 0.098 Angle : 0.523 12.087 28596 Z= 0.252 Chirality : 0.039 0.159 3132 Planarity : 0.004 0.047 3456 Dihedral : 12.332 87.088 4509 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.26 % Allowed : 13.52 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.18), residues: 2360 helix: 1.38 (0.14), residues: 1388 sheet: -2.42 (0.41), residues: 124 loop : -0.45 (0.22), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 321 HIS 0.003 0.001 HIS D 265 PHE 0.009 0.001 PHE D 537 TYR 0.006 0.001 TYR C 524 ARG 0.004 0.000 ARG D 359 Details of bonding type rmsd hydrogen bonds : bond 0.03407 ( 873) hydrogen bonds : angle 3.58663 ( 2499) covalent geometry : bond 0.00224 (21240) covalent geometry : angle 0.52263 (28596) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12486.00 seconds wall clock time: 213 minutes 43.41 seconds (12823.41 seconds total)