Starting phenix.real_space_refine on Fri Jul 3 17:36:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8epx_28534/07_2026/8epx_28534.cif Found real_map, /net/cci-nas-00/data/ceres_data/8epx_28534/07_2026/8epx_28534.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8epx_28534/07_2026/8epx_28534.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8epx_28534/07_2026/8epx_28534.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8epx_28534/07_2026/8epx_28534.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8epx_28534/07_2026/8epx_28534.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8epx_28534/07_2026/8epx_28534.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8epx_28534/07_2026/8epx_28534.map" } resolution = 3.15 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.202 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 2 9.91 5 P 144 5.49 5 S 30 5.16 5 C 9435 2.51 5 N 2795 2.21 5 O 3051 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15457 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 3609 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 492, 3600 Classifications: {'peptide': 492} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 29, 'TRANS': 462} Chain breaks: 1 Unresolved non-hydrogen bonds: 234 Unresolved non-hydrogen angles: 298 Unresolved non-hydrogen dihedrals: 175 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 18, 'ARG:plan': 10, 'ASP:plan': 12, 'TYR:plan': 1, 'GLN:plan1': 4, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 169 Conformer: "B" Number of residues, atoms: 492, 3600 Classifications: {'peptide': 492} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 29, 'TRANS': 462} Chain breaks: 1 Unresolved non-hydrogen bonds: 234 Unresolved non-hydrogen angles: 298 Unresolved non-hydrogen dihedrals: 175 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 18, 'ARG:plan': 10, 'ASP:plan': 12, 'TYR:plan': 1, 'GLN:plan1': 4, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 169 bond proxies already assigned to first conformer: 3683 Chain: "B" Number of atoms: 2606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2606 Classifications: {'peptide': 337} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 16, 'TRANS': 320} Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 109 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 9, 'ASP:plan': 6, 'ARG:plan': 3, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 62 Chain: "C" Number of atoms: 2536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2536 Classifications: {'peptide': 337} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 16, 'TRANS': 320} Unresolved non-hydrogen bonds: 155 Unresolved non-hydrogen angles: 196 Unresolved non-hydrogen dihedrals: 114 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ASP:plan': 9, 'ARG:plan': 8, 'GLU:plan': 10, 'ASN:plan1': 2, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 104 Chain: "D" Number of atoms: 3752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 3752 Classifications: {'peptide': 506} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 30, 'TRANS': 475} Chain breaks: 1 Unresolved non-hydrogen bonds: 195 Unresolved non-hydrogen angles: 252 Unresolved non-hydrogen dihedrals: 140 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ASP:plan': 14, 'GLU:plan': 16, 'ARG:plan': 9, 'GLN:plan1': 6, 'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 154 Chain: "E" Number of atoms: 319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 319 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "F" Number of atoms: 296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 296 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "H" Number of atoms: 316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 316 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "G" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 340 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "I" Number of atoms: 381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 381 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "J" Number of atoms: 357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 357 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "K" Number of atoms: 479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 479 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Chain: "L" Number of atoms: 464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 464 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AGLU A 184 " occ=0.82 ... (16 atoms not shown) pdb=" OE2BGLU A 184 " occ=0.18 Time building chain proxies: 4.24, per 1000 atoms: 0.27 Number of scatterers: 15457 At special positions: 0 Unit cell: (124.542, 152.592, 142.494, 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 2 19.99 S 30 16.00 P 144 15.00 O 3051 8.00 N 2795 7.00 C 9435 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.38 Conformation dependent library (CDL) restraints added in 765.4 milliseconds 3326 Ramachandran restraints generated. 1663 Oldfield, 0 Emsley, 1663 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3052 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 5 sheets defined 50.5% alpha, 3.9% beta 65 base pairs and 104 stacking pairs defined. Time for finding SS restraints: 1.98 Creating SS restraints... Processing helix chain 'A' and resid 8 through 23 removed outlier: 3.924A pdb=" N ALA A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL A 21 " --> pdb=" O ALA A 17 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA A 22 " --> pdb=" O ARG A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 28 removed outlier: 4.339A pdb=" N CYS A 27 " --> pdb=" O ASP A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 33 removed outlier: 4.171A pdb=" N LEU A 33 " --> pdb=" O ALA A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 98 removed outlier: 4.448A pdb=" N LEU A 85 " --> pdb=" O ILE A 81 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR A 86 " --> pdb=" O HIS A 82 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY A 98 " --> pdb=" O TYR A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 127 Processing helix chain 'A' and resid 188 through 205 Processing helix chain 'A' and resid 214 through 225 Processing helix chain 'A' and resid 229 through 235 Processing helix chain 'A' and resid 241 through 254 Processing helix chain 'A' and resid 266 through 270 removed outlier: 3.752A pdb=" N GLY A 269 " --> pdb=" O LEU A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 310 removed outlier: 3.839A pdb=" N ILE A 303 " --> pdb=" O LEU A 299 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ALA A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 324 Processing helix chain 'A' and resid 336 through 355 removed outlier: 3.639A pdb=" N HIS A 342 " --> pdb=" O ARG A 338 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER A 343 " --> pdb=" O ALA A 339 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASP A 347 " --> pdb=" O SER A 343 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE A 348 " --> pdb=" O TYR A 344 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N SER A 350 " --> pdb=" O GLU A 346 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA A 351 " --> pdb=" O ASP A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 378 Processing helix chain 'A' and resid 383 through 397 Processing helix chain 'A' and resid 399 through 418 removed outlier: 3.679A pdb=" N PHE A 403 " --> pdb=" O ARG A 399 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLU A 417 " --> pdb=" O ARG A 413 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASN A 418 " --> pdb=" O LYS A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 452 Processing helix chain 'A' and resid 471 through 481 Processing helix chain 'A' and resid 498 through 506 removed outlier: 3.550A pdb=" N VAL A 502 " --> pdb=" O ASP A 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 204 removed outlier: 3.508A pdb=" N PHE B 193 " --> pdb=" O ARG B 189 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA B 204 " --> pdb=" O LYS B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 225 Processing helix chain 'B' and resid 229 through 235 Processing helix chain 'B' and resid 241 through 255 removed outlier: 3.541A pdb=" N LEU B 252 " --> pdb=" O GLN B 248 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLU B 253 " --> pdb=" O PHE B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 309 Processing helix chain 'B' and resid 313 through 324 removed outlier: 3.671A pdb=" N VAL B 322 " --> pdb=" O TRP B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 355 removed outlier: 4.085A pdb=" N SER B 350 " --> pdb=" O GLU B 346 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ALA B 351 " --> pdb=" O ASP B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 379 Processing helix chain 'B' and resid 383 through 397 Processing helix chain 'B' and resid 399 through 413 Processing helix chain 'B' and resid 434 through 451 Processing helix chain 'B' and resid 471 through 481 removed outlier: 3.667A pdb=" N LEU B 475 " --> pdb=" O PHE B 471 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR B 476 " --> pdb=" O GLN B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 506 Processing helix chain 'C' and resid 188 through 204 removed outlier: 3.910A pdb=" N PHE C 195 " --> pdb=" O ALA C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 225 removed outlier: 3.778A pdb=" N VAL C 218 " --> pdb=" O ARG C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 254 Processing helix chain 'C' and resid 298 through 309 Processing helix chain 'C' and resid 313 through 324 removed outlier: 3.695A pdb=" N VAL C 322 " --> pdb=" O TRP C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 355 removed outlier: 3.612A pdb=" N LEU C 355 " --> pdb=" O ALA C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 379 removed outlier: 3.569A pdb=" N GLY C 379 " --> pdb=" O CYS C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 396 Processing helix chain 'C' and resid 399 through 418 removed outlier: 4.030A pdb=" N GLU C 417 " --> pdb=" O ARG C 413 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASN C 418 " --> pdb=" O LYS C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 434 through 452 Processing helix chain 'C' and resid 472 through 481 Processing helix chain 'C' and resid 498 through 507 removed outlier: 3.521A pdb=" N VAL C 502 " --> pdb=" O ASP C 498 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 23 removed outlier: 3.953A pdb=" N ASP D 10 " --> pdb=" O ASN D 6 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N PHE D 11 " --> pdb=" O ALA D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 27 removed outlier: 3.697A pdb=" N CYS D 27 " --> pdb=" O PRO D 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 24 through 27' Processing helix chain 'D' and resid 76 through 81 removed outlier: 6.433A pdb=" N ILE D 81 " --> pdb=" O GLN D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 98 removed outlier: 3.829A pdb=" N THR D 86 " --> pdb=" O HIS D 82 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY D 98 " --> pdb=" O TYR D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 127 Processing helix chain 'D' and resid 188 through 204 removed outlier: 3.509A pdb=" N ALA D 204 " --> pdb=" O LYS D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 225 Processing helix chain 'D' and resid 229 through 236 Processing helix chain 'D' and resid 241 through 252 removed outlier: 3.605A pdb=" N LEU D 252 " --> pdb=" O GLN D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 270 Processing helix chain 'D' and resid 298 through 309 Processing helix chain 'D' and resid 313 through 324 removed outlier: 3.700A pdb=" N VAL D 322 " --> pdb=" O TRP D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 355 removed outlier: 3.738A pdb=" N SER D 350 " --> pdb=" O GLU D 346 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA D 351 " --> pdb=" O ASP D 347 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 379 Processing helix chain 'D' and resid 383 through 397 Processing helix chain 'D' and resid 399 through 418 removed outlier: 3.856A pdb=" N GLU D 417 " --> pdb=" O ARG D 413 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASN D 418 " --> pdb=" O LYS D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 434 through 452 Processing helix chain 'D' and resid 472 through 481 Processing helix chain 'D' and resid 498 through 506 Processing sheet with id=AA1, first strand: chain 'A' and resid 38 through 42 removed outlier: 4.372A pdb=" N GLY A 55 " --> pdb=" O LEU A 72 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ALA A 102 " --> pdb=" O ALA A 134 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N PHE A 136 " --> pdb=" O ALA A 102 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ILE A 104 " --> pdb=" O PHE A 136 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N TYR A 138 " --> pdb=" O ILE A 104 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ILE A 106 " --> pdb=" O TYR A 138 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL A 135 " --> pdb=" O VAL A 156 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 424 through 425 Processing sheet with id=AA3, first strand: chain 'C' and resid 424 through 425 Processing sheet with id=AA4, first strand: chain 'D' and resid 38 through 42 removed outlier: 4.384A pdb=" N GLY D 55 " --> pdb=" O LEU D 72 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL D 59 " --> pdb=" O ARG D 68 " (cutoff:3.500A) removed outlier: 9.417A pdb=" N GLY D 101 " --> pdb=" O GLN D 67 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ALA D 69 " --> pdb=" O GLY D 101 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N ALA D 103 " --> pdb=" O ALA D 69 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ALA D 71 " --> pdb=" O ALA D 103 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N VAL D 105 " --> pdb=" O ALA D 71 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N GLU D 73 " --> pdb=" O VAL D 105 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N SER D 137 " --> pdb=" O CYS D 155 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N CYS D 155 " --> pdb=" O SER D 137 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 424 through 425 586 hydrogen bonds defined for protein. 1719 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 174 hydrogen bonds 348 hydrogen bond angles 0 basepair planarities 65 basepair parallelities 104 stacking parallelities Total time for adding SS restraints: 2.77 Time building geometry restraints manager: 1.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 3684 1.33 - 1.45: 3996 1.45 - 1.57: 8120 1.57 - 1.69: 278 1.69 - 1.81: 52 Bond restraints: 16130 Sorted by residual: bond pdb=" O3' DA G 26 " pdb=" P DA G 27 " ideal model delta sigma weight residual 1.607 1.444 0.163 1.50e-02 4.44e+03 1.18e+02 bond pdb=" C2' DA G 27 " pdb=" C1' DA G 27 " ideal model delta sigma weight residual 1.518 1.453 0.065 1.00e-02 1.00e+04 4.17e+01 bond pdb=" O4' DA G 27 " pdb=" C1' DA G 27 " ideal model delta sigma weight residual 1.420 1.353 0.067 1.10e-02 8.26e+03 3.67e+01 bond pdb=" N9 DA G 27 " pdb=" C8 DA G 27 " ideal model delta sigma weight residual 1.373 1.340 0.033 8.00e-03 1.56e+04 1.66e+01 bond pdb=" C5 DA G 27 " pdb=" C4 DA G 27 " ideal model delta sigma weight residual 1.383 1.355 0.028 7.00e-03 2.04e+04 1.59e+01 ... (remaining 16125 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.09: 22444 3.09 - 6.19: 102 6.19 - 9.28: 5 9.28 - 12.37: 3 12.37 - 15.46: 2 Bond angle restraints: 22556 Sorted by residual: angle pdb=" O5' DA G 29 " pdb=" C5' DA G 29 " pdb=" C4' DA G 29 " ideal model delta sigma weight residual 109.40 115.87 -6.47 8.00e-01 1.56e+00 6.55e+01 angle pdb=" O4' DA G 27 " pdb=" C1' DA G 27 " pdb=" C2' DA G 27 " ideal model delta sigma weight residual 105.90 100.49 5.41 8.00e-01 1.56e+00 4.58e+01 angle pdb=" C4' DG G 28 " pdb=" O4' DG G 28 " pdb=" C1' DG G 28 " ideal model delta sigma weight residual 110.10 104.39 5.71 1.00e+00 1.00e+00 3.26e+01 angle pdb=" C3' DA G 26 " pdb=" O3' DA G 26 " pdb=" P DA G 27 " ideal model delta sigma weight residual 120.20 128.74 -8.54 1.50e+00 4.44e-01 3.24e+01 angle pdb=" C4' DA G 27 " pdb=" C3' DA G 27 " pdb=" O3' DA G 27 " ideal model delta sigma weight residual 109.70 123.78 -14.08 2.50e+00 1.60e-01 3.17e+01 ... (remaining 22551 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.74: 8113 35.74 - 71.48: 881 71.48 - 107.22: 15 107.22 - 142.96: 4 142.96 - 178.70: 10 Dihedral angle restraints: 9023 sinusoidal: 4239 harmonic: 4784 Sorted by residual: dihedral pdb=" CA THR D 469 " pdb=" C THR D 469 " pdb=" N THR D 470 " pdb=" CA THR D 470 " ideal model delta harmonic sigma weight residual 180.00 -157.13 -22.87 0 5.00e+00 4.00e-02 2.09e+01 dihedral pdb=" CA ARG D 210 " pdb=" C ARG D 210 " pdb=" N PRO D 211 " pdb=" CA PRO D 211 " ideal model delta harmonic sigma weight residual 180.00 159.16 20.84 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" C4' DG K 15 " pdb=" C3' DG K 15 " pdb=" O3' DG K 15 " pdb=" P DC K 16 " ideal model delta sinusoidal sigma weight residual -140.00 38.70 -178.70 1 3.50e+01 8.16e-04 1.57e+01 ... (remaining 9020 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.122: 2477 0.122 - 0.244: 25 0.244 - 0.366: 2 0.366 - 0.488: 1 0.488 - 0.610: 1 Chirality restraints: 2506 Sorted by residual: chirality pdb=" C3' DA G 27 " pdb=" C4' DA G 27 " pdb=" O3' DA G 27 " pdb=" C2' DA G 27 " both_signs ideal model delta sigma weight residual False -2.73 -2.12 -0.61 2.00e-01 2.50e+01 9.29e+00 chirality pdb=" C1' DG G 28 " pdb=" O4' DG G 28 " pdb=" C2' DG G 28 " pdb=" N9 DG G 28 " both_signs ideal model delta sigma weight residual False 2.43 2.05 0.38 2.00e-01 2.50e+01 3.62e+00 chirality pdb=" C3' DG G 28 " pdb=" C4' DG G 28 " pdb=" O3' DG G 28 " pdb=" C2' DG G 28 " both_signs ideal model delta sigma weight residual False -2.73 -2.43 -0.31 2.00e-01 2.50e+01 2.33e+00 ... (remaining 2503 not shown) Planarity restraints: 2393 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA G 27 " 0.012 2.00e-02 2.50e+03 4.28e-02 5.04e+01 pdb=" N9 DA G 27 " -0.092 2.00e-02 2.50e+03 pdb=" C8 DA G 27 " 0.031 2.00e-02 2.50e+03 pdb=" N7 DA G 27 " 0.068 2.00e-02 2.50e+03 pdb=" C5 DA G 27 " -0.017 2.00e-02 2.50e+03 pdb=" C6 DA G 27 " -0.010 2.00e-02 2.50e+03 pdb=" N6 DA G 27 " -0.055 2.00e-02 2.50e+03 pdb=" N1 DA G 27 " 0.050 2.00e-02 2.50e+03 pdb=" C2 DA G 27 " 0.013 2.00e-02 2.50e+03 pdb=" N3 DA G 27 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DA G 27 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG G 28 " -0.080 2.00e-02 2.50e+03 3.42e-02 3.50e+01 pdb=" N9 DG G 28 " 0.044 2.00e-02 2.50e+03 pdb=" C8 DG G 28 " 0.012 2.00e-02 2.50e+03 pdb=" N7 DG G 28 " 0.023 2.00e-02 2.50e+03 pdb=" C5 DG G 28 " 0.009 2.00e-02 2.50e+03 pdb=" C6 DG G 28 " 0.018 2.00e-02 2.50e+03 pdb=" O6 DG G 28 " -0.063 2.00e-02 2.50e+03 pdb=" N1 DG G 28 " 0.003 2.00e-02 2.50e+03 pdb=" C2 DG G 28 " -0.003 2.00e-02 2.50e+03 pdb=" N2 DG G 28 " 0.005 2.00e-02 2.50e+03 pdb=" N3 DG G 28 " 0.017 2.00e-02 2.50e+03 pdb=" C4 DG G 28 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA G 29 " -0.032 2.00e-02 2.50e+03 2.10e-02 1.21e+01 pdb=" N9 DA G 29 " 0.001 2.00e-02 2.50e+03 pdb=" C8 DA G 29 " 0.011 2.00e-02 2.50e+03 pdb=" N7 DA G 29 " 0.016 2.00e-02 2.50e+03 pdb=" C5 DA G 29 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DA G 29 " 0.017 2.00e-02 2.50e+03 pdb=" N6 DA G 29 " -0.047 2.00e-02 2.50e+03 pdb=" N1 DA G 29 " 0.020 2.00e-02 2.50e+03 pdb=" C2 DA G 29 " -0.006 2.00e-02 2.50e+03 pdb=" N3 DA G 29 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DA G 29 " 0.021 2.00e-02 2.50e+03 ... (remaining 2390 not shown) Histogram of nonbonded interaction distances: 1.30 - 2.02: 6 2.02 - 2.74: 1324 2.74 - 3.46: 20831 3.46 - 4.18: 39221 4.18 - 4.90: 67429 Nonbonded interactions: 128811 Sorted by model distance: nonbonded pdb=" NE ARG A 464 " pdb=" OP1 DT G 22 " model vdw 1.297 3.120 nonbonded pdb=" NH2 ARG B 464 " pdb=" OP1 DT I 22 " model vdw 1.298 3.120 nonbonded pdb=" NE ARG A 468 " pdb=" N2 DG G 21 " model vdw 1.351 3.200 nonbonded pdb=" N4 DC H 23 " pdb=" O6 DG G 28 " model vdw 1.800 3.120 nonbonded pdb=" CZ ARG A 468 " pdb=" N2 DG G 21 " model vdw 1.909 3.350 ... (remaining 128806 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 6 through 10 and (name N or name CA or name C or name O o \ r name CB )) or resid 11 through 78 or (resid 79 and (name N or name CA or name \ C or name O or name CB or name CG )) or resid 80 through 108 or (resid 109 and ( \ name N or name CA or name C or name O or name CB )) or resid 110 or (resid 111 t \ hrough 112 and (name N or name CA or name C or name O or name CB )) or resid 113 \ through 117 or (resid 118 and (name N or name CA or name C or name O or name CB \ )) or resid 119 through 121 or (resid 122 and (name N or name CA or name C or n \ ame O or name CB )) or resid 123 through 127 or (resid 128 and (name N or name C \ A or name C or name O or name CB )) or resid 129 through 175 or (resid 176 and ( \ name N or name CA or name C or name O or name CB )) or resid 177 through 183 or \ resid 185 through 211 or (resid 212 and (name N or name CA or name C or name O o \ r name CB )) or resid 213 through 282 or (resid 283 and (name N or name CA or na \ me C or name O or name CB )) or resid 284 through 308 or (resid 309 and (name N \ or name CA or name C or name O or name CB or name CG or name CD or name NE )) or \ resid 310 through 313 or (resid 314 and (name N or name CA or name C or name O \ or name CB or name CG or name CD )) or resid 315 through 355 or (resid 356 and ( \ name N or name CA or name C or name O or name CB or name CG or name CD or name N \ E )) or resid 357 through 358 or (resid 359 through 361 and (name N or name CA o \ r name C or name O or name CB )) or resid 362 through 369 or (resid 370 and (nam \ e N or name CA or name C or name O or name CB or name CG or name CD or name NE ) \ ) or resid 371 through 376 or (resid 377 and (name N or name CA or name C or nam \ e O or name CB or name CG or name CD or name NE )) or resid 378 through 411 or ( \ resid 412 and (name N or name CA or name C or name O or name CB )) or resid 413 \ through 439 or (resid 440 and (name N or name CA or name C or name O or name CB \ )) or resid 441 through 442 or (resid 443 through 444 and (name N or name CA or \ name C or name O or name CB )) or resid 445 through 457 or (resid 458 and (name \ N or name CA or name C or name O or name CB or name CG or name CD or name CE )) \ or resid 459 through 473 or (resid 474 and (name N or name CA or name C or name \ O or name CB or name CG or name CD )) or resid 475 through 497 or (resid 498 and \ (name N or name CA or name C or name O or name CB )) or resid 499 through 503 o \ r (resid 504 and (name N or name CA or name C or name O or name CB or name CG )) \ or resid 505 through 510)) selection = (chain 'D' and ((resid 6 through 10 and (name N or name CA or name C or name O o \ r name CB )) or resid 11 through 17 or (resid 18 and (name N or name CA or name \ C or name O or name CB )) or resid 19 or (resid 20 and (name N or name CA or nam \ e C or name O or name CB )) or resid 21 through 22 or (resid 23 and (name N or n \ ame CA or name C or name O or name CB )) or resid 24 through 32 or (resid 33 and \ (name N or name CA or name C or name O or name CB or name CG )) or resid 34 thr \ ough 35 or (resid 36 and (name N or name CA or name C or name O or name CB )) or \ resid 37 or (resid 38 through 44 and (name N or name CA or name C or name O or \ name CB )) or resid 45 through 51 or (resid 52 and (name N or name CA or name C \ or name O or name CB or name CG or name CD )) or resid 53 through 59 or (resid 6 \ 0 through 61 and (name N or name CA or name C or name O or name CB )) or (resid \ 62 through 67 and (name N or name CA or name C or name O or name CB )) or resid \ 68 through 72 or (resid 73 and (name N or name CA or name C or name O or name CB \ )) or resid 74 through 80 or (resid 81 and (name N or name CA or name C or name \ O or name CB or name CG1 or name CG2)) or resid 82 through 96 or (resid 97 and \ (name N or name CA or name C or name O or name CB or name CG )) or resid 98 thro \ ugh 138 or (resid 139 and (name N or name CA or name C or name O or name CB )) o \ r resid 140 through 144 or (resid 145 and (name N or name CA or name C or name O \ or name CB )) or resid 146 or (resid 147 and (name N or name CA or name C or na \ me O or name CB )) or resid 148 through 151 or (resid 152 and (name N or name CA \ or name C or name O or name CB )) or resid 153 through 160 or (resid 161 and (n \ ame N or name CA or name C or name O or name CB )) or resid 175 through 183 or r \ esid 185 through 209 or (resid 210 and (name N or name CA or name C or name O or \ name CB or name CG or name CD or name NE )) or resid 211 through 214 or (resid \ 215 and (name N or name CA or name C or name O or name CB )) or (resid 216 and ( \ name N or name CA or name C or name O or name CB or name CG or name CD )) or res \ id 217 through 227 or (resid 228 and (name N or name CA or name C or name O or n \ ame CB or name CG )) or resid 229 through 231 or (resid 232 and (name N or name \ CA or name C or name O or name CB or name CG or name CD )) or resid 233 through \ 239 or (resid 240 and (name N or name CA or name C or name O or name CB )) or re \ sid 241 through 244 or (resid 245 and (name N or name CA or name C or name O or \ name CB or name CG or name CD or name CE )) or resid 246 through 265 or (resid 2 \ 66 through 268 and (name N or name CA or name C or name O or name CB )) or resid \ 269 through 285 or (resid 286 through 287 and (name N or name CA or name C or n \ ame O or name CB )) or resid 288 through 292 or (resid 293 and (name N or name C \ A or name C or name O or name CB )) or resid 294 through 297 or (resid 298 and ( \ name N or name CA or name C or name O or name CB )) or resid 299 through 315 or \ (resid 316 and (name N or name CA or name C or name O or name CB )) or resid 317 \ through 318 or (resid 319 through 320 and (name N or name CA or name C or name \ O or name CB )) or resid 321 through 325 or (resid 326 through 328 and (name N o \ r name CA or name C or name O or name CB )) or resid 329 through 360 or (resid 3 \ 61 and (name N or name CA or name C or name O or name CB )) or resid 362 through \ 383 or (resid 384 through 386 and (name N or name CA or name C or name O or nam \ e CB )) or resid 387 through 408 or (resid 409 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE )) or resid 410 through 41 \ 2 or (resid 413 and (name N or name CA or name C or name O or name CB or name CG \ or name CD or name NE )) or resid 414 through 416 or (resid 417 and (name N or \ name CA or name C or name O or name CB or name CG )) or resid 418 through 451 or \ (resid 452 and (name N or name CA or name C or name O or name CB )) or resid 45 \ 3 through 459 or (resid 460 and (name N or name CA or name C or name O or name C \ B )) or resid 461 through 507 or (resid 508 through 509 and (name N or name CA o \ r name C or name O or name CB )) or resid 510)) } ncs_group { reference = (chain 'B' and (resid 174 through 175 or (resid 176 and (name N or name CA or na \ me C or name O or name CB )) or resid 177 through 204 or (resid 205 and (name N \ or name CA or name C or name O or name CB )) or resid 206 through 209 or (resid \ 210 and (name N or name CA or name C or name O or name CB or name CG or name CD \ or name NE )) or resid 211 or (resid 212 and (name N or name CA or name C or nam \ e O or name CB )) or resid 213 or (resid 214 through 215 and (name N or name CA \ or name C or name O or name CB )) or resid 216 through 223 or (resid 224 through \ 225 and (name N or name CA or name C or name O or name CB )) or resid 226 throu \ gh 227 or (resid 228 through 229 and (name N or name CA or name C or name O or n \ ame CB )) or resid 230 through 231 or (resid 232 and (name N or name CA or name \ C or name O or name CB or name CG or name CD )) or resid 233 through 238 or (res \ id 239 and (name N or name CA or name C or name O or name CB )) or (resid 240 an \ d (name N or name CA or name C or name O or name CB or name CG )) or (resid 241 \ and (name N or name CA or name C or name O or name CB or name CG or name CD )) o \ r resid 242 through 244 or (resid 245 and (name N or name CA or name C or name O \ or name CB or name CG )) or resid 246 through 264 or (resid 265 through 268 and \ (name N or name CA or name C or name O or name CB )) or resid 269 or (resid 270 \ and (name N or name CA or name C or name O or name CB )) or resid 271 or (resid \ 272 through 273 and (name N or name CA or name C or name O or name CB )) or res \ id 274 through 282 or (resid 283 and (name N or name CA or name C or name O or n \ ame CB or name CG or name CD )) or resid 284 through 292 or (resid 293 and (name \ N or name CA or name C or name O or name CB )) or resid 294 through 296 or (res \ id 297 and (name N or name CA or name C or name O or name CB )) or resid 298 thr \ ough 308 or (resid 309 and (name N or name CA or name C or name O or name CB )) \ or (resid 310 through 312 and (name N or name CA or name C or name O or name CB \ )) or resid 313 through 315 or (resid 316 and (name N or name CA or name C or na \ me O or name CB or name CG or name CD )) or resid 317 through 355 or (resid 356 \ and (name N or name CA or name C or name O or name CB or name CG or name CD )) o \ r resid 357 through 360 or (resid 361 and (name N or name CA or name C or name O \ or name CB )) or resid 362 through 369 or (resid 370 and (name N or name CA or \ name C or name O or name CB or name CG or name CD or name NE )) or resid 371 thr \ ough 383 or (resid 384 through 386 and (name N or name CA or name C or name O or \ name CB )) or resid 387 through 413 or (resid 414 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name CE )) or resid 415 throug \ h 449 or (resid 450 through 452 and (name N or name CA or name C or name O or na \ me CB )) or resid 453 or (resid 454 and (name N or name CA or name C or name O o \ r name CB )) or resid 455 through 508 or (resid 509 through 510 and (name N or n \ ame CA or name C or name O or name CB )))) selection = (chain 'C' and (resid 174 through 411 or (resid 412 and (name N or name CA or na \ me C or name O or name CB or name CG )) or resid 413 through 442 or (resid 443 a \ nd (name N or name CA or name C or name O or name CB or name CG )) or resid 444 \ through 451 or (resid 452 and (name N or name CA or name C or name O or name CB \ )) or resid 453 through 457 or (resid 458 and (name N or name CA or name C or na \ me O or name CB or name CG or name CD )) or resid 459 through 510)) } ncs_group { reference = chain 'E' selection = (chain 'G' and resid 14 through 28) } ncs_group { reference = chain 'F' selection = (chain 'H' and resid 23 through 37) } 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=0.18 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: 2.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 17.840 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 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 : 0.004 0.163 16130 Z= 0.360 Angle : 0.656 15.465 22556 Z= 0.478 Chirality : 0.046 0.610 2506 Planarity : 0.004 0.046 2393 Dihedral : 24.053 178.705 5971 Min Nonbonded Distance : 1.297 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 4.99 % Allowed : 25.47 % Favored : 69.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.21), residues: 1663 helix: 1.21 (0.19), residues: 828 sheet: -1.24 (0.52), residues: 82 loop : -1.64 (0.21), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 189 TYR 0.010 0.001 TYR D 138 PHE 0.010 0.001 PHE A 403 TRP 0.014 0.001 TRP B 247 HIS 0.003 0.001 HIS D 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.36 (16130) covalent geometry : angle 0.65553 / 0.48 (22556) hydrogen bonds : bond 0.13591 / 9.63 ( 760) hydrogen bonds : angle 5.16106 / 3.81 ( 2067) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3326 Ramachandran restraints generated. 1663 Oldfield, 0 Emsley, 1663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3326 Ramachandran restraints generated. 1663 Oldfield, 0 Emsley, 1663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 82 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 217 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8189 (tp) REVERT: A 457 ARG cc_start: 0.8113 (ttt90) cc_final: 0.7444 (tmt170) outliers start: 55 outliers final: 52 residues processed: 135 average time/residue: 0.1308 time to fit residues: 26.8581 Evaluate side-chains 132 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 79 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 183 ARG Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 282 ARG Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 333 ASP Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain B residue 183 ARG Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 240 ASN Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 409 ARG Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain C residue 186 SER Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 282 ARG Chi-restraints excluded: chain C residue 409 ARG Chi-restraints excluded: chain C residue 437 SER Chi-restraints excluded: chain C residue 488 ARG Chi-restraints excluded: chain C residue 489 HIS Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 50 TRP Chi-restraints excluded: chain D residue 54 ASP Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 130 SER Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 186 SER Chi-restraints excluded: chain D residue 188 THR Chi-restraints excluded: chain D residue 200 LYS Chi-restraints excluded: chain D residue 237 THR Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 437 SER Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 469 THR Chi-restraints excluded: chain D residue 493 VAL Chi-restraints excluded: chain D residue 507 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 0.0050 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 3.9990 overall best weight: 1.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 297 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.118860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.095725 restraints weight = 29594.858| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 1.47 r_work: 0.3058 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2936 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2936 r_free = 0.2936 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2936 r_free = 0.2936 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (6 function evaluations) r_final: 0.2936 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.0541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16130 Z= 0.172 Angle : 0.599 10.784 22556 Z= 0.333 Chirality : 0.046 0.328 2506 Planarity : 0.005 0.051 2393 Dihedral : 24.819 178.778 3447 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 6.59 % Allowed : 22.71 % Favored : 70.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.21), residues: 1663 helix: 1.22 (0.19), residues: 825 sheet: -1.42 (0.51), residues: 83 loop : -1.62 (0.22), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 468 TYR 0.014 0.001 TYR D 441 PHE 0.010 0.001 PHE D 136 TRP 0.010 0.001 TRP B 247 HIS 0.005 0.001 HIS D 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.17 (16130) covalent geometry : angle 0.59894 / 0.33 (22556) hydrogen bonds : bond 0.04399 / 3.10 ( 760) hydrogen bonds : angle 3.92879 / 2.90 ( 2067) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3326 Ramachandran restraints generated. 1663 Oldfield, 0 Emsley, 1663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3326 Ramachandran restraints generated. 1663 Oldfield, 0 Emsley, 1663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 76 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 372 MET cc_start: 0.8472 (OUTLIER) cc_final: 0.7663 (mtt) REVERT: B 424 LYS cc_start: 0.8391 (OUTLIER) cc_final: 0.7183 (mppt) REVERT: C 301 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.6785 (mp0) REVERT: D 236 ASN cc_start: 0.8907 (OUTLIER) cc_final: 0.8251 (t0) outliers start: 73 outliers final: 50 residues processed: 138 average time/residue: 0.1064 time to fit residues: 23.2133 Evaluate side-chains 126 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 72 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 282 ARG Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 333 ASP Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 297 ASN Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 409 ARG Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 424 LYS Chi-restraints excluded: chain B residue 468 ARG Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 190 ASP Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 301 GLU Chi-restraints excluded: chain C residue 333 ASP Chi-restraints excluded: chain C residue 348 ILE Chi-restraints excluded: chain C residue 374 ILE Chi-restraints excluded: chain C residue 437 SER Chi-restraints excluded: chain C residue 468 ARG Chi-restraints excluded: chain C residue 489 HIS Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 50 TRP Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 186 SER Chi-restraints excluded: chain D residue 188 THR Chi-restraints excluded: chain D residue 200 LYS Chi-restraints excluded: chain D residue 236 ASN Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 390 MET Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain D residue 437 SER Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 456 MET Chi-restraints excluded: chain D residue 469 THR Chi-restraints excluded: chain D residue 493 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 144 optimal weight: 0.0370 chunk 66 optimal weight: 4.9990 chunk 19 optimal weight: 10.0000 chunk 149 optimal weight: 3.9990 chunk 21 optimal weight: 0.4980 chunk 96 optimal weight: 0.8980 chunk 105 optimal weight: 0.9980 chunk 138 optimal weight: 0.0570 chunk 127 optimal weight: 0.6980 chunk 94 optimal weight: 1.9990 chunk 151 optimal weight: 0.9980 overall best weight: 0.4376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 507 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.120801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.097289 restraints weight = 38931.358| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.06 r_work: 0.3039 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3042 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3042 r_free = 0.3042 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3042 r_free = 0.3042 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3042 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.0640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 16130 Z= 0.116 Angle : 0.545 10.476 22556 Z= 0.305 Chirality : 0.043 0.294 2506 Planarity : 0.004 0.074 2393 Dihedral : 24.779 179.751 3397 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 5.70 % Allowed : 23.24 % Favored : 71.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.21), residues: 1663 helix: 1.40 (0.19), residues: 827 sheet: -1.31 (0.51), residues: 88 loop : -1.58 (0.22), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 468 TYR 0.009 0.001 TYR D 138 PHE 0.010 0.001 PHE A 403 TRP 0.013 0.001 TRP A 247 HIS 0.003 0.001 HIS D 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.12 (16130) covalent geometry : angle 0.54518 / 0.30 (22556) hydrogen bonds : bond 0.03551 / 2.51 ( 760) hydrogen bonds : angle 3.69576 / 2.73 ( 2067) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3326 Ramachandran restraints generated. 1663 Oldfield, 0 Emsley, 1663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3326 Ramachandran restraints generated. 1663 Oldfield, 0 Emsley, 1663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 81 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 510 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7513 (mt) REVERT: B 372 MET cc_start: 0.8338 (OUTLIER) cc_final: 0.7619 (mtt) REVERT: C 301 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.6775 (mp0) REVERT: D 236 ASN cc_start: 0.8847 (OUTLIER) cc_final: 0.8257 (t0) REVERT: D 346 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7097 (mp0) REVERT: D 510 LEU cc_start: 0.7473 (OUTLIER) cc_final: 0.7146 (pp) outliers start: 63 outliers final: 39 residues processed: 134 average time/residue: 0.1170 time to fit residues: 24.3575 Evaluate side-chains 123 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 78 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 282 ARG Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 333 ASP Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 409 ARG Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 468 ARG Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 190 ASP Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 301 GLU Chi-restraints excluded: chain C residue 333 ASP Chi-restraints excluded: chain C residue 348 ILE Chi-restraints excluded: chain C residue 374 ILE Chi-restraints excluded: chain C residue 468 ARG Chi-restraints excluded: chain C residue 489 HIS Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain D residue 3 TYR Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 50 TRP Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 186 SER Chi-restraints excluded: chain D residue 236 ASN Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 346 GLU Chi-restraints excluded: chain D residue 390 MET Chi-restraints excluded: chain D residue 437 SER Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 469 THR Chi-restraints excluded: chain D residue 493 VAL Chi-restraints excluded: chain D residue 510 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 37 optimal weight: 0.5980 chunk 80 optimal weight: 0.0570 chunk 162 optimal weight: 0.9990 chunk 173 optimal weight: 8.9990 chunk 8 optimal weight: 0.6980 chunk 111 optimal weight: 0.9990 chunk 74 optimal weight: 0.2980 chunk 26 optimal weight: 0.0670 chunk 119 optimal weight: 0.9980 chunk 100 optimal weight: 0.6980 chunk 84 optimal weight: 3.9990 overall best weight: 0.3436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 ASN C 308 ASN D 507 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.122128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.098776 restraints weight = 37257.808| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.92 r_work: 0.3079 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3080 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3080 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.0854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 16130 Z= 0.110 Angle : 0.524 10.218 22556 Z= 0.291 Chirality : 0.042 0.301 2506 Planarity : 0.004 0.063 2393 Dihedral : 24.732 178.953 3388 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 4.90 % Allowed : 23.78 % Favored : 71.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.21), residues: 1663 helix: 1.56 (0.19), residues: 827 sheet: -1.16 (0.51), residues: 88 loop : -1.54 (0.22), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 468 TYR 0.009 0.001 TYR D 138 PHE 0.010 0.001 PHE A 403 TRP 0.013 0.001 TRP A 179 HIS 0.003 0.001 HIS D 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00200 / 0.11 (16130) covalent geometry : angle 0.52371 / 0.29 (22556) hydrogen bonds : bond 0.03138 / 2.23 ( 760) hydrogen bonds : angle 3.50376 / 2.59 ( 2067) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3326 Ramachandran restraints generated. 1663 Oldfield, 0 Emsley, 1663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3326 Ramachandran restraints generated. 1663 Oldfield, 0 Emsley, 1663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 86 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 457 ARG cc_start: 0.8097 (ttt90) cc_final: 0.7470 (tmt170) REVERT: B 372 MET cc_start: 0.8267 (OUTLIER) cc_final: 0.7660 (mtt) REVERT: C 301 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.6433 (mp0) REVERT: D 236 ASN cc_start: 0.8893 (OUTLIER) cc_final: 0.8280 (t0) REVERT: D 346 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7048 (mp0) REVERT: D 510 LEU cc_start: 0.7412 (OUTLIER) cc_final: 0.7090 (pp) outliers start: 54 outliers final: 35 residues processed: 130 average time/residue: 0.1070 time to fit residues: 22.4187 Evaluate side-chains 121 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 81 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 282 ARG Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 333 ASP Chi-restraints excluded: chain B residue 297 ASN Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 468 ARG Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 190 ASP Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 301 GLU Chi-restraints excluded: chain C residue 333 ASP Chi-restraints excluded: chain C residue 348 ILE Chi-restraints excluded: chain C residue 437 SER Chi-restraints excluded: chain C residue 468 ARG Chi-restraints excluded: chain C residue 489 HIS Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain D residue 3 TYR Chi-restraints excluded: chain D residue 50 TRP Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 186 SER Chi-restraints excluded: chain D residue 236 ASN Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 334 LYS Chi-restraints excluded: chain D residue 346 GLU Chi-restraints excluded: chain D residue 390 MET Chi-restraints excluded: chain D residue 402 SER Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 469 THR Chi-restraints excluded: chain D residue 493 VAL Chi-restraints excluded: chain D residue 510 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 161 optimal weight: 0.0020 chunk 121 optimal weight: 1.9990 chunk 3 optimal weight: 8.9990 chunk 101 optimal weight: 5.9990 chunk 9 optimal weight: 10.0000 chunk 152 optimal weight: 0.5980 chunk 153 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 chunk 26 optimal weight: 0.0470 chunk 78 optimal weight: 0.0170 chunk 65 optimal weight: 2.9990 overall best weight: 0.5326 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 90 GLN D 507 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.121845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.098126 restraints weight = 42121.546| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.21 r_work: 0.3049 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3052 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3052 r_free = 0.3052 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3052 r_free = 0.3052 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3052 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.0889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 16130 Z= 0.112 Angle : 0.524 10.073 22556 Z= 0.291 Chirality : 0.043 0.301 2506 Planarity : 0.004 0.055 2393 Dihedral : 24.742 179.006 3376 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 4.54 % Allowed : 24.04 % Favored : 71.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.21), residues: 1663 helix: 1.59 (0.19), residues: 827 sheet: -1.11 (0.51), residues: 88 loop : -1.52 (0.22), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 295 TYR 0.015 0.001 TYR D 94 PHE 0.009 0.001 PHE A 403 TRP 0.011 0.001 TRP A 247 HIS 0.003 0.001 HIS D 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.11 (16130) covalent geometry : angle 0.52443 / 0.29 (22556) hydrogen bonds : bond 0.03169 / 2.24 ( 760) hydrogen bonds : angle 3.47785 / 2.57 ( 2067) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3326 Ramachandran restraints generated. 1663 Oldfield, 0 Emsley, 1663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3326 Ramachandran restraints generated. 1663 Oldfield, 0 Emsley, 1663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 81 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 457 ARG cc_start: 0.8120 (ttt90) cc_final: 0.7489 (tmt170) REVERT: B 297 ASN cc_start: 0.7657 (OUTLIER) cc_final: 0.7393 (p0) REVERT: B 372 MET cc_start: 0.8308 (OUTLIER) cc_final: 0.7481 (mtp) REVERT: C 301 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.6446 (mp0) REVERT: D 236 ASN cc_start: 0.8909 (OUTLIER) cc_final: 0.8269 (t0) REVERT: D 346 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7091 (mp0) REVERT: D 510 LEU cc_start: 0.7408 (OUTLIER) cc_final: 0.7081 (pp) outliers start: 50 outliers final: 36 residues processed: 119 average time/residue: 0.0946 time to fit residues: 18.2307 Evaluate side-chains 122 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 80 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 282 ARG Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 333 ASP Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain B residue 297 ASN Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 468 ARG Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 190 ASP Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 301 GLU Chi-restraints excluded: chain C residue 333 ASP Chi-restraints excluded: chain C residue 348 ILE Chi-restraints excluded: chain C residue 437 SER Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 468 ARG Chi-restraints excluded: chain C residue 489 HIS Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain D residue 3 TYR Chi-restraints excluded: chain D residue 50 TRP Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 186 SER Chi-restraints excluded: chain D residue 236 ASN Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 346 GLU Chi-restraints excluded: chain D residue 390 MET Chi-restraints excluded: chain D residue 402 SER Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 456 MET Chi-restraints excluded: chain D residue 493 VAL Chi-restraints excluded: chain D residue 510 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 105 optimal weight: 0.8980 chunk 159 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 58 optimal weight: 0.0870 chunk 158 optimal weight: 0.9980 chunk 148 optimal weight: 3.9990 chunk 129 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 169 optimal weight: 10.0000 chunk 161 optimal weight: 0.0980 chunk 116 optimal weight: 0.7980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 236 ASN D 90 GLN D 507 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.121884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.099234 restraints weight = 43506.153| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 2.15 r_work: 0.3057 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3066 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3066 r_free = 0.3066 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3066 r_free = 0.3066 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3066 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.0958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 16130 Z= 0.111 Angle : 0.523 9.753 22556 Z= 0.289 Chirality : 0.043 0.298 2506 Planarity : 0.004 0.050 2393 Dihedral : 24.749 179.214 3375 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 4.54 % Allowed : 23.60 % Favored : 71.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.21), residues: 1663 helix: 1.63 (0.19), residues: 827 sheet: -1.04 (0.51), residues: 88 loop : -1.50 (0.22), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 189 TYR 0.013 0.001 TYR D 94 PHE 0.009 0.001 PHE A 403 TRP 0.011 0.001 TRP A 179 HIS 0.003 0.001 HIS D 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.11 (16130) covalent geometry : angle 0.52336 / 0.29 (22556) hydrogen bonds : bond 0.03113 / 2.21 ( 760) hydrogen bonds : angle 3.42115 / 2.52 ( 2067) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3326 Ramachandran restraints generated. 1663 Oldfield, 0 Emsley, 1663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3326 Ramachandran restraints generated. 1663 Oldfield, 0 Emsley, 1663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 82 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 457 ARG cc_start: 0.8101 (ttt90) cc_final: 0.7468 (tmt170) REVERT: B 372 MET cc_start: 0.8311 (OUTLIER) cc_final: 0.7519 (mtp) REVERT: C 301 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.6473 (mp0) REVERT: D 236 ASN cc_start: 0.8909 (OUTLIER) cc_final: 0.8282 (t0) REVERT: D 346 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.7081 (mp0) REVERT: D 510 LEU cc_start: 0.7404 (OUTLIER) cc_final: 0.7053 (pp) outliers start: 50 outliers final: 36 residues processed: 122 average time/residue: 0.0860 time to fit residues: 16.9587 Evaluate side-chains 124 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 83 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 282 ARG Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 333 ASP Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 468 ARG Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 190 ASP Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 301 GLU Chi-restraints excluded: chain C residue 333 ASP Chi-restraints excluded: chain C residue 348 ILE Chi-restraints excluded: chain C residue 374 ILE Chi-restraints excluded: chain C residue 437 SER Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 468 ARG Chi-restraints excluded: chain C residue 489 HIS Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain D residue 3 TYR Chi-restraints excluded: chain D residue 50 TRP Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 236 ASN Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 334 LYS Chi-restraints excluded: chain D residue 346 GLU Chi-restraints excluded: chain D residue 390 MET Chi-restraints excluded: chain D residue 402 SER Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 493 VAL Chi-restraints excluded: chain D residue 510 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 73 optimal weight: 0.2980 chunk 117 optimal weight: 0.0020 chunk 33 optimal weight: 0.9980 chunk 108 optimal weight: 0.7980 chunk 166 optimal weight: 10.0000 chunk 44 optimal weight: 0.0270 chunk 156 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 140 optimal weight: 0.8980 overall best weight: 0.3846 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 297 ASN D 90 GLN D 507 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.122897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.099661 restraints weight = 37029.987| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 1.90 r_work: 0.3088 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3091 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3091 r_free = 0.3091 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3091 r_free = 0.3091 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3091 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.1051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 16130 Z= 0.105 Angle : 0.514 9.410 22556 Z= 0.284 Chirality : 0.042 0.294 2506 Planarity : 0.004 0.048 2393 Dihedral : 24.727 179.481 3373 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 4.36 % Allowed : 23.60 % Favored : 72.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.21), residues: 1663 helix: 1.70 (0.19), residues: 825 sheet: -1.14 (0.50), residues: 88 loop : -1.49 (0.22), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 338 TYR 0.010 0.001 TYR D 94 PHE 0.010 0.001 PHE A 403 TRP 0.012 0.001 TRP A 179 HIS 0.003 0.000 HIS D 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00192 / 0.10 (16130) covalent geometry : angle 0.51433 / 0.28 (22556) hydrogen bonds : bond 0.02942 / 2.09 ( 760) hydrogen bonds : angle 3.37226 / 2.49 ( 2067) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3326 Ramachandran restraints generated. 1663 Oldfield, 0 Emsley, 1663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3326 Ramachandran restraints generated. 1663 Oldfield, 0 Emsley, 1663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 85 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 295 ARG cc_start: 0.7996 (OUTLIER) cc_final: 0.6544 (mtt180) REVERT: A 399 ARG cc_start: 0.8787 (OUTLIER) cc_final: 0.8536 (mtm110) REVERT: A 457 ARG cc_start: 0.8061 (ttt90) cc_final: 0.7467 (tmt170) REVERT: B 372 MET cc_start: 0.8282 (OUTLIER) cc_final: 0.7495 (mtp) REVERT: C 301 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.6418 (mp0) REVERT: D 236 ASN cc_start: 0.8859 (OUTLIER) cc_final: 0.8237 (t0) REVERT: D 346 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.7211 (mp0) REVERT: D 510 LEU cc_start: 0.7412 (OUTLIER) cc_final: 0.7069 (pp) outliers start: 48 outliers final: 36 residues processed: 123 average time/residue: 0.1085 time to fit residues: 20.6733 Evaluate side-chains 123 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 80 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 282 ARG Chi-restraints excluded: chain A residue 295 ARG Chi-restraints excluded: chain A residue 333 ASP Chi-restraints excluded: chain A residue 399 ARG Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain B residue 297 ASN Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 468 ARG Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain C residue 190 ASP Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 301 GLU Chi-restraints excluded: chain C residue 333 ASP Chi-restraints excluded: chain C residue 348 ILE Chi-restraints excluded: chain C residue 437 SER Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 468 ARG Chi-restraints excluded: chain C residue 489 HIS Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain D residue 3 TYR Chi-restraints excluded: chain D residue 50 TRP Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 236 ASN Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 346 GLU Chi-restraints excluded: chain D residue 390 MET Chi-restraints excluded: chain D residue 402 SER Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 493 VAL Chi-restraints excluded: chain D residue 507 ASN Chi-restraints excluded: chain D residue 510 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 68 optimal weight: 0.7980 chunk 121 optimal weight: 4.9990 chunk 88 optimal weight: 0.9980 chunk 162 optimal weight: 1.9990 chunk 146 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 135 optimal weight: 3.9990 chunk 148 optimal weight: 4.9990 chunk 14 optimal weight: 0.3980 chunk 15 optimal weight: 6.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 297 ASN D 90 GLN D 507 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.121900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.098416 restraints weight = 33434.772| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 1.60 r_work: 0.3102 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2986 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2986 r_free = 0.2986 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2986 r_free = 0.2986 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2986 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.1048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 16130 Z= 0.122 Angle : 0.530 9.538 22556 Z= 0.291 Chirality : 0.043 0.302 2506 Planarity : 0.004 0.048 2393 Dihedral : 24.739 178.974 3372 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 4.36 % Allowed : 23.78 % Favored : 71.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.21), residues: 1663 helix: 1.65 (0.19), residues: 827 sheet: -1.16 (0.50), residues: 88 loop : -1.48 (0.22), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 152 TYR 0.012 0.001 TYR B 441 PHE 0.008 0.001 PHE A 403 TRP 0.010 0.001 TRP A 179 HIS 0.003 0.001 HIS D 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.12 (16130) covalent geometry : angle 0.52998 / 0.29 (22556) hydrogen bonds : bond 0.03150 / 2.24 ( 760) hydrogen bonds : angle 3.39046 / 2.50 ( 2067) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3326 Ramachandran restraints generated. 1663 Oldfield, 0 Emsley, 1663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3326 Ramachandran restraints generated. 1663 Oldfield, 0 Emsley, 1663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 81 time to evaluate : 0.477 Fit side-chains revert: symmetry clash REVERT: A 295 ARG cc_start: 0.8040 (OUTLIER) cc_final: 0.6575 (mtt180) REVERT: A 399 ARG cc_start: 0.8857 (OUTLIER) cc_final: 0.8630 (mtm110) REVERT: A 457 ARG cc_start: 0.8153 (ttt90) cc_final: 0.7534 (tmt170) REVERT: B 372 MET cc_start: 0.8444 (OUTLIER) cc_final: 0.7627 (mtp) REVERT: C 301 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.6591 (mp0) REVERT: D 236 ASN cc_start: 0.8940 (OUTLIER) cc_final: 0.8291 (t0) REVERT: D 346 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.7335 (mp0) REVERT: D 510 LEU cc_start: 0.7558 (OUTLIER) cc_final: 0.7181 (pp) outliers start: 48 outliers final: 38 residues processed: 117 average time/residue: 0.0922 time to fit residues: 17.0119 Evaluate side-chains 124 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 79 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 295 ARG Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 333 ASP Chi-restraints excluded: chain A residue 399 ARG Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain B residue 297 ASN Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 468 ARG Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain C residue 190 ASP Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 301 GLU Chi-restraints excluded: chain C residue 333 ASP Chi-restraints excluded: chain C residue 348 ILE Chi-restraints excluded: chain C residue 437 SER Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 468 ARG Chi-restraints excluded: chain C residue 489 HIS Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain D residue 3 TYR Chi-restraints excluded: chain D residue 50 TRP Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 236 ASN Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 346 GLU Chi-restraints excluded: chain D residue 390 MET Chi-restraints excluded: chain D residue 402 SER Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 456 MET Chi-restraints excluded: chain D residue 469 THR Chi-restraints excluded: chain D residue 493 VAL Chi-restraints excluded: chain D residue 507 ASN Chi-restraints excluded: chain D residue 510 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 53.4175 > 50: distance: 19 - 24: 30.954 distance: 24 - 25: 42.217 distance: 24 - 74: 42.217 distance: 25 - 26: 17.970 distance: 25 - 28: 19.372 distance: 26 - 27: 16.831 distance: 26 - 33: 14.064 distance: 27 - 71: 4.935 distance: 28 - 29: 32.412 distance: 29 - 30: 19.723 distance: 30 - 31: 26.218 distance: 31 - 32: 18.425 distance: 33 - 34: 3.806 distance: 33 - 39: 11.720 distance: 34 - 35: 5.994 distance: 34 - 37: 6.475 distance: 35 - 36: 6.073 distance: 35 - 40: 17.657 distance: 37 - 38: 5.302 distance: 38 - 39: 7.799 distance: 40 - 41: 8.271 distance: 41 - 42: 3.866 distance: 42 - 43: 12.595 distance: 42 - 44: 7.541 distance: 44 - 45: 22.916 distance: 44 - 50: 11.695 distance: 45 - 46: 25.833 distance: 45 - 48: 9.849 distance: 46 - 47: 6.134 distance: 46 - 51: 12.017 distance: 48 - 49: 21.251 distance: 49 - 50: 10.675 distance: 51 - 52: 6.278 distance: 52 - 53: 6.831 distance: 53 - 54: 14.084 distance: 53 - 55: 22.627 distance: 55 - 56: 9.696 distance: 56 - 57: 7.981 distance: 57 - 58: 9.229 distance: 57 - 59: 11.464 distance: 59 - 60: 12.812 distance: 60 - 61: 19.187 distance: 60 - 63: 5.690 distance: 61 - 62: 7.100 distance: 61 - 64: 10.978 distance: 64 - 65: 17.818 distance: 64 - 70: 14.834 distance: 65 - 66: 9.032 distance: 65 - 68: 12.614 distance: 66 - 71: 8.332 distance: 68 - 69: 17.373 distance: 69 - 70: 22.457 distance: 71 - 72: 20.478 distance: 72 - 73: 13.695 distance: 72 - 75: 12.758 distance: 73 - 74: 8.275 distance: 73 - 78: 14.087 distance: 75 - 76: 18.238 distance: 75 - 77: 28.535 distance: 78 - 79: 4.098 distance: 79 - 80: 10.311 distance: 79 - 82: 4.780 distance: 80 - 81: 8.030 distance: 80 - 89: 10.762 distance: 82 - 83: 8.976 distance: 83 - 84: 9.070 distance: 83 - 85: 14.941 distance: 84 - 86: 12.987 distance: 85 - 87: 12.750 distance: 86 - 88: 13.881 distance: 87 - 88: 9.532