Starting phenix.real_space_refine on Fri Aug 7 20:47:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pmk_17762/08_2026/8pmk_17762.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pmk_17762/08_2026/8pmk_17762.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8pmk_17762/08_2026/8pmk_17762.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pmk_17762/08_2026/8pmk_17762.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8pmk_17762/08_2026/8pmk_17762.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pmk_17762/08_2026/8pmk_17762.map" } resolution = 2.43 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= 0.000 sd= 0.002 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: 7 Type Number sf(0) Gaussians K 6 8.98 5 Fe 18 7.16 5 P 6 5.49 5 S 162 5.16 5 C 15186 2.51 5 N 4110 2.21 5 O 4470 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23958 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 502, 3953 Classifications: {'peptide': 502} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 29, 'TRANS': 472} Chain breaks: 1 Chain: "A" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 40 Unusual residues: {' K': 1, ' FE': 3, 'BYN': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: B, C, D, E, F Time building chain proxies: 4.68, per 1000 atoms: 0.20 Number of scatterers: 23958 At special positions: 0 Unit cell: (137.268, 152.892, 94.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 18 26.01 K 6 19.00 S 162 16.00 P 6 15.00 O 4470 8.00 N 4110 7.00 C 15186 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: 2.07 Conformation dependent library (CDL) restraints added in 1.0 seconds 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5508 Finding SS restraints... Secondary structure from input PDB file: 114 helices and 36 sheets defined 35.1% alpha, 19.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'A' and resid 20 through 31 Processing helix chain 'A' and resid 46 through 54 Processing helix chain 'A' and resid 80 through 88 removed outlier: 3.510A pdb=" N VAL A 84 " --> pdb=" O ASP A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 106 removed outlier: 3.797A pdb=" N ASP A 105 " --> pdb=" O ALA A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 122 removed outlier: 3.756A pdb=" N GLU A 122 " --> pdb=" O PRO A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 135 removed outlier: 3.630A pdb=" N TRP A 134 " --> pdb=" O ASP A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 162 removed outlier: 3.633A pdb=" N ASP A 162 " --> pdb=" O PRO A 159 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 159 through 162' Processing helix chain 'A' and resid 188 through 197 Processing helix chain 'A' and resid 213 through 221 removed outlier: 3.856A pdb=" N GLY A 221 " --> pdb=" O THR A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 244 removed outlier: 3.592A pdb=" N ALA A 239 " --> pdb=" O GLU A 235 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN A 243 " --> pdb=" O ALA A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 286 removed outlier: 3.765A pdb=" N ALA A 286 " --> pdb=" O GLU A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 324 Processing helix chain 'A' and resid 334 through 342 Processing helix chain 'A' and resid 343 through 357 removed outlier: 3.644A pdb=" N SER A 347 " --> pdb=" O SER A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 402 removed outlier: 3.846A pdb=" N ASN A 393 " --> pdb=" O GLY A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 430 removed outlier: 3.664A pdb=" N ILE A 423 " --> pdb=" O SER A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 502 removed outlier: 3.507A pdb=" N ASN A 501 " --> pdb=" O LYS A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 513 removed outlier: 3.566A pdb=" N ASP A 509 " --> pdb=" O ALA A 505 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER A 513 " --> pdb=" O ASP A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 526 removed outlier: 4.106A pdb=" N SER A 521 " --> pdb=" O GLY A 517 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG A 524 " --> pdb=" O LEU A 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 31 Processing helix chain 'B' and resid 46 through 54 Processing helix chain 'B' and resid 80 through 88 removed outlier: 3.509A pdb=" N VAL B 84 " --> pdb=" O ASP B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 106 removed outlier: 3.797A pdb=" N ASP B 105 " --> pdb=" O ALA B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 122 removed outlier: 3.756A pdb=" N GLU B 122 " --> pdb=" O PRO B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 135 removed outlier: 3.630A pdb=" N TRP B 134 " --> pdb=" O ASP B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 162 removed outlier: 3.633A pdb=" N ASP B 162 " --> pdb=" O PRO B 159 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 159 through 162' Processing helix chain 'B' and resid 188 through 197 Processing helix chain 'B' and resid 213 through 221 removed outlier: 3.855A pdb=" N GLY B 221 " --> pdb=" O THR B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 244 removed outlier: 3.592A pdb=" N ALA B 239 " --> pdb=" O GLU B 235 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLN B 243 " --> pdb=" O ALA B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 286 removed outlier: 3.766A pdb=" N ALA B 286 " --> pdb=" O GLU B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 324 Processing helix chain 'B' and resid 334 through 342 Processing helix chain 'B' and resid 343 through 357 removed outlier: 3.644A pdb=" N SER B 347 " --> pdb=" O SER B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 402 removed outlier: 3.845A pdb=" N ASN B 393 " --> pdb=" O GLY B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 430 removed outlier: 3.665A pdb=" N ILE B 423 " --> pdb=" O SER B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 502 removed outlier: 3.507A pdb=" N ASN B 501 " --> pdb=" O LYS B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 513 removed outlier: 3.565A pdb=" N ASP B 509 " --> pdb=" O ALA B 505 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER B 513 " --> pdb=" O ASP B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 526 removed outlier: 4.106A pdb=" N SER B 521 " --> pdb=" O GLY B 517 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG B 524 " --> pdb=" O LEU B 520 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 31 Processing helix chain 'C' and resid 46 through 54 Processing helix chain 'C' and resid 80 through 88 removed outlier: 3.510A pdb=" N VAL C 84 " --> pdb=" O ASP C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 106 removed outlier: 3.797A pdb=" N ASP C 105 " --> pdb=" O ALA C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 122 removed outlier: 3.757A pdb=" N GLU C 122 " --> pdb=" O PRO C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 135 removed outlier: 3.631A pdb=" N TRP C 134 " --> pdb=" O ASP C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 162 removed outlier: 3.633A pdb=" N ASP C 162 " --> pdb=" O PRO C 159 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 159 through 162' Processing helix chain 'C' and resid 188 through 197 Processing helix chain 'C' and resid 213 through 221 removed outlier: 3.857A pdb=" N GLY C 221 " --> pdb=" O THR C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 244 removed outlier: 3.592A pdb=" N ALA C 239 " --> pdb=" O GLU C 235 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLN C 243 " --> pdb=" O ALA C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 286 removed outlier: 3.765A pdb=" N ALA C 286 " --> pdb=" O GLU C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 324 Processing helix chain 'C' and resid 334 through 342 Processing helix chain 'C' and resid 343 through 357 removed outlier: 3.645A pdb=" N SER C 347 " --> pdb=" O SER C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 389 through 402 removed outlier: 3.845A pdb=" N ASN C 393 " --> pdb=" O GLY C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 419 through 430 removed outlier: 3.665A pdb=" N ILE C 423 " --> pdb=" O SER C 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 502 removed outlier: 3.507A pdb=" N ASN C 501 " --> pdb=" O LYS C 498 " (cutoff:3.500A) Processing helix chain 'C' and resid 504 through 513 removed outlier: 3.565A pdb=" N ASP C 509 " --> pdb=" O ALA C 505 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER C 513 " --> pdb=" O ASP C 509 " (cutoff:3.500A) Processing helix chain 'C' and resid 517 through 526 removed outlier: 4.106A pdb=" N SER C 521 " --> pdb=" O GLY C 517 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG C 524 " --> pdb=" O LEU C 520 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 31 Processing helix chain 'D' and resid 46 through 54 Processing helix chain 'D' and resid 80 through 88 removed outlier: 3.510A pdb=" N VAL D 84 " --> pdb=" O ASP D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 106 removed outlier: 3.797A pdb=" N ASP D 105 " --> pdb=" O ALA D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 122 removed outlier: 3.756A pdb=" N GLU D 122 " --> pdb=" O PRO D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 135 removed outlier: 3.631A pdb=" N TRP D 134 " --> pdb=" O ASP D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 162 removed outlier: 3.632A pdb=" N ASP D 162 " --> pdb=" O PRO D 159 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 159 through 162' Processing helix chain 'D' and resid 188 through 197 Processing helix chain 'D' and resid 213 through 221 removed outlier: 3.856A pdb=" N GLY D 221 " --> pdb=" O THR D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 244 removed outlier: 3.593A pdb=" N ALA D 239 " --> pdb=" O GLU D 235 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN D 243 " --> pdb=" O ALA D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 286 removed outlier: 3.764A pdb=" N ALA D 286 " --> pdb=" O GLU D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 324 Processing helix chain 'D' and resid 334 through 342 Processing helix chain 'D' and resid 343 through 357 removed outlier: 3.644A pdb=" N SER D 347 " --> pdb=" O SER D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 402 removed outlier: 3.846A pdb=" N ASN D 393 " --> pdb=" O GLY D 389 " (cutoff:3.500A) Processing helix chain 'D' and resid 419 through 430 removed outlier: 3.664A pdb=" N ILE D 423 " --> pdb=" O SER D 419 " (cutoff:3.500A) Processing helix chain 'D' and resid 498 through 502 removed outlier: 3.506A pdb=" N ASN D 501 " --> pdb=" O LYS D 498 " (cutoff:3.500A) Processing helix chain 'D' and resid 504 through 513 removed outlier: 3.566A pdb=" N ASP D 509 " --> pdb=" O ALA D 505 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER D 513 " --> pdb=" O ASP D 509 " (cutoff:3.500A) Processing helix chain 'D' and resid 517 through 526 removed outlier: 4.106A pdb=" N SER D 521 " --> pdb=" O GLY D 517 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG D 524 " --> pdb=" O LEU D 520 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 31 Processing helix chain 'E' and resid 46 through 54 Processing helix chain 'E' and resid 80 through 88 removed outlier: 3.509A pdb=" N VAL E 84 " --> pdb=" O ASP E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 106 removed outlier: 3.796A pdb=" N ASP E 105 " --> pdb=" O ALA E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 122 removed outlier: 3.756A pdb=" N GLU E 122 " --> pdb=" O PRO E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 135 removed outlier: 3.631A pdb=" N TRP E 134 " --> pdb=" O ASP E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 159 through 162 removed outlier: 3.633A pdb=" N ASP E 162 " --> pdb=" O PRO E 159 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 159 through 162' Processing helix chain 'E' and resid 188 through 197 Processing helix chain 'E' and resid 213 through 221 removed outlier: 3.857A pdb=" N GLY E 221 " --> pdb=" O THR E 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 244 removed outlier: 3.592A pdb=" N ALA E 239 " --> pdb=" O GLU E 235 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLN E 243 " --> pdb=" O ALA E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 286 removed outlier: 3.765A pdb=" N ALA E 286 " --> pdb=" O GLU E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 320 through 324 Processing helix chain 'E' and resid 334 through 342 Processing helix chain 'E' and resid 343 through 357 removed outlier: 3.644A pdb=" N SER E 347 " --> pdb=" O SER E 343 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 402 removed outlier: 3.846A pdb=" N ASN E 393 " --> pdb=" O GLY E 389 " (cutoff:3.500A) Processing helix chain 'E' and resid 419 through 430 removed outlier: 3.665A pdb=" N ILE E 423 " --> pdb=" O SER E 419 " (cutoff:3.500A) Processing helix chain 'E' and resid 498 through 502 removed outlier: 3.507A pdb=" N ASN E 501 " --> pdb=" O LYS E 498 " (cutoff:3.500A) Processing helix chain 'E' and resid 504 through 513 removed outlier: 3.565A pdb=" N ASP E 509 " --> pdb=" O ALA E 505 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER E 513 " --> pdb=" O ASP E 509 " (cutoff:3.500A) Processing helix chain 'E' and resid 517 through 526 removed outlier: 4.107A pdb=" N SER E 521 " --> pdb=" O GLY E 517 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG E 524 " --> pdb=" O LEU E 520 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 31 Processing helix chain 'F' and resid 46 through 54 Processing helix chain 'F' and resid 80 through 88 removed outlier: 3.509A pdb=" N VAL F 84 " --> pdb=" O ASP F 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 106 removed outlier: 3.797A pdb=" N ASP F 105 " --> pdb=" O ALA F 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 118 through 122 removed outlier: 3.756A pdb=" N GLU F 122 " --> pdb=" O PRO F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 130 through 135 removed outlier: 3.631A pdb=" N TRP F 134 " --> pdb=" O ASP F 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 162 removed outlier: 3.633A pdb=" N ASP F 162 " --> pdb=" O PRO F 159 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 159 through 162' Processing helix chain 'F' and resid 188 through 197 Processing helix chain 'F' and resid 213 through 221 removed outlier: 3.856A pdb=" N GLY F 221 " --> pdb=" O THR F 217 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 244 removed outlier: 3.593A pdb=" N ALA F 239 " --> pdb=" O GLU F 235 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN F 243 " --> pdb=" O ALA F 239 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 286 removed outlier: 3.765A pdb=" N ALA F 286 " --> pdb=" O GLU F 282 " (cutoff:3.500A) Processing helix chain 'F' and resid 320 through 324 Processing helix chain 'F' and resid 334 through 342 Processing helix chain 'F' and resid 343 through 357 removed outlier: 3.645A pdb=" N SER F 347 " --> pdb=" O SER F 343 " (cutoff:3.500A) Processing helix chain 'F' and resid 389 through 402 removed outlier: 3.846A pdb=" N ASN F 393 " --> pdb=" O GLY F 389 " (cutoff:3.500A) Processing helix chain 'F' and resid 419 through 430 removed outlier: 3.664A pdb=" N ILE F 423 " --> pdb=" O SER F 419 " (cutoff:3.500A) Processing helix chain 'F' and resid 498 through 502 removed outlier: 3.506A pdb=" N ASN F 501 " --> pdb=" O LYS F 498 " (cutoff:3.500A) Processing helix chain 'F' and resid 504 through 513 removed outlier: 3.565A pdb=" N ASP F 509 " --> pdb=" O ALA F 505 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER F 513 " --> pdb=" O ASP F 509 " (cutoff:3.500A) Processing helix chain 'F' and resid 517 through 526 removed outlier: 4.106A pdb=" N SER F 521 " --> pdb=" O GLY F 517 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG F 524 " --> pdb=" O LEU F 520 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 41 removed outlier: 6.595A pdb=" N VAL A 35 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N ASN A 63 " --> pdb=" O VAL A 35 " (cutoff:3.500A) removed outlier: 8.451A pdb=" N THR A 37 " --> pdb=" O ASN A 63 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N VAL A 65 " --> pdb=" O THR A 37 " (cutoff:3.500A) removed outlier: 9.597A pdb=" N LYS A 39 " --> pdb=" O VAL A 65 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ARG A 72 " --> pdb=" O ILE A 327 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 111 through 112 removed outlier: 6.529A pdb=" N VAL A 111 " --> pdb=" O LEU A 249 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N LYS A 251 " --> pdb=" O VAL A 111 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL A 250 " --> pdb=" O THR A 259 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 123 through 125 removed outlier: 9.114A pdb=" N ALA A 308 " --> pdb=" O ARG A 274 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N ARG A 274 " --> pdb=" O ALA A 308 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR A 310 " --> pdb=" O HIS A 272 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N GLU A 268 " --> pdb=" O THR A 314 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ILE A 316 " --> pdb=" O VAL A 266 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL A 266 " --> pdb=" O ILE A 316 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL A 157 " --> pdb=" O PRO A 205 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR A 207 " --> pdb=" O CYS A 155 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 123 through 125 removed outlier: 3.771A pdb=" N ASN A 173 " --> pdb=" O THR A 181 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 293 through 296 removed outlier: 7.455A pdb=" N GLY A 303 " --> pdb=" O PHE A 294 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 361 through 365 removed outlier: 3.540A pdb=" N ASN A 363 " --> pdb=" O GLN A 379 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ALA A 408 " --> pdb=" O ILE A 475 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ALA A 477 " --> pdb=" O ALA A 408 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ALA A 410 " --> pdb=" O ALA A 477 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 35 through 41 removed outlier: 6.595A pdb=" N VAL B 35 " --> pdb=" O LEU B 61 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N ASN B 63 " --> pdb=" O VAL B 35 " (cutoff:3.500A) removed outlier: 8.452A pdb=" N THR B 37 " --> pdb=" O ASN B 63 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N VAL B 65 " --> pdb=" O THR B 37 " (cutoff:3.500A) removed outlier: 9.597A pdb=" N LYS B 39 " --> pdb=" O VAL B 65 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ARG B 72 " --> pdb=" O ILE B 327 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 111 through 112 removed outlier: 6.530A pdb=" N VAL B 111 " --> pdb=" O LEU B 249 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N LYS B 251 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL B 250 " --> pdb=" O THR B 259 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 123 through 125 removed outlier: 9.115A pdb=" N ALA B 308 " --> pdb=" O ARG B 274 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N ARG B 274 " --> pdb=" O ALA B 308 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR B 310 " --> pdb=" O HIS B 272 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N GLU B 268 " --> pdb=" O THR B 314 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ILE B 316 " --> pdb=" O VAL B 266 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL B 266 " --> pdb=" O ILE B 316 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL B 157 " --> pdb=" O PRO B 205 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR B 207 " --> pdb=" O CYS B 155 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 123 through 125 removed outlier: 3.770A pdb=" N ASN B 173 " --> pdb=" O THR B 181 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 293 through 296 removed outlier: 7.455A pdb=" N GLY B 303 " --> pdb=" O PHE B 294 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 361 through 365 removed outlier: 3.539A pdb=" N ASN B 363 " --> pdb=" O GLN B 379 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ALA B 408 " --> pdb=" O ILE B 475 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ALA B 477 " --> pdb=" O ALA B 408 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ALA B 410 " --> pdb=" O ALA B 477 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 35 through 41 removed outlier: 6.594A pdb=" N VAL C 35 " --> pdb=" O LEU C 61 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N ASN C 63 " --> pdb=" O VAL C 35 " (cutoff:3.500A) removed outlier: 8.451A pdb=" N THR C 37 " --> pdb=" O ASN C 63 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N VAL C 65 " --> pdb=" O THR C 37 " (cutoff:3.500A) removed outlier: 9.598A pdb=" N LYS C 39 " --> pdb=" O VAL C 65 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ARG C 72 " --> pdb=" O ILE C 327 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 111 through 112 removed outlier: 6.530A pdb=" N VAL C 111 " --> pdb=" O LEU C 249 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N LYS C 251 " --> pdb=" O VAL C 111 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL C 250 " --> pdb=" O THR C 259 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 123 through 125 removed outlier: 9.115A pdb=" N ALA C 308 " --> pdb=" O ARG C 274 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N ARG C 274 " --> pdb=" O ALA C 308 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR C 310 " --> pdb=" O HIS C 272 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N GLU C 268 " --> pdb=" O THR C 314 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ILE C 316 " --> pdb=" O VAL C 266 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL C 266 " --> pdb=" O ILE C 316 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL C 157 " --> pdb=" O PRO C 205 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR C 207 " --> pdb=" O CYS C 155 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 123 through 125 removed outlier: 3.770A pdb=" N ASN C 173 " --> pdb=" O THR C 181 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 293 through 296 removed outlier: 7.455A pdb=" N GLY C 303 " --> pdb=" O PHE C 294 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 361 through 365 removed outlier: 3.540A pdb=" N ASN C 363 " --> pdb=" O GLN C 379 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ALA C 408 " --> pdb=" O ILE C 475 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ALA C 477 " --> pdb=" O ALA C 408 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ALA C 410 " --> pdb=" O ALA C 477 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 35 through 41 removed outlier: 6.595A pdb=" N VAL D 35 " --> pdb=" O LEU D 61 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N ASN D 63 " --> pdb=" O VAL D 35 " (cutoff:3.500A) removed outlier: 8.452A pdb=" N THR D 37 " --> pdb=" O ASN D 63 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N VAL D 65 " --> pdb=" O THR D 37 " (cutoff:3.500A) removed outlier: 9.597A pdb=" N LYS D 39 " --> pdb=" O VAL D 65 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ARG D 72 " --> pdb=" O ILE D 327 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 111 through 112 removed outlier: 6.530A pdb=" N VAL D 111 " --> pdb=" O LEU D 249 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N LYS D 251 " --> pdb=" O VAL D 111 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL D 250 " --> pdb=" O THR D 259 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 123 through 125 removed outlier: 9.115A pdb=" N ALA D 308 " --> pdb=" O ARG D 274 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N ARG D 274 " --> pdb=" O ALA D 308 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR D 310 " --> pdb=" O HIS D 272 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N GLU D 268 " --> pdb=" O THR D 314 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ILE D 316 " --> pdb=" O VAL D 266 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL D 266 " --> pdb=" O ILE D 316 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL D 157 " --> pdb=" O PRO D 205 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR D 207 " --> pdb=" O CYS D 155 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 123 through 125 removed outlier: 3.771A pdb=" N ASN D 173 " --> pdb=" O THR D 181 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 293 through 296 removed outlier: 7.455A pdb=" N GLY D 303 " --> pdb=" O PHE D 294 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 361 through 365 removed outlier: 3.539A pdb=" N ASN D 363 " --> pdb=" O GLN D 379 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ALA D 408 " --> pdb=" O ILE D 475 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ALA D 477 " --> pdb=" O ALA D 408 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ALA D 410 " --> pdb=" O ALA D 477 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 35 through 41 removed outlier: 6.595A pdb=" N VAL E 35 " --> pdb=" O LEU E 61 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N ASN E 63 " --> pdb=" O VAL E 35 " (cutoff:3.500A) removed outlier: 8.451A pdb=" N THR E 37 " --> pdb=" O ASN E 63 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N VAL E 65 " --> pdb=" O THR E 37 " (cutoff:3.500A) removed outlier: 9.598A pdb=" N LYS E 39 " --> pdb=" O VAL E 65 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ARG E 72 " --> pdb=" O ILE E 327 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 111 through 112 removed outlier: 6.529A pdb=" N VAL E 111 " --> pdb=" O LEU E 249 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N LYS E 251 " --> pdb=" O VAL E 111 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL E 250 " --> pdb=" O THR E 259 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 123 through 125 removed outlier: 9.115A pdb=" N ALA E 308 " --> pdb=" O ARG E 274 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N ARG E 274 " --> pdb=" O ALA E 308 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR E 310 " --> pdb=" O HIS E 272 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N GLU E 268 " --> pdb=" O THR E 314 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ILE E 316 " --> pdb=" O VAL E 266 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL E 266 " --> pdb=" O ILE E 316 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL E 157 " --> pdb=" O PRO E 205 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR E 207 " --> pdb=" O CYS E 155 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 123 through 125 removed outlier: 3.770A pdb=" N ASN E 173 " --> pdb=" O THR E 181 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 293 through 296 removed outlier: 7.455A pdb=" N GLY E 303 " --> pdb=" O PHE E 294 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 361 through 365 removed outlier: 3.540A pdb=" N ASN E 363 " --> pdb=" O GLN E 379 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ALA E 408 " --> pdb=" O ILE E 475 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N ALA E 477 " --> pdb=" O ALA E 408 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ALA E 410 " --> pdb=" O ALA E 477 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 35 through 41 removed outlier: 6.595A pdb=" N VAL F 35 " --> pdb=" O LEU F 61 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N ASN F 63 " --> pdb=" O VAL F 35 " (cutoff:3.500A) removed outlier: 8.451A pdb=" N THR F 37 " --> pdb=" O ASN F 63 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N VAL F 65 " --> pdb=" O THR F 37 " (cutoff:3.500A) removed outlier: 9.598A pdb=" N LYS F 39 " --> pdb=" O VAL F 65 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ARG F 72 " --> pdb=" O ILE F 327 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 111 through 112 removed outlier: 6.530A pdb=" N VAL F 111 " --> pdb=" O LEU F 249 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N LYS F 251 " --> pdb=" O VAL F 111 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL F 250 " --> pdb=" O THR F 259 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 123 through 125 removed outlier: 9.114A pdb=" N ALA F 308 " --> pdb=" O ARG F 274 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N ARG F 274 " --> pdb=" O ALA F 308 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR F 310 " --> pdb=" O HIS F 272 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N GLU F 268 " --> pdb=" O THR F 314 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ILE F 316 " --> pdb=" O VAL F 266 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N VAL F 266 " --> pdb=" O ILE F 316 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL F 157 " --> pdb=" O PRO F 205 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR F 207 " --> pdb=" O CYS F 155 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 123 through 125 removed outlier: 3.770A pdb=" N ASN F 173 " --> pdb=" O THR F 181 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 293 through 296 removed outlier: 7.455A pdb=" N GLY F 303 " --> pdb=" O PHE F 294 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 361 through 365 removed outlier: 3.539A pdb=" N ASN F 363 " --> pdb=" O GLN F 379 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ALA F 408 " --> pdb=" O ILE F 475 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ALA F 477 " --> pdb=" O ALA F 408 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ALA F 410 " --> pdb=" O ALA F 477 " (cutoff:3.500A) 792 hydrogen bonds defined for protein. 2178 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.93 Time building geometry restraints manager: 2.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 7888 1.35 - 1.47: 5863 1.47 - 1.59: 10513 1.59 - 1.72: 12 1.72 - 1.84: 264 Bond restraints: 24540 Sorted by residual: bond pdb=" C2 BYN F 601 " pdb=" O3 BYN F 601 " ideal model delta sigma weight residual 1.226 1.399 -0.173 2.00e-02 2.50e+03 7.50e+01 bond pdb=" C2 BYN C 601 " pdb=" O3 BYN C 601 " ideal model delta sigma weight residual 1.226 1.399 -0.173 2.00e-02 2.50e+03 7.50e+01 bond pdb=" C2 BYN D 601 " pdb=" O3 BYN D 601 " ideal model delta sigma weight residual 1.226 1.399 -0.173 2.00e-02 2.50e+03 7.49e+01 bond pdb=" C2 BYN E 601 " pdb=" O3 BYN E 601 " ideal model delta sigma weight residual 1.226 1.399 -0.173 2.00e-02 2.50e+03 7.49e+01 bond pdb=" C2 BYN A 601 " pdb=" O3 BYN A 601 " ideal model delta sigma weight residual 1.226 1.399 -0.173 2.00e-02 2.50e+03 7.48e+01 ... (remaining 24535 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.34: 32746 3.34 - 6.68: 476 6.68 - 10.02: 114 10.02 - 13.36: 6 13.36 - 16.70: 18 Bond angle restraints: 33360 Sorted by residual: angle pdb=" CB MET A 68 " pdb=" CG MET A 68 " pdb=" SD MET A 68 " ideal model delta sigma weight residual 112.70 129.40 -16.70 3.00e+00 1.11e-01 3.10e+01 angle pdb=" CB MET D 68 " pdb=" CG MET D 68 " pdb=" SD MET D 68 " ideal model delta sigma weight residual 112.70 129.39 -16.69 3.00e+00 1.11e-01 3.09e+01 angle pdb=" CB MET F 68 " pdb=" CG MET F 68 " pdb=" SD MET F 68 " ideal model delta sigma weight residual 112.70 129.37 -16.67 3.00e+00 1.11e-01 3.09e+01 angle pdb=" CB MET C 68 " pdb=" CG MET C 68 " pdb=" SD MET C 68 " ideal model delta sigma weight residual 112.70 129.37 -16.67 3.00e+00 1.11e-01 3.09e+01 angle pdb=" CB MET B 68 " pdb=" CG MET B 68 " pdb=" SD MET B 68 " ideal model delta sigma weight residual 112.70 129.36 -16.66 3.00e+00 1.11e-01 3.09e+01 ... (remaining 33355 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.55: 13662 28.55 - 57.10: 954 57.10 - 85.66: 96 85.66 - 114.21: 12 114.21 - 142.76: 12 Dihedral angle restraints: 14736 sinusoidal: 6126 harmonic: 8610 Sorted by residual: dihedral pdb=" C22 BYN B 601 " pdb=" C20 BYN B 601 " pdb=" C21 BYN B 601 " pdb=" O5 BYN B 601 " ideal model delta sinusoidal sigma weight residual 68.64 -74.12 142.76 1 3.00e+01 1.11e-03 1.92e+01 dihedral pdb=" C22 BYN C 601 " pdb=" C20 BYN C 601 " pdb=" C21 BYN C 601 " pdb=" O5 BYN C 601 " ideal model delta sinusoidal sigma weight residual 68.64 -74.08 142.72 1 3.00e+01 1.11e-03 1.92e+01 dihedral pdb=" C22 BYN D 601 " pdb=" C20 BYN D 601 " pdb=" C21 BYN D 601 " pdb=" O5 BYN D 601 " ideal model delta sinusoidal sigma weight residual 68.64 -74.06 142.70 1 3.00e+01 1.11e-03 1.92e+01 ... (remaining 14733 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 3100 0.079 - 0.159: 393 0.159 - 0.238: 59 0.238 - 0.317: 12 0.317 - 0.397: 6 Chirality restraints: 3570 Sorted by residual: chirality pdb=" C19 BYN D 601 " pdb=" C18 BYN D 601 " pdb=" C20 BYN D 601 " pdb=" O4 BYN D 601 " both_signs ideal model delta sigma weight residual False -2.52 -2.12 -0.40 2.00e-01 2.50e+01 3.93e+00 chirality pdb=" C19 BYN C 601 " pdb=" C18 BYN C 601 " pdb=" C20 BYN C 601 " pdb=" O4 BYN C 601 " both_signs ideal model delta sigma weight residual False -2.52 -2.12 -0.40 2.00e-01 2.50e+01 3.92e+00 chirality pdb=" C19 BYN E 601 " pdb=" C18 BYN E 601 " pdb=" C20 BYN E 601 " pdb=" O4 BYN E 601 " both_signs ideal model delta sigma weight residual False -2.52 -2.12 -0.39 2.00e-01 2.50e+01 3.90e+00 ... (remaining 3567 not shown) Planarity restraints: 4338 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 BYN E 601 " -0.046 2.00e-02 2.50e+03 1.21e-01 4.03e+02 pdb=" C18 BYN E 601 " 0.189 2.00e-02 2.50e+03 pdb=" C2 BYN E 601 " 0.043 2.00e-02 2.50e+03 pdb=" C3 BYN E 601 " 0.081 2.00e-02 2.50e+03 pdb=" C4 BYN E 601 " 0.051 2.00e-02 2.50e+03 pdb=" C6 BYN E 601 " -0.304 2.00e-02 2.50e+03 pdb=" N1 BYN E 601 " -0.018 2.00e-02 2.50e+03 pdb=" N2 BYN E 601 " -0.004 2.00e-02 2.50e+03 pdb=" N4 BYN E 601 " 0.062 2.00e-02 2.50e+03 pdb=" O1 BYN E 601 " -0.111 2.00e-02 2.50e+03 pdb=" O3 BYN E 601 " 0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BYN F 601 " 0.046 2.00e-02 2.50e+03 1.21e-01 4.02e+02 pdb=" C18 BYN F 601 " -0.189 2.00e-02 2.50e+03 pdb=" C2 BYN F 601 " -0.043 2.00e-02 2.50e+03 pdb=" C3 BYN F 601 " -0.081 2.00e-02 2.50e+03 pdb=" C4 BYN F 601 " -0.051 2.00e-02 2.50e+03 pdb=" C6 BYN F 601 " 0.304 2.00e-02 2.50e+03 pdb=" N1 BYN F 601 " 0.018 2.00e-02 2.50e+03 pdb=" N2 BYN F 601 " 0.003 2.00e-02 2.50e+03 pdb=" N4 BYN F 601 " -0.063 2.00e-02 2.50e+03 pdb=" O1 BYN F 601 " 0.111 2.00e-02 2.50e+03 pdb=" O3 BYN F 601 " -0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BYN D 601 " -0.046 2.00e-02 2.50e+03 1.21e-01 4.02e+02 pdb=" C18 BYN D 601 " 0.189 2.00e-02 2.50e+03 pdb=" C2 BYN D 601 " 0.043 2.00e-02 2.50e+03 pdb=" C3 BYN D 601 " 0.081 2.00e-02 2.50e+03 pdb=" C4 BYN D 601 " 0.052 2.00e-02 2.50e+03 pdb=" C6 BYN D 601 " -0.304 2.00e-02 2.50e+03 pdb=" N1 BYN D 601 " -0.018 2.00e-02 2.50e+03 pdb=" N2 BYN D 601 " -0.003 2.00e-02 2.50e+03 pdb=" N4 BYN D 601 " 0.062 2.00e-02 2.50e+03 pdb=" O1 BYN D 601 " -0.111 2.00e-02 2.50e+03 pdb=" O3 BYN D 601 " 0.056 2.00e-02 2.50e+03 ... (remaining 4335 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.66: 518 2.66 - 3.28: 22526 3.28 - 3.90: 50991 3.90 - 4.52: 67921 4.52 - 5.14: 108790 Nonbonded interactions: 250746 Sorted by model distance: nonbonded pdb=" ND1 HIS D 166 " pdb="FE FE D 602 " model vdw 2.045 2.340 nonbonded pdb=" ND1 HIS A 166 " pdb="FE FE A 602 " model vdw 2.046 2.340 nonbonded pdb=" ND1 HIS E 166 " pdb="FE FE E 602 " model vdw 2.046 2.340 nonbonded pdb=" ND1 HIS F 166 " pdb="FE FE F 602 " model vdw 2.046 2.340 nonbonded pdb=" ND1 HIS B 166 " pdb="FE FE B 602 " model vdw 2.046 2.340 ... (remaining 250741 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.270 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: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 22.400 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8860 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 : 0.008 0.173 24540 Z= 0.360 Angle : 1.093 16.700 33360 Z= 0.535 Chirality : 0.060 0.397 3570 Planarity : 0.010 0.121 4338 Dihedral : 18.967 142.762 9228 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.46 % Allowed : 23.82 % Favored : 74.72 % 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: -4.01 (0.13), residues: 2988 helix: -4.67 (0.05), residues: 936 sheet: -0.96 (0.21), residues: 630 loop : -1.89 (0.14), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 345 TYR 0.029 0.002 TYR F 265 PHE 0.017 0.002 PHE A 210 TRP 0.009 0.002 TRP E 373 HIS 0.010 0.002 HIS B 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00786 / 0.36 (24540) covalent geometry : angle 1.09316 / 0.53 (33360) hydrogen bonds : bond 0.29439 / 19.25 ( 768) hydrogen bonds : angle 10.11178 / 7.07 ( 2178) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 126 time to evaluate : 0.958 Fit side-chains REVERT: A 302 MET cc_start: 0.5521 (mpt) cc_final: 0.5173 (mmt) REVERT: C 302 MET cc_start: 0.6015 (mpt) cc_final: 0.5585 (mmt) REVERT: D 302 MET cc_start: 0.5964 (mpt) cc_final: 0.5651 (mmt) REVERT: F 302 MET cc_start: 0.5566 (mpt) cc_final: 0.5217 (mmt) outliers start: 37 outliers final: 19 residues processed: 158 average time/residue: 0.6094 time to fit residues: 111.5510 Evaluate side-chains 142 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 123 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain C residue 151 SER Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 402 SER Chi-restraints excluded: chain D residue 151 SER Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain D residue 236 ILE Chi-restraints excluded: chain D residue 402 SER Chi-restraints excluded: chain E residue 151 SER Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 402 SER Chi-restraints excluded: chain F residue 151 SER Chi-restraints excluded: chain F residue 185 SER Chi-restraints excluded: chain F residue 402 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.0070 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.5980 chunk 298 optimal weight: 1.9990 overall best weight: 1.1202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 106 HIS B 106 HIS C 106 HIS D 106 HIS E 106 HIS F 106 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.076956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.056424 restraints weight = 55096.541| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 2.58 r_work: 0.2799 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2672 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.1150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 24540 Z= 0.123 Angle : 0.555 7.252 33360 Z= 0.283 Chirality : 0.042 0.122 3570 Planarity : 0.005 0.052 4338 Dihedral : 11.494 142.756 3578 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.86 % Allowed : 22.16 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.44 (0.13), residues: 2988 helix: -2.38 (0.12), residues: 918 sheet: -1.07 (0.21), residues: 660 loop : -1.19 (0.15), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 102 TYR 0.011 0.001 TYR F 226 PHE 0.009 0.001 PHE C 210 TRP 0.008 0.001 TRP D 298 HIS 0.002 0.001 HIS D 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 (24540) covalent geometry : angle 0.55504 / 0.28 (33360) hydrogen bonds : bond 0.04089 / 2.70 ( 768) hydrogen bonds : angle 5.46025 / 3.77 ( 2178) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 131 time to evaluate : 0.859 Fit side-chains REVERT: A 172 MET cc_start: 0.8827 (OUTLIER) cc_final: 0.7264 (mtp) REVERT: A 282 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.8195 (pp20) REVERT: A 302 MET cc_start: 0.6095 (mpt) cc_final: 0.5406 (mmt) REVERT: A 527 ARG cc_start: 0.7858 (OUTLIER) cc_final: 0.7413 (ttp-170) REVERT: B 172 MET cc_start: 0.8784 (OUTLIER) cc_final: 0.7538 (mpp) REVERT: B 424 MET cc_start: 0.9443 (OUTLIER) cc_final: 0.9206 (tpp) REVERT: C 282 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.8392 (pp20) REVERT: C 302 MET cc_start: 0.6113 (mpt) cc_final: 0.5449 (mmt) REVERT: C 506 LYS cc_start: 0.9110 (tptp) cc_final: 0.8450 (tptp) REVERT: C 509 ASP cc_start: 0.9018 (m-30) cc_final: 0.8779 (p0) REVERT: C 527 ARG cc_start: 0.7985 (OUTLIER) cc_final: 0.7020 (mtp180) REVERT: D 282 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.8343 (pp20) REVERT: D 302 MET cc_start: 0.6097 (mpt) cc_final: 0.5437 (mmt) REVERT: D 509 ASP cc_start: 0.8990 (m-30) cc_final: 0.8764 (p0) REVERT: D 527 ARG cc_start: 0.7974 (OUTLIER) cc_final: 0.6965 (mtp180) REVERT: E 172 MET cc_start: 0.8748 (OUTLIER) cc_final: 0.7517 (mpp) REVERT: E 282 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.8161 (pp20) REVERT: F 172 MET cc_start: 0.8866 (OUTLIER) cc_final: 0.7239 (mtp) REVERT: F 282 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.8187 (pp20) REVERT: F 302 MET cc_start: 0.6059 (mpt) cc_final: 0.5341 (mmt) REVERT: F 527 ARG cc_start: 0.7858 (OUTLIER) cc_final: 0.7476 (ttp-170) outliers start: 47 outliers final: 1 residues processed: 157 average time/residue: 0.7105 time to fit residues: 126.6772 Evaluate side-chains 138 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 123 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 MET Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 318 MET Chi-restraints excluded: chain A residue 527 ARG Chi-restraints excluded: chain B residue 172 MET Chi-restraints excluded: chain B residue 424 MET Chi-restraints excluded: chain C residue 282 GLU Chi-restraints excluded: chain C residue 527 ARG Chi-restraints excluded: chain D residue 282 GLU Chi-restraints excluded: chain D residue 527 ARG Chi-restraints excluded: chain E residue 172 MET Chi-restraints excluded: chain E residue 282 GLU Chi-restraints excluded: chain F residue 172 MET Chi-restraints excluded: chain F residue 282 GLU Chi-restraints excluded: chain F residue 527 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 58 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 109 optimal weight: 10.0000 chunk 92 optimal weight: 3.9990 chunk 290 optimal weight: 5.9990 chunk 171 optimal weight: 7.9990 chunk 119 optimal weight: 2.9990 chunk 287 optimal weight: 2.9990 chunk 60 optimal weight: 0.3980 chunk 70 optimal weight: 0.0370 chunk 174 optimal weight: 10.0000 overall best weight: 2.0864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 295 HIS F 295 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.075365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.054528 restraints weight = 55346.083| |-----------------------------------------------------------------------------| r_work (start): 0.2880 rms_B_bonded: 2.58 r_work: 0.2749 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2623 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 24540 Z= 0.162 Angle : 0.530 7.592 33360 Z= 0.267 Chirality : 0.043 0.124 3570 Planarity : 0.004 0.042 4338 Dihedral : 10.566 132.115 3558 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.94 % Allowed : 20.62 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.15), residues: 2988 helix: -0.62 (0.16), residues: 930 sheet: -1.02 (0.21), residues: 660 loop : -0.80 (0.16), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 406 TYR 0.013 0.001 TYR F 226 PHE 0.009 0.001 PHE D 174 TRP 0.005 0.001 TRP B 176 HIS 0.004 0.001 HIS E 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 (24540) covalent geometry : angle 0.52976 / 0.27 (33360) hydrogen bonds : bond 0.03691 / 2.44 ( 768) hydrogen bonds : angle 4.78381 / 3.31 ( 2178) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 132 time to evaluate : 0.864 Fit side-chains REVERT: A 172 MET cc_start: 0.8835 (OUTLIER) cc_final: 0.7482 (mpp) REVERT: A 282 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.8329 (pp20) REVERT: A 302 MET cc_start: 0.6356 (mpt) cc_final: 0.5795 (mmt) REVERT: A 509 ASP cc_start: 0.9013 (m-30) cc_final: 0.8803 (p0) REVERT: A 511 MET cc_start: 0.9354 (OUTLIER) cc_final: 0.9151 (mtm) REVERT: A 527 ARG cc_start: 0.7915 (OUTLIER) cc_final: 0.7645 (ttp-170) REVERT: B 282 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.8288 (pp20) REVERT: C 282 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.8327 (pp20) REVERT: C 302 MET cc_start: 0.6160 (mpt) cc_final: 0.5478 (mmt) REVERT: C 506 LYS cc_start: 0.9090 (tptp) cc_final: 0.8243 (tptp) REVERT: C 509 ASP cc_start: 0.8936 (m-30) cc_final: 0.8628 (p0) REVERT: C 527 ARG cc_start: 0.7944 (OUTLIER) cc_final: 0.6990 (mtp180) REVERT: D 282 GLU cc_start: 0.8602 (OUTLIER) cc_final: 0.8355 (pp20) REVERT: D 302 MET cc_start: 0.6148 (mpt) cc_final: 0.5471 (mmt) REVERT: D 506 LYS cc_start: 0.9082 (tptp) cc_final: 0.8352 (tptp) REVERT: D 509 ASP cc_start: 0.8964 (m-30) cc_final: 0.8665 (p0) REVERT: D 527 ARG cc_start: 0.7946 (OUTLIER) cc_final: 0.7000 (mtp180) REVERT: E 282 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.8292 (pp20) REVERT: F 172 MET cc_start: 0.8827 (OUTLIER) cc_final: 0.7584 (mtp) REVERT: F 282 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.8372 (pp20) REVERT: F 302 MET cc_start: 0.6023 (mpt) cc_final: 0.5508 (mmt) REVERT: F 527 ARG cc_start: 0.7918 (OUTLIER) cc_final: 0.7572 (ttp-170) outliers start: 49 outliers final: 10 residues processed: 155 average time/residue: 0.8066 time to fit residues: 140.3911 Evaluate side-chains 148 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 125 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 MET Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 473 MET Chi-restraints excluded: chain A residue 511 MET Chi-restraints excluded: chain A residue 527 ARG Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 511 MET Chi-restraints excluded: chain C residue 282 GLU Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 527 ARG Chi-restraints excluded: chain D residue 282 GLU Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 527 ARG Chi-restraints excluded: chain E residue 151 SER Chi-restraints excluded: chain E residue 282 GLU Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 511 MET Chi-restraints excluded: chain F residue 172 MET Chi-restraints excluded: chain F residue 282 GLU Chi-restraints excluded: chain F residue 511 MET Chi-restraints excluded: chain F residue 527 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 37 optimal weight: 3.9990 chunk 232 optimal weight: 1.9990 chunk 110 optimal weight: 9.9990 chunk 70 optimal weight: 0.0060 chunk 18 optimal weight: 3.9990 chunk 29 optimal weight: 9.9990 chunk 253 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 227 optimal weight: 10.0000 chunk 292 optimal weight: 1.9990 chunk 9 optimal weight: 7.9990 overall best weight: 2.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 295 HIS F 295 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.075070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.054103 restraints weight = 55262.988| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 2.59 r_work: 0.2736 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2610 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 24540 Z= 0.164 Angle : 0.522 8.132 33360 Z= 0.261 Chirality : 0.043 0.120 3570 Planarity : 0.003 0.039 4338 Dihedral : 10.116 134.912 3558 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.17 % Allowed : 19.15 % Favored : 78.67 % 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: -0.67 (0.15), residues: 2988 helix: 0.21 (0.17), residues: 930 sheet: -1.01 (0.21), residues: 654 loop : -0.45 (0.16), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 406 TYR 0.012 0.001 TYR B 226 PHE 0.008 0.001 PHE B 174 TRP 0.005 0.001 TRP B 176 HIS 0.005 0.001 HIS A 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 (24540) covalent geometry : angle 0.52225 / 0.26 (33360) hydrogen bonds : bond 0.03306 / 2.17 ( 768) hydrogen bonds : angle 4.64021 / 3.21 ( 2178) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 129 time to evaluate : 0.881 Fit side-chains REVERT: A 172 MET cc_start: 0.8802 (OUTLIER) cc_final: 0.7506 (mpp) REVERT: A 282 GLU cc_start: 0.8649 (OUTLIER) cc_final: 0.8368 (pp20) REVERT: A 302 MET cc_start: 0.6094 (OUTLIER) cc_final: 0.5618 (mmt) REVERT: A 509 ASP cc_start: 0.8946 (m-30) cc_final: 0.8740 (p0) REVERT: A 527 ARG cc_start: 0.7873 (OUTLIER) cc_final: 0.7625 (ttp-170) REVERT: B 282 GLU cc_start: 0.8710 (OUTLIER) cc_final: 0.8335 (pp20) REVERT: B 509 ASP cc_start: 0.8909 (m-30) cc_final: 0.8620 (p0) REVERT: C 282 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.8430 (pp20) REVERT: C 302 MET cc_start: 0.6184 (OUTLIER) cc_final: 0.5379 (mmt) REVERT: C 506 LYS cc_start: 0.9085 (tptp) cc_final: 0.8347 (tptp) REVERT: C 509 ASP cc_start: 0.8989 (m-30) cc_final: 0.8680 (p0) REVERT: C 527 ARG cc_start: 0.7984 (OUTLIER) cc_final: 0.7044 (mtp180) REVERT: D 282 GLU cc_start: 0.8630 (OUTLIER) cc_final: 0.8409 (pp20) REVERT: D 302 MET cc_start: 0.6187 (OUTLIER) cc_final: 0.5380 (mmt) REVERT: D 506 LYS cc_start: 0.9071 (tptp) cc_final: 0.8426 (tptp) REVERT: D 509 ASP cc_start: 0.8970 (m-30) cc_final: 0.8668 (p0) REVERT: D 527 ARG cc_start: 0.7976 (OUTLIER) cc_final: 0.7022 (mtp180) REVERT: E 282 GLU cc_start: 0.8688 (OUTLIER) cc_final: 0.8328 (pp20) REVERT: E 509 ASP cc_start: 0.8878 (m-30) cc_final: 0.8597 (p0) REVERT: F 172 MET cc_start: 0.8800 (OUTLIER) cc_final: 0.7455 (mpp) REVERT: F 282 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.8369 (pp20) REVERT: F 302 MET cc_start: 0.6094 (OUTLIER) cc_final: 0.5488 (mmt) REVERT: F 527 ARG cc_start: 0.7910 (OUTLIER) cc_final: 0.7668 (ttp-170) outliers start: 55 outliers final: 26 residues processed: 162 average time/residue: 0.7484 time to fit residues: 137.6126 Evaluate side-chains 167 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 125 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 172 MET Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 291 ARG Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 473 MET Chi-restraints excluded: chain A residue 511 MET Chi-restraints excluded: chain A residue 527 ARG Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 511 MET Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 151 SER Chi-restraints excluded: chain C residue 282 GLU Chi-restraints excluded: chain C residue 302 MET Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 527 ARG Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 151 SER Chi-restraints excluded: chain D residue 282 GLU Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain D residue 527 ARG Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 151 SER Chi-restraints excluded: chain E residue 282 GLU Chi-restraints excluded: chain E residue 422 ASP Chi-restraints excluded: chain E residue 511 MET Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 172 MET Chi-restraints excluded: chain F residue 282 GLU Chi-restraints excluded: chain F residue 291 ARG Chi-restraints excluded: chain F residue 302 MET Chi-restraints excluded: chain F residue 467 THR Chi-restraints excluded: chain F residue 473 MET Chi-restraints excluded: chain F residue 511 MET Chi-restraints excluded: chain F residue 527 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 21 optimal weight: 4.9990 chunk 240 optimal weight: 0.9980 chunk 226 optimal weight: 6.9990 chunk 269 optimal weight: 4.9990 chunk 58 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 294 optimal weight: 4.9990 chunk 190 optimal weight: 6.9990 chunk 144 optimal weight: 0.0970 chunk 287 optimal weight: 4.9990 chunk 234 optimal weight: 0.8980 overall best weight: 1.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.075162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.054187 restraints weight = 55004.834| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 2.59 r_work: 0.2735 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2609 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 24540 Z= 0.141 Angle : 0.512 6.694 33360 Z= 0.254 Chirality : 0.043 0.120 3570 Planarity : 0.003 0.037 4338 Dihedral : 9.904 135.423 3558 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.53 % Allowed : 18.68 % Favored : 78.79 % 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: -0.39 (0.16), residues: 2988 helix: 0.57 (0.18), residues: 930 sheet: -1.05 (0.21), residues: 654 loop : -0.27 (0.17), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 345 TYR 0.011 0.001 TYR F 226 PHE 0.007 0.001 PHE B 224 TRP 0.005 0.001 TRP A 298 HIS 0.005 0.001 HIS A 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 (24540) covalent geometry : angle 0.51180 / 0.25 (33360) hydrogen bonds : bond 0.03091 / 2.03 ( 768) hydrogen bonds : angle 4.56885 / 3.16 ( 2178) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 127 time to evaluate : 0.968 Fit side-chains REVERT: A 172 MET cc_start: 0.8769 (OUTLIER) cc_final: 0.7469 (mpp) REVERT: A 282 GLU cc_start: 0.8659 (OUTLIER) cc_final: 0.8383 (pp20) REVERT: A 302 MET cc_start: 0.6048 (OUTLIER) cc_final: 0.5518 (mmt) REVERT: A 527 ARG cc_start: 0.7897 (OUTLIER) cc_final: 0.7679 (ttp-170) REVERT: B 282 GLU cc_start: 0.8753 (OUTLIER) cc_final: 0.8391 (pp20) REVERT: B 509 ASP cc_start: 0.8886 (m-30) cc_final: 0.8581 (p0) REVERT: C 282 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.8373 (pp20) REVERT: C 302 MET cc_start: 0.6257 (OUTLIER) cc_final: 0.5476 (mmt) REVERT: C 422 ASP cc_start: 0.9355 (OUTLIER) cc_final: 0.9144 (t70) REVERT: C 506 LYS cc_start: 0.9074 (tptp) cc_final: 0.8293 (tptp) REVERT: C 509 ASP cc_start: 0.8986 (m-30) cc_final: 0.8695 (p0) REVERT: C 527 ARG cc_start: 0.7967 (OUTLIER) cc_final: 0.7092 (mtp180) REVERT: D 282 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.8328 (pp20) REVERT: D 302 MET cc_start: 0.6181 (OUTLIER) cc_final: 0.5420 (mmt) REVERT: D 422 ASP cc_start: 0.9358 (OUTLIER) cc_final: 0.9147 (t70) REVERT: D 506 LYS cc_start: 0.9054 (tptp) cc_final: 0.8329 (tptp) REVERT: D 509 ASP cc_start: 0.8972 (m-30) cc_final: 0.8684 (p0) REVERT: D 527 ARG cc_start: 0.7952 (OUTLIER) cc_final: 0.7072 (mtp180) REVERT: E 282 GLU cc_start: 0.8722 (OUTLIER) cc_final: 0.8369 (pp20) REVERT: E 509 ASP cc_start: 0.8892 (m-30) cc_final: 0.8598 (p0) REVERT: F 172 MET cc_start: 0.8778 (OUTLIER) cc_final: 0.7454 (mpp) REVERT: F 282 GLU cc_start: 0.8693 (OUTLIER) cc_final: 0.8410 (pp20) REVERT: F 302 MET cc_start: 0.6088 (OUTLIER) cc_final: 0.5387 (mmm) REVERT: F 527 ARG cc_start: 0.7892 (OUTLIER) cc_final: 0.7676 (ttp-170) outliers start: 64 outliers final: 28 residues processed: 171 average time/residue: 0.7320 time to fit residues: 142.8476 Evaluate side-chains 170 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 124 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 172 MET Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 291 ARG Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 473 MET Chi-restraints excluded: chain A residue 511 MET Chi-restraints excluded: chain A residue 527 ARG Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 511 MET Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 151 SER Chi-restraints excluded: chain C residue 282 GLU Chi-restraints excluded: chain C residue 302 MET Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 527 ARG Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 151 SER Chi-restraints excluded: chain D residue 282 GLU Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 422 ASP Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain D residue 527 ARG Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 282 GLU Chi-restraints excluded: chain E residue 422 ASP Chi-restraints excluded: chain E residue 511 MET Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 151 SER Chi-restraints excluded: chain F residue 172 MET Chi-restraints excluded: chain F residue 282 GLU Chi-restraints excluded: chain F residue 291 ARG Chi-restraints excluded: chain F residue 302 MET Chi-restraints excluded: chain F residue 467 THR Chi-restraints excluded: chain F residue 473 MET Chi-restraints excluded: chain F residue 511 MET Chi-restraints excluded: chain F residue 527 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 71 optimal weight: 0.2980 chunk 126 optimal weight: 5.9990 chunk 142 optimal weight: 0.5980 chunk 235 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 210 optimal weight: 10.0000 chunk 294 optimal weight: 10.0000 chunk 202 optimal weight: 7.9990 chunk 237 optimal weight: 5.9990 chunk 56 optimal weight: 10.0000 chunk 135 optimal weight: 6.9990 overall best weight: 3.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.073867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.052271 restraints weight = 54761.786| |-----------------------------------------------------------------------------| r_work (start): 0.2795 rms_B_bonded: 2.62 r_work: 0.2653 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2517 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 24540 Z= 0.258 Angle : 0.576 8.567 33360 Z= 0.287 Chirality : 0.045 0.138 3570 Planarity : 0.004 0.036 4338 Dihedral : 9.717 135.829 3558 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.13 % Allowed : 18.25 % Favored : 79.62 % 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: -0.30 (0.16), residues: 2988 helix: 0.64 (0.17), residues: 930 sheet: -1.09 (0.20), residues: 654 loop : -0.16 (0.17), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 406 TYR 0.011 0.001 TYR E 226 PHE 0.009 0.001 PHE D 224 TRP 0.006 0.001 TRP A 373 HIS 0.004 0.001 HIS E 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00595 / 0.26 (24540) covalent geometry : angle 0.57622 / 0.29 (33360) hydrogen bonds : bond 0.03536 / 2.31 ( 768) hydrogen bonds : angle 4.68686 / 3.25 ( 2178) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 129 time to evaluate : 0.976 Fit side-chains REVERT: A 282 GLU cc_start: 0.8691 (OUTLIER) cc_final: 0.8416 (pp20) REVERT: A 302 MET cc_start: 0.6205 (OUTLIER) cc_final: 0.5719 (mmt) REVERT: B 208 MET cc_start: 0.9030 (mmm) cc_final: 0.8706 (mtm) REVERT: B 282 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.8482 (pp20) REVERT: B 509 ASP cc_start: 0.8932 (m-30) cc_final: 0.8595 (p0) REVERT: C 282 GLU cc_start: 0.8722 (OUTLIER) cc_final: 0.8470 (pp20) REVERT: C 302 MET cc_start: 0.6397 (OUTLIER) cc_final: 0.5533 (mmt) REVERT: C 422 ASP cc_start: 0.9387 (OUTLIER) cc_final: 0.9105 (t0) REVERT: C 506 LYS cc_start: 0.9039 (tptp) cc_final: 0.8230 (tptp) REVERT: C 509 ASP cc_start: 0.8960 (m-30) cc_final: 0.8693 (p0) REVERT: C 527 ARG cc_start: 0.7879 (OUTLIER) cc_final: 0.6816 (mtp180) REVERT: D 282 GLU cc_start: 0.8688 (OUTLIER) cc_final: 0.8438 (pp20) REVERT: D 302 MET cc_start: 0.6378 (OUTLIER) cc_final: 0.5526 (mmt) REVERT: D 506 LYS cc_start: 0.9037 (tptp) cc_final: 0.8282 (tptp) REVERT: D 509 ASP cc_start: 0.8956 (m-30) cc_final: 0.8691 (p0) REVERT: D 527 ARG cc_start: 0.7865 (OUTLIER) cc_final: 0.6803 (mtp180) REVERT: E 208 MET cc_start: 0.9031 (mmm) cc_final: 0.8706 (mtm) REVERT: E 282 GLU cc_start: 0.8737 (OUTLIER) cc_final: 0.8413 (pp20) REVERT: E 509 ASP cc_start: 0.8941 (m-30) cc_final: 0.8612 (p0) REVERT: F 172 MET cc_start: 0.8745 (OUTLIER) cc_final: 0.7803 (mtp) REVERT: F 282 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.8420 (pp20) REVERT: F 302 MET cc_start: 0.6226 (OUTLIER) cc_final: 0.5737 (mmt) outliers start: 54 outliers final: 27 residues processed: 164 average time/residue: 0.7537 time to fit residues: 140.4698 Evaluate side-chains 167 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 126 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 291 ARG Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 511 MET Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 511 MET Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 151 SER Chi-restraints excluded: chain C residue 282 GLU Chi-restraints excluded: chain C residue 302 MET Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 527 ARG Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 151 SER Chi-restraints excluded: chain D residue 282 GLU Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain D residue 527 ARG Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 151 SER Chi-restraints excluded: chain E residue 282 GLU Chi-restraints excluded: chain E residue 422 ASP Chi-restraints excluded: chain E residue 511 MET Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 151 SER Chi-restraints excluded: chain F residue 172 MET Chi-restraints excluded: chain F residue 282 GLU Chi-restraints excluded: chain F residue 302 MET Chi-restraints excluded: chain F residue 467 THR Chi-restraints excluded: chain F residue 511 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 84 optimal weight: 1.9990 chunk 190 optimal weight: 1.9990 chunk 245 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 223 optimal weight: 5.9990 chunk 113 optimal weight: 0.0040 chunk 191 optimal weight: 0.6980 chunk 140 optimal weight: 0.9990 chunk 248 optimal weight: 6.9990 chunk 90 optimal weight: 5.9990 chunk 259 optimal weight: 1.9990 overall best weight: 1.1398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.075298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.053935 restraints weight = 54383.110| |-----------------------------------------------------------------------------| r_work (start): 0.2837 rms_B_bonded: 2.64 r_work: 0.2696 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2561 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 24540 Z= 0.107 Angle : 0.507 7.657 33360 Z= 0.250 Chirality : 0.042 0.124 3570 Planarity : 0.003 0.036 4338 Dihedral : 9.684 135.299 3558 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.01 % Allowed : 18.52 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.16), residues: 2988 helix: 0.88 (0.18), residues: 924 sheet: -1.13 (0.20), residues: 654 loop : -0.13 (0.17), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 345 TYR 0.012 0.001 TYR B 226 PHE 0.006 0.001 PHE B 224 TRP 0.004 0.001 TRP B 176 HIS 0.003 0.001 HIS A 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (24540) covalent geometry : angle 0.50653 / 0.25 (33360) hydrogen bonds : bond 0.02901 / 1.90 ( 768) hydrogen bonds : angle 4.56706 / 3.16 ( 2178) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 126 time to evaluate : 0.946 Fit side-chains REVERT: A 172 MET cc_start: 0.8631 (OUTLIER) cc_final: 0.7376 (mtp) REVERT: A 282 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.8387 (pp20) REVERT: A 302 MET cc_start: 0.6101 (OUTLIER) cc_final: 0.5668 (mmt) REVERT: B 282 GLU cc_start: 0.8782 (OUTLIER) cc_final: 0.8433 (pp20) REVERT: B 509 ASP cc_start: 0.8867 (m-30) cc_final: 0.8556 (p0) REVERT: C 282 GLU cc_start: 0.8740 (OUTLIER) cc_final: 0.8431 (pp20) REVERT: C 302 MET cc_start: 0.5911 (OUTLIER) cc_final: 0.5466 (mmt) REVERT: C 422 ASP cc_start: 0.9290 (OUTLIER) cc_final: 0.9087 (t70) REVERT: C 506 LYS cc_start: 0.9038 (tptp) cc_final: 0.8252 (tptp) REVERT: C 509 ASP cc_start: 0.8953 (m-30) cc_final: 0.8677 (p0) REVERT: C 527 ARG cc_start: 0.7877 (OUTLIER) cc_final: 0.7056 (mtp180) REVERT: D 282 GLU cc_start: 0.8708 (OUTLIER) cc_final: 0.8400 (pp20) REVERT: D 302 MET cc_start: 0.5876 (OUTLIER) cc_final: 0.5446 (mmt) REVERT: D 506 LYS cc_start: 0.9026 (tptp) cc_final: 0.8255 (tptp) REVERT: D 509 ASP cc_start: 0.8955 (m-30) cc_final: 0.8679 (p0) REVERT: D 527 ARG cc_start: 0.7865 (OUTLIER) cc_final: 0.7047 (mtp180) REVERT: E 282 GLU cc_start: 0.8791 (OUTLIER) cc_final: 0.8467 (pp20) REVERT: E 509 ASP cc_start: 0.8872 (m-30) cc_final: 0.8571 (p0) REVERT: F 172 MET cc_start: 0.8629 (OUTLIER) cc_final: 0.7388 (mtp) REVERT: F 282 GLU cc_start: 0.8732 (OUTLIER) cc_final: 0.8424 (pp20) REVERT: F 302 MET cc_start: 0.6128 (OUTLIER) cc_final: 0.5701 (mmt) outliers start: 51 outliers final: 21 residues processed: 161 average time/residue: 0.7320 time to fit residues: 134.3469 Evaluate side-chains 161 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 125 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 172 MET Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 291 ARG Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 511 MET Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 511 MET Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 151 SER Chi-restraints excluded: chain C residue 282 GLU Chi-restraints excluded: chain C residue 302 MET Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 527 ARG Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 151 SER Chi-restraints excluded: chain D residue 282 GLU Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain D residue 527 ARG Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 282 GLU Chi-restraints excluded: chain E residue 422 ASP Chi-restraints excluded: chain E residue 511 MET Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 172 MET Chi-restraints excluded: chain F residue 282 GLU Chi-restraints excluded: chain F residue 302 MET Chi-restraints excluded: chain F residue 511 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 1 optimal weight: 0.9980 chunk 249 optimal weight: 0.9980 chunk 151 optimal weight: 0.9990 chunk 80 optimal weight: 9.9990 chunk 184 optimal weight: 3.9990 chunk 231 optimal weight: 9.9990 chunk 96 optimal weight: 9.9990 chunk 191 optimal weight: 3.9990 chunk 59 optimal weight: 0.6980 chunk 271 optimal weight: 0.8980 chunk 210 optimal weight: 10.0000 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.075679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.054904 restraints weight = 55035.042| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 2.58 r_work: 0.2760 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2633 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 24540 Z= 0.100 Angle : 0.500 8.998 33360 Z= 0.246 Chirality : 0.042 0.154 3570 Planarity : 0.003 0.036 4338 Dihedral : 9.613 136.002 3558 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.66 % Allowed : 18.76 % Favored : 79.58 % 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: -0.03 (0.16), residues: 2988 helix: 0.98 (0.18), residues: 930 sheet: -1.06 (0.20), residues: 654 loop : -0.02 (0.17), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 175 TYR 0.012 0.001 TYR B 226 PHE 0.007 0.001 PHE D 182 TRP 0.004 0.001 TRP D 134 HIS 0.003 0.001 HIS B 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.10 (24540) covalent geometry : angle 0.50018 / 0.25 (33360) hydrogen bonds : bond 0.02690 / 1.77 ( 768) hydrogen bonds : angle 4.48674 / 3.10 ( 2178) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 130 time to evaluate : 0.916 Fit side-chains REVERT: A 282 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.8421 (pp20) REVERT: A 302 MET cc_start: 0.5904 (OUTLIER) cc_final: 0.5429 (mmt) REVERT: B 208 MET cc_start: 0.8799 (mmm) cc_final: 0.8554 (mtm) REVERT: B 282 GLU cc_start: 0.8851 (OUTLIER) cc_final: 0.8501 (pp20) REVERT: B 509 ASP cc_start: 0.8868 (m-30) cc_final: 0.8558 (p0) REVERT: C 282 GLU cc_start: 0.8802 (OUTLIER) cc_final: 0.8462 (pp20) REVERT: C 302 MET cc_start: 0.5813 (OUTLIER) cc_final: 0.5499 (mmt) REVERT: C 506 LYS cc_start: 0.9057 (tptp) cc_final: 0.8253 (tptp) REVERT: C 509 ASP cc_start: 0.8930 (m-30) cc_final: 0.8657 (p0) REVERT: C 527 ARG cc_start: 0.7982 (OUTLIER) cc_final: 0.7205 (mtp180) REVERT: D 282 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.8424 (pp20) REVERT: D 302 MET cc_start: 0.5834 (OUTLIER) cc_final: 0.5512 (mmt) REVERT: D 506 LYS cc_start: 0.9060 (tptp) cc_final: 0.8290 (tptp) REVERT: D 509 ASP cc_start: 0.8937 (m-30) cc_final: 0.8660 (p0) REVERT: D 527 ARG cc_start: 0.7965 (OUTLIER) cc_final: 0.7193 (mtp180) REVERT: E 208 MET cc_start: 0.8802 (mmm) cc_final: 0.8549 (mtm) REVERT: E 282 GLU cc_start: 0.8840 (OUTLIER) cc_final: 0.8518 (pp20) REVERT: E 509 ASP cc_start: 0.8857 (m-30) cc_final: 0.8552 (p0) REVERT: F 172 MET cc_start: 0.8689 (OUTLIER) cc_final: 0.7318 (mpp) REVERT: F 282 GLU cc_start: 0.8783 (OUTLIER) cc_final: 0.8477 (pp20) REVERT: F 302 MET cc_start: 0.5958 (OUTLIER) cc_final: 0.5535 (mmt) REVERT: F 506 LYS cc_start: 0.9218 (tptp) cc_final: 0.8616 (tptp) outliers start: 42 outliers final: 20 residues processed: 157 average time/residue: 0.7273 time to fit residues: 129.7662 Evaluate side-chains 161 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 128 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 291 ARG Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 511 MET Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 511 MET Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 151 SER Chi-restraints excluded: chain C residue 282 GLU Chi-restraints excluded: chain C residue 302 MET Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 527 ARG Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 151 SER Chi-restraints excluded: chain D residue 282 GLU Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 527 ARG Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 282 GLU Chi-restraints excluded: chain E residue 422 ASP Chi-restraints excluded: chain E residue 511 MET Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 60 MET Chi-restraints excluded: chain F residue 151 SER Chi-restraints excluded: chain F residue 172 MET Chi-restraints excluded: chain F residue 282 GLU Chi-restraints excluded: chain F residue 302 MET Chi-restraints excluded: chain F residue 511 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 149 optimal weight: 7.9990 chunk 105 optimal weight: 5.9990 chunk 126 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 261 optimal weight: 0.9990 chunk 218 optimal weight: 6.9990 chunk 151 optimal weight: 1.9990 chunk 60 optimal weight: 8.9990 chunk 217 optimal weight: 1.9990 chunk 54 optimal weight: 7.9990 chunk 13 optimal weight: 3.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 63 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.074906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.053947 restraints weight = 55384.081| |-----------------------------------------------------------------------------| r_work (start): 0.2859 rms_B_bonded: 2.59 r_work: 0.2724 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2595 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 24540 Z= 0.151 Angle : 0.528 11.971 33360 Z= 0.257 Chirality : 0.043 0.139 3570 Planarity : 0.003 0.036 4338 Dihedral : 9.563 136.128 3558 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.58 % Allowed : 19.31 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.16), residues: 2988 helix: 0.98 (0.18), residues: 930 sheet: -1.02 (0.20), residues: 654 loop : -0.00 (0.17), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 406 TYR 0.011 0.001 TYR E 226 PHE 0.008 0.001 PHE B 224 TRP 0.005 0.001 TRP E 176 HIS 0.004 0.001 HIS E 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 (24540) covalent geometry : angle 0.52754 / 0.26 (33360) hydrogen bonds : bond 0.02936 / 1.92 ( 768) hydrogen bonds : angle 4.52580 / 3.13 ( 2178) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 130 time to evaluate : 0.927 Fit side-chains REVERT: A 172 MET cc_start: 0.8569 (OUTLIER) cc_final: 0.7454 (mtp) REVERT: A 282 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.8443 (pp20) REVERT: A 302 MET cc_start: 0.5993 (OUTLIER) cc_final: 0.5566 (mmt) REVERT: B 208 MET cc_start: 0.8898 (mmm) cc_final: 0.8496 (mtm) REVERT: B 282 GLU cc_start: 0.8832 (OUTLIER) cc_final: 0.8491 (pp20) REVERT: B 509 ASP cc_start: 0.8864 (m-30) cc_final: 0.8556 (p0) REVERT: C 282 GLU cc_start: 0.8789 (OUTLIER) cc_final: 0.8491 (pp20) REVERT: C 302 MET cc_start: 0.5830 (OUTLIER) cc_final: 0.5524 (mmt) REVERT: C 506 LYS cc_start: 0.9054 (tptp) cc_final: 0.8239 (tptp) REVERT: C 509 ASP cc_start: 0.8930 (m-30) cc_final: 0.8662 (p0) REVERT: C 527 ARG cc_start: 0.8012 (OUTLIER) cc_final: 0.7272 (mtp180) REVERT: D 282 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.8460 (pp20) REVERT: D 302 MET cc_start: 0.5858 (OUTLIER) cc_final: 0.5531 (mmt) REVERT: D 506 LYS cc_start: 0.9055 (tptp) cc_final: 0.8276 (tptp) REVERT: D 509 ASP cc_start: 0.8936 (m-30) cc_final: 0.8655 (p0) REVERT: D 527 ARG cc_start: 0.8006 (OUTLIER) cc_final: 0.7257 (mtp180) REVERT: E 282 GLU cc_start: 0.8861 (OUTLIER) cc_final: 0.8539 (pp20) REVERT: E 509 ASP cc_start: 0.8842 (m-30) cc_final: 0.8534 (p0) REVERT: F 172 MET cc_start: 0.8667 (OUTLIER) cc_final: 0.7616 (mtp) REVERT: F 282 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.8426 (pp20) REVERT: F 302 MET cc_start: 0.6027 (OUTLIER) cc_final: 0.5584 (mmt) outliers start: 40 outliers final: 24 residues processed: 157 average time/residue: 0.7339 time to fit residues: 130.4841 Evaluate side-chains 163 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 125 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 172 MET Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 291 ARG Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 511 MET Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 511 MET Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 151 SER Chi-restraints excluded: chain C residue 282 GLU Chi-restraints excluded: chain C residue 302 MET Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 527 ARG Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 151 SER Chi-restraints excluded: chain D residue 282 GLU Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 527 ARG Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 282 GLU Chi-restraints excluded: chain E residue 422 ASP Chi-restraints excluded: chain E residue 511 MET Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 60 MET Chi-restraints excluded: chain F residue 151 SER Chi-restraints excluded: chain F residue 172 MET Chi-restraints excluded: chain F residue 282 GLU Chi-restraints excluded: chain F residue 291 ARG Chi-restraints excluded: chain F residue 302 MET Chi-restraints excluded: chain F residue 511 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 144 optimal weight: 0.3980 chunk 77 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 299 optimal weight: 1.9990 chunk 74 optimal weight: 6.9990 chunk 149 optimal weight: 7.9990 chunk 72 optimal weight: 0.9990 chunk 262 optimal weight: 9.9990 chunk 208 optimal weight: 6.9990 chunk 83 optimal weight: 0.6980 chunk 212 optimal weight: 10.0000 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.075496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.054664 restraints weight = 55087.555| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 2.57 r_work: 0.2743 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2614 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 24540 Z= 0.111 Angle : 0.511 9.755 33360 Z= 0.249 Chirality : 0.042 0.121 3570 Planarity : 0.003 0.036 4338 Dihedral : 9.534 136.120 3558 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.58 % Allowed : 19.63 % Favored : 78.79 % 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: 0.03 (0.16), residues: 2988 helix: 1.02 (0.18), residues: 930 sheet: -0.99 (0.20), residues: 654 loop : -0.00 (0.17), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 175 TYR 0.011 0.001 TYR E 226 PHE 0.006 0.001 PHE B 224 TRP 0.004 0.001 TRP F 298 HIS 0.003 0.001 HIS E 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.11 (24540) covalent geometry : angle 0.51128 / 0.25 (33360) hydrogen bonds : bond 0.02743 / 1.80 ( 768) hydrogen bonds : angle 4.48020 / 3.10 ( 2178) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 128 time to evaluate : 0.891 Fit side-chains REVERT: A 282 GLU cc_start: 0.8766 (OUTLIER) cc_final: 0.8443 (pp20) REVERT: B 282 GLU cc_start: 0.8839 (OUTLIER) cc_final: 0.8486 (pp20) REVERT: B 509 ASP cc_start: 0.8854 (m-30) cc_final: 0.8557 (p0) REVERT: C 282 GLU cc_start: 0.8800 (OUTLIER) cc_final: 0.8465 (pp20) REVERT: C 302 MET cc_start: 0.5791 (OUTLIER) cc_final: 0.5500 (mmt) REVERT: C 449 PHE cc_start: 0.8169 (OUTLIER) cc_final: 0.7928 (m-10) REVERT: C 506 LYS cc_start: 0.9054 (tptp) cc_final: 0.8241 (tptp) REVERT: C 509 ASP cc_start: 0.8935 (m-30) cc_final: 0.8653 (p0) REVERT: C 527 ARG cc_start: 0.7987 (OUTLIER) cc_final: 0.7286 (mtp180) REVERT: D 282 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.8436 (pp20) REVERT: D 302 MET cc_start: 0.5821 (OUTLIER) cc_final: 0.5512 (mmt) REVERT: D 506 LYS cc_start: 0.9054 (tptp) cc_final: 0.8271 (tptp) REVERT: D 509 ASP cc_start: 0.8929 (m-30) cc_final: 0.8650 (p0) REVERT: D 527 ARG cc_start: 0.7980 (OUTLIER) cc_final: 0.7271 (mtp180) REVERT: E 282 GLU cc_start: 0.8876 (OUTLIER) cc_final: 0.8548 (pp20) REVERT: E 509 ASP cc_start: 0.8828 (m-30) cc_final: 0.8534 (p0) REVERT: F 172 MET cc_start: 0.8676 (OUTLIER) cc_final: 0.7457 (mtp) REVERT: F 208 MET cc_start: 0.8955 (mtp) cc_final: 0.8647 (mmm) REVERT: F 282 GLU cc_start: 0.8765 (OUTLIER) cc_final: 0.8436 (pp20) outliers start: 40 outliers final: 21 residues processed: 155 average time/residue: 0.7456 time to fit residues: 131.3412 Evaluate side-chains 160 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 127 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 291 ARG Chi-restraints excluded: chain A residue 511 MET Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 511 MET Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 151 SER Chi-restraints excluded: chain C residue 282 GLU Chi-restraints excluded: chain C residue 302 MET Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 449 PHE Chi-restraints excluded: chain C residue 527 ARG Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 151 SER Chi-restraints excluded: chain D residue 282 GLU Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 527 ARG Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 282 GLU Chi-restraints excluded: chain E residue 422 ASP Chi-restraints excluded: chain E residue 511 MET Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 60 MET Chi-restraints excluded: chain F residue 151 SER Chi-restraints excluded: chain F residue 172 MET Chi-restraints excluded: chain F residue 282 GLU Chi-restraints excluded: chain F residue 291 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 153 optimal weight: 3.9990 chunk 282 optimal weight: 4.9990 chunk 29 optimal weight: 0.6980 chunk 278 optimal weight: 6.9990 chunk 294 optimal weight: 1.9990 chunk 291 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 295 optimal weight: 5.9990 chunk 223 optimal weight: 0.7980 chunk 130 optimal weight: 9.9990 chunk 90 optimal weight: 0.5980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 293 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.075783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.055113 restraints weight = 54849.667| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 2.57 r_work: 0.2769 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2640 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 24540 Z= 0.102 Angle : 0.511 9.216 33360 Z= 0.247 Chirality : 0.042 0.120 3570 Planarity : 0.003 0.036 4338 Dihedral : 9.501 136.401 3558 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.46 % Allowed : 19.71 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.16), residues: 2988 helix: 1.08 (0.18), residues: 930 sheet: -0.96 (0.20), residues: 654 loop : -0.01 (0.17), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 171 TYR 0.011 0.001 TYR E 226 PHE 0.007 0.001 PHE E 210 TRP 0.005 0.001 TRP A 298 HIS 0.005 0.001 HIS A 293 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.10 (24540) covalent geometry : angle 0.51095 / 0.25 (33360) hydrogen bonds : bond 0.02641 / 1.73 ( 768) hydrogen bonds : angle 4.45957 / 3.08 ( 2178) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9656.44 seconds wall clock time: 164 minutes 54.70 seconds (9894.70 seconds total)