Starting phenix.real_space_refine on Wed Jun 11 16:31:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6sh4_10193/06_2025/6sh4_10193.cif Found real_map, /net/cci-nas-00/data/ceres_data/6sh4_10193/06_2025/6sh4_10193.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6sh4_10193/06_2025/6sh4_10193.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6sh4_10193/06_2025/6sh4_10193.map" model { file = "/net/cci-nas-00/data/ceres_data/6sh4_10193/06_2025/6sh4_10193.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6sh4_10193/06_2025/6sh4_10193.cif" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 3 Type Number sf(0) Gaussians C 7693 2.51 5 N 2632 2.21 5 O 2632 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 12957 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 1851 Classifications: {'peptide': 376} Incomplete info: {'truncation_to_alanine': 324} Link IDs: {'PTRANS': 17, 'TRANS': 358} Chain breaks: 3 Unresolved chain link angles: 17 Unresolved non-hydrogen bonds: 1195 Unresolved non-hydrogen angles: 1528 Unresolved non-hydrogen dihedrals: 1012 Unresolved non-hydrogen chiralities: 108 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 8, 'TYR:plan': 16, 'ASN:plan1': 17, 'TRP:plan': 5, 'ASP:plan': 24, 'PHE:plan': 17, 'GLU:plan': 16, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 617 Restraints were copied for chains: C, B, E, D, G, F Time building chain proxies: 4.93, per 1000 atoms: 0.38 Number of scatterers: 12957 At special positions: 0 Unit cell: (151.437, 148.26, 133.434, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 2632 8.00 N 2632 7.00 C 7693 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: 3.41 Conformation dependent library (CDL) restraints added in 2.4 seconds 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4858 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 21 sheets defined 45.5% alpha, 20.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.93 Creating SS restraints... Processing helix chain 'A' and resid 52 through 83 removed outlier: 4.502A pdb=" N GLY A 56 " --> pdb=" O PHE A 52 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLY A 57 " --> pdb=" O ALA A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 105 removed outlier: 3.510A pdb=" N LYS A 105 " --> pdb=" O THR A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 181 No H-bonds generated for 'chain 'A' and resid 179 through 181' Processing helix chain 'A' and resid 182 through 197 removed outlier: 4.120A pdb=" N ASP A 186 " --> pdb=" O HIS A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 228 Processing helix chain 'A' and resid 233 through 240 removed outlier: 3.617A pdb=" N ILE A 238 " --> pdb=" O ILE A 234 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU A 239 " --> pdb=" O LYS A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 246 Processing helix chain 'A' and resid 248 through 255 removed outlier: 3.678A pdb=" N ARG A 255 " --> pdb=" O TRP A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 284 Processing helix chain 'A' and resid 300 through 309 removed outlier: 3.729A pdb=" N ASN A 304 " --> pdb=" O ASP A 300 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N HIS A 305 " --> pdb=" O ASP A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 324 removed outlier: 3.849A pdb=" N ALA A 324 " --> pdb=" O ILE A 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 321 through 324' Processing helix chain 'A' and resid 342 through 350 Processing helix chain 'A' and resid 390 through 402 Processing helix chain 'A' and resid 405 through 417 removed outlier: 4.016A pdb=" N CYS A 409 " --> pdb=" O GLU A 405 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS A 410 " --> pdb=" O THR A 406 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS A 411 " --> pdb=" O ASP A 407 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N SER A 415 " --> pdb=" O LYS A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 434 Processing helix chain 'A' and resid 438 through 446 removed outlier: 3.616A pdb=" N ALA A 442 " --> pdb=" O ALA A 438 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYS A 444 " --> pdb=" O HIS A 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 83 removed outlier: 4.503A pdb=" N GLY B 56 " --> pdb=" O PHE B 52 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLY B 57 " --> pdb=" O ALA B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 105 removed outlier: 3.509A pdb=" N LYS B 105 " --> pdb=" O THR B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 181 No H-bonds generated for 'chain 'B' and resid 179 through 181' Processing helix chain 'B' and resid 182 through 197 removed outlier: 4.120A pdb=" N ASP B 186 " --> pdb=" O HIS B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 228 Processing helix chain 'B' and resid 233 through 240 removed outlier: 3.617A pdb=" N ILE B 238 " --> pdb=" O ILE B 234 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU B 239 " --> pdb=" O LYS B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 246 Processing helix chain 'B' and resid 248 through 255 removed outlier: 3.678A pdb=" N ARG B 255 " --> pdb=" O TRP B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 284 Processing helix chain 'B' and resid 300 through 309 removed outlier: 3.729A pdb=" N ASN B 304 " --> pdb=" O ASP B 300 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N HIS B 305 " --> pdb=" O ASP B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 324 removed outlier: 3.848A pdb=" N ALA B 324 " --> pdb=" O ILE B 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 321 through 324' Processing helix chain 'B' and resid 342 through 350 Processing helix chain 'B' and resid 390 through 402 Processing helix chain 'B' and resid 405 through 417 removed outlier: 4.016A pdb=" N CYS B 409 " --> pdb=" O GLU B 405 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS B 410 " --> pdb=" O THR B 406 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS B 411 " --> pdb=" O ASP B 407 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N SER B 415 " --> pdb=" O LYS B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 434 Processing helix chain 'B' and resid 438 through 446 removed outlier: 3.617A pdb=" N ALA B 442 " --> pdb=" O ALA B 438 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS B 444 " --> pdb=" O HIS B 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 83 removed outlier: 4.502A pdb=" N GLY C 56 " --> pdb=" O PHE C 52 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLY C 57 " --> pdb=" O ALA C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 105 removed outlier: 3.510A pdb=" N LYS C 105 " --> pdb=" O THR C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 181 No H-bonds generated for 'chain 'C' and resid 179 through 181' Processing helix chain 'C' and resid 182 through 197 removed outlier: 4.120A pdb=" N ASP C 186 " --> pdb=" O HIS C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 228 Processing helix chain 'C' and resid 233 through 240 removed outlier: 3.617A pdb=" N ILE C 238 " --> pdb=" O ILE C 234 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU C 239 " --> pdb=" O LYS C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 246 Processing helix chain 'C' and resid 248 through 255 removed outlier: 3.678A pdb=" N ARG C 255 " --> pdb=" O TRP C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 284 Processing helix chain 'C' and resid 300 through 309 removed outlier: 3.728A pdb=" N ASN C 304 " --> pdb=" O ASP C 300 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N HIS C 305 " --> pdb=" O ASP C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 324 removed outlier: 3.849A pdb=" N ALA C 324 " --> pdb=" O ILE C 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 321 through 324' Processing helix chain 'C' and resid 342 through 350 Processing helix chain 'C' and resid 390 through 402 Processing helix chain 'C' and resid 405 through 417 removed outlier: 4.015A pdb=" N CYS C 409 " --> pdb=" O GLU C 405 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS C 410 " --> pdb=" O THR C 406 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS C 411 " --> pdb=" O ASP C 407 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N SER C 415 " --> pdb=" O LYS C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 434 Processing helix chain 'C' and resid 438 through 446 removed outlier: 3.617A pdb=" N ALA C 442 " --> pdb=" O ALA C 438 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYS C 444 " --> pdb=" O HIS C 440 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 83 removed outlier: 4.502A pdb=" N GLY D 56 " --> pdb=" O PHE D 52 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLY D 57 " --> pdb=" O ALA D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 105 removed outlier: 3.509A pdb=" N LYS D 105 " --> pdb=" O THR D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 181 No H-bonds generated for 'chain 'D' and resid 179 through 181' Processing helix chain 'D' and resid 182 through 197 removed outlier: 4.121A pdb=" N ASP D 186 " --> pdb=" O HIS D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 228 Processing helix chain 'D' and resid 233 through 240 removed outlier: 3.617A pdb=" N ILE D 238 " --> pdb=" O ILE D 234 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU D 239 " --> pdb=" O LYS D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 246 Processing helix chain 'D' and resid 248 through 255 removed outlier: 3.678A pdb=" N ARG D 255 " --> pdb=" O TRP D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 284 Processing helix chain 'D' and resid 300 through 309 removed outlier: 3.729A pdb=" N ASN D 304 " --> pdb=" O ASP D 300 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N HIS D 305 " --> pdb=" O ASP D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 324 removed outlier: 3.849A pdb=" N ALA D 324 " --> pdb=" O ILE D 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 321 through 324' Processing helix chain 'D' and resid 342 through 350 Processing helix chain 'D' and resid 390 through 402 Processing helix chain 'D' and resid 405 through 417 removed outlier: 4.016A pdb=" N CYS D 409 " --> pdb=" O GLU D 405 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS D 410 " --> pdb=" O THR D 406 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS D 411 " --> pdb=" O ASP D 407 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N SER D 415 " --> pdb=" O LYS D 411 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 434 Processing helix chain 'D' and resid 438 through 446 removed outlier: 3.616A pdb=" N ALA D 442 " --> pdb=" O ALA D 438 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYS D 444 " --> pdb=" O HIS D 440 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 83 removed outlier: 4.502A pdb=" N GLY E 56 " --> pdb=" O PHE E 52 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY E 57 " --> pdb=" O ALA E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 105 removed outlier: 3.509A pdb=" N LYS E 105 " --> pdb=" O THR E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 181 No H-bonds generated for 'chain 'E' and resid 179 through 181' Processing helix chain 'E' and resid 182 through 197 removed outlier: 4.120A pdb=" N ASP E 186 " --> pdb=" O HIS E 182 " (cutoff:3.500A) Processing helix chain 'E' and resid 224 through 228 Processing helix chain 'E' and resid 233 through 240 removed outlier: 3.617A pdb=" N ILE E 238 " --> pdb=" O ILE E 234 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU E 239 " --> pdb=" O LYS E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 240 through 246 Processing helix chain 'E' and resid 248 through 255 removed outlier: 3.678A pdb=" N ARG E 255 " --> pdb=" O TRP E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 272 through 284 Processing helix chain 'E' and resid 300 through 309 removed outlier: 3.729A pdb=" N ASN E 304 " --> pdb=" O ASP E 300 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N HIS E 305 " --> pdb=" O ASP E 301 " (cutoff:3.500A) Processing helix chain 'E' and resid 321 through 324 removed outlier: 3.849A pdb=" N ALA E 324 " --> pdb=" O ILE E 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 321 through 324' Processing helix chain 'E' and resid 342 through 350 Processing helix chain 'E' and resid 390 through 402 Processing helix chain 'E' and resid 405 through 417 removed outlier: 4.015A pdb=" N CYS E 409 " --> pdb=" O GLU E 405 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS E 410 " --> pdb=" O THR E 406 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS E 411 " --> pdb=" O ASP E 407 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N SER E 415 " --> pdb=" O LYS E 411 " (cutoff:3.500A) Processing helix chain 'E' and resid 424 through 434 Processing helix chain 'E' and resid 438 through 446 removed outlier: 3.617A pdb=" N ALA E 442 " --> pdb=" O ALA E 438 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYS E 444 " --> pdb=" O HIS E 440 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 83 removed outlier: 4.502A pdb=" N GLY F 56 " --> pdb=" O PHE F 52 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLY F 57 " --> pdb=" O ALA F 53 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 105 removed outlier: 3.509A pdb=" N LYS F 105 " --> pdb=" O THR F 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 179 through 181 No H-bonds generated for 'chain 'F' and resid 179 through 181' Processing helix chain 'F' and resid 182 through 197 removed outlier: 4.120A pdb=" N ASP F 186 " --> pdb=" O HIS F 182 " (cutoff:3.500A) Processing helix chain 'F' and resid 224 through 228 Processing helix chain 'F' and resid 233 through 240 removed outlier: 3.617A pdb=" N ILE F 238 " --> pdb=" O ILE F 234 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU F 239 " --> pdb=" O LYS F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 240 through 246 Processing helix chain 'F' and resid 248 through 255 removed outlier: 3.678A pdb=" N ARG F 255 " --> pdb=" O TRP F 251 " (cutoff:3.500A) Processing helix chain 'F' and resid 272 through 284 Processing helix chain 'F' and resid 300 through 309 removed outlier: 3.729A pdb=" N ASN F 304 " --> pdb=" O ASP F 300 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N HIS F 305 " --> pdb=" O ASP F 301 " (cutoff:3.500A) Processing helix chain 'F' and resid 321 through 324 removed outlier: 3.849A pdb=" N ALA F 324 " --> pdb=" O ILE F 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 321 through 324' Processing helix chain 'F' and resid 342 through 350 Processing helix chain 'F' and resid 390 through 402 Processing helix chain 'F' and resid 405 through 417 removed outlier: 4.016A pdb=" N CYS F 409 " --> pdb=" O GLU F 405 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS F 410 " --> pdb=" O THR F 406 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS F 411 " --> pdb=" O ASP F 407 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N SER F 415 " --> pdb=" O LYS F 411 " (cutoff:3.500A) Processing helix chain 'F' and resid 424 through 434 Processing helix chain 'F' and resid 438 through 446 removed outlier: 3.616A pdb=" N ALA F 442 " --> pdb=" O ALA F 438 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYS F 444 " --> pdb=" O HIS F 440 " (cutoff:3.500A) Processing helix chain 'G' and resid 52 through 83 removed outlier: 4.502A pdb=" N GLY G 56 " --> pdb=" O PHE G 52 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLY G 57 " --> pdb=" O ALA G 53 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 105 removed outlier: 3.510A pdb=" N LYS G 105 " --> pdb=" O THR G 101 " (cutoff:3.500A) Processing helix chain 'G' and resid 179 through 181 No H-bonds generated for 'chain 'G' and resid 179 through 181' Processing helix chain 'G' and resid 182 through 197 removed outlier: 4.120A pdb=" N ASP G 186 " --> pdb=" O HIS G 182 " (cutoff:3.500A) Processing helix chain 'G' and resid 224 through 228 Processing helix chain 'G' and resid 233 through 240 removed outlier: 3.617A pdb=" N ILE G 238 " --> pdb=" O ILE G 234 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU G 239 " --> pdb=" O LYS G 235 " (cutoff:3.500A) Processing helix chain 'G' and resid 240 through 246 Processing helix chain 'G' and resid 248 through 255 removed outlier: 3.678A pdb=" N ARG G 255 " --> pdb=" O TRP G 251 " (cutoff:3.500A) Processing helix chain 'G' and resid 272 through 284 Processing helix chain 'G' and resid 300 through 309 removed outlier: 3.729A pdb=" N ASN G 304 " --> pdb=" O ASP G 300 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N HIS G 305 " --> pdb=" O ASP G 301 " (cutoff:3.500A) Processing helix chain 'G' and resid 321 through 324 removed outlier: 3.850A pdb=" N ALA G 324 " --> pdb=" O ILE G 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 321 through 324' Processing helix chain 'G' and resid 342 through 350 Processing helix chain 'G' and resid 390 through 402 Processing helix chain 'G' and resid 405 through 417 removed outlier: 4.016A pdb=" N CYS G 409 " --> pdb=" O GLU G 405 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS G 410 " --> pdb=" O THR G 406 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS G 411 " --> pdb=" O ASP G 407 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N SER G 415 " --> pdb=" O LYS G 411 " (cutoff:3.500A) Processing helix chain 'G' and resid 424 through 434 Processing helix chain 'G' and resid 438 through 446 removed outlier: 3.616A pdb=" N ALA G 442 " --> pdb=" O ALA G 438 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYS G 444 " --> pdb=" O HIS G 440 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 90 removed outlier: 4.589A pdb=" N PHE A 169 " --> pdb=" O SER A 157 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE A 152 " --> pdb=" O HIS A 141 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 115 through 122 Processing sheet with id=AA3, first strand: chain 'A' and resid 213 through 216 removed outlier: 4.073A pdb=" N ILE A 205 " --> pdb=" O PHE A 216 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N SER A 208 " --> pdb=" O ILE A 290 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N ASN A 292 " --> pdb=" O SER A 208 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ASN A 287 " --> pdb=" O ILE A 315 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N LEU A 317 " --> pdb=" O ASN A 287 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N CYS A 289 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N GLU A 319 " --> pdb=" O CYS A 289 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N LEU A 291 " --> pdb=" O GLU A 319 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N ILE A 359 " --> pdb=" O SER A 314 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ARG A 261 " --> pdb=" O THR A 360 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N MET A 362 " --> pdb=" O ARG A 261 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N TYR A 263 " --> pdb=" O MET A 362 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N THR A 364 " --> pdb=" O TYR A 263 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N LEU A 265 " --> pdb=" O THR A 364 " (cutoff:3.500A) removed outlier: 8.557A pdb=" N ILE A 380 " --> pdb=" O ARG A 260 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N GLY A 262 " --> pdb=" O ILE A 380 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N TYR A 382 " --> pdb=" O GLY A 262 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 84 through 90 removed outlier: 4.590A pdb=" N PHE B 169 " --> pdb=" O SER B 157 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE B 152 " --> pdb=" O HIS B 141 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 115 through 122 Processing sheet with id=AA6, first strand: chain 'B' and resid 213 through 216 removed outlier: 4.072A pdb=" N ILE B 205 " --> pdb=" O PHE B 216 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N SER B 208 " --> pdb=" O ILE B 290 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N ASN B 292 " --> pdb=" O SER B 208 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ASN B 287 " --> pdb=" O ILE B 315 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N LEU B 317 " --> pdb=" O ASN B 287 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N CYS B 289 " --> pdb=" O LEU B 317 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N GLU B 319 " --> pdb=" O CYS B 289 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N LEU B 291 " --> pdb=" O GLU B 319 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N ILE B 359 " --> pdb=" O SER B 314 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ARG B 261 " --> pdb=" O THR B 360 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N MET B 362 " --> pdb=" O ARG B 261 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N TYR B 263 " --> pdb=" O MET B 362 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N THR B 364 " --> pdb=" O TYR B 263 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N LEU B 265 " --> pdb=" O THR B 364 " (cutoff:3.500A) removed outlier: 8.557A pdb=" N ILE B 380 " --> pdb=" O ARG B 260 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N GLY B 262 " --> pdb=" O ILE B 380 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N TYR B 382 " --> pdb=" O GLY B 262 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 84 through 90 removed outlier: 4.589A pdb=" N PHE C 169 " --> pdb=" O SER C 157 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE C 152 " --> pdb=" O HIS C 141 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 115 through 122 Processing sheet with id=AA9, first strand: chain 'C' and resid 213 through 216 removed outlier: 4.072A pdb=" N ILE C 205 " --> pdb=" O PHE C 216 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N SER C 208 " --> pdb=" O ILE C 290 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N ASN C 292 " --> pdb=" O SER C 208 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ASN C 287 " --> pdb=" O ILE C 315 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N LEU C 317 " --> pdb=" O ASN C 287 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N CYS C 289 " --> pdb=" O LEU C 317 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N GLU C 319 " --> pdb=" O CYS C 289 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N LEU C 291 " --> pdb=" O GLU C 319 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N ILE C 359 " --> pdb=" O SER C 314 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ARG C 261 " --> pdb=" O THR C 360 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N MET C 362 " --> pdb=" O ARG C 261 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N TYR C 263 " --> pdb=" O MET C 362 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N THR C 364 " --> pdb=" O TYR C 263 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N LEU C 265 " --> pdb=" O THR C 364 " (cutoff:3.500A) removed outlier: 8.556A pdb=" N ILE C 380 " --> pdb=" O ARG C 260 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N GLY C 262 " --> pdb=" O ILE C 380 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N TYR C 382 " --> pdb=" O GLY C 262 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 84 through 90 removed outlier: 4.590A pdb=" N PHE D 169 " --> pdb=" O SER D 157 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE D 152 " --> pdb=" O HIS D 141 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 115 through 122 Processing sheet with id=AB3, first strand: chain 'D' and resid 213 through 216 removed outlier: 4.073A pdb=" N ILE D 205 " --> pdb=" O PHE D 216 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N SER D 208 " --> pdb=" O ILE D 290 " (cutoff:3.500A) removed outlier: 8.362A pdb=" N ASN D 292 " --> pdb=" O SER D 208 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ASN D 287 " --> pdb=" O ILE D 315 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N LEU D 317 " --> pdb=" O ASN D 287 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N CYS D 289 " --> pdb=" O LEU D 317 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N GLU D 319 " --> pdb=" O CYS D 289 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LEU D 291 " --> pdb=" O GLU D 319 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N ILE D 359 " --> pdb=" O SER D 314 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ARG D 261 " --> pdb=" O THR D 360 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N MET D 362 " --> pdb=" O ARG D 261 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N TYR D 263 " --> pdb=" O MET D 362 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N THR D 364 " --> pdb=" O TYR D 263 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N LEU D 265 " --> pdb=" O THR D 364 " (cutoff:3.500A) removed outlier: 8.557A pdb=" N ILE D 380 " --> pdb=" O ARG D 260 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N GLY D 262 " --> pdb=" O ILE D 380 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N TYR D 382 " --> pdb=" O GLY D 262 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 84 through 90 removed outlier: 4.590A pdb=" N PHE E 169 " --> pdb=" O SER E 157 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE E 152 " --> pdb=" O HIS E 141 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 115 through 122 Processing sheet with id=AB6, first strand: chain 'E' and resid 213 through 216 removed outlier: 4.072A pdb=" N ILE E 205 " --> pdb=" O PHE E 216 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N SER E 208 " --> pdb=" O ILE E 290 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N ASN E 292 " --> pdb=" O SER E 208 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N ASN E 287 " --> pdb=" O ILE E 315 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N LEU E 317 " --> pdb=" O ASN E 287 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N CYS E 289 " --> pdb=" O LEU E 317 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N GLU E 319 " --> pdb=" O CYS E 289 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N LEU E 291 " --> pdb=" O GLU E 319 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N ILE E 359 " --> pdb=" O SER E 314 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ARG E 261 " --> pdb=" O THR E 360 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N MET E 362 " --> pdb=" O ARG E 261 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N TYR E 263 " --> pdb=" O MET E 362 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N THR E 364 " --> pdb=" O TYR E 263 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N LEU E 265 " --> pdb=" O THR E 364 " (cutoff:3.500A) removed outlier: 8.557A pdb=" N ILE E 380 " --> pdb=" O ARG E 260 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N GLY E 262 " --> pdb=" O ILE E 380 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N TYR E 382 " --> pdb=" O GLY E 262 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 84 through 90 removed outlier: 4.589A pdb=" N PHE F 169 " --> pdb=" O SER F 157 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE F 152 " --> pdb=" O HIS F 141 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 115 through 122 Processing sheet with id=AB9, first strand: chain 'F' and resid 213 through 216 removed outlier: 4.072A pdb=" N ILE F 205 " --> pdb=" O PHE F 216 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N SER F 208 " --> pdb=" O ILE F 290 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N ASN F 292 " --> pdb=" O SER F 208 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N ASN F 287 " --> pdb=" O ILE F 315 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N LEU F 317 " --> pdb=" O ASN F 287 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N CYS F 289 " --> pdb=" O LEU F 317 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N GLU F 319 " --> pdb=" O CYS F 289 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N LEU F 291 " --> pdb=" O GLU F 319 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N ILE F 359 " --> pdb=" O SER F 314 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ARG F 261 " --> pdb=" O THR F 360 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N MET F 362 " --> pdb=" O ARG F 261 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N TYR F 263 " --> pdb=" O MET F 362 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N THR F 364 " --> pdb=" O TYR F 263 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N LEU F 265 " --> pdb=" O THR F 364 " (cutoff:3.500A) removed outlier: 8.557A pdb=" N ILE F 380 " --> pdb=" O ARG F 260 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N GLY F 262 " --> pdb=" O ILE F 380 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N TYR F 382 " --> pdb=" O GLY F 262 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 84 through 90 removed outlier: 4.590A pdb=" N PHE G 169 " --> pdb=" O SER G 157 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE G 152 " --> pdb=" O HIS G 141 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 115 through 122 Processing sheet with id=AC3, first strand: chain 'G' and resid 213 through 216 removed outlier: 4.073A pdb=" N ILE G 205 " --> pdb=" O PHE G 216 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N SER G 208 " --> pdb=" O ILE G 290 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N ASN G 292 " --> pdb=" O SER G 208 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ASN G 287 " --> pdb=" O ILE G 315 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N LEU G 317 " --> pdb=" O ASN G 287 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N CYS G 289 " --> pdb=" O LEU G 317 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N GLU G 319 " --> pdb=" O CYS G 289 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N LEU G 291 " --> pdb=" O GLU G 319 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N ILE G 359 " --> pdb=" O SER G 314 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ARG G 261 " --> pdb=" O THR G 360 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N MET G 362 " --> pdb=" O ARG G 261 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N TYR G 263 " --> pdb=" O MET G 362 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N THR G 364 " --> pdb=" O TYR G 263 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N LEU G 265 " --> pdb=" O THR G 364 " (cutoff:3.500A) removed outlier: 8.557A pdb=" N ILE G 380 " --> pdb=" O ARG G 260 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N GLY G 262 " --> pdb=" O ILE G 380 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N TYR G 382 " --> pdb=" O GLY G 262 " (cutoff:3.500A) 924 hydrogen bonds defined for protein. 2667 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: 4.83 Time building geometry restraints manager: 3.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.28: 2632 1.28 - 1.35: 2590 1.35 - 1.42: 14 1.42 - 1.48: 2506 1.48 - 1.55: 5187 Bond restraints: 12929 Sorted by residual: bond pdb=" N VAL E 352 " pdb=" CA VAL E 352 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.38e+00 bond pdb=" N VAL G 352 " pdb=" CA VAL G 352 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.22e+00 bond pdb=" N VAL D 352 " pdb=" CA VAL D 352 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.22e+00 bond pdb=" N VAL C 352 " pdb=" CA VAL C 352 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.07e+00 bond pdb=" N VAL B 352 " pdb=" CA VAL B 352 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.99e+00 ... (remaining 12924 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 17336 2.38 - 4.77: 507 4.77 - 7.15: 70 7.15 - 9.54: 7 9.54 - 11.92: 14 Bond angle restraints: 17934 Sorted by residual: angle pdb=" N PRO F 403 " pdb=" CA PRO F 403 " pdb=" CB PRO F 403 " ideal model delta sigma weight residual 103.31 110.43 -7.12 8.90e-01 1.26e+00 6.40e+01 angle pdb=" N PRO G 403 " pdb=" CA PRO G 403 " pdb=" CB PRO G 403 " ideal model delta sigma weight residual 103.31 110.38 -7.07 8.90e-01 1.26e+00 6.32e+01 angle pdb=" N PRO A 403 " pdb=" CA PRO A 403 " pdb=" CB PRO A 403 " ideal model delta sigma weight residual 103.31 110.38 -7.07 8.90e-01 1.26e+00 6.31e+01 angle pdb=" N PRO D 403 " pdb=" CA PRO D 403 " pdb=" CB PRO D 403 " ideal model delta sigma weight residual 103.31 110.38 -7.07 8.90e-01 1.26e+00 6.31e+01 angle pdb=" N PRO B 403 " pdb=" CA PRO B 403 " pdb=" CB PRO B 403 " ideal model delta sigma weight residual 103.31 110.37 -7.06 8.90e-01 1.26e+00 6.30e+01 ... (remaining 17929 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 3.87: 6317 3.87 - 7.74: 788 7.74 - 11.61: 280 11.61 - 15.47: 56 15.47 - 19.34: 21 Dihedral angle restraints: 7462 sinusoidal: 0 harmonic: 7462 Sorted by residual: dihedral pdb=" CA GLY B 378 " pdb=" C GLY B 378 " pdb=" N ARG B 379 " pdb=" CA ARG B 379 " ideal model delta harmonic sigma weight residual 180.00 160.66 19.34 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA GLY C 378 " pdb=" C GLY C 378 " pdb=" N ARG C 379 " pdb=" CA ARG C 379 " ideal model delta harmonic sigma weight residual 180.00 160.66 19.34 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA GLY A 378 " pdb=" C GLY A 378 " pdb=" N ARG A 379 " pdb=" CA ARG A 379 " ideal model delta harmonic sigma weight residual 180.00 160.69 19.31 0 5.00e+00 4.00e-02 1.49e+01 ... (remaining 7459 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1825 0.062 - 0.123: 442 0.123 - 0.185: 106 0.185 - 0.246: 28 0.246 - 0.308: 28 Chirality restraints: 2429 Sorted by residual: chirality pdb=" CA TYR E 80 " pdb=" N TYR E 80 " pdb=" C TYR E 80 " pdb=" CB TYR E 80 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.37e+00 chirality pdb=" CA TYR F 80 " pdb=" N TYR F 80 " pdb=" C TYR F 80 " pdb=" CB TYR F 80 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" CA TYR D 80 " pdb=" N TYR D 80 " pdb=" C TYR D 80 " pdb=" CB TYR D 80 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.35e+00 ... (remaining 2426 not shown) Planarity restraints: 2604 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN E 429 " -0.012 2.00e-02 2.50e+03 2.41e-02 5.79e+00 pdb=" C GLN E 429 " 0.042 2.00e-02 2.50e+03 pdb=" O GLN E 429 " -0.016 2.00e-02 2.50e+03 pdb=" N GLY E 430 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN G 429 " 0.012 2.00e-02 2.50e+03 2.39e-02 5.69e+00 pdb=" C GLN G 429 " -0.041 2.00e-02 2.50e+03 pdb=" O GLN G 429 " 0.015 2.00e-02 2.50e+03 pdb=" N GLY G 430 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN D 429 " -0.012 2.00e-02 2.50e+03 2.39e-02 5.69e+00 pdb=" C GLN D 429 " 0.041 2.00e-02 2.50e+03 pdb=" O GLN D 429 " -0.015 2.00e-02 2.50e+03 pdb=" N GLY D 430 " -0.014 2.00e-02 2.50e+03 ... (remaining 2601 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 5550 2.90 - 3.40: 12337 3.40 - 3.90: 17529 3.90 - 4.40: 16867 4.40 - 4.90: 28472 Nonbonded interactions: 80755 Sorted by model distance: nonbonded pdb=" O LEU B 196 " pdb=" N THR B 198 " model vdw 2.405 3.120 nonbonded pdb=" O LEU G 196 " pdb=" N THR G 198 " model vdw 2.405 3.120 nonbonded pdb=" O LEU C 196 " pdb=" N THR C 198 " model vdw 2.405 3.120 nonbonded pdb=" O LEU F 196 " pdb=" N THR F 198 " model vdw 2.405 3.120 nonbonded pdb=" O LEU D 196 " pdb=" N THR D 198 " model vdw 2.405 3.120 ... (remaining 80750 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: 0.30 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.530 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 31.130 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 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 : 0.005 0.040 12929 Z= 0.385 Angle : 1.005 11.924 17934 Z= 0.684 Chirality : 0.066 0.308 2429 Planarity : 0.004 0.024 2604 Dihedral : 5.132 19.343 2604 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.82 % Allowed : 6.79 % Favored : 92.39 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.94 (0.15), residues: 2576 helix: -0.50 (0.15), residues: 1064 sheet: -3.15 (0.18), residues: 574 loop : -2.69 (0.18), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 98 PHE 0.000 0.000 PHE A 52 TYR 0.000 0.000 TYR A 51 Details of bonding type rmsd hydrogen bonds : bond 0.17472 ( 924) hydrogen bonds : angle 6.77670 ( 2667) covalent geometry : bond 0.00505 (12929) covalent geometry : angle 1.00546 (17934) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 1.482 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.1097 time to fit residues: 22.1622 Evaluate side-chains 98 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 1.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 218 optimal weight: 9.9990 chunk 196 optimal weight: 9.9990 chunk 108 optimal weight: 30.0000 chunk 67 optimal weight: 0.4980 chunk 132 optimal weight: 20.0000 chunk 104 optimal weight: 0.0980 chunk 203 optimal weight: 0.0070 chunk 78 optimal weight: 20.0000 chunk 123 optimal weight: 20.0000 chunk 151 optimal weight: 20.0000 chunk 235 optimal weight: 6.9990 overall best weight: 3.5202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.075693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.062999 restraints weight = 75794.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.063657 restraints weight = 57254.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.064139 restraints weight = 47043.792| |-----------------------------------------------------------------------------| r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 12929 Z= 0.152 Angle : 0.487 5.115 17934 Z= 0.297 Chirality : 0.043 0.147 2429 Planarity : 0.002 0.011 2604 Dihedral : 4.469 28.453 2604 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.17), residues: 2576 helix: 0.73 (0.16), residues: 1134 sheet: -2.51 (0.19), residues: 518 loop : -2.07 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 98 PHE 0.000 0.000 PHE A 52 TYR 0.000 0.000 TYR A 51 Details of bonding type rmsd hydrogen bonds : bond 0.04255 ( 924) hydrogen bonds : angle 4.37344 ( 2667) covalent geometry : bond 0.00209 (12929) covalent geometry : angle 0.48694 (17934) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 1.495 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.1160 time to fit residues: 23.4331 Evaluate side-chains 98 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 1.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 108 optimal weight: 0.3980 chunk 145 optimal weight: 2.9990 chunk 11 optimal weight: 10.0000 chunk 177 optimal weight: 20.0000 chunk 135 optimal weight: 20.0000 chunk 57 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 98 optimal weight: 0.9980 chunk 151 optimal weight: 30.0000 chunk 32 optimal weight: 20.0000 chunk 130 optimal weight: 0.0870 overall best weight: 2.0962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.073967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.061426 restraints weight = 76778.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.062124 restraints weight = 57740.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.062540 restraints weight = 46708.474| |-----------------------------------------------------------------------------| r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.011 12929 Z= 0.085 Angle : 0.378 5.661 17934 Z= 0.222 Chirality : 0.041 0.130 2429 Planarity : 0.002 0.009 2604 Dihedral : 3.610 25.724 2604 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.18), residues: 2576 helix: 1.92 (0.17), residues: 1092 sheet: -1.68 (0.19), residues: 644 loop : -1.60 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 98 PHE 0.000 0.000 PHE A 52 TYR 0.000 0.000 TYR A 51 Details of bonding type rmsd hydrogen bonds : bond 0.03141 ( 924) hydrogen bonds : angle 3.37923 ( 2667) covalent geometry : bond 0.00117 (12929) covalent geometry : angle 0.37794 (17934) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 1.486 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.1125 time to fit residues: 22.8759 Evaluate side-chains 98 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 1.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 230 optimal weight: 20.0000 chunk 183 optimal weight: 30.0000 chunk 134 optimal weight: 9.9990 chunk 69 optimal weight: 30.0000 chunk 52 optimal weight: 0.0980 chunk 119 optimal weight: 20.0000 chunk 232 optimal weight: 30.0000 chunk 76 optimal weight: 5.9990 chunk 79 optimal weight: 8.9990 chunk 99 optimal weight: 4.9990 chunk 231 optimal weight: 5.9990 overall best weight: 5.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.069103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.059108 restraints weight = 79510.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.059584 restraints weight = 61968.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.059980 restraints weight = 52027.986| |-----------------------------------------------------------------------------| r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.4557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 12929 Z= 0.189 Angle : 0.522 6.479 17934 Z= 0.315 Chirality : 0.043 0.136 2429 Planarity : 0.003 0.008 2604 Dihedral : 4.924 26.708 2604 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 0.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.17), residues: 2576 helix: 1.53 (0.17), residues: 1127 sheet: -1.22 (0.20), residues: 574 loop : -1.87 (0.21), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 98 PHE 0.000 0.000 PHE A 52 TYR 0.000 0.000 TYR A 51 Details of bonding type rmsd hydrogen bonds : bond 0.03920 ( 924) hydrogen bonds : angle 4.63535 ( 2667) covalent geometry : bond 0.00265 (12929) covalent geometry : angle 0.52162 (17934) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 1.533 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.1130 time to fit residues: 22.6914 Evaluate side-chains 98 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 1.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 134 optimal weight: 8.9990 chunk 257 optimal weight: 30.0000 chunk 37 optimal weight: 0.8980 chunk 238 optimal weight: 0.0670 chunk 65 optimal weight: 10.0000 chunk 219 optimal weight: 0.6980 chunk 103 optimal weight: 7.9990 chunk 207 optimal weight: 9.9990 chunk 83 optimal weight: 40.0000 chunk 191 optimal weight: 9.9990 chunk 52 optimal weight: 7.9990 overall best weight: 3.5322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.070254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.058334 restraints weight = 78472.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.058973 restraints weight = 57760.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.059422 restraints weight = 46630.990| |-----------------------------------------------------------------------------| r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.4865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.011 12929 Z= 0.116 Angle : 0.393 5.403 17934 Z= 0.233 Chirality : 0.041 0.131 2429 Planarity : 0.002 0.009 2604 Dihedral : 3.951 28.487 2604 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 0.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.18), residues: 2576 helix: 2.32 (0.17), residues: 1092 sheet: -0.74 (0.21), residues: 574 loop : -1.69 (0.20), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 98 PHE 0.000 0.000 PHE A 52 TYR 0.000 0.000 TYR A 51 Details of bonding type rmsd hydrogen bonds : bond 0.02879 ( 924) hydrogen bonds : angle 3.61999 ( 2667) covalent geometry : bond 0.00161 (12929) covalent geometry : angle 0.39303 (17934) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 1.348 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.1060 time to fit residues: 21.3166 Evaluate side-chains 98 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 107 optimal weight: 10.0000 chunk 214 optimal weight: 20.0000 chunk 108 optimal weight: 10.0000 chunk 19 optimal weight: 0.9980 chunk 118 optimal weight: 20.0000 chunk 102 optimal weight: 4.9990 chunk 12 optimal weight: 30.0000 chunk 17 optimal weight: 5.9990 chunk 177 optimal weight: 10.0000 chunk 57 optimal weight: 30.0000 chunk 90 optimal weight: 0.7980 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.069637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.059232 restraints weight = 78195.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.059839 restraints weight = 58353.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.060220 restraints weight = 47307.981| |-----------------------------------------------------------------------------| r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.5488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 12929 Z= 0.158 Angle : 0.460 6.450 17934 Z= 0.275 Chirality : 0.042 0.136 2429 Planarity : 0.002 0.008 2604 Dihedral : 4.442 25.722 2604 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 0.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.18), residues: 2576 helix: 2.21 (0.17), residues: 1106 sheet: -0.47 (0.23), residues: 574 loop : -1.68 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 98 PHE 0.000 0.000 PHE A 52 TYR 0.000 0.000 TYR A 51 Details of bonding type rmsd hydrogen bonds : bond 0.03364 ( 924) hydrogen bonds : angle 4.17561 ( 2667) covalent geometry : bond 0.00221 (12929) covalent geometry : angle 0.46039 (17934) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 1.511 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.1102 time to fit residues: 22.4524 Evaluate side-chains 98 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 1.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 191 optimal weight: 9.9990 chunk 99 optimal weight: 3.9990 chunk 228 optimal weight: 10.0000 chunk 4 optimal weight: 10.0000 chunk 180 optimal weight: 20.0000 chunk 58 optimal weight: 20.0000 chunk 238 optimal weight: 8.9990 chunk 83 optimal weight: 40.0000 chunk 206 optimal weight: 20.0000 chunk 70 optimal weight: 10.0000 chunk 107 optimal weight: 10.0000 overall best weight: 8.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.066304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.054666 restraints weight = 79854.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.055285 restraints weight = 57840.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.055645 restraints weight = 46794.869| |-----------------------------------------------------------------------------| r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.6384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 12929 Z= 0.277 Angle : 0.593 6.106 17934 Z= 0.367 Chirality : 0.045 0.149 2429 Planarity : 0.003 0.014 2604 Dihedral : 5.755 31.584 2604 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.17), residues: 2576 helix: 0.93 (0.16), residues: 1120 sheet: -0.82 (0.23), residues: 574 loop : -2.01 (0.21), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 98 PHE 0.000 0.000 PHE A 52 TYR 0.000 0.000 TYR A 51 Details of bonding type rmsd hydrogen bonds : bond 0.04702 ( 924) hydrogen bonds : angle 5.58438 ( 2667) covalent geometry : bond 0.00389 (12929) covalent geometry : angle 0.59255 (17934) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 1.436 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.1113 time to fit residues: 22.4553 Evaluate side-chains 98 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 1.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 112 optimal weight: 5.9990 chunk 95 optimal weight: 5.9990 chunk 105 optimal weight: 5.9990 chunk 141 optimal weight: 0.8980 chunk 190 optimal weight: 2.9990 chunk 254 optimal weight: 20.0000 chunk 238 optimal weight: 5.9990 chunk 231 optimal weight: 40.0000 chunk 154 optimal weight: 8.9990 chunk 121 optimal weight: 8.9990 chunk 128 optimal weight: 1.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.067819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.056114 restraints weight = 79180.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.056840 restraints weight = 56812.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.057208 restraints weight = 45206.033| |-----------------------------------------------------------------------------| r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.6317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.011 12929 Z= 0.129 Angle : 0.429 6.573 17934 Z= 0.256 Chirality : 0.042 0.140 2429 Planarity : 0.002 0.010 2604 Dihedral : 4.593 29.045 2604 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 0.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.18), residues: 2576 helix: 1.79 (0.16), residues: 1106 sheet: -0.61 (0.24), residues: 532 loop : -1.78 (0.21), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 98 PHE 0.000 0.000 PHE A 52 TYR 0.000 0.000 TYR A 51 Details of bonding type rmsd hydrogen bonds : bond 0.03089 ( 924) hydrogen bonds : angle 4.30240 ( 2667) covalent geometry : bond 0.00179 (12929) covalent geometry : angle 0.42946 (17934) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 1.558 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.1113 time to fit residues: 22.7700 Evaluate side-chains 98 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 25 optimal weight: 8.9990 chunk 195 optimal weight: 6.9990 chunk 248 optimal weight: 9.9990 chunk 149 optimal weight: 6.9990 chunk 222 optimal weight: 0.6980 chunk 101 optimal weight: 0.8980 chunk 196 optimal weight: 5.9990 chunk 216 optimal weight: 20.0000 chunk 190 optimal weight: 7.9990 chunk 140 optimal weight: 9.9990 chunk 20 optimal weight: 9.9990 overall best weight: 4.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.067405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.055738 restraints weight = 78597.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.056421 restraints weight = 56750.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.056899 restraints weight = 45585.245| |-----------------------------------------------------------------------------| r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.6465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 12929 Z= 0.144 Angle : 0.430 5.993 17934 Z= 0.257 Chirality : 0.042 0.138 2429 Planarity : 0.002 0.010 2604 Dihedral : 4.382 28.739 2604 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 0.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.18), residues: 2576 helix: 2.07 (0.17), residues: 1106 sheet: -0.77 (0.22), residues: 574 loop : -1.79 (0.22), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 98 PHE 0.000 0.000 PHE A 52 TYR 0.000 0.000 TYR A 51 Details of bonding type rmsd hydrogen bonds : bond 0.03050 ( 924) hydrogen bonds : angle 4.19599 ( 2667) covalent geometry : bond 0.00201 (12929) covalent geometry : angle 0.42958 (17934) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 1.595 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.1121 time to fit residues: 22.8414 Evaluate side-chains 98 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 1.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 181 optimal weight: 6.9990 chunk 135 optimal weight: 20.0000 chunk 98 optimal weight: 20.0000 chunk 4 optimal weight: 20.0000 chunk 185 optimal weight: 8.9990 chunk 110 optimal weight: 20.0000 chunk 244 optimal weight: 0.6980 chunk 160 optimal weight: 30.0000 chunk 174 optimal weight: 9.9990 chunk 224 optimal weight: 10.0000 chunk 222 optimal weight: 0.8980 overall best weight: 5.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.066703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.055191 restraints weight = 78665.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.055885 restraints weight = 56656.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.056252 restraints weight = 45211.005| |-----------------------------------------------------------------------------| r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.6734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 12929 Z= 0.181 Angle : 0.476 6.779 17934 Z= 0.287 Chirality : 0.042 0.140 2429 Planarity : 0.002 0.011 2604 Dihedral : 4.774 29.437 2604 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 0.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.18), residues: 2576 helix: 1.85 (0.16), residues: 1113 sheet: -0.87 (0.23), residues: 574 loop : -1.80 (0.22), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 98 PHE 0.000 0.000 PHE A 52 TYR 0.000 0.000 TYR A 51 Details of bonding type rmsd hydrogen bonds : bond 0.03458 ( 924) hydrogen bonds : angle 4.56943 ( 2667) covalent geometry : bond 0.00254 (12929) covalent geometry : angle 0.47640 (17934) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 1.577 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.1148 time to fit residues: 23.2528 Evaluate side-chains 98 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 1.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 57 optimal weight: 10.0000 chunk 84 optimal weight: 0.9980 chunk 242 optimal weight: 20.0000 chunk 208 optimal weight: 6.9990 chunk 198 optimal weight: 0.4980 chunk 10 optimal weight: 0.9990 chunk 172 optimal weight: 20.0000 chunk 115 optimal weight: 20.0000 chunk 54 optimal weight: 9.9990 chunk 40 optimal weight: 30.0000 chunk 21 optimal weight: 8.9990 overall best weight: 3.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.067270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.055783 restraints weight = 79071.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.056447 restraints weight = 56681.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.056834 restraints weight = 45003.011| |-----------------------------------------------------------------------------| r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.6762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.011 12929 Z= 0.127 Angle : 0.414 6.026 17934 Z= 0.247 Chirality : 0.041 0.135 2429 Planarity : 0.002 0.011 2604 Dihedral : 4.248 28.951 2604 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 0.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.18), residues: 2576 helix: 2.30 (0.17), residues: 1099 sheet: -0.75 (0.23), residues: 574 loop : -1.76 (0.22), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 98 PHE 0.000 0.000 PHE A 52 TYR 0.000 0.000 TYR A 51 Details of bonding type rmsd hydrogen bonds : bond 0.02864 ( 924) hydrogen bonds : angle 4.02099 ( 2667) covalent geometry : bond 0.00177 (12929) covalent geometry : angle 0.41432 (17934) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3140.00 seconds wall clock time: 54 minutes 23.66 seconds (3263.66 seconds total)