Starting phenix.real_space_refine on Thu Sep 18 01:41:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6sh4_10193/09_2025/6sh4_10193.cif Found real_map, /net/cci-nas-00/data/ceres_data/6sh4_10193/09_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_10193/09_2025/6sh4_10193.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6sh4_10193/09_2025/6sh4_10193.map" model { file = "/net/cci-nas-00/data/ceres_data/6sh4_10193/09_2025/6sh4_10193.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6sh4_10193/09_2025/6sh4_10193.cif" } resolution = 4.4 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= 0.003 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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'ASN:plan1': 17, 'TYR:plan': 16, 'PHE:plan': 17, 'ARG:plan': 19, 'GLN:plan1': 9, 'ASP:plan': 24, 'GLU:plan': 16, 'TRP:plan': 5, 'HIS:plan': 8} Unresolved non-hydrogen planarities: 617 Restraints were copied for chains: B, C, D, E, F, G Time building chain proxies: 2.23, per 1000 atoms: 0.17 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: 1.34 Conformation dependent library (CDL) restraints added in 845.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.68 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: 2.17 Time building geometry restraints manager: 1.74 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: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } 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: 1.320 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.130 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.480 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 TYR 0.000 0.000 TYR A 51 PHE 0.000 0.000 PHE A 52 TRP 0.000 0.000 TRP A 98 Details of bonding type rmsd covalent geometry : bond 0.00505 (12929) covalent geometry : angle 1.00546 (17934) hydrogen bonds : bond 0.17472 ( 924) hydrogen bonds : angle 6.77670 ( 2667) *********************** 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 : 0.475 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.0538 time to fit residues: 10.4144 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 : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 197 optimal weight: 30.0000 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 20.0000 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 30.0000 chunk 111 optimal weight: 4.9990 chunk 258 optimal weight: 5.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- 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 = 0.3265 r_free = 0.3265 target = 0.072497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.060138 restraints weight = 78058.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.060743 restraints weight = 58737.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.061208 restraints weight = 48244.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.061522 restraints weight = 41852.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.061700 restraints weight = 38051.238| |-----------------------------------------------------------------------------| r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12929 Z= 0.212 Angle : 0.585 4.931 17934 Z= 0.360 Chirality : 0.044 0.162 2429 Planarity : 0.003 0.013 2604 Dihedral : 5.309 31.791 2604 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 0.43 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 : 3.36 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.01 (0.16), residues: 2576 helix: 0.05 (0.15), residues: 1148 sheet: -2.46 (0.18), residues: 588 loop : -2.24 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 51 PHE 0.000 0.000 PHE A 52 TRP 0.000 0.000 TRP A 98 Details of bonding type rmsd covalent geometry : bond 0.00299 (12929) covalent geometry : angle 0.58505 (17934) hydrogen bonds : bond 0.04904 ( 924) hydrogen bonds : angle 5.07582 ( 2667) *********************** 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 : 0.504 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.0542 time to fit residues: 10.6680 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 : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 208 optimal weight: 8.9990 chunk 119 optimal weight: 20.0000 chunk 129 optimal weight: 2.9990 chunk 83 optimal weight: 40.0000 chunk 69 optimal weight: 20.0000 chunk 120 optimal weight: 20.0000 chunk 95 optimal weight: 20.0000 chunk 48 optimal weight: 4.9990 chunk 145 optimal weight: 0.9990 chunk 131 optimal weight: 20.0000 chunk 19 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 = 0.3221 r_free = 0.3221 target = 0.070342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.058233 restraints weight = 78774.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.058873 restraints weight = 58078.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.059334 restraints weight = 47274.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.059484 restraints weight = 40993.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.059721 restraints weight = 38178.921| |-----------------------------------------------------------------------------| r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.4107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 12929 Z= 0.167 Angle : 0.477 6.008 17934 Z= 0.288 Chirality : 0.042 0.136 2429 Planarity : 0.002 0.011 2604 Dihedral : 4.467 28.185 2604 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 0.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.91 (0.17), residues: 2576 helix: 1.19 (0.16), residues: 1120 sheet: -1.72 (0.19), residues: 574 loop : -2.13 (0.19), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 51 PHE 0.000 0.000 PHE A 52 TRP 0.000 0.000 TRP A 98 Details of bonding type rmsd covalent geometry : bond 0.00232 (12929) covalent geometry : angle 0.47687 (17934) hydrogen bonds : bond 0.04317 ( 924) hydrogen bonds : angle 4.11241 ( 2667) *********************** 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 : 0.505 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.0558 time to fit residues: 10.8313 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 : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 38 optimal weight: 7.9990 chunk 119 optimal weight: 5.9990 chunk 65 optimal weight: 9.9990 chunk 147 optimal weight: 0.9990 chunk 237 optimal weight: 20.0000 chunk 249 optimal weight: 9.9990 chunk 143 optimal weight: 20.0000 chunk 169 optimal weight: 20.0000 chunk 146 optimal weight: 8.9990 chunk 213 optimal weight: 30.0000 chunk 159 optimal weight: 7.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- 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 = 0.3190 r_free = 0.3190 target = 0.069419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.059415 restraints weight = 79177.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.059970 restraints weight = 58775.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.060380 restraints weight = 48246.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.060688 restraints weight = 41920.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.060889 restraints weight = 37799.501| |-----------------------------------------------------------------------------| r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.5011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 12929 Z= 0.211 Angle : 0.524 6.308 17934 Z= 0.318 Chirality : 0.043 0.138 2429 Planarity : 0.003 0.009 2604 Dihedral : 5.037 29.209 2604 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 0.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.59 (0.17), residues: 2576 helix: 1.51 (0.17), residues: 1092 sheet: -1.43 (0.20), residues: 574 loop : -2.04 (0.20), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 51 PHE 0.000 0.000 PHE A 52 TRP 0.000 0.000 TRP A 98 Details of bonding type rmsd covalent geometry : bond 0.00296 (12929) covalent geometry : angle 0.52352 (17934) hydrogen bonds : bond 0.03988 ( 924) hydrogen bonds : angle 4.72945 ( 2667) *********************** 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 : 0.552 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.0561 time to fit residues: 11.0105 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 : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 241 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 4 optimal weight: 10.0000 chunk 198 optimal weight: 1.9990 chunk 182 optimal weight: 0.4980 chunk 15 optimal weight: 3.9990 chunk 199 optimal weight: 40.0000 chunk 230 optimal weight: 10.0000 chunk 45 optimal weight: 7.9990 chunk 256 optimal weight: 0.1980 chunk 38 optimal weight: 6.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 = 0.3217 r_free = 0.3217 target = 0.070145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.058047 restraints weight = 78175.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.058712 restraints weight = 57013.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.059091 restraints weight = 45781.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.059497 restraints weight = 39980.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.059699 restraints weight = 36078.799| |-----------------------------------------------------------------------------| r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.5055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.009 12929 Z= 0.086 Angle : 0.379 5.354 17934 Z= 0.222 Chirality : 0.041 0.129 2429 Planarity : 0.001 0.008 2604 Dihedral : 3.908 28.920 2604 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 0.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.19 (0.18), residues: 2576 helix: 2.21 (0.17), residues: 1092 sheet: -0.85 (0.22), residues: 532 loop : -1.83 (0.20), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 51 PHE 0.000 0.000 PHE A 52 TRP 0.000 0.000 TRP A 98 Details of bonding type rmsd covalent geometry : bond 0.00118 (12929) covalent geometry : angle 0.37864 (17934) hydrogen bonds : bond 0.02740 ( 924) hydrogen bonds : angle 3.57227 ( 2667) *********************** 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 : 0.476 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.0549 time to fit residues: 10.7936 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 : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 142 optimal weight: 10.0000 chunk 147 optimal weight: 20.0000 chunk 8 optimal weight: 20.0000 chunk 54 optimal weight: 1.9990 chunk 199 optimal weight: 3.9990 chunk 114 optimal weight: 20.0000 chunk 222 optimal weight: 20.0000 chunk 89 optimal weight: 9.9990 chunk 184 optimal weight: 20.0000 chunk 174 optimal weight: 4.9990 chunk 107 optimal weight: 9.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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 = 0.3172 r_free = 0.3172 target = 0.068707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.058462 restraints weight = 77889.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.059018 restraints weight = 58090.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.059421 restraints weight = 47533.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.059701 restraints weight = 41353.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.059889 restraints weight = 37583.415| |-----------------------------------------------------------------------------| r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.5762 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= 0.203 Angle : 0.505 6.422 17934 Z= 0.306 Chirality : 0.043 0.137 2429 Planarity : 0.003 0.010 2604 Dihedral : 4.953 28.192 2604 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 1.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.05 (0.18), residues: 2576 helix: 1.78 (0.17), residues: 1106 sheet: -0.88 (0.23), residues: 574 loop : -1.78 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 51 PHE 0.000 0.000 PHE A 52 TRP 0.000 0.000 TRP A 98 Details of bonding type rmsd covalent geometry : bond 0.00286 (12929) covalent geometry : angle 0.50529 (17934) hydrogen bonds : bond 0.03846 ( 924) hydrogen bonds : angle 4.76149 ( 2667) *********************** 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 : 0.537 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.0559 time to fit residues: 10.9830 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 : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 93 optimal weight: 0.9980 chunk 257 optimal weight: 20.0000 chunk 248 optimal weight: 20.0000 chunk 172 optimal weight: 20.0000 chunk 129 optimal weight: 20.0000 chunk 227 optimal weight: 10.0000 chunk 121 optimal weight: 5.9990 chunk 142 optimal weight: 10.0000 chunk 12 optimal weight: 30.0000 chunk 196 optimal weight: 0.3980 chunk 59 optimal weight: 4.9990 overall best weight: 4.4788 ------------------------------------------------------------------------------- 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 = 0.3172 r_free = 0.3172 target = 0.068035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.056205 restraints weight = 78670.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.056894 restraints weight = 56987.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.057303 restraints weight = 45697.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.057610 restraints weight = 39646.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.057850 restraints weight = 35877.391| |-----------------------------------------------------------------------------| r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.5916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 12929 Z= 0.152 Angle : 0.429 5.859 17934 Z= 0.258 Chirality : 0.042 0.137 2429 Planarity : 0.002 0.010 2604 Dihedral : 4.385 29.237 2604 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 0.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.18), residues: 2576 helix: 2.00 (0.16), residues: 1113 sheet: -0.74 (0.23), residues: 574 loop : -1.78 (0.21), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 51 PHE 0.000 0.000 PHE A 52 TRP 0.000 0.000 TRP A 98 Details of bonding type rmsd covalent geometry : bond 0.00211 (12929) covalent geometry : angle 0.42925 (17934) hydrogen bonds : bond 0.03140 ( 924) hydrogen bonds : angle 4.15363 ( 2667) *********************** 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 : 0.352 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.0558 time to fit residues: 10.9375 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 : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 63 optimal weight: 30.0000 chunk 15 optimal weight: 0.9990 chunk 221 optimal weight: 20.0000 chunk 173 optimal weight: 7.9990 chunk 152 optimal weight: 20.0000 chunk 92 optimal weight: 20.0000 chunk 80 optimal weight: 20.0000 chunk 125 optimal weight: 5.9990 chunk 218 optimal weight: 20.0000 chunk 105 optimal weight: 10.0000 chunk 90 optimal weight: 0.3980 overall best weight: 5.0790 ------------------------------------------------------------------------------- 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 = 0.3154 r_free = 0.3154 target = 0.067251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.055559 restraints weight = 78711.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.056237 restraints weight = 57003.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.056671 restraints weight = 45865.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.057014 restraints weight = 39544.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.057092 restraints weight = 35643.926| |-----------------------------------------------------------------------------| r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.6357 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= 0.173 Angle : 0.469 6.412 17934 Z= 0.282 Chirality : 0.043 0.141 2429 Planarity : 0.002 0.010 2604 Dihedral : 4.654 28.723 2604 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 0.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.18), residues: 2576 helix: 1.95 (0.17), residues: 1113 sheet: -0.92 (0.22), residues: 574 loop : -1.79 (0.21), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 51 PHE 0.000 0.000 PHE A 52 TRP 0.000 0.000 TRP A 98 Details of bonding type rmsd covalent geometry : bond 0.00241 (12929) covalent geometry : angle 0.46869 (17934) hydrogen bonds : bond 0.03366 ( 924) hydrogen bonds : angle 4.45842 ( 2667) *********************** 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 : 0.473 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.0556 time to fit residues: 10.8866 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 : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 219 optimal weight: 7.9990 chunk 179 optimal weight: 10.0000 chunk 207 optimal weight: 20.0000 chunk 194 optimal weight: 40.0000 chunk 170 optimal weight: 0.0980 chunk 113 optimal weight: 9.9990 chunk 43 optimal weight: 8.9990 chunk 34 optimal weight: 2.9990 chunk 158 optimal weight: 6.9990 chunk 173 optimal weight: 6.9990 chunk 196 optimal weight: 7.9990 overall best weight: 5.0188 ------------------------------------------------------------------------------- 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 = 0.3155 r_free = 0.3155 target = 0.067255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.055624 restraints weight = 78928.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.056321 restraints weight = 56889.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.056774 restraints weight = 45439.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.057027 restraints weight = 39007.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.057313 restraints weight = 35463.869| |-----------------------------------------------------------------------------| r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.6505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 12929 Z= 0.160 Angle : 0.440 5.800 17934 Z= 0.265 Chirality : 0.042 0.135 2429 Planarity : 0.002 0.010 2604 Dihedral : 4.519 29.423 2604 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 0.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.04 (0.18), residues: 2576 helix: 2.00 (0.16), residues: 1106 sheet: -0.93 (0.22), residues: 574 loop : -1.87 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 51 PHE 0.000 0.000 PHE A 52 TRP 0.000 0.000 TRP A 98 Details of bonding type rmsd covalent geometry : bond 0.00224 (12929) covalent geometry : angle 0.43982 (17934) hydrogen bonds : bond 0.03233 ( 924) hydrogen bonds : angle 4.32482 ( 2667) *********************** 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 : 0.504 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.0562 time to fit residues: 11.0212 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 : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 39 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 248 optimal weight: 10.0000 chunk 258 optimal weight: 9.9990 chunk 53 optimal weight: 20.0000 chunk 193 optimal weight: 7.9990 chunk 111 optimal weight: 0.0370 chunk 85 optimal weight: 6.9990 chunk 134 optimal weight: 5.9990 chunk 190 optimal weight: 9.9990 chunk 236 optimal weight: 0.8980 overall best weight: 4.3864 ------------------------------------------------------------------------------- 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 = 0.3155 r_free = 0.3155 target = 0.067241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.055737 restraints weight = 78972.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.056394 restraints weight = 56678.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.056869 restraints weight = 45404.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 18)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.057111 restraints weight = 38864.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.057111 restraints weight = 35379.453| |-----------------------------------------------------------------------------| r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.6652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 12929 Z= 0.146 Angle : 0.434 6.303 17934 Z= 0.259 Chirality : 0.042 0.137 2429 Planarity : 0.002 0.010 2604 Dihedral : 4.375 29.059 2604 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 0.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.18), residues: 2576 helix: 2.18 (0.17), residues: 1106 sheet: -0.94 (0.22), residues: 574 loop : -1.84 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 51 PHE 0.000 0.000 PHE A 52 TRP 0.000 0.000 TRP A 98 Details of bonding type rmsd covalent geometry : bond 0.00204 (12929) covalent geometry : angle 0.43391 (17934) hydrogen bonds : bond 0.02998 ( 924) hydrogen bonds : angle 4.15836 ( 2667) ********************** 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 : 0.507 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.0558 time to fit residues: 10.9848 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 : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 43 optimal weight: 7.9990 chunk 86 optimal weight: 30.0000 chunk 127 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 67 optimal weight: 0.0040 chunk 221 optimal weight: 0.0370 chunk 163 optimal weight: 20.0000 chunk 151 optimal weight: 40.0000 chunk 157 optimal weight: 40.0000 chunk 31 optimal weight: 30.0000 chunk 10 optimal weight: 4.9990 overall best weight: 2.8076 ------------------------------------------------------------------------------- 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 = 0.3171 r_free = 0.3171 target = 0.067931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.056409 restraints weight = 77971.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.057061 restraints weight = 56072.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.057538 restraints weight = 44674.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.057921 restraints weight = 38298.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.058079 restraints weight = 34628.540| |-----------------------------------------------------------------------------| r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.6665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.009 12929 Z= 0.103 Angle : 0.387 5.576 17934 Z= 0.228 Chirality : 0.041 0.134 2429 Planarity : 0.001 0.010 2604 Dihedral : 3.943 28.453 2604 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 0.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.46 (0.18), residues: 2576 helix: 2.49 (0.17), residues: 1106 sheet: -0.79 (0.23), residues: 574 loop : -1.80 (0.22), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 51 PHE 0.000 0.000 PHE A 52 TRP 0.000 0.000 TRP A 98 Details of bonding type rmsd covalent geometry : bond 0.00143 (12929) covalent geometry : angle 0.38705 (17934) hydrogen bonds : bond 0.02548 ( 924) hydrogen bonds : angle 3.71500 ( 2667) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1655.56 seconds wall clock time: 28 minutes 58.76 seconds (1738.76 seconds total)