Starting phenix.real_space_refine on Thu Sep 26 11:32:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sh4_10193/09_2024/6sh4_10193.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sh4_10193/09_2024/6sh4_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sh4_10193/09_2024/6sh4_10193.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sh4_10193/09_2024/6sh4_10193.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sh4_10193/09_2024/6sh4_10193.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sh4_10193/09_2024/6sh4_10193.cif" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 7693 2.51 5 N 2632 2.21 5 O 2632 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 12957 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 1851 Classifications: {'peptide': 376} Incomplete info: {'truncation_to_alanine': 324} Link IDs: {'PTRANS': 17, 'TRANS': 358} Chain breaks: 3 Unresolved chain link angles: 17 Unresolved non-hydrogen bonds: 1195 Unresolved non-hydrogen angles: 1528 Unresolved non-hydrogen dihedrals: 1012 Unresolved non-hydrogen chiralities: 108 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 8, 'TYR:plan': 16, 'ASN:plan1': 17, 'TRP:plan': 5, 'ASP:plan': 24, 'PHE:plan': 17, 'GLU:plan': 16, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 617 Restraints were copied for chains: C, B, E, D, G, F Time building chain proxies: 4.80, per 1000 atoms: 0.37 Number of scatterers: 12957 At special positions: 0 Unit cell: (151.437, 148.26, 133.434, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 2632 8.00 N 2632 7.00 C 7693 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.50 Conformation dependent library (CDL) restraints added in 2.5 seconds 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4858 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 21 sheets defined 45.5% alpha, 20.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.03 Creating SS restraints... Processing helix chain 'A' and resid 52 through 83 removed outlier: 4.502A pdb=" N GLY A 56 " --> pdb=" O PHE A 52 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLY A 57 " --> pdb=" O ALA A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 105 removed outlier: 3.510A pdb=" N LYS A 105 " --> pdb=" O THR A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 181 No H-bonds generated for 'chain 'A' and resid 179 through 181' Processing helix chain 'A' and resid 182 through 197 removed outlier: 4.120A pdb=" N ASP A 186 " --> pdb=" O HIS A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 228 Processing helix chain 'A' and resid 233 through 240 removed outlier: 3.617A pdb=" N ILE A 238 " --> pdb=" O ILE A 234 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU A 239 " --> pdb=" O LYS A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 246 Processing helix chain 'A' and resid 248 through 255 removed outlier: 3.678A pdb=" N ARG A 255 " --> pdb=" O TRP A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 284 Processing helix chain 'A' and resid 300 through 309 removed outlier: 3.729A pdb=" N ASN A 304 " --> pdb=" O ASP A 300 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N HIS A 305 " --> pdb=" O ASP A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 324 removed outlier: 3.849A pdb=" N ALA A 324 " --> pdb=" O ILE A 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 321 through 324' Processing helix chain 'A' and resid 342 through 350 Processing helix chain 'A' and resid 390 through 402 Processing helix chain 'A' and resid 405 through 417 removed outlier: 4.016A pdb=" N CYS A 409 " --> pdb=" O GLU A 405 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS A 410 " --> pdb=" O THR A 406 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS A 411 " --> pdb=" O ASP A 407 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N SER A 415 " --> pdb=" O LYS A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 434 Processing helix chain 'A' and resid 438 through 446 removed outlier: 3.616A pdb=" N ALA A 442 " --> pdb=" O ALA A 438 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYS A 444 " --> pdb=" O HIS A 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 83 removed outlier: 4.503A pdb=" N GLY B 56 " --> pdb=" O PHE B 52 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLY B 57 " --> pdb=" O ALA B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 105 removed outlier: 3.509A pdb=" N LYS B 105 " --> pdb=" O THR B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 181 No H-bonds generated for 'chain 'B' and resid 179 through 181' Processing helix chain 'B' and resid 182 through 197 removed outlier: 4.120A pdb=" N ASP B 186 " --> pdb=" O HIS B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 228 Processing helix chain 'B' and resid 233 through 240 removed outlier: 3.617A pdb=" N ILE B 238 " --> pdb=" O ILE B 234 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU B 239 " --> pdb=" O LYS B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 246 Processing helix chain 'B' and resid 248 through 255 removed outlier: 3.678A pdb=" N ARG B 255 " --> pdb=" O TRP B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 284 Processing helix chain 'B' and resid 300 through 309 removed outlier: 3.729A pdb=" N ASN B 304 " --> pdb=" O ASP B 300 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N HIS B 305 " --> pdb=" O ASP B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 324 removed outlier: 3.848A pdb=" N ALA B 324 " --> pdb=" O ILE B 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 321 through 324' Processing helix chain 'B' and resid 342 through 350 Processing helix chain 'B' and resid 390 through 402 Processing helix chain 'B' and resid 405 through 417 removed outlier: 4.016A pdb=" N CYS B 409 " --> pdb=" O GLU B 405 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS B 410 " --> pdb=" O THR B 406 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS B 411 " --> pdb=" O ASP B 407 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N SER B 415 " --> pdb=" O LYS B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 434 Processing helix chain 'B' and resid 438 through 446 removed outlier: 3.617A pdb=" N ALA B 442 " --> pdb=" O ALA B 438 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS B 444 " --> pdb=" O HIS B 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 83 removed outlier: 4.502A pdb=" N GLY C 56 " --> pdb=" O PHE C 52 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLY C 57 " --> pdb=" O ALA C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 105 removed outlier: 3.510A pdb=" N LYS C 105 " --> pdb=" O THR C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 181 No H-bonds generated for 'chain 'C' and resid 179 through 181' Processing helix chain 'C' and resid 182 through 197 removed outlier: 4.120A pdb=" N ASP C 186 " --> pdb=" O HIS C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 228 Processing helix chain 'C' and resid 233 through 240 removed outlier: 3.617A pdb=" N ILE C 238 " --> pdb=" O ILE C 234 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU C 239 " --> pdb=" O LYS C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 246 Processing helix chain 'C' and resid 248 through 255 removed outlier: 3.678A pdb=" N ARG C 255 " --> pdb=" O TRP C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 284 Processing helix chain 'C' and resid 300 through 309 removed outlier: 3.728A pdb=" N ASN C 304 " --> pdb=" O ASP C 300 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N HIS C 305 " --> pdb=" O ASP C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 324 removed outlier: 3.849A pdb=" N ALA C 324 " --> pdb=" O ILE C 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 321 through 324' Processing helix chain 'C' and resid 342 through 350 Processing helix chain 'C' and resid 390 through 402 Processing helix chain 'C' and resid 405 through 417 removed outlier: 4.015A pdb=" N CYS C 409 " --> pdb=" O GLU C 405 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS C 410 " --> pdb=" O THR C 406 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS C 411 " --> pdb=" O ASP C 407 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N SER C 415 " --> pdb=" O LYS C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 434 Processing helix chain 'C' and resid 438 through 446 removed outlier: 3.617A pdb=" N ALA C 442 " --> pdb=" O ALA C 438 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYS C 444 " --> pdb=" O HIS C 440 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 83 removed outlier: 4.502A pdb=" N GLY D 56 " --> pdb=" O PHE D 52 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLY D 57 " --> pdb=" O ALA D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 105 removed outlier: 3.509A pdb=" N LYS D 105 " --> pdb=" O THR D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 181 No H-bonds generated for 'chain 'D' and resid 179 through 181' Processing helix chain 'D' and resid 182 through 197 removed outlier: 4.121A pdb=" N ASP D 186 " --> pdb=" O HIS D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 228 Processing helix chain 'D' and resid 233 through 240 removed outlier: 3.617A pdb=" N ILE D 238 " --> pdb=" O ILE D 234 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU D 239 " --> pdb=" O LYS D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 246 Processing helix chain 'D' and resid 248 through 255 removed outlier: 3.678A pdb=" N ARG D 255 " --> pdb=" O TRP D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 284 Processing helix chain 'D' and resid 300 through 309 removed outlier: 3.729A pdb=" N ASN D 304 " --> pdb=" O ASP D 300 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N HIS D 305 " --> pdb=" O ASP D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 324 removed outlier: 3.849A pdb=" N ALA D 324 " --> pdb=" O ILE D 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 321 through 324' Processing helix chain 'D' and resid 342 through 350 Processing helix chain 'D' and resid 390 through 402 Processing helix chain 'D' and resid 405 through 417 removed outlier: 4.016A pdb=" N CYS D 409 " --> pdb=" O GLU D 405 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS D 410 " --> pdb=" O THR D 406 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS D 411 " --> pdb=" O ASP D 407 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N SER D 415 " --> pdb=" O LYS D 411 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 434 Processing helix chain 'D' and resid 438 through 446 removed outlier: 3.616A pdb=" N ALA D 442 " --> pdb=" O ALA D 438 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYS D 444 " --> pdb=" O HIS D 440 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 83 removed outlier: 4.502A pdb=" N GLY E 56 " --> pdb=" O PHE E 52 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY E 57 " --> pdb=" O ALA E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 105 removed outlier: 3.509A pdb=" N LYS E 105 " --> pdb=" O THR E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 181 No H-bonds generated for 'chain 'E' and resid 179 through 181' Processing helix chain 'E' and resid 182 through 197 removed outlier: 4.120A pdb=" N ASP E 186 " --> pdb=" O HIS E 182 " (cutoff:3.500A) Processing helix chain 'E' and resid 224 through 228 Processing helix chain 'E' and resid 233 through 240 removed outlier: 3.617A pdb=" N ILE E 238 " --> pdb=" O ILE E 234 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU E 239 " --> pdb=" O LYS E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 240 through 246 Processing helix chain 'E' and resid 248 through 255 removed outlier: 3.678A pdb=" N ARG E 255 " --> pdb=" O TRP E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 272 through 284 Processing helix chain 'E' and resid 300 through 309 removed outlier: 3.729A pdb=" N ASN E 304 " --> pdb=" O ASP E 300 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N HIS E 305 " --> pdb=" O ASP E 301 " (cutoff:3.500A) Processing helix chain 'E' and resid 321 through 324 removed outlier: 3.849A pdb=" N ALA E 324 " --> pdb=" O ILE E 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 321 through 324' Processing helix chain 'E' and resid 342 through 350 Processing helix chain 'E' and resid 390 through 402 Processing helix chain 'E' and resid 405 through 417 removed outlier: 4.015A pdb=" N CYS E 409 " --> pdb=" O GLU E 405 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS E 410 " --> pdb=" O THR E 406 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS E 411 " --> pdb=" O ASP E 407 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N SER E 415 " --> pdb=" O LYS E 411 " (cutoff:3.500A) Processing helix chain 'E' and resid 424 through 434 Processing helix chain 'E' and resid 438 through 446 removed outlier: 3.617A pdb=" N ALA E 442 " --> pdb=" O ALA E 438 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYS E 444 " --> pdb=" O HIS E 440 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 83 removed outlier: 4.502A pdb=" N GLY F 56 " --> pdb=" O PHE F 52 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLY F 57 " --> pdb=" O ALA F 53 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 105 removed outlier: 3.509A pdb=" N LYS F 105 " --> pdb=" O THR F 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 179 through 181 No H-bonds generated for 'chain 'F' and resid 179 through 181' Processing helix chain 'F' and resid 182 through 197 removed outlier: 4.120A pdb=" N ASP F 186 " --> pdb=" O HIS F 182 " (cutoff:3.500A) Processing helix chain 'F' and resid 224 through 228 Processing helix chain 'F' and resid 233 through 240 removed outlier: 3.617A pdb=" N ILE F 238 " --> pdb=" O ILE F 234 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU F 239 " --> pdb=" O LYS F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 240 through 246 Processing helix chain 'F' and resid 248 through 255 removed outlier: 3.678A pdb=" N ARG F 255 " --> pdb=" O TRP F 251 " (cutoff:3.500A) Processing helix chain 'F' and resid 272 through 284 Processing helix chain 'F' and resid 300 through 309 removed outlier: 3.729A pdb=" N ASN F 304 " --> pdb=" O ASP F 300 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N HIS F 305 " --> pdb=" O ASP F 301 " (cutoff:3.500A) Processing helix chain 'F' and resid 321 through 324 removed outlier: 3.849A pdb=" N ALA F 324 " --> pdb=" O ILE F 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 321 through 324' Processing helix chain 'F' and resid 342 through 350 Processing helix chain 'F' and resid 390 through 402 Processing helix chain 'F' and resid 405 through 417 removed outlier: 4.016A pdb=" N CYS F 409 " --> pdb=" O GLU F 405 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS F 410 " --> pdb=" O THR F 406 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS F 411 " --> pdb=" O ASP F 407 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N SER F 415 " --> pdb=" O LYS F 411 " (cutoff:3.500A) Processing helix chain 'F' and resid 424 through 434 Processing helix chain 'F' and resid 438 through 446 removed outlier: 3.616A pdb=" N ALA F 442 " --> pdb=" O ALA F 438 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYS F 444 " --> pdb=" O HIS F 440 " (cutoff:3.500A) Processing helix chain 'G' and resid 52 through 83 removed outlier: 4.502A pdb=" N GLY G 56 " --> pdb=" O PHE G 52 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLY G 57 " --> pdb=" O ALA G 53 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 105 removed outlier: 3.510A pdb=" N LYS G 105 " --> pdb=" O THR G 101 " (cutoff:3.500A) Processing helix chain 'G' and resid 179 through 181 No H-bonds generated for 'chain 'G' and resid 179 through 181' Processing helix chain 'G' and resid 182 through 197 removed outlier: 4.120A pdb=" N ASP G 186 " --> pdb=" O HIS G 182 " (cutoff:3.500A) Processing helix chain 'G' and resid 224 through 228 Processing helix chain 'G' and resid 233 through 240 removed outlier: 3.617A pdb=" N ILE G 238 " --> pdb=" O ILE G 234 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU G 239 " --> pdb=" O LYS G 235 " (cutoff:3.500A) Processing helix chain 'G' and resid 240 through 246 Processing helix chain 'G' and resid 248 through 255 removed outlier: 3.678A pdb=" N ARG G 255 " --> pdb=" O TRP G 251 " (cutoff:3.500A) Processing helix chain 'G' and resid 272 through 284 Processing helix chain 'G' and resid 300 through 309 removed outlier: 3.729A pdb=" N ASN G 304 " --> pdb=" O ASP G 300 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N HIS G 305 " --> pdb=" O ASP G 301 " (cutoff:3.500A) Processing helix chain 'G' and resid 321 through 324 removed outlier: 3.850A pdb=" N ALA G 324 " --> pdb=" O ILE G 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 321 through 324' Processing helix chain 'G' and resid 342 through 350 Processing helix chain 'G' and resid 390 through 402 Processing helix chain 'G' and resid 405 through 417 removed outlier: 4.016A pdb=" N CYS G 409 " --> pdb=" O GLU G 405 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS G 410 " --> pdb=" O THR G 406 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS G 411 " --> pdb=" O ASP G 407 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N SER G 415 " --> pdb=" O LYS G 411 " (cutoff:3.500A) Processing helix chain 'G' and resid 424 through 434 Processing helix chain 'G' and resid 438 through 446 removed outlier: 3.616A pdb=" N ALA G 442 " --> pdb=" O ALA G 438 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYS G 444 " --> pdb=" O HIS G 440 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 90 removed outlier: 4.589A pdb=" N PHE A 169 " --> pdb=" O SER A 157 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE A 152 " --> pdb=" O HIS A 141 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 115 through 122 Processing sheet with id=AA3, first strand: chain 'A' and resid 213 through 216 removed outlier: 4.073A pdb=" N ILE A 205 " --> pdb=" O PHE A 216 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N SER A 208 " --> pdb=" O ILE A 290 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N ASN A 292 " --> pdb=" O SER A 208 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ASN A 287 " --> pdb=" O ILE A 315 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N LEU A 317 " --> pdb=" O ASN A 287 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N CYS A 289 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N GLU A 319 " --> pdb=" O CYS A 289 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N LEU A 291 " --> pdb=" O GLU A 319 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N ILE A 359 " --> pdb=" O SER A 314 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ARG A 261 " --> pdb=" O THR A 360 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N MET A 362 " --> pdb=" O ARG A 261 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N TYR A 263 " --> pdb=" O MET A 362 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N THR A 364 " --> pdb=" O TYR A 263 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N LEU A 265 " --> pdb=" O THR A 364 " (cutoff:3.500A) removed outlier: 8.557A pdb=" N ILE A 380 " --> pdb=" O ARG A 260 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N GLY A 262 " --> pdb=" O ILE A 380 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N TYR A 382 " --> pdb=" O GLY A 262 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 84 through 90 removed outlier: 4.590A pdb=" N PHE B 169 " --> pdb=" O SER B 157 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE B 152 " --> pdb=" O HIS B 141 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 115 through 122 Processing sheet with id=AA6, first strand: chain 'B' and resid 213 through 216 removed outlier: 4.072A pdb=" N ILE B 205 " --> pdb=" O PHE B 216 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N SER B 208 " --> pdb=" O ILE B 290 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N ASN B 292 " --> pdb=" O SER B 208 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ASN B 287 " --> pdb=" O ILE B 315 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N LEU B 317 " --> pdb=" O ASN B 287 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N CYS B 289 " --> pdb=" O LEU B 317 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N GLU B 319 " --> pdb=" O CYS B 289 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N LEU B 291 " --> pdb=" O GLU B 319 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N ILE B 359 " --> pdb=" O SER B 314 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ARG B 261 " --> pdb=" O THR B 360 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N MET B 362 " --> pdb=" O ARG B 261 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N TYR B 263 " --> pdb=" O MET B 362 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N THR B 364 " --> pdb=" O TYR B 263 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N LEU B 265 " --> pdb=" O THR B 364 " (cutoff:3.500A) removed outlier: 8.557A pdb=" N ILE B 380 " --> pdb=" O ARG B 260 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N GLY B 262 " --> pdb=" O ILE B 380 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N TYR B 382 " --> pdb=" O GLY B 262 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 84 through 90 removed outlier: 4.589A pdb=" N PHE C 169 " --> pdb=" O SER C 157 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE C 152 " --> pdb=" O HIS C 141 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 115 through 122 Processing sheet with id=AA9, first strand: chain 'C' and resid 213 through 216 removed outlier: 4.072A pdb=" N ILE C 205 " --> pdb=" O PHE C 216 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N SER C 208 " --> pdb=" O ILE C 290 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N ASN C 292 " --> pdb=" O SER C 208 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ASN C 287 " --> pdb=" O ILE C 315 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N LEU C 317 " --> pdb=" O ASN C 287 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N CYS C 289 " --> pdb=" O LEU C 317 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N GLU C 319 " --> pdb=" O CYS C 289 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N LEU C 291 " --> pdb=" O GLU C 319 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N ILE C 359 " --> pdb=" O SER C 314 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ARG C 261 " --> pdb=" O THR C 360 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N MET C 362 " --> pdb=" O ARG C 261 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N TYR C 263 " --> pdb=" O MET C 362 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N THR C 364 " --> pdb=" O TYR C 263 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N LEU C 265 " --> pdb=" O THR C 364 " (cutoff:3.500A) removed outlier: 8.556A pdb=" N ILE C 380 " --> pdb=" O ARG C 260 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N GLY C 262 " --> pdb=" O ILE C 380 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N TYR C 382 " --> pdb=" O GLY C 262 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 84 through 90 removed outlier: 4.590A pdb=" N PHE D 169 " --> pdb=" O SER D 157 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE D 152 " --> pdb=" O HIS D 141 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 115 through 122 Processing sheet with id=AB3, first strand: chain 'D' and resid 213 through 216 removed outlier: 4.073A pdb=" N ILE D 205 " --> pdb=" O PHE D 216 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N SER D 208 " --> pdb=" O ILE D 290 " (cutoff:3.500A) removed outlier: 8.362A pdb=" N ASN D 292 " --> pdb=" O SER D 208 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ASN D 287 " --> pdb=" O ILE D 315 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N LEU D 317 " --> pdb=" O ASN D 287 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N CYS D 289 " --> pdb=" O LEU D 317 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N GLU D 319 " --> pdb=" O CYS D 289 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LEU D 291 " --> pdb=" O GLU D 319 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N ILE D 359 " --> pdb=" O SER D 314 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ARG D 261 " --> pdb=" O THR D 360 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N MET D 362 " --> pdb=" O ARG D 261 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N TYR D 263 " --> pdb=" O MET D 362 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N THR D 364 " --> pdb=" O TYR D 263 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N LEU D 265 " --> pdb=" O THR D 364 " (cutoff:3.500A) removed outlier: 8.557A pdb=" N ILE D 380 " --> pdb=" O ARG D 260 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N GLY D 262 " --> pdb=" O ILE D 380 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N TYR D 382 " --> pdb=" O GLY D 262 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 84 through 90 removed outlier: 4.590A pdb=" N PHE E 169 " --> pdb=" O SER E 157 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE E 152 " --> pdb=" O HIS E 141 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 115 through 122 Processing sheet with id=AB6, first strand: chain 'E' and resid 213 through 216 removed outlier: 4.072A pdb=" N ILE E 205 " --> pdb=" O PHE E 216 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N SER E 208 " --> pdb=" O ILE E 290 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N ASN E 292 " --> pdb=" O SER E 208 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N ASN E 287 " --> pdb=" O ILE E 315 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N LEU E 317 " --> pdb=" O ASN E 287 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N CYS E 289 " --> pdb=" O LEU E 317 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N GLU E 319 " --> pdb=" O CYS E 289 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N LEU E 291 " --> pdb=" O GLU E 319 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N ILE E 359 " --> pdb=" O SER E 314 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ARG E 261 " --> pdb=" O THR E 360 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N MET E 362 " --> pdb=" O ARG E 261 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N TYR E 263 " --> pdb=" O MET E 362 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N THR E 364 " --> pdb=" O TYR E 263 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N LEU E 265 " --> pdb=" O THR E 364 " (cutoff:3.500A) removed outlier: 8.557A pdb=" N ILE E 380 " --> pdb=" O ARG E 260 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N GLY E 262 " --> pdb=" O ILE E 380 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N TYR E 382 " --> pdb=" O GLY E 262 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 84 through 90 removed outlier: 4.589A pdb=" N PHE F 169 " --> pdb=" O SER F 157 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE F 152 " --> pdb=" O HIS F 141 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 115 through 122 Processing sheet with id=AB9, first strand: chain 'F' and resid 213 through 216 removed outlier: 4.072A pdb=" N ILE F 205 " --> pdb=" O PHE F 216 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N SER F 208 " --> pdb=" O ILE F 290 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N ASN F 292 " --> pdb=" O SER F 208 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N ASN F 287 " --> pdb=" O ILE F 315 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N LEU F 317 " --> pdb=" O ASN F 287 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N CYS F 289 " --> pdb=" O LEU F 317 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N GLU F 319 " --> pdb=" O CYS F 289 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N LEU F 291 " --> pdb=" O GLU F 319 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N ILE F 359 " --> pdb=" O SER F 314 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ARG F 261 " --> pdb=" O THR F 360 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N MET F 362 " --> pdb=" O ARG F 261 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N TYR F 263 " --> pdb=" O MET F 362 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N THR F 364 " --> pdb=" O TYR F 263 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N LEU F 265 " --> pdb=" O THR F 364 " (cutoff:3.500A) removed outlier: 8.557A pdb=" N ILE F 380 " --> pdb=" O ARG F 260 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N GLY F 262 " --> pdb=" O ILE F 380 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N TYR F 382 " --> pdb=" O GLY F 262 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 84 through 90 removed outlier: 4.590A pdb=" N PHE G 169 " --> pdb=" O SER G 157 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE G 152 " --> pdb=" O HIS G 141 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 115 through 122 Processing sheet with id=AC3, first strand: chain 'G' and resid 213 through 216 removed outlier: 4.073A pdb=" N ILE G 205 " --> pdb=" O PHE G 216 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N SER G 208 " --> pdb=" O ILE G 290 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N ASN G 292 " --> pdb=" O SER G 208 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ASN G 287 " --> pdb=" O ILE G 315 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N LEU G 317 " --> pdb=" O ASN G 287 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N CYS G 289 " --> pdb=" O LEU G 317 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N GLU G 319 " --> pdb=" O CYS G 289 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N LEU G 291 " --> pdb=" O GLU G 319 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N ILE G 359 " --> pdb=" O SER G 314 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ARG G 261 " --> pdb=" O THR G 360 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N MET G 362 " --> pdb=" O ARG G 261 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N TYR G 263 " --> pdb=" O MET G 362 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N THR G 364 " --> pdb=" O TYR G 263 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N LEU G 265 " --> pdb=" O THR G 364 " (cutoff:3.500A) removed outlier: 8.557A pdb=" N ILE G 380 " --> pdb=" O ARG G 260 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N GLY G 262 " --> pdb=" O ILE G 380 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N TYR G 382 " --> pdb=" O GLY G 262 " (cutoff:3.500A) 924 hydrogen bonds defined for protein. 2667 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.53 Time building geometry restraints manager: 4.02 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: 0.00 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: 1.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.590 Check model and map are aligned: 0.090 Set scattering table: 0.150 Process input model: 30.240 Find NCS groups from input model: 0.450 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:2.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.070 ------------------------------------------------------------------------------- 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= 0.367 Angle : 1.005 11.924 17934 Z= 0.684 Chirality : 0.066 0.308 2429 Planarity : 0.004 0.024 2604 Dihedral : 5.132 19.343 2604 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.82 % Allowed : 6.79 % Favored : 92.39 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.94 (0.15), residues: 2576 helix: -0.50 (0.15), residues: 1064 sheet: -3.15 (0.18), residues: 574 loop : -2.69 (0.18), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 98 PHE 0.000 0.000 PHE A 52 TYR 0.000 0.000 TYR A 51 *********************** 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 fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 1.550 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.1065 time to fit residues: 21.3892 Evaluate side-chains 98 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 218 optimal weight: 9.9990 chunk 196 optimal weight: 9.9990 chunk 108 optimal weight: 30.0000 chunk 67 optimal weight: 0.4980 chunk 132 optimal weight: 20.0000 chunk 104 optimal weight: 0.0980 chunk 203 optimal weight: 0.0070 chunk 78 optimal weight: 20.0000 chunk 123 optimal weight: 20.0000 chunk 151 optimal weight: 20.0000 chunk 235 optimal weight: 6.9990 overall best weight: 3.5202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 12929 Z= 0.154 Angle : 0.487 5.115 17934 Z= 0.297 Chirality : 0.043 0.147 2429 Planarity : 0.002 0.011 2604 Dihedral : 4.469 28.454 2604 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.17), residues: 2576 helix: 0.73 (0.16), residues: 1134 sheet: -2.51 (0.19), residues: 518 loop : -2.07 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 98 PHE 0.000 0.000 PHE A 52 TYR 0.000 0.000 TYR A 51 *********************** 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 fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 1.424 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.1076 time to fit residues: 21.7044 Evaluate side-chains 98 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 1.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 130 optimal weight: 10.0000 chunk 72 optimal weight: 1.9990 chunk 195 optimal weight: 5.9990 chunk 160 optimal weight: 30.0000 chunk 64 optimal weight: 8.9990 chunk 235 optimal weight: 0.5980 chunk 254 optimal weight: 20.0000 chunk 209 optimal weight: 0.8980 chunk 233 optimal weight: 4.9990 chunk 80 optimal weight: 30.0000 chunk 189 optimal weight: 20.0000 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.3430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.011 12929 Z= 0.118 Angle : 0.415 6.712 17934 Z= 0.246 Chirality : 0.042 0.134 2429 Planarity : 0.002 0.010 2604 Dihedral : 3.831 25.144 2604 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.17), residues: 2576 helix: 1.86 (0.17), residues: 1099 sheet: -1.48 (0.20), residues: 588 loop : -1.78 (0.21), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 98 PHE 0.000 0.000 PHE A 52 TYR 0.000 0.000 TYR A 51 *********************** 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 fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 1.307 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.1083 time to fit residues: 21.7453 Evaluate side-chains 98 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 1.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 232 optimal weight: 9.9990 chunk 177 optimal weight: 20.0000 chunk 122 optimal weight: 8.9990 chunk 26 optimal weight: 20.0000 chunk 112 optimal weight: 6.9990 chunk 158 optimal weight: 1.9990 chunk 236 optimal weight: 5.9990 chunk 250 optimal weight: 6.9990 chunk 123 optimal weight: 30.0000 chunk 224 optimal weight: 7.9990 chunk 67 optimal weight: 0.0040 overall best weight: 4.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.4752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 12929 Z= 0.165 Angle : 0.483 6.452 17934 Z= 0.290 Chirality : 0.042 0.134 2429 Planarity : 0.002 0.010 2604 Dihedral : 4.659 27.174 2604 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 0.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.17), residues: 2576 helix: 1.82 (0.17), residues: 1092 sheet: -1.10 (0.20), residues: 574 loop : -1.71 (0.20), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 98 PHE 0.000 0.000 PHE A 52 TYR 0.000 0.000 TYR A 51 *********************** 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 fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 1.418 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.1169 time to fit residues: 23.4147 Evaluate side-chains 98 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 208 optimal weight: 6.9990 chunk 142 optimal weight: 4.9990 chunk 3 optimal weight: 20.0000 chunk 186 optimal weight: 5.9990 chunk 103 optimal weight: 30.0000 chunk 213 optimal weight: 30.0000 chunk 173 optimal weight: 6.9990 chunk 0 optimal weight: 50.0000 chunk 127 optimal weight: 2.9990 chunk 224 optimal weight: 7.9990 chunk 63 optimal weight: 0.8980 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.5125 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= 0.147 Angle : 0.422 5.906 17934 Z= 0.252 Chirality : 0.042 0.137 2429 Planarity : 0.002 0.008 2604 Dihedral : 4.170 28.148 2604 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 0.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.18), residues: 2576 helix: 2.07 (0.17), residues: 1106 sheet: -0.72 (0.21), residues: 574 loop : -1.71 (0.20), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 98 PHE 0.000 0.000 PHE A 52 TYR 0.000 0.000 TYR A 51 *********************** 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 fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 1.410 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.1092 time to fit residues: 22.0173 Evaluate side-chains 98 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 84 optimal weight: 2.9990 chunk 225 optimal weight: 10.0000 chunk 49 optimal weight: 20.0000 chunk 146 optimal weight: 30.0000 chunk 61 optimal weight: 20.0000 chunk 250 optimal weight: 0.7980 chunk 208 optimal weight: 10.0000 chunk 116 optimal weight: 9.9990 chunk 20 optimal weight: 10.0000 chunk 82 optimal weight: 10.0000 chunk 131 optimal weight: 20.0000 overall best weight: 6.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.5906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 12929 Z= 0.230 Angle : 0.542 7.047 17934 Z= 0.329 Chirality : 0.043 0.141 2429 Planarity : 0.003 0.012 2604 Dihedral : 5.231 28.129 2604 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 1.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.17), residues: 2576 helix: 1.62 (0.16), residues: 1106 sheet: -0.52 (0.24), residues: 539 loop : -1.76 (0.20), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 98 PHE 0.000 0.000 PHE A 52 TYR 0.000 0.000 TYR A 51 *********************** 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 fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 1.421 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.1081 time to fit residues: 21.7198 Evaluate side-chains 98 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 1.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 241 optimal weight: 9.9990 chunk 28 optimal weight: 10.0000 chunk 142 optimal weight: 9.9990 chunk 182 optimal weight: 6.9990 chunk 141 optimal weight: 9.9990 chunk 210 optimal weight: 4.9990 chunk 139 optimal weight: 30.0000 chunk 249 optimal weight: 4.9990 chunk 156 optimal weight: 7.9990 chunk 152 optimal weight: 20.0000 chunk 115 optimal weight: 9.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.6389 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= 0.225 Angle : 0.509 5.867 17934 Z= 0.312 Chirality : 0.043 0.149 2429 Planarity : 0.003 0.012 2604 Dihedral : 5.058 30.407 2604 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 1.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.20 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.17), residues: 2576 helix: 1.36 (0.16), residues: 1106 sheet: -0.73 (0.23), residues: 574 loop : -2.01 (0.20), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 98 PHE 0.000 0.000 PHE A 52 TYR 0.000 0.000 TYR A 51 *********************** 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 fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 1.380 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.1099 time to fit residues: 22.4121 Evaluate side-chains 98 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 1.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 154 optimal weight: 9.9990 chunk 99 optimal weight: 7.9990 chunk 149 optimal weight: 7.9990 chunk 75 optimal weight: 6.9990 chunk 49 optimal weight: 20.0000 chunk 48 optimal weight: 10.0000 chunk 158 optimal weight: 4.9990 chunk 170 optimal weight: 20.0000 chunk 123 optimal weight: 20.0000 chunk 23 optimal weight: 10.0000 chunk 196 optimal weight: 1.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.6552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 12929 Z= 0.199 Angle : 0.495 6.973 17934 Z= 0.299 Chirality : 0.042 0.143 2429 Planarity : 0.002 0.010 2604 Dihedral : 4.957 29.176 2604 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 1.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.17), residues: 2576 helix: 1.50 (0.16), residues: 1106 sheet: -0.89 (0.23), residues: 574 loop : -1.97 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 98 PHE 0.000 0.000 PHE A 52 TYR 0.000 0.000 TYR A 51 *********************** 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 fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 1.439 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.1091 time to fit residues: 22.1301 Evaluate side-chains 98 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 1.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 227 optimal weight: 8.9990 chunk 239 optimal weight: 20.0000 chunk 218 optimal weight: 7.9990 chunk 232 optimal weight: 5.9990 chunk 140 optimal weight: 20.0000 chunk 101 optimal weight: 10.0000 chunk 182 optimal weight: 9.9990 chunk 71 optimal weight: 7.9990 chunk 210 optimal weight: 5.9990 chunk 220 optimal weight: 20.0000 chunk 231 optimal weight: 7.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.6939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 12929 Z= 0.236 Angle : 0.531 6.416 17934 Z= 0.325 Chirality : 0.044 0.142 2429 Planarity : 0.003 0.013 2604 Dihedral : 5.341 30.535 2604 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 1.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.54 % Favored : 91.46 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.17), residues: 2576 helix: 1.18 (0.16), residues: 1113 sheet: -1.06 (0.22), residues: 574 loop : -2.05 (0.21), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 98 PHE 0.000 0.000 PHE A 52 TYR 0.000 0.000 TYR A 51 *********************** 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 fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 1.400 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.1100 time to fit residues: 22.1591 Evaluate side-chains 98 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 1.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 152 optimal weight: 20.0000 chunk 245 optimal weight: 5.9990 chunk 150 optimal weight: 40.0000 chunk 116 optimal weight: 10.0000 chunk 171 optimal weight: 4.9990 chunk 258 optimal weight: 20.0000 chunk 237 optimal weight: 2.9990 chunk 205 optimal weight: 8.9990 chunk 21 optimal weight: 5.9990 chunk 158 optimal weight: 3.9990 chunk 125 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.6942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 12929 Z= 0.160 Angle : 0.456 6.739 17934 Z= 0.273 Chirality : 0.042 0.140 2429 Planarity : 0.002 0.011 2604 Dihedral : 4.762 29.893 2604 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 0.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.18), residues: 2576 helix: 1.70 (0.16), residues: 1113 sheet: -1.11 (0.22), residues: 574 loop : -1.99 (0.22), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 98 PHE 0.000 0.000 PHE A 52 TYR 0.000 0.000 TYR A 51 ********************** 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 fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 1.460 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.1096 time to fit residues: 22.0618 Evaluate side-chains 98 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 1.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 163 optimal weight: 6.9990 chunk 218 optimal weight: 7.9990 chunk 62 optimal weight: 7.9990 chunk 189 optimal weight: 20.0000 chunk 30 optimal weight: 0.8980 chunk 57 optimal weight: 5.9990 chunk 205 optimal weight: 6.9990 chunk 86 optimal weight: 30.0000 chunk 211 optimal weight: 20.0000 chunk 26 optimal weight: 0.0270 chunk 37 optimal weight: 20.0000 overall best weight: 4.1844 ------------------------------------------------------------------------------- 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 = 0.3146 r_free = 0.3146 target = 0.066831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.055628 restraints weight = 79341.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.056282 restraints weight = 56261.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.056823 restraints weight = 44439.404| |-----------------------------------------------------------------------------| r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.7005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.011 12929 Z= 0.143 Angle : 0.428 6.098 17934 Z= 0.255 Chirality : 0.042 0.138 2429 Planarity : 0.002 0.011 2604 Dihedral : 4.384 29.413 2604 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 0.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.18), residues: 2576 helix: 2.15 (0.17), residues: 1106 sheet: -1.09 (0.22), residues: 574 loop : -1.98 (0.22), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 98 PHE 0.000 0.000 PHE A 52 TYR 0.000 0.000 TYR A 51 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1671.77 seconds wall clock time: 30 minutes 16.93 seconds (1816.93 seconds total)