Starting phenix.real_space_refine on Thu Jan 23 20:40:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6kff_9971/01_2025/6kff_9971.cif Found real_map, /net/cci-nas-00/data/ceres_data/6kff_9971/01_2025/6kff_9971.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6kff_9971/01_2025/6kff_9971.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6kff_9971/01_2025/6kff_9971.map" model { file = "/net/cci-nas-00/data/ceres_data/6kff_9971/01_2025/6kff_9971.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6kff_9971/01_2025/6kff_9971.cif" } resolution = 3.8 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= 0.011 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: 4 Type Number sf(0) Gaussians S 96 5.16 5 C 14072 2.51 5 N 3432 2.21 5 O 3592 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 96 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 21192 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2649 Classifications: {'peptide': 322} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 11, 'TRANS': 310} Chain breaks: 4 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Restraints were copied for chains: C, B, E, D, G, F, H Time building chain proxies: 6.47, per 1000 atoms: 0.31 Number of scatterers: 21192 At special positions: 0 Unit cell: (121.968, 121.968, 108.416, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 96 16.00 O 3592 8.00 N 3432 7.00 C 14072 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 58 " - pdb=" SG CYS A 265 " distance=2.03 Simple disulfide: pdb=" SG CYS A 76 " - pdb=" SG CYS A 248 " distance=2.03 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: 5.51 Conformation dependent library (CDL) restraints added in 2.5 seconds 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4960 Finding SS restraints... Secondary structure from input PDB file: 128 helices and 8 sheets defined 71.7% alpha, 1.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.93 Creating SS restraints... Processing helix chain 'A' and resid 29 through 53 removed outlier: 4.058A pdb=" N ARG A 33 " --> pdb=" O ARG A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 79 removed outlier: 4.758A pdb=" N GLN A 74 " --> pdb=" O ASN A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 134 removed outlier: 4.480A pdb=" N ALA A 113 " --> pdb=" O PRO A 109 " (cutoff:3.500A) Proline residue: A 122 - end of helix removed outlier: 3.830A pdb=" N GLY A 134 " --> pdb=" O ILE A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 152 removed outlier: 3.878A pdb=" N ALA A 140 " --> pdb=" O ASP A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 159 removed outlier: 4.147A pdb=" N LYS A 159 " --> pdb=" O ASP A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 168 Processing helix chain 'A' and resid 168 through 182 removed outlier: 3.916A pdb=" N TYR A 172 " --> pdb=" O ARG A 168 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LYS A 182 " --> pdb=" O ARG A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 212 Processing helix chain 'A' and resid 223 through 232 Processing helix chain 'A' and resid 269 through 273 Processing helix chain 'A' and resid 276 through 305 removed outlier: 4.071A pdb=" N PHE A 282 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS A 305 " --> pdb=" O TYR A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 308 No H-bonds generated for 'chain 'A' and resid 306 through 308' Processing helix chain 'A' and resid 309 through 316 Processing helix chain 'A' and resid 326 through 335 removed outlier: 3.549A pdb=" N PHE A 330 " --> pdb=" O SER A 326 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE A 331 " --> pdb=" O ASP A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 350 Processing helix chain 'A' and resid 351 through 364 removed outlier: 3.536A pdb=" N LEU A 357 " --> pdb=" O PRO A 353 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ARG A 362 " --> pdb=" O THR A 358 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ASN A 363 " --> pdb=" O ILE A 359 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE A 364 " --> pdb=" O SER A 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 53 removed outlier: 4.058A pdb=" N ARG B 33 " --> pdb=" O ARG B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 79 removed outlier: 4.758A pdb=" N GLN B 74 " --> pdb=" O ASN B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 134 removed outlier: 4.480A pdb=" N ALA B 113 " --> pdb=" O PRO B 109 " (cutoff:3.500A) Proline residue: B 122 - end of helix removed outlier: 3.829A pdb=" N GLY B 134 " --> pdb=" O ILE B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 152 removed outlier: 3.878A pdb=" N ALA B 140 " --> pdb=" O ASP B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 159 removed outlier: 4.147A pdb=" N LYS B 159 " --> pdb=" O ASP B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 168 Processing helix chain 'B' and resid 168 through 182 removed outlier: 3.916A pdb=" N TYR B 172 " --> pdb=" O ARG B 168 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LYS B 182 " --> pdb=" O ARG B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 212 Processing helix chain 'B' and resid 223 through 232 Processing helix chain 'B' and resid 269 through 273 Processing helix chain 'B' and resid 276 through 305 removed outlier: 4.071A pdb=" N PHE B 282 " --> pdb=" O ILE B 278 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS B 305 " --> pdb=" O TYR B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 308 No H-bonds generated for 'chain 'B' and resid 306 through 308' Processing helix chain 'B' and resid 309 through 316 Processing helix chain 'B' and resid 326 through 335 removed outlier: 3.549A pdb=" N PHE B 330 " --> pdb=" O SER B 326 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE B 331 " --> pdb=" O ASP B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 350 Processing helix chain 'B' and resid 351 through 364 removed outlier: 3.537A pdb=" N LEU B 357 " --> pdb=" O PRO B 353 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ARG B 362 " --> pdb=" O THR B 358 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ASN B 363 " --> pdb=" O ILE B 359 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE B 364 " --> pdb=" O SER B 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 53 removed outlier: 4.058A pdb=" N ARG C 33 " --> pdb=" O ARG C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 79 removed outlier: 4.758A pdb=" N GLN C 74 " --> pdb=" O ASN C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 134 removed outlier: 4.480A pdb=" N ALA C 113 " --> pdb=" O PRO C 109 " (cutoff:3.500A) Proline residue: C 122 - end of helix removed outlier: 3.829A pdb=" N GLY C 134 " --> pdb=" O ILE C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 152 removed outlier: 3.878A pdb=" N ALA C 140 " --> pdb=" O ASP C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 159 removed outlier: 4.147A pdb=" N LYS C 159 " --> pdb=" O ASP C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 168 Processing helix chain 'C' and resid 168 through 182 removed outlier: 3.916A pdb=" N TYR C 172 " --> pdb=" O ARG C 168 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LYS C 182 " --> pdb=" O ARG C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 212 Processing helix chain 'C' and resid 223 through 232 Processing helix chain 'C' and resid 269 through 273 Processing helix chain 'C' and resid 276 through 305 removed outlier: 4.070A pdb=" N PHE C 282 " --> pdb=" O ILE C 278 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS C 305 " --> pdb=" O TYR C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 308 No H-bonds generated for 'chain 'C' and resid 306 through 308' Processing helix chain 'C' and resid 309 through 316 Processing helix chain 'C' and resid 326 through 335 removed outlier: 3.549A pdb=" N PHE C 330 " --> pdb=" O SER C 326 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE C 331 " --> pdb=" O ASP C 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 350 Processing helix chain 'C' and resid 351 through 364 removed outlier: 3.537A pdb=" N LEU C 357 " --> pdb=" O PRO C 353 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ARG C 362 " --> pdb=" O THR C 358 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ASN C 363 " --> pdb=" O ILE C 359 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE C 364 " --> pdb=" O SER C 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 53 removed outlier: 4.057A pdb=" N ARG D 33 " --> pdb=" O ARG D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 79 removed outlier: 4.759A pdb=" N GLN D 74 " --> pdb=" O ASN D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 134 removed outlier: 4.480A pdb=" N ALA D 113 " --> pdb=" O PRO D 109 " (cutoff:3.500A) Proline residue: D 122 - end of helix removed outlier: 3.830A pdb=" N GLY D 134 " --> pdb=" O ILE D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 152 removed outlier: 3.879A pdb=" N ALA D 140 " --> pdb=" O ASP D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 159 removed outlier: 4.147A pdb=" N LYS D 159 " --> pdb=" O ASP D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 168 Processing helix chain 'D' and resid 168 through 182 removed outlier: 3.915A pdb=" N TYR D 172 " --> pdb=" O ARG D 168 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LYS D 182 " --> pdb=" O ARG D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 212 Processing helix chain 'D' and resid 223 through 232 Processing helix chain 'D' and resid 269 through 273 Processing helix chain 'D' and resid 276 through 305 removed outlier: 4.071A pdb=" N PHE D 282 " --> pdb=" O ILE D 278 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS D 305 " --> pdb=" O TYR D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 308 No H-bonds generated for 'chain 'D' and resid 306 through 308' Processing helix chain 'D' and resid 309 through 316 Processing helix chain 'D' and resid 326 through 335 removed outlier: 3.549A pdb=" N PHE D 330 " --> pdb=" O SER D 326 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE D 331 " --> pdb=" O ASP D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 350 Processing helix chain 'D' and resid 351 through 364 removed outlier: 3.536A pdb=" N LEU D 357 " --> pdb=" O PRO D 353 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ARG D 362 " --> pdb=" O THR D 358 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ASN D 363 " --> pdb=" O ILE D 359 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE D 364 " --> pdb=" O SER D 360 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 53 removed outlier: 4.058A pdb=" N ARG E 33 " --> pdb=" O ARG E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 79 removed outlier: 4.759A pdb=" N GLN E 74 " --> pdb=" O ASN E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 134 removed outlier: 4.480A pdb=" N ALA E 113 " --> pdb=" O PRO E 109 " (cutoff:3.500A) Proline residue: E 122 - end of helix removed outlier: 3.829A pdb=" N GLY E 134 " --> pdb=" O ILE E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 152 removed outlier: 3.878A pdb=" N ALA E 140 " --> pdb=" O ASP E 136 " (cutoff:3.500A) Processing helix chain 'E' and resid 155 through 159 removed outlier: 4.146A pdb=" N LYS E 159 " --> pdb=" O ASP E 156 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 168 Processing helix chain 'E' and resid 168 through 182 removed outlier: 3.916A pdb=" N TYR E 172 " --> pdb=" O ARG E 168 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LYS E 182 " --> pdb=" O ARG E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 212 Processing helix chain 'E' and resid 223 through 232 Processing helix chain 'E' and resid 269 through 273 Processing helix chain 'E' and resid 276 through 305 removed outlier: 4.071A pdb=" N PHE E 282 " --> pdb=" O ILE E 278 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS E 305 " --> pdb=" O TYR E 301 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 308 No H-bonds generated for 'chain 'E' and resid 306 through 308' Processing helix chain 'E' and resid 309 through 316 Processing helix chain 'E' and resid 326 through 335 removed outlier: 3.549A pdb=" N PHE E 330 " --> pdb=" O SER E 326 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE E 331 " --> pdb=" O ASP E 327 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 350 Processing helix chain 'E' and resid 351 through 364 removed outlier: 3.536A pdb=" N LEU E 357 " --> pdb=" O PRO E 353 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ARG E 362 " --> pdb=" O THR E 358 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ASN E 363 " --> pdb=" O ILE E 359 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE E 364 " --> pdb=" O SER E 360 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 53 removed outlier: 4.058A pdb=" N ARG F 33 " --> pdb=" O ARG F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 68 through 79 removed outlier: 4.758A pdb=" N GLN F 74 " --> pdb=" O ASN F 70 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 134 removed outlier: 4.479A pdb=" N ALA F 113 " --> pdb=" O PRO F 109 " (cutoff:3.500A) Proline residue: F 122 - end of helix removed outlier: 3.830A pdb=" N GLY F 134 " --> pdb=" O ILE F 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 136 through 152 removed outlier: 3.878A pdb=" N ALA F 140 " --> pdb=" O ASP F 136 " (cutoff:3.500A) Processing helix chain 'F' and resid 155 through 159 removed outlier: 4.147A pdb=" N LYS F 159 " --> pdb=" O ASP F 156 " (cutoff:3.500A) Processing helix chain 'F' and resid 160 through 168 Processing helix chain 'F' and resid 168 through 182 removed outlier: 3.917A pdb=" N TYR F 172 " --> pdb=" O ARG F 168 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LYS F 182 " --> pdb=" O ARG F 178 " (cutoff:3.500A) Processing helix chain 'F' and resid 187 through 212 Processing helix chain 'F' and resid 223 through 232 Processing helix chain 'F' and resid 269 through 273 Processing helix chain 'F' and resid 276 through 305 removed outlier: 4.071A pdb=" N PHE F 282 " --> pdb=" O ILE F 278 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS F 305 " --> pdb=" O TYR F 301 " (cutoff:3.500A) Processing helix chain 'F' and resid 306 through 308 No H-bonds generated for 'chain 'F' and resid 306 through 308' Processing helix chain 'F' and resid 309 through 316 Processing helix chain 'F' and resid 326 through 335 removed outlier: 3.549A pdb=" N PHE F 330 " --> pdb=" O SER F 326 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE F 331 " --> pdb=" O ASP F 327 " (cutoff:3.500A) Processing helix chain 'F' and resid 337 through 350 Processing helix chain 'F' and resid 351 through 364 removed outlier: 3.536A pdb=" N LEU F 357 " --> pdb=" O PRO F 353 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ARG F 362 " --> pdb=" O THR F 358 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ASN F 363 " --> pdb=" O ILE F 359 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE F 364 " --> pdb=" O SER F 360 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 53 removed outlier: 4.058A pdb=" N ARG G 33 " --> pdb=" O ARG G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 68 through 79 removed outlier: 4.758A pdb=" N GLN G 74 " --> pdb=" O ASN G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 107 through 134 removed outlier: 4.479A pdb=" N ALA G 113 " --> pdb=" O PRO G 109 " (cutoff:3.500A) Proline residue: G 122 - end of helix removed outlier: 3.829A pdb=" N GLY G 134 " --> pdb=" O ILE G 130 " (cutoff:3.500A) Processing helix chain 'G' and resid 136 through 152 removed outlier: 3.879A pdb=" N ALA G 140 " --> pdb=" O ASP G 136 " (cutoff:3.500A) Processing helix chain 'G' and resid 155 through 159 removed outlier: 4.146A pdb=" N LYS G 159 " --> pdb=" O ASP G 156 " (cutoff:3.500A) Processing helix chain 'G' and resid 160 through 168 Processing helix chain 'G' and resid 168 through 182 removed outlier: 3.916A pdb=" N TYR G 172 " --> pdb=" O ARG G 168 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LYS G 182 " --> pdb=" O ARG G 178 " (cutoff:3.500A) Processing helix chain 'G' and resid 187 through 212 Processing helix chain 'G' and resid 223 through 232 Processing helix chain 'G' and resid 269 through 273 Processing helix chain 'G' and resid 276 through 305 removed outlier: 4.070A pdb=" N PHE G 282 " --> pdb=" O ILE G 278 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS G 305 " --> pdb=" O TYR G 301 " (cutoff:3.500A) Processing helix chain 'G' and resid 306 through 308 No H-bonds generated for 'chain 'G' and resid 306 through 308' Processing helix chain 'G' and resid 309 through 316 Processing helix chain 'G' and resid 326 through 335 removed outlier: 3.548A pdb=" N PHE G 330 " --> pdb=" O SER G 326 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE G 331 " --> pdb=" O ASP G 327 " (cutoff:3.500A) Processing helix chain 'G' and resid 337 through 350 Processing helix chain 'G' and resid 351 through 364 removed outlier: 3.536A pdb=" N LEU G 357 " --> pdb=" O PRO G 353 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ARG G 362 " --> pdb=" O THR G 358 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ASN G 363 " --> pdb=" O ILE G 359 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE G 364 " --> pdb=" O SER G 360 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 53 removed outlier: 4.057A pdb=" N ARG H 33 " --> pdb=" O ARG H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 68 through 79 removed outlier: 4.759A pdb=" N GLN H 74 " --> pdb=" O ASN H 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 134 removed outlier: 4.480A pdb=" N ALA H 113 " --> pdb=" O PRO H 109 " (cutoff:3.500A) Proline residue: H 122 - end of helix removed outlier: 3.829A pdb=" N GLY H 134 " --> pdb=" O ILE H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 136 through 152 removed outlier: 3.879A pdb=" N ALA H 140 " --> pdb=" O ASP H 136 " (cutoff:3.500A) Processing helix chain 'H' and resid 155 through 159 removed outlier: 4.147A pdb=" N LYS H 159 " --> pdb=" O ASP H 156 " (cutoff:3.500A) Processing helix chain 'H' and resid 160 through 168 Processing helix chain 'H' and resid 168 through 182 removed outlier: 3.916A pdb=" N TYR H 172 " --> pdb=" O ARG H 168 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LYS H 182 " --> pdb=" O ARG H 178 " (cutoff:3.500A) Processing helix chain 'H' and resid 187 through 212 Processing helix chain 'H' and resid 223 through 232 Processing helix chain 'H' and resid 269 through 273 Processing helix chain 'H' and resid 276 through 305 removed outlier: 4.071A pdb=" N PHE H 282 " --> pdb=" O ILE H 278 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS H 305 " --> pdb=" O TYR H 301 " (cutoff:3.500A) Processing helix chain 'H' and resid 306 through 308 No H-bonds generated for 'chain 'H' and resid 306 through 308' Processing helix chain 'H' and resid 309 through 316 Processing helix chain 'H' and resid 326 through 335 removed outlier: 3.549A pdb=" N PHE H 330 " --> pdb=" O SER H 326 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE H 331 " --> pdb=" O ASP H 327 " (cutoff:3.500A) Processing helix chain 'H' and resid 337 through 350 Processing helix chain 'H' and resid 351 through 364 removed outlier: 3.536A pdb=" N LEU H 357 " --> pdb=" O PRO H 353 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ARG H 362 " --> pdb=" O THR H 358 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ASN H 363 " --> pdb=" O ILE H 359 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE H 364 " --> pdb=" O SER H 360 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 57 Processing sheet with id=AA2, first strand: chain 'B' and resid 56 through 57 Processing sheet with id=AA3, first strand: chain 'C' and resid 56 through 57 Processing sheet with id=AA4, first strand: chain 'D' and resid 56 through 57 Processing sheet with id=AA5, first strand: chain 'E' and resid 56 through 57 Processing sheet with id=AA6, first strand: chain 'F' and resid 56 through 57 Processing sheet with id=AA7, first strand: chain 'G' and resid 56 through 57 Processing sheet with id=AA8, first strand: chain 'H' and resid 56 through 57 1240 hydrogen bonds defined for protein. 3624 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: 6.97 Time building geometry restraints manager: 6.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6312 1.34 - 1.46: 5601 1.46 - 1.58: 9791 1.58 - 1.69: 0 1.69 - 1.81: 128 Bond restraints: 21832 Sorted by residual: bond pdb=" C ARG G 168 " pdb=" N PRO G 169 " ideal model delta sigma weight residual 1.334 1.356 -0.022 2.34e-02 1.83e+03 9.17e-01 bond pdb=" C ARG H 168 " pdb=" N PRO H 169 " ideal model delta sigma weight residual 1.334 1.356 -0.022 2.34e-02 1.83e+03 9.07e-01 bond pdb=" C ARG D 168 " pdb=" N PRO D 169 " ideal model delta sigma weight residual 1.334 1.356 -0.022 2.34e-02 1.83e+03 9.06e-01 bond pdb=" C ARG E 168 " pdb=" N PRO E 169 " ideal model delta sigma weight residual 1.334 1.356 -0.022 2.34e-02 1.83e+03 8.74e-01 bond pdb=" C ARG A 168 " pdb=" N PRO A 169 " ideal model delta sigma weight residual 1.334 1.356 -0.022 2.34e-02 1.83e+03 8.66e-01 ... (remaining 21827 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 28985 1.49 - 2.98: 591 2.98 - 4.46: 79 4.46 - 5.95: 65 5.95 - 7.44: 24 Bond angle restraints: 29744 Sorted by residual: angle pdb=" C TRP G 107 " pdb=" N VAL G 108 " pdb=" CA VAL G 108 " ideal model delta sigma weight residual 120.33 122.46 -2.13 8.00e-01 1.56e+00 7.06e+00 angle pdb=" C TRP B 107 " pdb=" N VAL B 108 " pdb=" CA VAL B 108 " ideal model delta sigma weight residual 120.33 122.45 -2.12 8.00e-01 1.56e+00 7.00e+00 angle pdb=" C TRP C 107 " pdb=" N VAL C 108 " pdb=" CA VAL C 108 " ideal model delta sigma weight residual 120.33 122.45 -2.12 8.00e-01 1.56e+00 6.99e+00 angle pdb=" C TRP F 107 " pdb=" N VAL F 108 " pdb=" CA VAL F 108 " ideal model delta sigma weight residual 120.33 122.45 -2.12 8.00e-01 1.56e+00 6.99e+00 angle pdb=" C TRP E 107 " pdb=" N VAL E 108 " pdb=" CA VAL E 108 " ideal model delta sigma weight residual 120.33 122.44 -2.11 8.00e-01 1.56e+00 6.93e+00 ... (remaining 29739 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.32: 10928 17.32 - 34.64: 1244 34.64 - 51.96: 210 51.96 - 69.28: 16 69.28 - 86.60: 40 Dihedral angle restraints: 12438 sinusoidal: 4798 harmonic: 7640 Sorted by residual: dihedral pdb=" CB CYS A 76 " pdb=" SG CYS A 76 " pdb=" SG CYS A 248 " pdb=" CB CYS A 248 " ideal model delta sinusoidal sigma weight residual 93.00 137.00 -44.00 1 1.00e+01 1.00e-02 2.69e+01 dihedral pdb=" CA GLU C 274 " pdb=" C GLU C 274 " pdb=" N LYS C 275 " pdb=" CA LYS C 275 " ideal model delta harmonic sigma weight residual 180.00 158.90 21.10 0 5.00e+00 4.00e-02 1.78e+01 dihedral pdb=" CA GLU H 274 " pdb=" C GLU H 274 " pdb=" N LYS H 275 " pdb=" CA LYS H 275 " ideal model delta harmonic sigma weight residual 180.00 158.90 21.10 0 5.00e+00 4.00e-02 1.78e+01 ... (remaining 12435 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1859 0.026 - 0.051: 855 0.051 - 0.077: 412 0.077 - 0.103: 108 0.103 - 0.129: 54 Chirality restraints: 3288 Sorted by residual: chirality pdb=" CA TRP B 236 " pdb=" N TRP B 236 " pdb=" C TRP B 236 " pdb=" CB TRP B 236 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.13e-01 chirality pdb=" CA TRP G 236 " pdb=" N TRP G 236 " pdb=" C TRP G 236 " pdb=" CB TRP G 236 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.09e-01 chirality pdb=" CA TRP F 236 " pdb=" N TRP F 236 " pdb=" C TRP F 236 " pdb=" CB TRP F 236 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.06e-01 ... (remaining 3285 not shown) Planarity restraints: 3632 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE D 119 " -0.010 2.00e-02 2.50e+03 9.91e-03 1.72e+00 pdb=" CG PHE D 119 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 PHE D 119 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE D 119 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE D 119 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE D 119 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE D 119 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 119 " -0.010 2.00e-02 2.50e+03 9.75e-03 1.66e+00 pdb=" CG PHE F 119 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 PHE F 119 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE F 119 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE F 119 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE F 119 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE F 119 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 119 " -0.009 2.00e-02 2.50e+03 9.75e-03 1.66e+00 pdb=" CG PHE C 119 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 PHE C 119 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE C 119 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE C 119 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE C 119 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE C 119 " -0.002 2.00e-02 2.50e+03 ... (remaining 3629 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 133 2.60 - 3.18: 19389 3.18 - 3.75: 32896 3.75 - 4.33: 41863 4.33 - 4.90: 69294 Nonbonded interactions: 163575 Sorted by model distance: nonbonded pdb=" SG CYS G 76 " pdb=" SG CYS G 248 " model vdw 2.029 3.760 nonbonded pdb=" SG CYS D 76 " pdb=" SG CYS D 248 " model vdw 2.029 3.760 nonbonded pdb=" SG CYS E 76 " pdb=" SG CYS E 248 " model vdw 2.030 3.760 nonbonded pdb=" SG CYS H 76 " pdb=" SG CYS H 248 " model vdw 2.030 3.760 nonbonded pdb=" SG CYS B 76 " pdb=" SG CYS B 248 " model vdw 2.030 3.760 ... (remaining 163570 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: 0.18 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.730 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 39.400 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 21832 Z= 0.226 Angle : 0.604 7.440 29744 Z= 0.321 Chirality : 0.038 0.129 3288 Planarity : 0.003 0.021 3632 Dihedral : 15.084 86.599 7472 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.17 % Favored : 90.83 % Rotamer: Outliers : 0.35 % Allowed : 6.96 % Favored : 92.69 % 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: -2.57 (0.15), residues: 2496 helix: -0.50 (0.11), residues: 1672 sheet: -4.64 (0.29), residues: 80 loop : -4.12 (0.18), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 68 HIS 0.004 0.001 HIS A 50 PHE 0.023 0.001 PHE D 119 TYR 0.009 0.001 TYR B 110 ARG 0.002 0.000 ARG H 362 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 934 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 926 time to evaluate : 2.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 LEU cc_start: 0.9301 (tt) cc_final: 0.9094 (tt) REVERT: A 153 ASP cc_start: 0.8634 (m-30) cc_final: 0.8271 (m-30) REVERT: A 166 GLU cc_start: 0.7628 (pt0) cc_final: 0.7270 (pt0) REVERT: A 175 ASP cc_start: 0.8000 (m-30) cc_final: 0.7429 (m-30) REVERT: A 194 LEU cc_start: 0.9418 (mt) cc_final: 0.9043 (mt) REVERT: A 208 TYR cc_start: 0.8326 (t80) cc_final: 0.7846 (t80) REVERT: A 304 ASN cc_start: 0.8695 (t0) cc_final: 0.8389 (t0) REVERT: A 310 LYS cc_start: 0.6931 (ttpt) cc_final: 0.6552 (tptt) REVERT: A 339 LEU cc_start: 0.9254 (tp) cc_final: 0.9036 (tp) REVERT: A 353 PRO cc_start: 0.9486 (Cg_endo) cc_final: 0.9219 (Cg_exo) REVERT: B 58 CYS cc_start: 0.6717 (m) cc_final: 0.6494 (m) REVERT: B 146 ARG cc_start: 0.8918 (ttp80) cc_final: 0.8343 (mtm110) REVERT: B 153 ASP cc_start: 0.8678 (m-30) cc_final: 0.8243 (m-30) REVERT: B 172 TYR cc_start: 0.9068 (t80) cc_final: 0.8817 (t80) REVERT: B 270 ASN cc_start: 0.9167 (t0) cc_final: 0.8855 (t0) REVERT: B 304 ASN cc_start: 0.8321 (t0) cc_final: 0.7817 (t0) REVERT: B 310 LYS cc_start: 0.7220 (ttpt) cc_final: 0.6514 (tptt) REVERT: B 332 SER cc_start: 0.9205 (t) cc_final: 0.8999 (t) REVERT: B 353 PRO cc_start: 0.9576 (Cg_endo) cc_final: 0.9325 (Cg_exo) REVERT: B 359 ILE cc_start: 0.9395 (tp) cc_final: 0.9132 (tp) REVERT: C 154 LYS cc_start: 0.8794 (mtmt) cc_final: 0.8066 (mtmt) REVERT: C 157 LYS cc_start: 0.8268 (tptt) cc_final: 0.7688 (ttpp) REVERT: C 198 TRP cc_start: 0.8737 (t-100) cc_final: 0.8528 (t-100) REVERT: C 208 TYR cc_start: 0.8275 (t80) cc_final: 0.7811 (t80) REVERT: C 310 LYS cc_start: 0.6681 (ttpt) cc_final: 0.6165 (tptt) REVERT: C 339 LEU cc_start: 0.9253 (tp) cc_final: 0.9039 (tp) REVERT: C 353 PRO cc_start: 0.9551 (Cg_endo) cc_final: 0.9235 (Cg_exo) REVERT: C 359 ILE cc_start: 0.9411 (tp) cc_final: 0.9207 (tp) REVERT: D 58 CYS cc_start: 0.7177 (m) cc_final: 0.6803 (m) REVERT: D 146 ARG cc_start: 0.8910 (ttp80) cc_final: 0.8286 (mtp-110) REVERT: D 192 TYR cc_start: 0.9016 (t80) cc_final: 0.8656 (t80) REVERT: D 270 ASN cc_start: 0.9148 (t0) cc_final: 0.8821 (t0) REVERT: D 304 ASN cc_start: 0.8353 (t0) cc_final: 0.8030 (t0) REVERT: D 310 LYS cc_start: 0.6960 (ttpt) cc_final: 0.6510 (tptt) REVERT: D 325 ILE cc_start: 0.8840 (mp) cc_final: 0.8622 (mp) REVERT: D 353 PRO cc_start: 0.9527 (Cg_endo) cc_final: 0.9307 (Cg_exo) REVERT: D 359 ILE cc_start: 0.9389 (tp) cc_final: 0.9184 (tp) REVERT: E 65 ASN cc_start: 0.7162 (p0) cc_final: 0.6726 (p0) REVERT: E 68 TRP cc_start: 0.7866 (t-100) cc_final: 0.7656 (t-100) REVERT: E 157 LYS cc_start: 0.8300 (tptt) cc_final: 0.7881 (ttpp) REVERT: E 166 GLU cc_start: 0.7558 (pt0) cc_final: 0.7223 (pt0) REVERT: E 178 ARG cc_start: 0.8938 (ttm-80) cc_final: 0.8667 (ttp-110) REVERT: E 208 TYR cc_start: 0.8103 (t80) cc_final: 0.7539 (t80) REVERT: E 310 LYS cc_start: 0.7104 (ttpt) cc_final: 0.6594 (tptt) REVERT: E 339 LEU cc_start: 0.9204 (tp) cc_final: 0.9002 (tp) REVERT: F 58 CYS cc_start: 0.7240 (m) cc_final: 0.6896 (m) REVERT: F 157 LYS cc_start: 0.8360 (tptt) cc_final: 0.7717 (ttmm) REVERT: F 194 LEU cc_start: 0.9221 (mt) cc_final: 0.8908 (mt) REVERT: F 310 LYS cc_start: 0.7153 (ttpt) cc_final: 0.6762 (tptt) REVERT: F 353 PRO cc_start: 0.9581 (Cg_endo) cc_final: 0.9301 (Cg_exo) REVERT: G 154 LYS cc_start: 0.8831 (mtmt) cc_final: 0.8243 (mtpt) REVERT: G 157 LYS cc_start: 0.8301 (tptt) cc_final: 0.7725 (ttpp) REVERT: G 208 TYR cc_start: 0.8240 (t80) cc_final: 0.7752 (t80) REVERT: G 310 LYS cc_start: 0.6964 (ttpt) cc_final: 0.6236 (tptt) REVERT: G 322 LYS cc_start: 0.7669 (pttm) cc_final: 0.6898 (mptt) REVERT: G 339 LEU cc_start: 0.9308 (tp) cc_final: 0.9078 (tp) REVERT: G 353 PRO cc_start: 0.9542 (Cg_endo) cc_final: 0.9273 (Cg_exo) REVERT: G 359 ILE cc_start: 0.9350 (tp) cc_final: 0.9144 (tp) REVERT: H 58 CYS cc_start: 0.7131 (m) cc_final: 0.6644 (m) REVERT: H 192 TYR cc_start: 0.8960 (t80) cc_final: 0.8760 (t80) REVERT: H 310 LYS cc_start: 0.7196 (ttpt) cc_final: 0.6603 (tptt) REVERT: H 313 LYS cc_start: 0.9300 (ttmt) cc_final: 0.9082 (ttmm) outliers start: 8 outliers final: 6 residues processed: 928 average time/residue: 0.3596 time to fit residues: 491.8178 Evaluate side-chains 753 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 747 time to evaluate : 2.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain F residue 171 VAL Chi-restraints excluded: chain H residue 171 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 216 optimal weight: 0.8980 chunk 194 optimal weight: 6.9990 chunk 107 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 5.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 3.9990 chunk 149 optimal weight: 5.9990 chunk 232 optimal weight: 5.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 HIS A 67 GLN A 234 ASN A 247 HIS A 329 GLN B 21 GLN B 73 ASN B 234 ASN B 247 HIS B 329 GLN C 206 GLN C 234 ASN C 247 HIS C 329 GLN D 21 GLN D 73 ASN D 234 ASN D 247 HIS D 329 GLN E 50 HIS ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 234 ASN E 247 HIS E 329 GLN F 21 GLN F 50 HIS F 73 ASN F 234 ASN F 247 HIS F 329 GLN G 234 ASN G 247 HIS G 329 GLN H 21 GLN H 50 HIS H 73 ASN H 234 ASN H 247 HIS H 329 GLN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.121758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.099299 restraints weight = 32913.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.102933 restraints weight = 17942.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.105405 restraints weight = 12073.339| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 21832 Z= 0.307 Angle : 0.669 10.610 29744 Z= 0.326 Chirality : 0.043 0.188 3288 Planarity : 0.004 0.029 3632 Dihedral : 4.978 23.608 2798 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 3.77 % Allowed : 21.19 % Favored : 75.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.18 (0.17), residues: 2496 helix: 0.53 (0.12), residues: 1688 sheet: -3.99 (0.47), residues: 80 loop : -3.59 (0.21), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 59 HIS 0.010 0.002 HIS F 50 PHE 0.022 0.002 PHE D 242 TYR 0.017 0.002 TYR G 301 ARG 0.005 0.000 ARG E 244 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 865 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 780 time to evaluate : 2.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ASN cc_start: 0.6852 (p0) cc_final: 0.6606 (p0) REVERT: A 68 TRP cc_start: 0.8039 (t-100) cc_final: 0.7774 (t-100) REVERT: A 123 ARG cc_start: 0.8377 (ttm170) cc_final: 0.8005 (ttp-170) REVERT: A 137 LEU cc_start: 0.9345 (tt) cc_final: 0.9141 (tt) REVERT: A 153 ASP cc_start: 0.8613 (m-30) cc_final: 0.8071 (m-30) REVERT: A 157 LYS cc_start: 0.8207 (tptt) cc_final: 0.7613 (ttmm) REVERT: A 206 GLN cc_start: 0.9084 (mm-40) cc_final: 0.8446 (mm110) REVERT: A 208 TYR cc_start: 0.8352 (t80) cc_final: 0.7871 (t80) REVERT: A 310 LYS cc_start: 0.7030 (ttpt) cc_final: 0.6542 (tptt) REVERT: A 353 PRO cc_start: 0.9489 (Cg_endo) cc_final: 0.9262 (Cg_exo) REVERT: B 65 ASN cc_start: 0.7677 (p0) cc_final: 0.7232 (p0) REVERT: B 146 ARG cc_start: 0.8974 (ttp80) cc_final: 0.8383 (mtm110) REVERT: B 153 ASP cc_start: 0.8809 (m-30) cc_final: 0.8438 (m-30) REVERT: B 158 PHE cc_start: 0.8439 (OUTLIER) cc_final: 0.7962 (t80) REVERT: B 161 ARG cc_start: 0.8137 (ttp-110) cc_final: 0.7922 (ttp-110) REVERT: B 206 GLN cc_start: 0.9000 (mm-40) cc_final: 0.8687 (mm-40) REVERT: B 208 TYR cc_start: 0.8509 (t80) cc_final: 0.8248 (t80) REVERT: B 263 VAL cc_start: 0.8892 (t) cc_final: 0.8649 (p) REVERT: B 305 LYS cc_start: 0.8608 (tttm) cc_final: 0.8358 (tmtt) REVERT: B 310 LYS cc_start: 0.7194 (ttpt) cc_final: 0.6523 (tptt) REVERT: B 332 SER cc_start: 0.9085 (t) cc_final: 0.8869 (t) REVERT: B 359 ILE cc_start: 0.9469 (tp) cc_final: 0.9181 (tp) REVERT: C 58 CYS cc_start: 0.8850 (m) cc_final: 0.8423 (m) REVERT: C 64 PHE cc_start: 0.8281 (m-80) cc_final: 0.8036 (m-10) REVERT: C 65 ASN cc_start: 0.7599 (p0) cc_final: 0.7092 (p0) REVERT: C 105 TYR cc_start: 0.7527 (OUTLIER) cc_final: 0.7221 (m-10) REVERT: C 153 ASP cc_start: 0.8856 (m-30) cc_final: 0.8202 (m-30) REVERT: C 154 LYS cc_start: 0.8825 (mtmt) cc_final: 0.8243 (mtpt) REVERT: C 157 LYS cc_start: 0.8217 (tptt) cc_final: 0.7727 (ttpp) REVERT: C 198 TRP cc_start: 0.8713 (t-100) cc_final: 0.8334 (t-100) REVERT: C 208 TYR cc_start: 0.8375 (t80) cc_final: 0.7886 (t80) REVERT: C 310 LYS cc_start: 0.6851 (ttpt) cc_final: 0.6165 (tptt) REVERT: C 353 PRO cc_start: 0.9500 (Cg_endo) cc_final: 0.9274 (Cg_exo) REVERT: D 65 ASN cc_start: 0.7788 (p0) cc_final: 0.7358 (p0) REVERT: D 146 ARG cc_start: 0.8977 (ttp80) cc_final: 0.8304 (mtp-110) REVERT: D 153 ASP cc_start: 0.8891 (m-30) cc_final: 0.8453 (m-30) REVERT: D 158 PHE cc_start: 0.8438 (t80) cc_final: 0.8208 (t80) REVERT: D 192 TYR cc_start: 0.9199 (t80) cc_final: 0.8923 (t80) REVERT: D 263 VAL cc_start: 0.8928 (t) cc_final: 0.8683 (p) REVERT: D 310 LYS cc_start: 0.7285 (ttpt) cc_final: 0.6792 (tptt) REVERT: D 332 SER cc_start: 0.9131 (m) cc_final: 0.8890 (t) REVERT: D 359 ILE cc_start: 0.9464 (tp) cc_final: 0.9235 (tp) REVERT: E 58 CYS cc_start: 0.8830 (m) cc_final: 0.8279 (m) REVERT: E 65 ASN cc_start: 0.7435 (p0) cc_final: 0.7086 (p0) REVERT: E 157 LYS cc_start: 0.8365 (tptt) cc_final: 0.7863 (ttmm) REVERT: E 206 GLN cc_start: 0.9196 (mm-40) cc_final: 0.8348 (mm-40) REVERT: E 208 TYR cc_start: 0.8213 (t80) cc_final: 0.7555 (t80) REVERT: E 310 LYS cc_start: 0.7333 (ttpt) cc_final: 0.6735 (tptt) REVERT: F 137 LEU cc_start: 0.9194 (tt) cc_final: 0.8972 (tt) REVERT: F 157 LYS cc_start: 0.8200 (tptt) cc_final: 0.7699 (ttmm) REVERT: F 310 LYS cc_start: 0.7224 (ttpt) cc_final: 0.6750 (tptt) REVERT: G 58 CYS cc_start: 0.8849 (m) cc_final: 0.8432 (m) REVERT: G 63 GLN cc_start: 0.8195 (tp40) cc_final: 0.7988 (tp40) REVERT: G 65 ASN cc_start: 0.7672 (p0) cc_final: 0.7280 (p0) REVERT: G 67 GLN cc_start: 0.8185 (mt0) cc_final: 0.7818 (mt0) REVERT: G 68 TRP cc_start: 0.8220 (t-100) cc_final: 0.8012 (t-100) REVERT: G 105 TYR cc_start: 0.7521 (OUTLIER) cc_final: 0.7218 (m-10) REVERT: G 153 ASP cc_start: 0.8880 (m-30) cc_final: 0.8508 (m-30) REVERT: G 154 LYS cc_start: 0.8828 (mtmt) cc_final: 0.8242 (mtpt) REVERT: G 157 LYS cc_start: 0.8266 (tptt) cc_final: 0.7711 (ttpp) REVERT: G 208 TYR cc_start: 0.8338 (t80) cc_final: 0.7857 (t80) REVERT: G 304 ASN cc_start: 0.8738 (t0) cc_final: 0.8394 (t0) REVERT: G 310 LYS cc_start: 0.6983 (ttpt) cc_final: 0.6303 (tptt) REVERT: G 322 LYS cc_start: 0.7841 (pttm) cc_final: 0.6681 (mptt) REVERT: H 137 LEU cc_start: 0.9278 (tt) cc_final: 0.9048 (tt) REVERT: H 146 ARG cc_start: 0.8960 (ttp80) cc_final: 0.8493 (mtp-110) REVERT: H 192 TYR cc_start: 0.9275 (t80) cc_final: 0.9016 (t80) REVERT: H 206 GLN cc_start: 0.9014 (mm-40) cc_final: 0.8559 (mm-40) REVERT: H 263 VAL cc_start: 0.8931 (t) cc_final: 0.8656 (p) REVERT: H 310 LYS cc_start: 0.7209 (ttpt) cc_final: 0.6608 (tptt) REVERT: H 313 LYS cc_start: 0.9372 (ttmt) cc_final: 0.9101 (ttmm) outliers start: 85 outliers final: 55 residues processed: 822 average time/residue: 0.3543 time to fit residues: 433.7455 Evaluate side-chains 790 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 732 time to evaluate : 2.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 50 HIS Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 158 PHE Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 352 ILE Chi-restraints excluded: chain C residue 360 SER Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 226 ILE Chi-restraints excluded: chain E residue 360 SER Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 50 HIS Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 360 SER Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 105 TYR Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 332 SER Chi-restraints excluded: chain G residue 360 SER Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 50 HIS Chi-restraints excluded: chain H residue 67 GLN Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 332 SER Chi-restraints excluded: chain H residue 360 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 71 optimal weight: 0.8980 chunk 115 optimal weight: 4.9990 chunk 109 optimal weight: 5.9990 chunk 173 optimal weight: 2.9990 chunk 174 optimal weight: 2.9990 chunk 114 optimal weight: 0.0770 chunk 44 optimal weight: 5.9990 chunk 100 optimal weight: 0.0010 chunk 207 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 203 optimal weight: 4.9990 overall best weight: 0.9948 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 50 HIS ** B 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 73 ASN C 67 GLN C 73 ASN C 363 ASN D 50 HIS D 73 ASN E 73 ASN F 73 ASN F 206 GLN F 329 GLN G 50 HIS G 73 ASN G 363 ASN H 73 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.127812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.105485 restraints weight = 32204.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.109259 restraints weight = 17373.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.111814 restraints weight = 11577.686| |-----------------------------------------------------------------------------| r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 21832 Z= 0.172 Angle : 0.591 8.368 29744 Z= 0.290 Chirality : 0.039 0.144 3288 Planarity : 0.003 0.028 3632 Dihedral : 4.649 21.884 2792 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 2.84 % Allowed : 25.18 % Favored : 71.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.62 (0.18), residues: 2496 helix: 0.90 (0.13), residues: 1688 sheet: -3.58 (0.55), residues: 80 loop : -3.25 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 68 HIS 0.012 0.002 HIS B 50 PHE 0.020 0.001 PHE G 64 TYR 0.014 0.001 TYR F 301 ARG 0.007 0.000 ARG D 17 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 854 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 790 time to evaluate : 2.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ASP cc_start: 0.6911 (m-30) cc_final: 0.6652 (m-30) REVERT: A 65 ASN cc_start: 0.6677 (p0) cc_final: 0.6135 (p0) REVERT: A 67 GLN cc_start: 0.8399 (mp10) cc_final: 0.8110 (mp-120) REVERT: A 68 TRP cc_start: 0.7982 (t-100) cc_final: 0.7779 (t-100) REVERT: A 123 ARG cc_start: 0.8340 (ttm170) cc_final: 0.7960 (ttp-170) REVERT: A 137 LEU cc_start: 0.9250 (tt) cc_final: 0.9038 (tt) REVERT: A 153 ASP cc_start: 0.8627 (m-30) cc_final: 0.7256 (m-30) REVERT: A 157 LYS cc_start: 0.8251 (tptt) cc_final: 0.7588 (ttmm) REVERT: A 158 PHE cc_start: 0.8005 (OUTLIER) cc_final: 0.7265 (t80) REVERT: A 208 TYR cc_start: 0.8329 (t80) cc_final: 0.7634 (t80) REVERT: A 305 LYS cc_start: 0.8563 (tttm) cc_final: 0.8097 (tmtt) REVERT: A 310 LYS cc_start: 0.7102 (ttpt) cc_final: 0.6368 (tptm) REVERT: B 65 ASN cc_start: 0.7703 (p0) cc_final: 0.7210 (p0) REVERT: B 146 ARG cc_start: 0.8915 (ttp80) cc_final: 0.8235 (mtp-110) REVERT: B 153 ASP cc_start: 0.8803 (m-30) cc_final: 0.8366 (m-30) REVERT: B 158 PHE cc_start: 0.8280 (OUTLIER) cc_final: 0.7753 (t80) REVERT: B 170 SER cc_start: 0.9404 (t) cc_final: 0.9174 (m) REVERT: B 206 GLN cc_start: 0.8919 (mm-40) cc_final: 0.8548 (mm-40) REVERT: B 208 TYR cc_start: 0.8470 (t80) cc_final: 0.8135 (t80) REVERT: B 263 VAL cc_start: 0.8925 (t) cc_final: 0.8616 (p) REVERT: B 305 LYS cc_start: 0.8686 (tttm) cc_final: 0.8355 (tmtt) REVERT: B 310 LYS cc_start: 0.7224 (ttpt) cc_final: 0.6451 (tptt) REVERT: B 315 TYR cc_start: 0.8269 (m-10) cc_final: 0.7499 (m-10) REVERT: B 322 LYS cc_start: 0.7876 (pttm) cc_final: 0.7064 (mptt) REVERT: B 332 SER cc_start: 0.9019 (t) cc_final: 0.8787 (t) REVERT: B 359 ILE cc_start: 0.9439 (tp) cc_final: 0.9144 (tp) REVERT: C 105 TYR cc_start: 0.7527 (OUTLIER) cc_final: 0.7144 (m-10) REVERT: C 123 ARG cc_start: 0.8478 (ttm170) cc_final: 0.8083 (ttp-170) REVERT: C 153 ASP cc_start: 0.8830 (m-30) cc_final: 0.7608 (m-30) REVERT: C 154 LYS cc_start: 0.8802 (mtmt) cc_final: 0.8215 (mtpt) REVERT: C 157 LYS cc_start: 0.8252 (tptt) cc_final: 0.7596 (ttpp) REVERT: C 158 PHE cc_start: 0.8181 (OUTLIER) cc_final: 0.7905 (t80) REVERT: C 198 TRP cc_start: 0.8672 (t-100) cc_final: 0.8283 (t-100) REVERT: C 208 TYR cc_start: 0.8338 (t80) cc_final: 0.7580 (t80) REVERT: C 267 LEU cc_start: 0.9221 (mp) cc_final: 0.8890 (mp) REVERT: C 305 LYS cc_start: 0.8428 (tttm) cc_final: 0.7999 (tmtt) REVERT: C 310 LYS cc_start: 0.7126 (ttpt) cc_final: 0.6267 (tptm) REVERT: C 322 LYS cc_start: 0.7548 (pttm) cc_final: 0.6692 (mptt) REVERT: C 353 PRO cc_start: 0.9410 (Cg_endo) cc_final: 0.9168 (Cg_exo) REVERT: D 47 LEU cc_start: 0.9530 (mm) cc_final: 0.9329 (mm) REVERT: D 64 PHE cc_start: 0.8399 (m-10) cc_final: 0.8165 (m-10) REVERT: D 65 ASN cc_start: 0.7457 (p0) cc_final: 0.6938 (p0) REVERT: D 105 TYR cc_start: 0.7606 (OUTLIER) cc_final: 0.7284 (m-10) REVERT: D 146 ARG cc_start: 0.8938 (ttp80) cc_final: 0.8269 (mtp-110) REVERT: D 153 ASP cc_start: 0.8871 (m-30) cc_final: 0.8397 (m-30) REVERT: D 170 SER cc_start: 0.9290 (t) cc_final: 0.9080 (m) REVERT: D 192 TYR cc_start: 0.9119 (t80) cc_final: 0.8866 (t80) REVERT: D 206 GLN cc_start: 0.8909 (mm-40) cc_final: 0.8442 (mm-40) REVERT: D 275 LYS cc_start: 0.8764 (mptt) cc_final: 0.8560 (mmtt) REVERT: D 310 LYS cc_start: 0.7208 (ttpt) cc_final: 0.6759 (tptt) REVERT: D 322 LYS cc_start: 0.7659 (pttm) cc_final: 0.6900 (mptt) REVERT: D 332 SER cc_start: 0.9159 (m) cc_final: 0.8946 (t) REVERT: D 359 ILE cc_start: 0.9414 (tp) cc_final: 0.9135 (tp) REVERT: E 65 ASN cc_start: 0.7140 (p0) cc_final: 0.6557 (p0) REVERT: E 67 GLN cc_start: 0.8524 (mp10) cc_final: 0.8157 (mp10) REVERT: E 68 TRP cc_start: 0.8192 (t-100) cc_final: 0.7937 (t-100) REVERT: E 129 MET cc_start: 0.8156 (tpp) cc_final: 0.7924 (tpp) REVERT: E 157 LYS cc_start: 0.8362 (tptt) cc_final: 0.7805 (ttpp) REVERT: E 158 PHE cc_start: 0.8099 (OUTLIER) cc_final: 0.7864 (t80) REVERT: E 206 GLN cc_start: 0.9227 (mm-40) cc_final: 0.8399 (mm-40) REVERT: E 208 TYR cc_start: 0.8164 (t80) cc_final: 0.7686 (t80) REVERT: E 310 LYS cc_start: 0.7188 (ttpt) cc_final: 0.6629 (tptt) REVERT: E 322 LYS cc_start: 0.7548 (pttm) cc_final: 0.6488 (mptt) REVERT: E 353 PRO cc_start: 0.9399 (Cg_endo) cc_final: 0.9155 (Cg_exo) REVERT: F 157 LYS cc_start: 0.8173 (tptt) cc_final: 0.7681 (ttmm) REVERT: F 158 PHE cc_start: 0.7945 (OUTLIER) cc_final: 0.7702 (t80) REVERT: F 275 LYS cc_start: 0.8767 (mptt) cc_final: 0.8555 (mmtt) REVERT: F 304 ASN cc_start: 0.8593 (t0) cc_final: 0.7926 (t0) REVERT: F 310 LYS cc_start: 0.7301 (ttpt) cc_final: 0.6847 (tptt) REVERT: G 65 ASN cc_start: 0.7354 (p0) cc_final: 0.6805 (p0) REVERT: G 68 TRP cc_start: 0.8199 (t-100) cc_final: 0.7878 (t-100) REVERT: G 70 ASN cc_start: 0.8930 (t0) cc_final: 0.8529 (t0) REVERT: G 105 TYR cc_start: 0.7511 (OUTLIER) cc_final: 0.7121 (m-10) REVERT: G 123 ARG cc_start: 0.8437 (ttm170) cc_final: 0.8067 (ttp-170) REVERT: G 153 ASP cc_start: 0.8854 (m-30) cc_final: 0.8524 (m-30) REVERT: G 154 LYS cc_start: 0.8802 (mtmt) cc_final: 0.8230 (mtpt) REVERT: G 157 LYS cc_start: 0.8302 (tptt) cc_final: 0.7650 (ttpp) REVERT: G 158 PHE cc_start: 0.8166 (OUTLIER) cc_final: 0.7804 (t80) REVERT: G 208 TYR cc_start: 0.8265 (t80) cc_final: 0.7567 (t80) REVERT: G 267 LEU cc_start: 0.9219 (mp) cc_final: 0.8885 (mp) REVERT: G 305 LYS cc_start: 0.8452 (tttm) cc_final: 0.8030 (tmtt) REVERT: G 310 LYS cc_start: 0.7174 (ttpt) cc_final: 0.6511 (tptt) REVERT: G 322 LYS cc_start: 0.7522 (pttm) cc_final: 0.6661 (mptt) REVERT: G 353 PRO cc_start: 0.9424 (Cg_endo) cc_final: 0.9192 (Cg_exo) REVERT: H 47 LEU cc_start: 0.9440 (mm) cc_final: 0.9211 (mm) REVERT: H 65 ASN cc_start: 0.7354 (p0) cc_final: 0.6786 (p0) REVERT: H 146 ARG cc_start: 0.8944 (ttp80) cc_final: 0.8243 (mtp-110) REVERT: H 153 ASP cc_start: 0.8745 (m-30) cc_final: 0.8321 (m-30) REVERT: H 157 LYS cc_start: 0.8227 (tptt) cc_final: 0.7878 (ttmm) REVERT: H 158 PHE cc_start: 0.8111 (OUTLIER) cc_final: 0.7853 (t80) REVERT: H 161 ARG cc_start: 0.8252 (ttp-110) cc_final: 0.8033 (ttp-110) REVERT: H 206 GLN cc_start: 0.8791 (mm-40) cc_final: 0.8482 (mm-40) REVERT: H 310 LYS cc_start: 0.7217 (ttpt) cc_final: 0.6695 (tptt) REVERT: H 313 LYS cc_start: 0.9332 (ttmt) cc_final: 0.9119 (ttmm) REVERT: H 322 LYS cc_start: 0.7858 (pttm) cc_final: 0.7049 (mptt) outliers start: 64 outliers final: 39 residues processed: 816 average time/residue: 0.3472 time to fit residues: 424.9204 Evaluate side-chains 788 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 739 time to evaluate : 2.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain B residue 50 HIS Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 158 PHE Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 158 PHE Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 265 CYS Chi-restraints excluded: chain C residue 352 ILE Chi-restraints excluded: chain C residue 360 SER Chi-restraints excluded: chain D residue 50 HIS Chi-restraints excluded: chain D residue 105 TYR Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain E residue 158 PHE Chi-restraints excluded: chain E residue 226 ILE Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 360 SER Chi-restraints excluded: chain F residue 51 PHE Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain F residue 158 PHE Chi-restraints excluded: chain F residue 162 LEU Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain F residue 299 ILE Chi-restraints excluded: chain F residue 359 ILE Chi-restraints excluded: chain F residue 360 SER Chi-restraints excluded: chain G residue 50 HIS Chi-restraints excluded: chain G residue 105 TYR Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain G residue 158 PHE Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 265 CYS Chi-restraints excluded: chain G residue 299 ILE Chi-restraints excluded: chain G residue 360 SER Chi-restraints excluded: chain H residue 67 GLN Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 158 PHE Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 360 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 206 optimal weight: 1.9990 chunk 114 optimal weight: 9.9990 chunk 133 optimal weight: 0.8980 chunk 203 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 chunk 141 optimal weight: 5.9990 chunk 199 optimal weight: 3.9990 chunk 254 optimal weight: 0.7980 chunk 129 optimal weight: 7.9990 chunk 104 optimal weight: 2.9990 chunk 249 optimal weight: 0.0020 overall best weight: 1.3392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 HIS ** B 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 HIS C 73 ASN C 206 GLN D 50 HIS ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 HIS F 50 HIS G 50 HIS G 206 GLN H 50 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.128195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.105706 restraints weight = 32751.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.109522 restraints weight = 17480.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.112128 restraints weight = 11589.542| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 21832 Z= 0.180 Angle : 0.575 7.900 29744 Z= 0.283 Chirality : 0.039 0.136 3288 Planarity : 0.003 0.032 3632 Dihedral : 4.491 20.698 2792 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 4.39 % Allowed : 25.84 % Favored : 69.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.18), residues: 2496 helix: 1.04 (0.13), residues: 1696 sheet: -3.50 (0.56), residues: 80 loop : -3.10 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 68 HIS 0.018 0.003 HIS B 50 PHE 0.019 0.001 PHE H 64 TYR 0.014 0.001 TYR F 301 ARG 0.009 0.000 ARG E 362 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 865 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 766 time to evaluate : 2.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 TRP cc_start: 0.8135 (t-100) cc_final: 0.7894 (t-100) REVERT: A 123 ARG cc_start: 0.8352 (ttm170) cc_final: 0.7952 (ttp-170) REVERT: A 137 LEU cc_start: 0.9230 (tt) cc_final: 0.9017 (tt) REVERT: A 153 ASP cc_start: 0.8622 (m-30) cc_final: 0.7185 (m-30) REVERT: A 157 LYS cc_start: 0.8207 (tptt) cc_final: 0.7212 (ttmm) REVERT: A 158 PHE cc_start: 0.7820 (OUTLIER) cc_final: 0.7133 (t80) REVERT: A 170 SER cc_start: 0.9435 (OUTLIER) cc_final: 0.9017 (m) REVERT: A 208 TYR cc_start: 0.8320 (t80) cc_final: 0.7605 (t80) REVERT: A 274 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.6084 (mp0) REVERT: A 305 LYS cc_start: 0.8567 (tttm) cc_final: 0.8170 (tmtt) REVERT: A 310 LYS cc_start: 0.7143 (ttpt) cc_final: 0.6439 (tptm) REVERT: B 47 LEU cc_start: 0.9418 (mm) cc_final: 0.9202 (mm) REVERT: B 65 ASN cc_start: 0.7566 (p0) cc_final: 0.7117 (p0) REVERT: B 146 ARG cc_start: 0.8937 (ttp80) cc_final: 0.8414 (mtm110) REVERT: B 153 ASP cc_start: 0.8781 (m-30) cc_final: 0.8379 (m-30) REVERT: B 170 SER cc_start: 0.9311 (t) cc_final: 0.9061 (m) REVERT: B 206 GLN cc_start: 0.8861 (mm-40) cc_final: 0.8479 (mm-40) REVERT: B 208 TYR cc_start: 0.8533 (t80) cc_final: 0.8224 (t80) REVERT: B 274 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.6317 (mp0) REVERT: B 305 LYS cc_start: 0.8681 (tttm) cc_final: 0.8370 (tmtt) REVERT: B 310 LYS cc_start: 0.7236 (ttpt) cc_final: 0.6496 (tptt) REVERT: B 315 TYR cc_start: 0.8285 (m-10) cc_final: 0.7521 (m-10) REVERT: B 322 LYS cc_start: 0.7837 (pttm) cc_final: 0.7018 (mptt) REVERT: B 332 SER cc_start: 0.9044 (t) cc_final: 0.8831 (t) REVERT: B 359 ILE cc_start: 0.9474 (tp) cc_final: 0.9194 (tp) REVERT: C 64 PHE cc_start: 0.8229 (m-80) cc_final: 0.7895 (m-10) REVERT: C 70 ASN cc_start: 0.8930 (t0) cc_final: 0.8551 (t0) REVERT: C 105 TYR cc_start: 0.7417 (OUTLIER) cc_final: 0.7079 (m-10) REVERT: C 123 ARG cc_start: 0.8443 (ttm170) cc_final: 0.8141 (ttp-170) REVERT: C 153 ASP cc_start: 0.8778 (m-30) cc_final: 0.8144 (m-30) REVERT: C 154 LYS cc_start: 0.8847 (mtmt) cc_final: 0.8308 (mtpt) REVERT: C 157 LYS cc_start: 0.8285 (tptt) cc_final: 0.7509 (ttpp) REVERT: C 158 PHE cc_start: 0.8191 (OUTLIER) cc_final: 0.7873 (t80) REVERT: C 208 TYR cc_start: 0.8367 (t80) cc_final: 0.7898 (t80) REVERT: C 267 LEU cc_start: 0.9235 (mp) cc_final: 0.8916 (mp) REVERT: C 274 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.6224 (mp0) REVERT: C 305 LYS cc_start: 0.8506 (tttm) cc_final: 0.8064 (tmtt) REVERT: C 310 LYS cc_start: 0.7072 (ttpt) cc_final: 0.6263 (tptm) REVERT: C 322 LYS cc_start: 0.7498 (pttm) cc_final: 0.6666 (mptt) REVERT: C 353 PRO cc_start: 0.9382 (Cg_endo) cc_final: 0.9168 (Cg_exo) REVERT: D 47 LEU cc_start: 0.9484 (mm) cc_final: 0.9283 (mm) REVERT: D 65 ASN cc_start: 0.7506 (p0) cc_final: 0.7110 (p0) REVERT: D 105 TYR cc_start: 0.7646 (OUTLIER) cc_final: 0.7286 (m-10) REVERT: D 146 ARG cc_start: 0.8955 (ttp80) cc_final: 0.8276 (mtp-110) REVERT: D 153 ASP cc_start: 0.8865 (m-30) cc_final: 0.8425 (m-30) REVERT: D 192 TYR cc_start: 0.9084 (t80) cc_final: 0.8852 (t80) REVERT: D 206 GLN cc_start: 0.8894 (mm-40) cc_final: 0.8426 (mm-40) REVERT: D 274 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.6398 (mp0) REVERT: D 310 LYS cc_start: 0.7228 (ttpt) cc_final: 0.6774 (tptt) REVERT: D 322 LYS cc_start: 0.7633 (pttm) cc_final: 0.6873 (mptt) REVERT: D 332 SER cc_start: 0.9193 (m) cc_final: 0.8939 (t) REVERT: D 359 ILE cc_start: 0.9437 (tp) cc_final: 0.9160 (tp) REVERT: E 29 ARG cc_start: 0.7726 (tpp-160) cc_final: 0.7298 (tpp-160) REVERT: E 65 ASN cc_start: 0.6576 (p0) cc_final: 0.6074 (p0) REVERT: E 68 TRP cc_start: 0.8206 (t-100) cc_final: 0.7977 (t-100) REVERT: E 70 ASN cc_start: 0.8921 (t0) cc_final: 0.8552 (t0) REVERT: E 129 MET cc_start: 0.8168 (tpp) cc_final: 0.7929 (tpp) REVERT: E 153 ASP cc_start: 0.8811 (m-30) cc_final: 0.7601 (m-30) REVERT: E 157 LYS cc_start: 0.8371 (tptt) cc_final: 0.7932 (ttmm) REVERT: E 158 PHE cc_start: 0.8033 (OUTLIER) cc_final: 0.7791 (t80) REVERT: E 199 GLN cc_start: 0.7976 (tp40) cc_final: 0.7519 (tp40) REVERT: E 206 GLN cc_start: 0.9239 (mm-40) cc_final: 0.8326 (mm-40) REVERT: E 208 TYR cc_start: 0.8153 (t80) cc_final: 0.7659 (t80) REVERT: E 274 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.6306 (mp0) REVERT: E 310 LYS cc_start: 0.7186 (ttpt) cc_final: 0.6656 (tptt) REVERT: E 322 LYS cc_start: 0.7464 (pttm) cc_final: 0.6468 (tttm) REVERT: E 353 PRO cc_start: 0.9388 (Cg_endo) cc_final: 0.9158 (Cg_exo) REVERT: F 105 TYR cc_start: 0.7770 (OUTLIER) cc_final: 0.7391 (m-10) REVERT: F 157 LYS cc_start: 0.8133 (tptt) cc_final: 0.7487 (ttmm) REVERT: F 158 PHE cc_start: 0.7956 (OUTLIER) cc_final: 0.7679 (t80) REVERT: F 304 ASN cc_start: 0.8579 (t0) cc_final: 0.7937 (t0) REVERT: F 310 LYS cc_start: 0.7310 (ttpt) cc_final: 0.6856 (tptt) REVERT: F 322 LYS cc_start: 0.7816 (pttm) cc_final: 0.7069 (mptt) REVERT: G 67 GLN cc_start: 0.8505 (mp10) cc_final: 0.7962 (mp10) REVERT: G 68 TRP cc_start: 0.8272 (t-100) cc_final: 0.7973 (t-100) REVERT: G 105 TYR cc_start: 0.7402 (OUTLIER) cc_final: 0.7079 (m-10) REVERT: G 123 ARG cc_start: 0.8465 (ttm170) cc_final: 0.8119 (ttp-170) REVERT: G 153 ASP cc_start: 0.8799 (m-30) cc_final: 0.8473 (m-30) REVERT: G 154 LYS cc_start: 0.8833 (mtmt) cc_final: 0.8301 (mtpt) REVERT: G 157 LYS cc_start: 0.8312 (tptt) cc_final: 0.7541 (ttpp) REVERT: G 158 PHE cc_start: 0.8163 (OUTLIER) cc_final: 0.7741 (t80) REVERT: G 208 TYR cc_start: 0.8285 (t80) cc_final: 0.7794 (t80) REVERT: G 267 LEU cc_start: 0.9227 (mp) cc_final: 0.8905 (mp) REVERT: G 274 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.6350 (mp0) REVERT: G 304 ASN cc_start: 0.8640 (t0) cc_final: 0.8323 (t0) REVERT: G 305 LYS cc_start: 0.8640 (tttm) cc_final: 0.8333 (tmtt) REVERT: G 310 LYS cc_start: 0.7179 (ttpt) cc_final: 0.6424 (tptm) REVERT: G 322 LYS cc_start: 0.7398 (pttm) cc_final: 0.6644 (mptt) REVERT: H 28 ASP cc_start: 0.6940 (m-30) cc_final: 0.6647 (m-30) REVERT: H 47 LEU cc_start: 0.9515 (mm) cc_final: 0.9269 (mm) REVERT: H 65 ASN cc_start: 0.7401 (p0) cc_final: 0.6889 (p0) REVERT: H 105 TYR cc_start: 0.7837 (OUTLIER) cc_final: 0.7446 (m-10) REVERT: H 146 ARG cc_start: 0.8963 (ttp80) cc_final: 0.8233 (mtp-110) REVERT: H 153 ASP cc_start: 0.8703 (m-30) cc_final: 0.8281 (m-30) REVERT: H 157 LYS cc_start: 0.8287 (tptt) cc_final: 0.7944 (ttmm) REVERT: H 158 PHE cc_start: 0.8063 (OUTLIER) cc_final: 0.7798 (t80) REVERT: H 208 TYR cc_start: 0.8520 (t80) cc_final: 0.8172 (t80) REVERT: H 229 ASP cc_start: 0.8602 (m-30) cc_final: 0.8342 (m-30) REVERT: H 274 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.6188 (mp0) REVERT: H 305 LYS cc_start: 0.8649 (tttm) cc_final: 0.8313 (tmtt) REVERT: H 310 LYS cc_start: 0.7251 (ttpt) cc_final: 0.6556 (tptt) REVERT: H 313 LYS cc_start: 0.9340 (ttmt) cc_final: 0.9062 (ttmm) REVERT: H 315 TYR cc_start: 0.8343 (m-10) cc_final: 0.7601 (m-10) REVERT: H 322 LYS cc_start: 0.7821 (pttm) cc_final: 0.7051 (mptt) REVERT: H 359 ILE cc_start: 0.9458 (tp) cc_final: 0.9110 (tp) outliers start: 99 outliers final: 58 residues processed: 820 average time/residue: 0.3411 time to fit residues: 423.3698 Evaluate side-chains 809 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 732 time to evaluate : 2.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 HIS Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 50 HIS Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 158 PHE Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 265 CYS Chi-restraints excluded: chain C residue 274 GLU Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 351 ASP Chi-restraints excluded: chain C residue 352 ILE Chi-restraints excluded: chain C residue 360 SER Chi-restraints excluded: chain D residue 105 TYR Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 274 GLU Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 158 PHE Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain E residue 226 ILE Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 352 ILE Chi-restraints excluded: chain E residue 360 SER Chi-restraints excluded: chain F residue 50 HIS Chi-restraints excluded: chain F residue 105 TYR Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain F residue 158 PHE Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 299 ILE Chi-restraints excluded: chain F residue 360 SER Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 105 TYR Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain G residue 158 PHE Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 274 GLU Chi-restraints excluded: chain G residue 299 ILE Chi-restraints excluded: chain G residue 360 SER Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 50 HIS Chi-restraints excluded: chain H residue 67 GLN Chi-restraints excluded: chain H residue 105 TYR Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 158 PHE Chi-restraints excluded: chain H residue 162 LEU Chi-restraints excluded: chain H residue 170 SER Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 274 GLU Chi-restraints excluded: chain H residue 332 SER Chi-restraints excluded: chain H residue 360 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 202 optimal weight: 9.9990 chunk 248 optimal weight: 9.9990 chunk 192 optimal weight: 20.0000 chunk 25 optimal weight: 1.9990 chunk 226 optimal weight: 0.7980 chunk 51 optimal weight: 9.9990 chunk 117 optimal weight: 5.9990 chunk 178 optimal weight: 10.0000 chunk 195 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 HIS A 67 GLN B 50 HIS ** B 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 ASN E 50 HIS F 50 HIS ** F 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 50 HIS H 115 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.127213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.104644 restraints weight = 32692.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.108375 restraints weight = 17449.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.110912 restraints weight = 11595.393| |-----------------------------------------------------------------------------| r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 21832 Z= 0.252 Angle : 0.604 11.685 29744 Z= 0.295 Chirality : 0.040 0.185 3288 Planarity : 0.004 0.045 3632 Dihedral : 4.485 21.281 2792 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 4.96 % Allowed : 26.33 % Favored : 68.71 % 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: 2496 helix: 1.08 (0.13), residues: 1712 sheet: -3.61 (0.54), residues: 80 loop : -3.00 (0.23), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP G 59 HIS 0.017 0.002 HIS H 50 PHE 0.015 0.001 PHE E 330 TYR 0.016 0.001 TYR F 301 ARG 0.010 0.001 ARG G 362 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 861 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 749 time to evaluate : 2.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 TRP cc_start: 0.8168 (t-100) cc_final: 0.7926 (t-100) REVERT: A 123 ARG cc_start: 0.8417 (ttm170) cc_final: 0.7999 (ttp-170) REVERT: A 153 ASP cc_start: 0.8619 (m-30) cc_final: 0.7923 (m-30) REVERT: A 154 LYS cc_start: 0.8816 (mtpt) cc_final: 0.8511 (mtpt) REVERT: A 157 LYS cc_start: 0.8215 (tptt) cc_final: 0.7329 (ttpp) REVERT: A 170 SER cc_start: 0.9447 (OUTLIER) cc_final: 0.8978 (m) REVERT: A 208 TYR cc_start: 0.8292 (t80) cc_final: 0.7615 (t80) REVERT: A 236 TRP cc_start: 0.8812 (p-90) cc_final: 0.8476 (p-90) REVERT: A 274 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.6119 (mp0) REVERT: A 305 LYS cc_start: 0.8684 (tttm) cc_final: 0.8188 (tmtt) REVERT: A 310 LYS cc_start: 0.7196 (ttpt) cc_final: 0.6475 (tptm) REVERT: B 65 ASN cc_start: 0.7751 (p0) cc_final: 0.7216 (p0) REVERT: B 146 ARG cc_start: 0.8950 (ttp80) cc_final: 0.8407 (mtm110) REVERT: B 153 ASP cc_start: 0.8796 (m-30) cc_final: 0.8345 (m-30) REVERT: B 206 GLN cc_start: 0.8886 (mm-40) cc_final: 0.8414 (mm-40) REVERT: B 208 TYR cc_start: 0.8548 (t80) cc_final: 0.8234 (t80) REVERT: B 274 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.6210 (mp0) REVERT: B 305 LYS cc_start: 0.8697 (tttm) cc_final: 0.8361 (tmtt) REVERT: B 310 LYS cc_start: 0.7279 (ttpt) cc_final: 0.6550 (tptt) REVERT: B 322 LYS cc_start: 0.7851 (pttm) cc_final: 0.7082 (mptt) REVERT: B 332 SER cc_start: 0.9071 (t) cc_final: 0.8867 (t) REVERT: B 359 ILE cc_start: 0.9440 (tp) cc_final: 0.9150 (tp) REVERT: C 64 PHE cc_start: 0.8328 (m-80) cc_final: 0.7969 (m-10) REVERT: C 70 ASN cc_start: 0.8950 (t0) cc_final: 0.8574 (t0) REVERT: C 105 TYR cc_start: 0.7492 (OUTLIER) cc_final: 0.7148 (m-10) REVERT: C 123 ARG cc_start: 0.8450 (ttm170) cc_final: 0.8071 (ttp-170) REVERT: C 153 ASP cc_start: 0.8776 (m-30) cc_final: 0.8155 (m-30) REVERT: C 154 LYS cc_start: 0.8870 (mtmt) cc_final: 0.8328 (mtpt) REVERT: C 157 LYS cc_start: 0.8283 (tptt) cc_final: 0.7498 (ttpp) REVERT: C 158 PHE cc_start: 0.8284 (OUTLIER) cc_final: 0.7933 (t80) REVERT: C 208 TYR cc_start: 0.8342 (t80) cc_final: 0.7859 (t80) REVERT: C 267 LEU cc_start: 0.9270 (mp) cc_final: 0.8968 (mp) REVERT: C 274 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.6221 (mp0) REVERT: C 305 LYS cc_start: 0.8599 (tttm) cc_final: 0.8103 (tmtt) REVERT: C 310 LYS cc_start: 0.7121 (ttpt) cc_final: 0.6305 (tptm) REVERT: C 322 LYS cc_start: 0.7521 (pttm) cc_final: 0.6687 (mptt) REVERT: C 353 PRO cc_start: 0.9428 (Cg_endo) cc_final: 0.9200 (Cg_exo) REVERT: D 65 ASN cc_start: 0.7687 (p0) cc_final: 0.7215 (p0) REVERT: D 105 TYR cc_start: 0.7765 (OUTLIER) cc_final: 0.7357 (m-10) REVERT: D 153 ASP cc_start: 0.8876 (m-30) cc_final: 0.8397 (m-30) REVERT: D 183 LYS cc_start: 0.9093 (ttpt) cc_final: 0.8878 (ttpt) REVERT: D 192 TYR cc_start: 0.9069 (t80) cc_final: 0.8837 (t80) REVERT: D 206 GLN cc_start: 0.8951 (mm-40) cc_final: 0.8407 (mm-40) REVERT: D 208 TYR cc_start: 0.8516 (t80) cc_final: 0.8196 (t80) REVERT: D 274 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.6223 (mp0) REVERT: D 310 LYS cc_start: 0.7264 (ttpt) cc_final: 0.6802 (tptt) REVERT: D 322 LYS cc_start: 0.7678 (pttm) cc_final: 0.6913 (mptt) REVERT: D 332 SER cc_start: 0.9194 (m) cc_final: 0.8963 (t) REVERT: D 359 ILE cc_start: 0.9444 (tp) cc_final: 0.9157 (tp) REVERT: E 65 ASN cc_start: 0.6704 (p0) cc_final: 0.6175 (p0) REVERT: E 68 TRP cc_start: 0.8254 (t-100) cc_final: 0.8052 (t-100) REVERT: E 129 MET cc_start: 0.8216 (tpp) cc_final: 0.7977 (tpp) REVERT: E 153 ASP cc_start: 0.8826 (m-30) cc_final: 0.8490 (m-30) REVERT: E 157 LYS cc_start: 0.8407 (tptt) cc_final: 0.7884 (ttmm) REVERT: E 158 PHE cc_start: 0.8137 (OUTLIER) cc_final: 0.7856 (t80) REVERT: E 206 GLN cc_start: 0.9239 (mm-40) cc_final: 0.8306 (mm-40) REVERT: E 208 TYR cc_start: 0.8223 (t80) cc_final: 0.7731 (t80) REVERT: E 274 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.6339 (mp0) REVERT: E 305 LYS cc_start: 0.8568 (tttm) cc_final: 0.8035 (tmtt) REVERT: E 310 LYS cc_start: 0.7218 (ttpt) cc_final: 0.6684 (tptt) REVERT: E 322 LYS cc_start: 0.7456 (pttm) cc_final: 0.6345 (mptt) REVERT: E 353 PRO cc_start: 0.9417 (Cg_endo) cc_final: 0.9194 (Cg_exo) REVERT: F 65 ASN cc_start: 0.7670 (p0) cc_final: 0.7361 (p0) REVERT: F 105 TYR cc_start: 0.7885 (OUTLIER) cc_final: 0.7443 (m-10) REVERT: F 137 LEU cc_start: 0.9222 (tt) cc_final: 0.9010 (tt) REVERT: F 153 ASP cc_start: 0.8775 (m-30) cc_final: 0.8340 (m-30) REVERT: F 157 LYS cc_start: 0.8114 (tptt) cc_final: 0.7836 (ttmm) REVERT: F 158 PHE cc_start: 0.8011 (OUTLIER) cc_final: 0.7720 (t80) REVERT: F 274 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.6358 (mp0) REVERT: F 304 ASN cc_start: 0.8644 (t0) cc_final: 0.8025 (t0) REVERT: F 310 LYS cc_start: 0.7343 (ttpt) cc_final: 0.6869 (tptt) REVERT: F 322 LYS cc_start: 0.7818 (pttm) cc_final: 0.7066 (mptt) REVERT: G 105 TYR cc_start: 0.7467 (OUTLIER) cc_final: 0.7111 (m-10) REVERT: G 123 ARG cc_start: 0.8452 (ttm170) cc_final: 0.8061 (ttp-170) REVERT: G 153 ASP cc_start: 0.8766 (m-30) cc_final: 0.8477 (m-30) REVERT: G 154 LYS cc_start: 0.8830 (mtmt) cc_final: 0.8279 (mtpt) REVERT: G 157 LYS cc_start: 0.8326 (tptt) cc_final: 0.7543 (ttpp) REVERT: G 158 PHE cc_start: 0.8236 (OUTLIER) cc_final: 0.7797 (t80) REVERT: G 170 SER cc_start: 0.9473 (OUTLIER) cc_final: 0.9012 (m) REVERT: G 208 TYR cc_start: 0.8305 (t80) cc_final: 0.7608 (t80) REVERT: G 267 LEU cc_start: 0.9246 (mp) cc_final: 0.8918 (mp) REVERT: G 274 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.6370 (mp0) REVERT: G 304 ASN cc_start: 0.8647 (t0) cc_final: 0.8330 (t0) REVERT: G 305 LYS cc_start: 0.8576 (tttm) cc_final: 0.8346 (tmtt) REVERT: G 310 LYS cc_start: 0.7209 (ttpt) cc_final: 0.6458 (tptm) REVERT: G 322 LYS cc_start: 0.7431 (pttm) cc_final: 0.6579 (mptt) REVERT: H 47 LEU cc_start: 0.9448 (mm) cc_final: 0.9222 (mm) REVERT: H 64 PHE cc_start: 0.8356 (m-80) cc_final: 0.8032 (m-10) REVERT: H 65 ASN cc_start: 0.7542 (p0) cc_final: 0.7019 (p0) REVERT: H 105 TYR cc_start: 0.7688 (OUTLIER) cc_final: 0.7353 (m-10) REVERT: H 137 LEU cc_start: 0.9259 (tt) cc_final: 0.9046 (tt) REVERT: H 146 ARG cc_start: 0.8990 (ttp80) cc_final: 0.8393 (mtp-110) REVERT: H 153 ASP cc_start: 0.8708 (m-30) cc_final: 0.8283 (m-30) REVERT: H 157 LYS cc_start: 0.8172 (tptt) cc_final: 0.7806 (ttmm) REVERT: H 158 PHE cc_start: 0.7908 (OUTLIER) cc_final: 0.7613 (t80) REVERT: H 208 TYR cc_start: 0.8533 (t80) cc_final: 0.8183 (t80) REVERT: H 229 ASP cc_start: 0.8614 (m-30) cc_final: 0.8341 (m-30) REVERT: H 274 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.6218 (mp0) REVERT: H 305 LYS cc_start: 0.8652 (tttm) cc_final: 0.8318 (tmtt) REVERT: H 310 LYS cc_start: 0.7253 (ttpt) cc_final: 0.6539 (tptt) REVERT: H 313 LYS cc_start: 0.9342 (ttmt) cc_final: 0.9091 (ttmm) REVERT: H 322 LYS cc_start: 0.7829 (pttm) cc_final: 0.7038 (mptt) REVERT: H 359 ILE cc_start: 0.9460 (tp) cc_final: 0.9117 (tp) outliers start: 112 outliers final: 71 residues processed: 809 average time/residue: 0.3316 time to fit residues: 408.0807 Evaluate side-chains 825 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 734 time to evaluate : 2.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 50 HIS Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 158 PHE Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 265 CYS Chi-restraints excluded: chain C residue 274 GLU Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 352 ILE Chi-restraints excluded: chain C residue 360 SER Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 105 TYR Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 274 GLU Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 137 LEU Chi-restraints excluded: chain E residue 158 PHE Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 226 ILE Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain E residue 352 ILE Chi-restraints excluded: chain E residue 360 SER Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 51 PHE Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 105 TYR Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain F residue 158 PHE Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 274 GLU Chi-restraints excluded: chain F residue 360 SER Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 58 CYS Chi-restraints excluded: chain G residue 60 THR Chi-restraints excluded: chain G residue 105 TYR Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain G residue 158 PHE Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 170 SER Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 274 GLU Chi-restraints excluded: chain G residue 299 ILE Chi-restraints excluded: chain G residue 360 SER Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 105 TYR Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 158 PHE Chi-restraints excluded: chain H residue 162 LEU Chi-restraints excluded: chain H residue 170 SER Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 274 GLU Chi-restraints excluded: chain H residue 360 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 90 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 chunk 200 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 50 optimal weight: 9.9990 chunk 123 optimal weight: 3.9990 chunk 116 optimal weight: 10.0000 chunk 180 optimal weight: 7.9990 chunk 52 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 chunk 246 optimal weight: 6.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 HIS B 50 HIS ** B 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 HIS C 206 GLN ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 ASN ** F 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 79 HIS G 115 GLN H 115 GLN ** H 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.128901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.106311 restraints weight = 32271.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.110155 restraints weight = 17199.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.112778 restraints weight = 11400.856| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 21832 Z= 0.185 Angle : 0.581 12.712 29744 Z= 0.282 Chirality : 0.039 0.197 3288 Planarity : 0.003 0.028 3632 Dihedral : 4.360 21.873 2792 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 4.61 % Allowed : 26.46 % Favored : 68.93 % 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: -0.14 (0.18), residues: 2496 helix: 1.15 (0.13), residues: 1728 sheet: -3.64 (0.53), residues: 80 loop : -2.92 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP G 59 HIS 0.021 0.001 HIS B 50 PHE 0.027 0.001 PHE H 124 TYR 0.015 0.001 TYR F 301 ARG 0.008 0.000 ARG G 362 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 851 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 747 time to evaluate : 2.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 TRP cc_start: 0.8148 (t-100) cc_final: 0.7919 (t-100) REVERT: A 123 ARG cc_start: 0.8394 (ttm170) cc_final: 0.8000 (ttp-170) REVERT: A 153 ASP cc_start: 0.8605 (m-30) cc_final: 0.7308 (m-30) REVERT: A 154 LYS cc_start: 0.8817 (mtpt) cc_final: 0.8562 (mtpt) REVERT: A 157 LYS cc_start: 0.8206 (tptt) cc_final: 0.7323 (ttpp) REVERT: A 170 SER cc_start: 0.9432 (OUTLIER) cc_final: 0.8975 (m) REVERT: A 208 TYR cc_start: 0.8270 (t80) cc_final: 0.7647 (t80) REVERT: A 236 TRP cc_start: 0.8793 (p-90) cc_final: 0.8434 (p-90) REVERT: A 274 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.6129 (mp0) REVERT: A 305 LYS cc_start: 0.8537 (tttm) cc_final: 0.8179 (tmtt) REVERT: A 310 LYS cc_start: 0.7183 (ttpt) cc_final: 0.6464 (tptm) REVERT: A 345 MET cc_start: 0.9376 (tpp) cc_final: 0.9091 (tpp) REVERT: B 65 ASN cc_start: 0.7641 (p0) cc_final: 0.7066 (p0) REVERT: B 146 ARG cc_start: 0.8878 (ttp80) cc_final: 0.8379 (mtm110) REVERT: B 153 ASP cc_start: 0.8764 (m-30) cc_final: 0.8350 (m-30) REVERT: B 199 GLN cc_start: 0.8253 (tp40) cc_final: 0.7801 (tt0) REVERT: B 206 GLN cc_start: 0.8837 (mm-40) cc_final: 0.8374 (mm-40) REVERT: B 208 TYR cc_start: 0.8540 (t80) cc_final: 0.8228 (t80) REVERT: B 274 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.6082 (mp0) REVERT: B 305 LYS cc_start: 0.8718 (tttm) cc_final: 0.8387 (tmtt) REVERT: B 310 LYS cc_start: 0.7364 (ttpt) cc_final: 0.6645 (tptt) REVERT: B 315 TYR cc_start: 0.8284 (m-10) cc_final: 0.7555 (m-10) REVERT: B 322 LYS cc_start: 0.7841 (pttm) cc_final: 0.7035 (mptt) REVERT: B 359 ILE cc_start: 0.9403 (tp) cc_final: 0.9132 (tp) REVERT: C 70 ASN cc_start: 0.8939 (t0) cc_final: 0.8566 (t0) REVERT: C 123 ARG cc_start: 0.8435 (ttm170) cc_final: 0.8039 (ttp-170) REVERT: C 153 ASP cc_start: 0.8777 (m-30) cc_final: 0.8180 (m-30) REVERT: C 154 LYS cc_start: 0.8848 (mtmt) cc_final: 0.8369 (mtpt) REVERT: C 157 LYS cc_start: 0.8280 (tptt) cc_final: 0.7510 (ttpp) REVERT: C 158 PHE cc_start: 0.8235 (OUTLIER) cc_final: 0.7904 (t80) REVERT: C 208 TYR cc_start: 0.8326 (t80) cc_final: 0.7843 (t80) REVERT: C 274 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.6213 (mp0) REVERT: C 305 LYS cc_start: 0.8553 (tttm) cc_final: 0.8161 (tmtt) REVERT: C 310 LYS cc_start: 0.7168 (ttpt) cc_final: 0.6352 (tptm) REVERT: C 322 LYS cc_start: 0.7395 (pttm) cc_final: 0.6650 (mptt) REVERT: C 353 PRO cc_start: 0.9374 (Cg_endo) cc_final: 0.9163 (Cg_exo) REVERT: D 65 ASN cc_start: 0.7589 (p0) cc_final: 0.7091 (p0) REVERT: D 105 TYR cc_start: 0.7731 (OUTLIER) cc_final: 0.7342 (m-10) REVERT: D 153 ASP cc_start: 0.8803 (m-30) cc_final: 0.8345 (m-30) REVERT: D 183 LYS cc_start: 0.9106 (ttpt) cc_final: 0.8897 (ttpt) REVERT: D 192 TYR cc_start: 0.9039 (t80) cc_final: 0.8839 (t80) REVERT: D 206 GLN cc_start: 0.8917 (mm-40) cc_final: 0.8388 (mm-40) REVERT: D 208 TYR cc_start: 0.8459 (t80) cc_final: 0.8087 (t80) REVERT: D 274 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.6096 (mp0) REVERT: D 310 LYS cc_start: 0.7297 (ttpt) cc_final: 0.6823 (tptt) REVERT: D 315 TYR cc_start: 0.8369 (m-10) cc_final: 0.7627 (m-10) REVERT: D 322 LYS cc_start: 0.7603 (pttm) cc_final: 0.6823 (mptt) REVERT: D 332 SER cc_start: 0.9181 (m) cc_final: 0.8970 (t) REVERT: D 359 ILE cc_start: 0.9390 (tp) cc_final: 0.9129 (tp) REVERT: E 70 ASN cc_start: 0.8946 (t0) cc_final: 0.8535 (t0) REVERT: E 129 MET cc_start: 0.8199 (tpp) cc_final: 0.7967 (tpp) REVERT: E 153 ASP cc_start: 0.8783 (m-30) cc_final: 0.8491 (m-30) REVERT: E 157 LYS cc_start: 0.8309 (tptt) cc_final: 0.7742 (ttmm) REVERT: E 158 PHE cc_start: 0.8192 (OUTLIER) cc_final: 0.7922 (t80) REVERT: E 206 GLN cc_start: 0.9254 (mm-40) cc_final: 0.8314 (mm-40) REVERT: E 208 TYR cc_start: 0.8246 (t80) cc_final: 0.7766 (t80) REVERT: E 274 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.6406 (mp0) REVERT: E 305 LYS cc_start: 0.8568 (tttm) cc_final: 0.8056 (tmtt) REVERT: E 310 LYS cc_start: 0.7198 (ttpt) cc_final: 0.6575 (tptt) REVERT: E 322 LYS cc_start: 0.7397 (pttm) cc_final: 0.6586 (mptt) REVERT: E 353 PRO cc_start: 0.9341 (Cg_endo) cc_final: 0.9133 (Cg_exo) REVERT: F 65 ASN cc_start: 0.7647 (p0) cc_final: 0.7233 (p0) REVERT: F 105 TYR cc_start: 0.7832 (OUTLIER) cc_final: 0.7343 (m-10) REVERT: F 137 LEU cc_start: 0.9163 (tt) cc_final: 0.8943 (tt) REVERT: F 153 ASP cc_start: 0.8835 (m-30) cc_final: 0.8413 (m-30) REVERT: F 157 LYS cc_start: 0.8108 (tptt) cc_final: 0.7516 (ttmm) REVERT: F 158 PHE cc_start: 0.7943 (OUTLIER) cc_final: 0.7680 (t80) REVERT: F 206 GLN cc_start: 0.8963 (mm-40) cc_final: 0.8524 (mm-40) REVERT: F 274 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.6234 (mp0) REVERT: F 304 ASN cc_start: 0.8496 (t0) cc_final: 0.8010 (t0) REVERT: F 310 LYS cc_start: 0.7337 (ttpt) cc_final: 0.6894 (tptt) REVERT: F 322 LYS cc_start: 0.7675 (pttm) cc_final: 0.6939 (mptt) REVERT: F 332 SER cc_start: 0.9245 (m) cc_final: 0.8970 (t) REVERT: G 70 ASN cc_start: 0.8943 (t0) cc_final: 0.8558 (t0) REVERT: G 123 ARG cc_start: 0.8407 (ttm170) cc_final: 0.8080 (ttp-170) REVERT: G 153 ASP cc_start: 0.8782 (m-30) cc_final: 0.8494 (m-30) REVERT: G 154 LYS cc_start: 0.8812 (mtmt) cc_final: 0.8312 (mtpt) REVERT: G 157 LYS cc_start: 0.8296 (tptt) cc_final: 0.7502 (ttpp) REVERT: G 158 PHE cc_start: 0.8182 (OUTLIER) cc_final: 0.7764 (t80) REVERT: G 208 TYR cc_start: 0.8295 (t80) cc_final: 0.7827 (t80) REVERT: G 274 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.6344 (mp0) REVERT: G 305 LYS cc_start: 0.8619 (tttm) cc_final: 0.8197 (tmtt) REVERT: G 310 LYS cc_start: 0.7150 (ttpt) cc_final: 0.6420 (tptm) REVERT: G 322 LYS cc_start: 0.7360 (pttm) cc_final: 0.6536 (mptt) REVERT: H 65 ASN cc_start: 0.7418 (p0) cc_final: 0.6878 (p0) REVERT: H 105 TYR cc_start: 0.7847 (OUTLIER) cc_final: 0.7367 (m-10) REVERT: H 137 LEU cc_start: 0.9233 (tt) cc_final: 0.9013 (tt) REVERT: H 146 ARG cc_start: 0.8958 (ttp80) cc_final: 0.8274 (mtp-110) REVERT: H 153 ASP cc_start: 0.8698 (m-30) cc_final: 0.8308 (m-30) REVERT: H 157 LYS cc_start: 0.8221 (tptt) cc_final: 0.7633 (ttmm) REVERT: H 158 PHE cc_start: 0.7908 (OUTLIER) cc_final: 0.7641 (t80) REVERT: H 199 GLN cc_start: 0.8183 (tp40) cc_final: 0.7760 (tt0) REVERT: H 208 TYR cc_start: 0.8528 (t80) cc_final: 0.8161 (t80) REVERT: H 229 ASP cc_start: 0.8629 (m-30) cc_final: 0.8383 (m-30) REVERT: H 274 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.6121 (mp0) REVERT: H 305 LYS cc_start: 0.8561 (tttm) cc_final: 0.8233 (tmtt) REVERT: H 310 LYS cc_start: 0.7310 (ttpt) cc_final: 0.6638 (tptt) REVERT: H 313 LYS cc_start: 0.9361 (ttmt) cc_final: 0.9108 (ttmm) REVERT: H 315 TYR cc_start: 0.8332 (m-10) cc_final: 0.7567 (m-10) REVERT: H 322 LYS cc_start: 0.7821 (pttm) cc_final: 0.7064 (mptt) REVERT: H 331 PHE cc_start: 0.9030 (m-10) cc_final: 0.8754 (m-10) REVERT: H 359 ILE cc_start: 0.9444 (tp) cc_final: 0.9102 (tp) outliers start: 104 outliers final: 67 residues processed: 809 average time/residue: 0.3413 time to fit residues: 418.1166 Evaluate side-chains 806 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 722 time to evaluate : 2.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 50 HIS Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 50 HIS Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 158 PHE Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 265 CYS Chi-restraints excluded: chain C residue 274 GLU Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 360 SER Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 50 HIS Chi-restraints excluded: chain D residue 105 TYR Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 274 GLU Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 137 LEU Chi-restraints excluded: chain E residue 158 PHE Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 226 ILE Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 360 SER Chi-restraints excluded: chain F residue 50 HIS Chi-restraints excluded: chain F residue 105 TYR Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain F residue 158 PHE Chi-restraints excluded: chain F residue 162 LEU Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain F residue 229 ASP Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 274 GLU Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain F residue 299 ILE Chi-restraints excluded: chain F residue 360 SER Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 50 HIS Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain G residue 158 PHE Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 274 GLU Chi-restraints excluded: chain G residue 299 ILE Chi-restraints excluded: chain G residue 360 SER Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 105 TYR Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 158 PHE Chi-restraints excluded: chain H residue 162 LEU Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 274 GLU Chi-restraints excluded: chain H residue 284 LEU Chi-restraints excluded: chain H residue 285 VAL Chi-restraints excluded: chain H residue 332 SER Chi-restraints excluded: chain H residue 360 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 72.1834 > 50: distance: 5 - 21: 36.667 distance: 10 - 29: 28.350 distance: 14 - 35: 34.393 distance: 17 - 21: 35.200 distance: 18 - 41: 28.003 distance: 22 - 23: 39.724 distance: 22 - 25: 57.482 distance: 23 - 24: 69.314 distance: 23 - 29: 10.965 distance: 24 - 51: 54.092 distance: 25 - 26: 56.412 distance: 26 - 27: 67.881 distance: 26 - 28: 69.212 distance: 29 - 30: 41.960 distance: 30 - 31: 57.394 distance: 30 - 33: 41.356 distance: 31 - 32: 48.483 distance: 32 - 62: 44.104 distance: 33 - 34: 40.172 distance: 35 - 36: 67.903 distance: 36 - 37: 55.974 distance: 36 - 39: 41.705 distance: 37 - 38: 56.890 distance: 37 - 41: 24.123 distance: 38 - 70: 42.715 distance: 39 - 40: 39.611 distance: 41 - 42: 43.946 distance: 42 - 43: 55.268 distance: 42 - 45: 40.852 distance: 43 - 44: 34.146 distance: 43 - 51: 40.788 distance: 45 - 46: 56.897 distance: 46 - 48: 34.823 distance: 47 - 49: 56.509 distance: 48 - 50: 49.694 distance: 49 - 50: 39.217 distance: 51 - 52: 56.524 distance: 52 - 53: 56.929 distance: 52 - 55: 57.961 distance: 53 - 54: 56.321 distance: 53 - 62: 46.910 distance: 56 - 57: 55.652 distance: 56 - 58: 39.452 distance: 57 - 59: 39.935 distance: 58 - 60: 57.476 distance: 59 - 61: 57.700 distance: 62 - 63: 47.729 distance: 63 - 64: 55.799 distance: 63 - 66: 70.570 distance: 64 - 65: 40.949 distance: 64 - 70: 55.951 distance: 66 - 67: 42.886 distance: 66 - 68: 69.361 distance: 67 - 69: 41.765 distance: 70 - 71: 57.425 distance: 71 - 72: 68.979 distance: 72 - 73: 39.642 distance: 72 - 74: 40.997 distance: 74 - 75: 40.201 distance: 75 - 76: 38.552 distance: 75 - 78: 40.093 distance: 76 - 77: 69.257 distance: 76 - 82: 41.216 distance: 78 - 79: 39.905 distance: 82 - 83: 39.781 distance: 82 - 88: 39.826 distance: 83 - 84: 38.778 distance: 84 - 85: 40.043 distance: 84 - 89: 46.693 distance: 86 - 87: 39.140 distance: 87 - 88: 39.149 distance: 89 - 90: 54.619 distance: 90 - 93: 57.277 distance: 91 - 92: 56.561 distance: 91 - 97: 34.178 distance: 93 - 94: 41.028 distance: 93 - 95: 56.082 distance: 94 - 96: 55.765