Starting phenix.real_space_refine on Fri Sep 19 03:56:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/3jd0_6631/09_2025/3jd0_6631.cif Found real_map, /net/cci-nas-00/data/ceres_data/3jd0_6631/09_2025/3jd0_6631.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/3jd0_6631/09_2025/3jd0_6631.map" default_real_map = "/net/cci-nas-00/data/ceres_data/3jd0_6631/09_2025/3jd0_6631.map" model { file = "/net/cci-nas-00/data/ceres_data/3jd0_6631/09_2025/3jd0_6631.cif" } default_model = "/net/cci-nas-00/data/ceres_data/3jd0_6631/09_2025/3jd0_6631.cif" } resolution = 3.47 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.004 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: 5 Type Number sf(0) Gaussians P 18 5.49 5 S 114 5.16 5 C 14784 2.51 5 N 4104 2.21 5 O 4458 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23478 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3881 Classifications: {'peptide': 496} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 474} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, C, D, E, F Time building chain proxies: 3.58, per 1000 atoms: 0.15 Number of scatterers: 23478 At special positions: 0 Unit cell: (111.569, 123.045, 161.298, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 114 16.00 P 18 15.00 O 4458 8.00 N 4104 7.00 C 14784 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.16 Conformation dependent library (CDL) restraints added in 780.8 milliseconds Enol-peptide restraints added in 1.4 microseconds 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5400 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 24 sheets defined 55.7% alpha, 9.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 8 through 29 removed outlier: 3.977A pdb=" N ASP A 26 " --> pdb=" O SER A 22 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N LYS A 27 " --> pdb=" O ILE A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 52 removed outlier: 3.768A pdb=" N SER A 47 " --> pdb=" O ASN A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 118 removed outlier: 3.589A pdb=" N ALA A 106 " --> pdb=" O ASP A 102 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LEU A 107 " --> pdb=" O GLU A 103 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N TYR A 113 " --> pdb=" O SER A 109 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL A 118 " --> pdb=" O LYS A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 136 Processing helix chain 'A' and resid 137 through 155 removed outlier: 3.757A pdb=" N ARG A 146 " --> pdb=" O GLU A 142 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N MET A 150 " --> pdb=" O ARG A 146 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA A 153 " --> pdb=" O THR A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 185 Processing helix chain 'A' and resid 191 through 197 removed outlier: 3.659A pdb=" N HIS A 195 " --> pdb=" O ILE A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 206 removed outlier: 3.748A pdb=" N GLN A 205 " --> pdb=" O PRO A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 228 removed outlier: 4.318A pdb=" N THR A 215 " --> pdb=" O ARG A 211 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N GLY A 216 " --> pdb=" O ILE A 212 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N PHE A 226 " --> pdb=" O GLY A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 234 Processing helix chain 'A' and resid 255 through 266 removed outlier: 3.523A pdb=" N SER A 259 " --> pdb=" O VAL A 255 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N PHE A 266 " --> pdb=" O TYR A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 298 removed outlier: 3.519A pdb=" N PHE A 294 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU A 296 " --> pdb=" O GLU A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 317 Processing helix chain 'A' and resid 353 through 364 Processing helix chain 'A' and resid 369 through 374 removed outlier: 3.601A pdb=" N LEU A 373 " --> pdb=" O PRO A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 388 removed outlier: 4.170A pdb=" N SER A 381 " --> pdb=" O GLY A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 421 removed outlier: 4.719A pdb=" N LEU A 410 " --> pdb=" O ASN A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 442 Processing helix chain 'A' and resid 444 through 472 removed outlier: 3.626A pdb=" N ILE A 448 " --> pdb=" O SER A 444 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N THR A 456 " --> pdb=" O GLY A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 495 Processing helix chain 'B' and resid 8 through 29 removed outlier: 3.977A pdb=" N ASP B 26 " --> pdb=" O SER B 22 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N LYS B 27 " --> pdb=" O ILE B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 52 removed outlier: 3.767A pdb=" N SER B 47 " --> pdb=" O ASN B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 118 removed outlier: 3.589A pdb=" N ALA B 106 " --> pdb=" O ASP B 102 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LEU B 107 " --> pdb=" O GLU B 103 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N TYR B 113 " --> pdb=" O SER B 109 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL B 118 " --> pdb=" O LYS B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 136 Processing helix chain 'B' and resid 137 through 155 removed outlier: 3.758A pdb=" N ARG B 146 " --> pdb=" O GLU B 142 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N MET B 150 " --> pdb=" O ARG B 146 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA B 153 " --> pdb=" O THR B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 185 Processing helix chain 'B' and resid 191 through 197 removed outlier: 3.659A pdb=" N HIS B 195 " --> pdb=" O ILE B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 206 removed outlier: 3.747A pdb=" N GLN B 205 " --> pdb=" O PRO B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 228 removed outlier: 4.317A pdb=" N THR B 215 " --> pdb=" O ARG B 211 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N GLY B 216 " --> pdb=" O ILE B 212 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N PHE B 226 " --> pdb=" O GLY B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 234 Processing helix chain 'B' and resid 255 through 266 removed outlier: 3.523A pdb=" N SER B 259 " --> pdb=" O VAL B 255 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N PHE B 266 " --> pdb=" O TYR B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 298 removed outlier: 3.519A pdb=" N PHE B 294 " --> pdb=" O GLU B 290 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU B 296 " --> pdb=" O GLU B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 317 Processing helix chain 'B' and resid 353 through 364 Processing helix chain 'B' and resid 369 through 374 removed outlier: 3.600A pdb=" N LEU B 373 " --> pdb=" O PRO B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 388 removed outlier: 4.170A pdb=" N SER B 381 " --> pdb=" O GLY B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 421 removed outlier: 4.720A pdb=" N LEU B 410 " --> pdb=" O ASN B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 442 Processing helix chain 'B' and resid 444 through 472 removed outlier: 3.625A pdb=" N ILE B 448 " --> pdb=" O SER B 444 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N THR B 456 " --> pdb=" O GLY B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 495 Processing helix chain 'C' and resid 8 through 29 removed outlier: 3.977A pdb=" N ASP C 26 " --> pdb=" O SER C 22 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N LYS C 27 " --> pdb=" O ILE C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 52 removed outlier: 3.768A pdb=" N SER C 47 " --> pdb=" O ASN C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 118 removed outlier: 3.589A pdb=" N ALA C 106 " --> pdb=" O ASP C 102 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LEU C 107 " --> pdb=" O GLU C 103 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N TYR C 113 " --> pdb=" O SER C 109 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL C 118 " --> pdb=" O LYS C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 136 Processing helix chain 'C' and resid 137 through 155 removed outlier: 3.758A pdb=" N ARG C 146 " --> pdb=" O GLU C 142 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N MET C 150 " --> pdb=" O ARG C 146 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA C 153 " --> pdb=" O THR C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 185 Processing helix chain 'C' and resid 191 through 197 removed outlier: 3.659A pdb=" N HIS C 195 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 206 removed outlier: 3.747A pdb=" N GLN C 205 " --> pdb=" O PRO C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 228 removed outlier: 4.317A pdb=" N THR C 215 " --> pdb=" O ARG C 211 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N GLY C 216 " --> pdb=" O ILE C 212 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N PHE C 226 " --> pdb=" O GLY C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 234 Processing helix chain 'C' and resid 255 through 266 removed outlier: 3.523A pdb=" N SER C 259 " --> pdb=" O VAL C 255 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N PHE C 266 " --> pdb=" O TYR C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 298 removed outlier: 3.519A pdb=" N PHE C 294 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU C 296 " --> pdb=" O GLU C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 317 Processing helix chain 'C' and resid 353 through 364 Processing helix chain 'C' and resid 369 through 374 removed outlier: 3.600A pdb=" N LEU C 373 " --> pdb=" O PRO C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 375 through 388 removed outlier: 4.170A pdb=" N SER C 381 " --> pdb=" O GLY C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 422 removed outlier: 4.720A pdb=" N LEU C 410 " --> pdb=" O ASN C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 442 Processing helix chain 'C' and resid 444 through 472 removed outlier: 3.626A pdb=" N ILE C 448 " --> pdb=" O SER C 444 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N THR C 456 " --> pdb=" O GLY C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 495 Processing helix chain 'D' and resid 8 through 29 removed outlier: 3.977A pdb=" N ASP D 26 " --> pdb=" O SER D 22 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N LYS D 27 " --> pdb=" O ILE D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 52 removed outlier: 3.767A pdb=" N SER D 47 " --> pdb=" O ASN D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 118 removed outlier: 3.589A pdb=" N ALA D 106 " --> pdb=" O ASP D 102 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LEU D 107 " --> pdb=" O GLU D 103 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N TYR D 113 " --> pdb=" O SER D 109 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL D 118 " --> pdb=" O LYS D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 136 Processing helix chain 'D' and resid 137 through 155 removed outlier: 3.757A pdb=" N ARG D 146 " --> pdb=" O GLU D 142 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N MET D 150 " --> pdb=" O ARG D 146 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA D 153 " --> pdb=" O THR D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 185 Processing helix chain 'D' and resid 191 through 197 removed outlier: 3.658A pdb=" N HIS D 195 " --> pdb=" O ILE D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 206 removed outlier: 3.747A pdb=" N GLN D 205 " --> pdb=" O PRO D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 228 removed outlier: 4.318A pdb=" N THR D 215 " --> pdb=" O ARG D 211 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N GLY D 216 " --> pdb=" O ILE D 212 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N PHE D 226 " --> pdb=" O GLY D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 234 Processing helix chain 'D' and resid 255 through 266 removed outlier: 3.522A pdb=" N SER D 259 " --> pdb=" O VAL D 255 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N PHE D 266 " --> pdb=" O TYR D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 298 removed outlier: 3.519A pdb=" N PHE D 294 " --> pdb=" O GLU D 290 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU D 296 " --> pdb=" O GLU D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 317 Processing helix chain 'D' and resid 353 through 364 Processing helix chain 'D' and resid 369 through 374 removed outlier: 3.600A pdb=" N LEU D 373 " --> pdb=" O PRO D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 375 through 388 removed outlier: 4.169A pdb=" N SER D 381 " --> pdb=" O GLY D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 398 through 421 removed outlier: 4.719A pdb=" N LEU D 410 " --> pdb=" O ASN D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 433 through 442 Processing helix chain 'D' and resid 444 through 472 removed outlier: 3.626A pdb=" N ILE D 448 " --> pdb=" O SER D 444 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N THR D 456 " --> pdb=" O GLY D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 476 through 495 Processing helix chain 'E' and resid 8 through 29 removed outlier: 3.977A pdb=" N ASP E 26 " --> pdb=" O SER E 22 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N LYS E 27 " --> pdb=" O ILE E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 52 removed outlier: 3.768A pdb=" N SER E 47 " --> pdb=" O ASN E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 118 removed outlier: 3.589A pdb=" N ALA E 106 " --> pdb=" O ASP E 102 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LEU E 107 " --> pdb=" O GLU E 103 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N TYR E 113 " --> pdb=" O SER E 109 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL E 118 " --> pdb=" O LYS E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 136 Processing helix chain 'E' and resid 137 through 155 removed outlier: 3.758A pdb=" N ARG E 146 " --> pdb=" O GLU E 142 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N MET E 150 " --> pdb=" O ARG E 146 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA E 153 " --> pdb=" O THR E 149 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 185 Processing helix chain 'E' and resid 191 through 197 removed outlier: 3.659A pdb=" N HIS E 195 " --> pdb=" O ILE E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 206 removed outlier: 3.748A pdb=" N GLN E 205 " --> pdb=" O PRO E 202 " (cutoff:3.500A) Processing helix chain 'E' and resid 210 through 228 removed outlier: 4.318A pdb=" N THR E 215 " --> pdb=" O ARG E 211 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N GLY E 216 " --> pdb=" O ILE E 212 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N PHE E 226 " --> pdb=" O GLY E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 234 Processing helix chain 'E' and resid 255 through 266 removed outlier: 3.522A pdb=" N SER E 259 " --> pdb=" O VAL E 255 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N PHE E 266 " --> pdb=" O TYR E 262 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 298 removed outlier: 3.519A pdb=" N PHE E 294 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU E 296 " --> pdb=" O GLU E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 313 through 317 Processing helix chain 'E' and resid 353 through 364 Processing helix chain 'E' and resid 369 through 374 removed outlier: 3.600A pdb=" N LEU E 373 " --> pdb=" O PRO E 369 " (cutoff:3.500A) Processing helix chain 'E' and resid 375 through 388 removed outlier: 4.170A pdb=" N SER E 381 " --> pdb=" O GLY E 377 " (cutoff:3.500A) Processing helix chain 'E' and resid 398 through 421 removed outlier: 4.720A pdb=" N LEU E 410 " --> pdb=" O ASN E 406 " (cutoff:3.500A) Processing helix chain 'E' and resid 433 through 442 Processing helix chain 'E' and resid 444 through 472 removed outlier: 3.626A pdb=" N ILE E 448 " --> pdb=" O SER E 444 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N THR E 456 " --> pdb=" O GLY E 452 " (cutoff:3.500A) Processing helix chain 'E' and resid 476 through 495 Processing helix chain 'F' and resid 8 through 29 removed outlier: 3.977A pdb=" N ASP F 26 " --> pdb=" O SER F 22 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N LYS F 27 " --> pdb=" O ILE F 23 " (cutoff:3.500A) Processing helix chain 'F' and resid 37 through 52 removed outlier: 3.768A pdb=" N SER F 47 " --> pdb=" O ASN F 43 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 118 removed outlier: 3.589A pdb=" N ALA F 106 " --> pdb=" O ASP F 102 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LEU F 107 " --> pdb=" O GLU F 103 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N TYR F 113 " --> pdb=" O SER F 109 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL F 118 " --> pdb=" O LYS F 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 136 Processing helix chain 'F' and resid 137 through 155 removed outlier: 3.758A pdb=" N ARG F 146 " --> pdb=" O GLU F 142 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N MET F 150 " --> pdb=" O ARG F 146 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA F 153 " --> pdb=" O THR F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 185 Processing helix chain 'F' and resid 191 through 197 removed outlier: 3.659A pdb=" N HIS F 195 " --> pdb=" O ILE F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 202 through 206 removed outlier: 3.747A pdb=" N GLN F 205 " --> pdb=" O PRO F 202 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 228 removed outlier: 4.318A pdb=" N THR F 215 " --> pdb=" O ARG F 211 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N GLY F 216 " --> pdb=" O ILE F 212 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N PHE F 226 " --> pdb=" O GLY F 222 " (cutoff:3.500A) Processing helix chain 'F' and resid 229 through 234 Processing helix chain 'F' and resid 255 through 266 removed outlier: 3.522A pdb=" N SER F 259 " --> pdb=" O VAL F 255 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N PHE F 266 " --> pdb=" O TYR F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 287 through 298 removed outlier: 3.519A pdb=" N PHE F 294 " --> pdb=" O GLU F 290 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU F 296 " --> pdb=" O GLU F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 317 Processing helix chain 'F' and resid 353 through 364 Processing helix chain 'F' and resid 369 through 374 removed outlier: 3.600A pdb=" N LEU F 373 " --> pdb=" O PRO F 369 " (cutoff:3.500A) Processing helix chain 'F' and resid 375 through 388 removed outlier: 4.170A pdb=" N SER F 381 " --> pdb=" O GLY F 377 " (cutoff:3.500A) Processing helix chain 'F' and resid 398 through 422 removed outlier: 4.720A pdb=" N LEU F 410 " --> pdb=" O ASN F 406 " (cutoff:3.500A) Processing helix chain 'F' and resid 433 through 442 Processing helix chain 'F' and resid 444 through 472 removed outlier: 3.626A pdb=" N ILE F 448 " --> pdb=" O SER F 444 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N THR F 456 " --> pdb=" O GLY F 452 " (cutoff:3.500A) Processing helix chain 'F' and resid 476 through 495 Processing sheet with id=A, first strand: chain 'A' and resid 93 through 96 Processing sheet with id=B, first strand: chain 'A' and resid 163 through 164 removed outlier: 6.830A pdb=" N CYS A 89 " --> pdb=" O VAL A 164 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N CYS E 89 " --> pdb=" O VAL E 164 " (cutoff:3.500A) Processing sheet with id=C, first strand: chain 'A' and resid 63 through 66 Processing sheet with id=D, first strand: chain 'A' and resid 246 through 247 Processing sheet with id=E, first strand: chain 'A' and resid 272 through 275 removed outlier: 3.831A pdb=" N VAL A 273 " --> pdb=" O ILE A 280 " (cutoff:3.500A) Processing sheet with id=F, first strand: chain 'B' and resid 93 through 96 Processing sheet with id=G, first strand: chain 'B' and resid 163 through 164 removed outlier: 6.831A pdb=" N CYS B 89 " --> pdb=" O VAL B 164 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N CYS D 89 " --> pdb=" O VAL D 164 " (cutoff:3.500A) Processing sheet with id=H, first strand: chain 'B' and resid 63 through 66 Processing sheet with id=I, first strand: chain 'B' and resid 246 through 247 Processing sheet with id=J, first strand: chain 'B' and resid 272 through 275 removed outlier: 3.832A pdb=" N VAL B 273 " --> pdb=" O ILE B 280 " (cutoff:3.500A) Processing sheet with id=K, first strand: chain 'C' and resid 93 through 96 Processing sheet with id=L, first strand: chain 'C' and resid 163 through 164 removed outlier: 6.830A pdb=" N CYS C 89 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N CYS F 89 " --> pdb=" O VAL F 164 " (cutoff:3.500A) Processing sheet with id=M, first strand: chain 'C' and resid 63 through 66 Processing sheet with id=N, first strand: chain 'C' and resid 246 through 247 Processing sheet with id=O, first strand: chain 'C' and resid 272 through 275 removed outlier: 3.831A pdb=" N VAL C 273 " --> pdb=" O ILE C 280 " (cutoff:3.500A) Processing sheet with id=P, first strand: chain 'D' and resid 63 through 66 Processing sheet with id=Q, first strand: chain 'D' and resid 246 through 247 Processing sheet with id=R, first strand: chain 'D' and resid 272 through 275 removed outlier: 3.832A pdb=" N VAL D 273 " --> pdb=" O ILE D 280 " (cutoff:3.500A) Processing sheet with id=S, first strand: chain 'E' and resid 63 through 66 Processing sheet with id=T, first strand: chain 'E' and resid 246 through 247 Processing sheet with id=U, first strand: chain 'E' and resid 272 through 275 removed outlier: 3.832A pdb=" N VAL E 273 " --> pdb=" O ILE E 280 " (cutoff:3.500A) Processing sheet with id=V, first strand: chain 'F' and resid 63 through 66 Processing sheet with id=W, first strand: chain 'F' and resid 246 through 247 Processing sheet with id=X, first strand: chain 'F' and resid 272 through 275 removed outlier: 3.832A pdb=" N VAL F 273 " --> pdb=" O ILE F 280 " (cutoff:3.500A) 1256 hydrogen bonds defined for protein. 3552 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: 3.87 Time building geometry restraints manager: 2.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7782 1.34 - 1.46: 5523 1.46 - 1.58: 10461 1.58 - 1.69: 30 1.69 - 1.81: 192 Bond restraints: 23988 Sorted by residual: bond pdb=" CB VAL D 449 " pdb=" CG1 VAL D 449 " ideal model delta sigma weight residual 1.521 1.451 0.070 3.30e-02 9.18e+02 4.51e+00 bond pdb=" CB VAL E 449 " pdb=" CG1 VAL E 449 " ideal model delta sigma weight residual 1.521 1.451 0.070 3.30e-02 9.18e+02 4.50e+00 bond pdb=" CB VAL A 449 " pdb=" CG1 VAL A 449 " ideal model delta sigma weight residual 1.521 1.452 0.069 3.30e-02 9.18e+02 4.42e+00 bond pdb=" CB VAL B 449 " pdb=" CG1 VAL B 449 " ideal model delta sigma weight residual 1.521 1.452 0.069 3.30e-02 9.18e+02 4.40e+00 bond pdb=" CB VAL C 449 " pdb=" CG1 VAL C 449 " ideal model delta sigma weight residual 1.521 1.452 0.069 3.30e-02 9.18e+02 4.35e+00 ... (remaining 23983 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 31204 1.87 - 3.75: 1130 3.75 - 5.62: 90 5.62 - 7.49: 6 7.49 - 9.36: 12 Bond angle restraints: 32442 Sorted by residual: angle pdb=" CA LEU B 371 " pdb=" CB LEU B 371 " pdb=" CG LEU B 371 " ideal model delta sigma weight residual 116.30 125.66 -9.36 3.50e+00 8.16e-02 7.16e+00 angle pdb=" CA LEU C 371 " pdb=" CB LEU C 371 " pdb=" CG LEU C 371 " ideal model delta sigma weight residual 116.30 125.65 -9.35 3.50e+00 8.16e-02 7.14e+00 angle pdb=" CA LEU E 371 " pdb=" CB LEU E 371 " pdb=" CG LEU E 371 " ideal model delta sigma weight residual 116.30 125.64 -9.34 3.50e+00 8.16e-02 7.13e+00 angle pdb=" CA LEU A 371 " pdb=" CB LEU A 371 " pdb=" CG LEU A 371 " ideal model delta sigma weight residual 116.30 125.64 -9.34 3.50e+00 8.16e-02 7.12e+00 angle pdb=" CA LEU D 371 " pdb=" CB LEU D 371 " pdb=" CG LEU D 371 " ideal model delta sigma weight residual 116.30 125.64 -9.34 3.50e+00 8.16e-02 7.12e+00 ... (remaining 32437 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.85: 14268 35.85 - 71.71: 42 71.71 - 107.56: 6 107.56 - 143.41: 6 143.41 - 179.27: 12 Dihedral angle restraints: 14334 sinusoidal: 5856 harmonic: 8478 Sorted by residual: dihedral pdb=" C5' GTP F 601 " pdb=" O5' GTP F 601 " pdb=" PA GTP F 601 " pdb=" O3A GTP F 601 " ideal model delta sinusoidal sigma weight residual 69.27 -110.00 179.27 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' GTP D 601 " pdb=" O5' GTP D 601 " pdb=" PA GTP D 601 " pdb=" O3A GTP D 601 " ideal model delta sinusoidal sigma weight residual 69.27 -109.99 179.26 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' GTP E 601 " pdb=" O5' GTP E 601 " pdb=" PA GTP E 601 " pdb=" O3A GTP E 601 " ideal model delta sinusoidal sigma weight residual 69.27 -109.98 179.25 1 2.00e+01 2.50e-03 4.80e+01 ... (remaining 14331 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1725 0.029 - 0.058: 943 0.058 - 0.087: 516 0.087 - 0.116: 213 0.116 - 0.145: 119 Chirality restraints: 3516 Sorted by residual: chirality pdb=" CB THR F 456 " pdb=" CA THR F 456 " pdb=" OG1 THR F 456 " pdb=" CG2 THR F 456 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.15 2.00e-01 2.50e+01 5.27e-01 chirality pdb=" CA TYR E 407 " pdb=" N TYR E 407 " pdb=" C TYR E 407 " pdb=" CB TYR E 407 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.19e-01 chirality pdb=" CB THR A 456 " pdb=" CA THR A 456 " pdb=" OG1 THR A 456 " pdb=" CG2 THR A 456 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.14 2.00e-01 2.50e+01 5.17e-01 ... (remaining 3513 not shown) Planarity restraints: 4194 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA E 166 " 0.037 5.00e-02 4.00e+02 5.55e-02 4.92e+00 pdb=" N PRO E 167 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO E 167 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO E 167 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA F 166 " -0.037 5.00e-02 4.00e+02 5.54e-02 4.91e+00 pdb=" N PRO F 167 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO F 167 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO F 167 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 166 " 0.037 5.00e-02 4.00e+02 5.52e-02 4.88e+00 pdb=" N PRO C 167 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO C 167 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 167 " 0.030 5.00e-02 4.00e+02 ... (remaining 4191 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 423 2.57 - 3.15: 23944 3.15 - 3.74: 34965 3.74 - 4.32: 54461 4.32 - 4.90: 85304 Nonbonded interactions: 199097 Sorted by model distance: nonbonded pdb=" O LEU B 409 " pdb=" OG SER B 412 " model vdw 1.989 3.040 nonbonded pdb=" O LEU E 409 " pdb=" OG SER E 412 " model vdw 1.989 3.040 nonbonded pdb=" O LEU A 409 " pdb=" OG SER A 412 " model vdw 1.989 3.040 nonbonded pdb=" O LEU C 409 " pdb=" OG SER C 412 " model vdw 1.989 3.040 nonbonded pdb=" O LEU F 409 " pdb=" OG SER F 412 " model vdw 1.989 3.040 ... (remaining 199092 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.080 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: 0.010 Extract box with map and model: 0.500 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 18.660 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 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 : 0.012 0.072 23988 Z= 0.510 Angle : 0.817 9.363 32442 Z= 0.478 Chirality : 0.050 0.145 3516 Planarity : 0.005 0.055 4194 Dihedral : 10.314 179.267 8934 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.81 % Allowed : 13.26 % Favored : 85.93 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.89 (0.10), residues: 2964 helix: -4.31 (0.07), residues: 1488 sheet: -2.62 (0.24), residues: 330 loop : -3.45 (0.14), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 147 TYR 0.013 0.002 TYR F 382 PHE 0.020 0.002 PHE F 421 TRP 0.014 0.002 TRP D 281 HIS 0.007 0.002 HIS A 57 Details of bonding type rmsd covalent geometry : bond 0.01189 (23988) covalent geometry : angle 0.81728 (32442) hydrogen bonds : bond 0.26858 ( 1196) hydrogen bonds : angle 10.63518 ( 3552) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 532 time to evaluate : 0.888 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 LEU cc_start: 0.8193 (mp) cc_final: 0.7822 (mm) REVERT: A 364 ASN cc_start: 0.8465 (t0) cc_final: 0.8259 (t0) REVERT: B 187 ILE cc_start: 0.8347 (mm) cc_final: 0.8146 (mm) REVERT: B 384 GLU cc_start: 0.8034 (tt0) cc_final: 0.7749 (tt0) REVERT: C 315 LEU cc_start: 0.8203 (mp) cc_final: 0.7992 (mm) REVERT: D 315 LEU cc_start: 0.8188 (mp) cc_final: 0.7830 (mm) REVERT: D 364 ASN cc_start: 0.8463 (t0) cc_final: 0.8258 (t0) REVERT: E 384 GLU cc_start: 0.8036 (tt0) cc_final: 0.7752 (tt0) REVERT: F 315 LEU cc_start: 0.8203 (mp) cc_final: 0.7995 (mm) outliers start: 0 outliers final: 0 residues processed: 532 average time/residue: 0.1758 time to fit residues: 139.5970 Evaluate side-chains 264 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 264 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 6.9990 chunk 111 optimal weight: 5.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 408 HIS B 388 ASN B 408 HIS C 408 HIS ** D 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 408 HIS E 388 ASN E 408 HIS F 408 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.097870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.074960 restraints weight = 59673.456| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 3.91 r_work: 0.3109 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.3274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 23988 Z= 0.183 Angle : 0.744 9.926 32442 Z= 0.379 Chirality : 0.046 0.177 3516 Planarity : 0.005 0.043 4194 Dihedral : 13.154 169.279 3342 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.40 % Allowed : 5.40 % Favored : 94.20 % Rotamer: Outliers : 1.60 % Allowed : 5.57 % Favored : 92.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.27 (0.14), residues: 2964 helix: -0.98 (0.12), residues: 1506 sheet: -2.09 (0.24), residues: 342 loop : -1.85 (0.17), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 338 TYR 0.026 0.002 TYR D 407 PHE 0.029 0.003 PHE D 16 TRP 0.016 0.002 TRP C 72 HIS 0.014 0.002 HIS D 189 Details of bonding type rmsd covalent geometry : bond 0.00428 (23988) covalent geometry : angle 0.74352 (32442) hydrogen bonds : bond 0.04848 ( 1196) hydrogen bonds : angle 5.49154 ( 3552) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 332 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 ASP cc_start: 0.8684 (t0) cc_final: 0.8444 (t0) REVERT: A 190 TYR cc_start: 0.6995 (OUTLIER) cc_final: 0.6634 (m-80) REVERT: A 364 ASN cc_start: 0.8718 (t0) cc_final: 0.8449 (t0) REVERT: A 384 GLU cc_start: 0.8746 (tt0) cc_final: 0.8540 (tt0) REVERT: B 190 TYR cc_start: 0.7134 (OUTLIER) cc_final: 0.6737 (m-80) REVERT: B 281 TRP cc_start: 0.8542 (t60) cc_final: 0.8294 (t60) REVERT: B 384 GLU cc_start: 0.8772 (tt0) cc_final: 0.8423 (tt0) REVERT: C 12 MET cc_start: 0.8875 (mtm) cc_final: 0.8392 (mtm) REVERT: C 169 MET cc_start: 0.8985 (mmp) cc_final: 0.8773 (mmt) REVERT: C 181 ASP cc_start: 0.8690 (t0) cc_final: 0.8281 (t0) REVERT: C 190 TYR cc_start: 0.7066 (OUTLIER) cc_final: 0.6667 (m-80) REVERT: C 330 GLN cc_start: 0.8893 (tm-30) cc_final: 0.8655 (tm-30) REVERT: C 421 PHE cc_start: 0.8048 (p90) cc_final: 0.7550 (p90) REVERT: D 181 ASP cc_start: 0.8695 (t0) cc_final: 0.8452 (t0) REVERT: D 190 TYR cc_start: 0.7046 (OUTLIER) cc_final: 0.6705 (m-80) REVERT: D 364 ASN cc_start: 0.8715 (t0) cc_final: 0.8450 (t0) REVERT: D 384 GLU cc_start: 0.8766 (tt0) cc_final: 0.8556 (tt0) REVERT: E 190 TYR cc_start: 0.7142 (OUTLIER) cc_final: 0.6770 (m-80) REVERT: E 281 TRP cc_start: 0.8550 (t60) cc_final: 0.8301 (t60) REVERT: E 384 GLU cc_start: 0.8771 (tt0) cc_final: 0.8424 (tt0) REVERT: F 12 MET cc_start: 0.8877 (mtm) cc_final: 0.8401 (mtm) REVERT: F 169 MET cc_start: 0.8972 (mmp) cc_final: 0.8758 (mmt) REVERT: F 181 ASP cc_start: 0.8691 (t0) cc_final: 0.8279 (t0) REVERT: F 190 TYR cc_start: 0.7107 (OUTLIER) cc_final: 0.6714 (m-80) REVERT: F 330 GLN cc_start: 0.8891 (tm-30) cc_final: 0.8652 (tm-30) REVERT: F 421 PHE cc_start: 0.8051 (p90) cc_final: 0.7554 (p90) outliers start: 40 outliers final: 20 residues processed: 356 average time/residue: 0.1300 time to fit residues: 77.3030 Evaluate side-chains 263 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 237 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 TYR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain B residue 190 TYR Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain C residue 190 TYR Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain C residue 411 MET Chi-restraints excluded: chain D residue 190 TYR Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 393 SER Chi-restraints excluded: chain E residue 190 TYR Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 314 ILE Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain F residue 190 TYR Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 273 VAL Chi-restraints excluded: chain F residue 393 SER Chi-restraints excluded: chain F residue 411 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 18 optimal weight: 20.0000 chunk 36 optimal weight: 0.9990 chunk 188 optimal weight: 8.9990 chunk 94 optimal weight: 9.9990 chunk 130 optimal weight: 20.0000 chunk 137 optimal weight: 7.9990 chunk 216 optimal weight: 9.9990 chunk 280 optimal weight: 7.9990 chunk 55 optimal weight: 0.0670 chunk 201 optimal weight: 7.9990 chunk 51 optimal weight: 20.0000 overall best weight: 5.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 GLN ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 135 ASN ** C 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 GLN ** D 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 40 GLN ** E 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.095464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.072111 restraints weight = 60599.337| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 3.91 r_work: 0.3045 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.3986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 23988 Z= 0.197 Angle : 0.699 10.254 32442 Z= 0.350 Chirality : 0.046 0.196 3516 Planarity : 0.005 0.048 4194 Dihedral : 12.817 163.191 3342 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.93 % Favored : 94.87 % Rotamer: Outliers : 1.52 % Allowed : 7.09 % Favored : 91.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.75 (0.15), residues: 2964 helix: 0.48 (0.13), residues: 1548 sheet: -1.61 (0.28), residues: 282 loop : -1.51 (0.18), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 79 TYR 0.026 0.002 TYR C 407 PHE 0.024 0.003 PHE D 360 TRP 0.019 0.003 TRP C 72 HIS 0.011 0.001 HIS E 189 Details of bonding type rmsd covalent geometry : bond 0.00458 (23988) covalent geometry : angle 0.69863 (32442) hydrogen bonds : bond 0.04015 ( 1196) hydrogen bonds : angle 4.93545 ( 3552) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 306 time to evaluate : 0.942 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: A 119 ASP cc_start: 0.9209 (OUTLIER) cc_final: 0.8971 (m-30) REVERT: A 181 ASP cc_start: 0.8869 (t0) cc_final: 0.8537 (t0) REVERT: A 281 TRP cc_start: 0.8391 (t60) cc_final: 0.8155 (t60) REVERT: A 330 GLN cc_start: 0.8922 (tm-30) cc_final: 0.8650 (tm-30) REVERT: A 364 ASN cc_start: 0.8822 (t0) cc_final: 0.8585 (t0) REVERT: A 384 GLU cc_start: 0.8833 (tt0) cc_final: 0.8576 (tt0) REVERT: B 190 TYR cc_start: 0.7201 (p90) cc_final: 0.6948 (m-80) REVERT: B 384 GLU cc_start: 0.8859 (tt0) cc_final: 0.8559 (tt0) REVERT: B 421 PHE cc_start: 0.8034 (p90) cc_final: 0.7191 (p90) REVERT: C 12 MET cc_start: 0.8776 (mtm) cc_final: 0.8306 (mtm) REVERT: C 181 ASP cc_start: 0.8873 (t0) cc_final: 0.8393 (t0) REVERT: C 190 TYR cc_start: 0.7202 (p90) cc_final: 0.6935 (m-80) REVERT: C 205 GLN cc_start: 0.8584 (mp10) cc_final: 0.8368 (mp10) REVERT: C 330 GLN cc_start: 0.8953 (tm-30) cc_final: 0.8685 (tm-30) REVERT: C 411 MET cc_start: 0.9154 (OUTLIER) cc_final: 0.8860 (tpp) REVERT: C 421 PHE cc_start: 0.7962 (p90) cc_final: 0.7733 (p90) REVERT: D 119 ASP cc_start: 0.9188 (OUTLIER) cc_final: 0.8952 (m-30) REVERT: D 181 ASP cc_start: 0.8872 (t0) cc_final: 0.8542 (t0) REVERT: D 281 TRP cc_start: 0.8405 (t60) cc_final: 0.8160 (t60) REVERT: D 330 GLN cc_start: 0.8925 (tm-30) cc_final: 0.8654 (tm-30) REVERT: D 364 ASN cc_start: 0.8803 (t0) cc_final: 0.8562 (t0) REVERT: D 384 GLU cc_start: 0.8848 (tt0) cc_final: 0.8592 (tt0) REVERT: E 190 TYR cc_start: 0.7227 (p90) cc_final: 0.6969 (m-80) REVERT: E 384 GLU cc_start: 0.8851 (tt0) cc_final: 0.8550 (tt0) REVERT: E 421 PHE cc_start: 0.8032 (p90) cc_final: 0.7189 (p90) REVERT: F 12 MET cc_start: 0.8776 (mtm) cc_final: 0.8307 (mtm) REVERT: F 181 ASP cc_start: 0.8880 (t0) cc_final: 0.8397 (t0) REVERT: F 190 TYR cc_start: 0.7215 (p90) cc_final: 0.6948 (m-80) REVERT: F 330 GLN cc_start: 0.8954 (tm-30) cc_final: 0.8686 (tm-30) REVERT: F 411 MET cc_start: 0.9160 (OUTLIER) cc_final: 0.8870 (tpp) REVERT: F 421 PHE cc_start: 0.7972 (p90) cc_final: 0.7744 (p90) outliers start: 38 outliers final: 19 residues processed: 329 average time/residue: 0.1337 time to fit residues: 73.9299 Evaluate side-chains 266 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 243 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain C residue 407 TYR Chi-restraints excluded: chain C residue 411 MET Chi-restraints excluded: chain D residue 119 ASP Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 393 SER Chi-restraints excluded: chain D residue 460 SER Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain F residue 236 LEU Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 393 SER Chi-restraints excluded: chain F residue 407 TYR Chi-restraints excluded: chain F residue 411 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 175 optimal weight: 4.9990 chunk 190 optimal weight: 2.9990 chunk 42 optimal weight: 40.0000 chunk 145 optimal weight: 10.0000 chunk 265 optimal weight: 4.9990 chunk 130 optimal weight: 10.0000 chunk 266 optimal weight: 7.9990 chunk 95 optimal weight: 6.9990 chunk 70 optimal weight: 6.9990 chunk 25 optimal weight: 0.9990 chunk 284 optimal weight: 0.0870 overall best weight: 2.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 391 HIS B 391 HIS ** C 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 391 HIS E 391 HIS ** F 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.096623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.073487 restraints weight = 59832.870| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 3.88 r_work: 0.3067 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.4434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23988 Z= 0.140 Angle : 0.647 9.011 32442 Z= 0.325 Chirality : 0.044 0.183 3516 Planarity : 0.004 0.053 4194 Dihedral : 12.471 156.260 3342 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.82 % Favored : 94.97 % Rotamer: Outliers : 1.56 % Allowed : 9.05 % Favored : 89.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.01 (0.16), residues: 2964 helix: 1.24 (0.13), residues: 1512 sheet: -1.52 (0.28), residues: 312 loop : -1.20 (0.18), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 363 TYR 0.026 0.002 TYR F 407 PHE 0.020 0.002 PHE A 360 TRP 0.025 0.002 TRP B 281 HIS 0.003 0.001 HIS B 82 Details of bonding type rmsd covalent geometry : bond 0.00333 (23988) covalent geometry : angle 0.64747 (32442) hydrogen bonds : bond 0.03665 ( 1196) hydrogen bonds : angle 4.57136 ( 3552) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 317 time to evaluate : 0.857 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: A 119 ASP cc_start: 0.9212 (OUTLIER) cc_final: 0.8977 (m-30) REVERT: A 163 ASP cc_start: 0.8390 (t0) cc_final: 0.8182 (t0) REVERT: A 181 ASP cc_start: 0.8864 (t0) cc_final: 0.8456 (t0) REVERT: A 281 TRP cc_start: 0.8346 (t60) cc_final: 0.8099 (t60) REVERT: A 330 GLN cc_start: 0.8936 (tm-30) cc_final: 0.8655 (tm-30) REVERT: A 364 ASN cc_start: 0.8898 (t0) cc_final: 0.8647 (t0) REVERT: A 384 GLU cc_start: 0.8837 (tt0) cc_final: 0.8566 (tt0) REVERT: A 411 MET cc_start: 0.9109 (OUTLIER) cc_final: 0.8848 (tpp) REVERT: B 111 MET cc_start: 0.9155 (tpp) cc_final: 0.8731 (tpp) REVERT: B 190 TYR cc_start: 0.7234 (p90) cc_final: 0.6953 (m-80) REVERT: B 281 TRP cc_start: 0.8484 (t60) cc_final: 0.8183 (t60) REVERT: B 364 ASN cc_start: 0.8771 (t0) cc_final: 0.8553 (t0) REVERT: B 384 GLU cc_start: 0.8850 (tt0) cc_final: 0.8508 (tt0) REVERT: C 12 MET cc_start: 0.8753 (mtm) cc_final: 0.8339 (mtm) REVERT: C 181 ASP cc_start: 0.8855 (t0) cc_final: 0.8285 (t0) REVERT: C 190 TYR cc_start: 0.7198 (p90) cc_final: 0.6985 (m-80) REVERT: C 205 GLN cc_start: 0.8371 (mp10) cc_final: 0.8050 (mp10) REVERT: C 281 TRP cc_start: 0.8476 (t60) cc_final: 0.8249 (t60) REVERT: C 330 GLN cc_start: 0.8951 (tm-30) cc_final: 0.8654 (tm-30) REVERT: C 411 MET cc_start: 0.9131 (OUTLIER) cc_final: 0.8871 (tpp) REVERT: D 119 ASP cc_start: 0.9195 (OUTLIER) cc_final: 0.8956 (m-30) REVERT: D 163 ASP cc_start: 0.8382 (t0) cc_final: 0.8173 (t0) REVERT: D 181 ASP cc_start: 0.8866 (t0) cc_final: 0.8452 (t0) REVERT: D 281 TRP cc_start: 0.8331 (t60) cc_final: 0.8077 (t60) REVERT: D 330 GLN cc_start: 0.8940 (tm-30) cc_final: 0.8661 (tm-30) REVERT: D 364 ASN cc_start: 0.8881 (t0) cc_final: 0.8627 (t0) REVERT: D 384 GLU cc_start: 0.8849 (tt0) cc_final: 0.8577 (tt0) REVERT: D 411 MET cc_start: 0.9117 (OUTLIER) cc_final: 0.8854 (tpp) REVERT: E 111 MET cc_start: 0.9149 (tpp) cc_final: 0.8725 (tpp) REVERT: E 190 TYR cc_start: 0.7240 (p90) cc_final: 0.6975 (m-80) REVERT: E 281 TRP cc_start: 0.8486 (t60) cc_final: 0.8184 (t60) REVERT: E 364 ASN cc_start: 0.8775 (t0) cc_final: 0.8559 (t0) REVERT: E 384 GLU cc_start: 0.8857 (tt0) cc_final: 0.8514 (tt0) REVERT: F 12 MET cc_start: 0.8751 (mtm) cc_final: 0.8337 (mtm) REVERT: F 181 ASP cc_start: 0.8854 (t0) cc_final: 0.8289 (t0) REVERT: F 205 GLN cc_start: 0.8361 (mp10) cc_final: 0.8029 (mp10) REVERT: F 281 TRP cc_start: 0.8469 (t60) cc_final: 0.8234 (t60) REVERT: F 330 GLN cc_start: 0.8944 (tm-30) cc_final: 0.8647 (tm-30) REVERT: F 411 MET cc_start: 0.9143 (OUTLIER) cc_final: 0.8883 (tpp) outliers start: 39 outliers final: 22 residues processed: 340 average time/residue: 0.1431 time to fit residues: 79.6593 Evaluate side-chains 286 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 258 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 411 MET Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain C residue 411 MET Chi-restraints excluded: chain D residue 119 ASP Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 393 SER Chi-restraints excluded: chain D residue 411 MET Chi-restraints excluded: chain E residue 81 GLN Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 314 ILE Chi-restraints excluded: chain E residue 392 VAL Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 393 SER Chi-restraints excluded: chain F residue 411 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 230 optimal weight: 50.0000 chunk 235 optimal weight: 9.9990 chunk 216 optimal weight: 20.0000 chunk 202 optimal weight: 10.0000 chunk 106 optimal weight: 5.9990 chunk 88 optimal weight: 10.0000 chunk 112 optimal weight: 9.9990 chunk 15 optimal weight: 7.9990 chunk 52 optimal weight: 10.0000 chunk 17 optimal weight: 5.9990 chunk 80 optimal weight: 5.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN ** A 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 GLN ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 40 GLN ** C 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 391 HIS D 40 GLN ** D 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 40 GLN ** E 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 40 GLN ** F 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 391 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.092646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.069372 restraints weight = 60685.101| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 3.73 r_work: 0.2997 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.4744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 23988 Z= 0.250 Angle : 0.724 11.421 32442 Z= 0.362 Chirality : 0.046 0.198 3516 Planarity : 0.005 0.057 4194 Dihedral : 11.880 144.697 3342 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.43 % Favored : 94.30 % Rotamer: Outliers : 2.00 % Allowed : 10.46 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (0.16), residues: 2964 helix: 1.10 (0.13), residues: 1548 sheet: -1.04 (0.27), residues: 372 loop : -1.27 (0.19), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 146 TYR 0.024 0.002 TYR F 407 PHE 0.021 0.002 PHE C 247 TRP 0.018 0.002 TRP D 72 HIS 0.006 0.002 HIS A 408 Details of bonding type rmsd covalent geometry : bond 0.00580 (23988) covalent geometry : angle 0.72424 (32442) hydrogen bonds : bond 0.04067 ( 1196) hydrogen bonds : angle 4.84384 ( 3552) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 294 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 PHE cc_start: 0.8146 (m-10) cc_final: 0.7774 (m-10) REVERT: A 181 ASP cc_start: 0.8962 (t0) cc_final: 0.8600 (t0) REVERT: A 269 LYS cc_start: 0.7774 (tttt) cc_final: 0.7394 (tttt) REVERT: A 297 GLN cc_start: 0.9246 (mm-40) cc_final: 0.8782 (tm-30) REVERT: A 330 GLN cc_start: 0.8994 (tm-30) cc_final: 0.8606 (tm-30) REVERT: A 364 ASN cc_start: 0.8843 (t0) cc_final: 0.8609 (t0) REVERT: A 384 GLU cc_start: 0.8910 (tt0) cc_final: 0.8643 (tt0) REVERT: A 411 MET cc_start: 0.9174 (OUTLIER) cc_final: 0.8935 (tpp) REVERT: B 297 GLN cc_start: 0.9230 (mm-40) cc_final: 0.8747 (tm-30) REVERT: B 364 ASN cc_start: 0.8760 (t0) cc_final: 0.8521 (t0) REVERT: B 384 GLU cc_start: 0.8867 (tt0) cc_final: 0.8602 (tt0) REVERT: C 12 MET cc_start: 0.8832 (mtm) cc_final: 0.8369 (mtm) REVERT: C 281 TRP cc_start: 0.8439 (t60) cc_final: 0.8187 (t60) REVERT: C 297 GLN cc_start: 0.9260 (mm-40) cc_final: 0.8771 (tm-30) REVERT: C 330 GLN cc_start: 0.8995 (tm-30) cc_final: 0.8606 (tm-30) REVERT: C 411 MET cc_start: 0.9194 (OUTLIER) cc_final: 0.8965 (tpp) REVERT: D 63 PHE cc_start: 0.8146 (m-10) cc_final: 0.7775 (m-10) REVERT: D 181 ASP cc_start: 0.8971 (t0) cc_final: 0.8601 (t0) REVERT: D 269 LYS cc_start: 0.7779 (tttt) cc_final: 0.7405 (tttt) REVERT: D 281 TRP cc_start: 0.8390 (t60) cc_final: 0.8162 (t60) REVERT: D 297 GLN cc_start: 0.9253 (mm-40) cc_final: 0.8781 (tm-30) REVERT: D 330 GLN cc_start: 0.9001 (tm-30) cc_final: 0.8614 (tm-30) REVERT: D 364 ASN cc_start: 0.8812 (t0) cc_final: 0.8581 (t0) REVERT: D 384 GLU cc_start: 0.8925 (tt0) cc_final: 0.8646 (tt0) REVERT: D 411 MET cc_start: 0.9169 (OUTLIER) cc_final: 0.8932 (tpp) REVERT: E 297 GLN cc_start: 0.9236 (mm-40) cc_final: 0.8748 (tm-30) REVERT: E 364 ASN cc_start: 0.8785 (t0) cc_final: 0.8548 (t0) REVERT: E 384 GLU cc_start: 0.8894 (tt0) cc_final: 0.8635 (tt0) REVERT: F 12 MET cc_start: 0.8830 (mtm) cc_final: 0.8363 (mtm) REVERT: F 281 TRP cc_start: 0.8446 (t60) cc_final: 0.8204 (t60) REVERT: F 297 GLN cc_start: 0.9266 (mm-40) cc_final: 0.8774 (tm-30) REVERT: F 330 GLN cc_start: 0.8993 (tm-30) cc_final: 0.8591 (tm-30) REVERT: F 411 MET cc_start: 0.9198 (OUTLIER) cc_final: 0.8969 (tpp) outliers start: 50 outliers final: 37 residues processed: 319 average time/residue: 0.1530 time to fit residues: 78.9976 Evaluate side-chains 296 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 255 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 407 TYR Chi-restraints excluded: chain A residue 411 MET Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain B residue 189 HIS Chi-restraints excluded: chain B residue 195 HIS Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain C residue 189 HIS Chi-restraints excluded: chain C residue 195 HIS Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain C residue 407 TYR Chi-restraints excluded: chain C residue 411 MET Chi-restraints excluded: chain C residue 428 ILE Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 407 TYR Chi-restraints excluded: chain D residue 411 MET Chi-restraints excluded: chain D residue 460 SER Chi-restraints excluded: chain E residue 81 GLN Chi-restraints excluded: chain E residue 189 HIS Chi-restraints excluded: chain E residue 195 HIS Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 314 ILE Chi-restraints excluded: chain E residue 392 VAL Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain E residue 407 TYR Chi-restraints excluded: chain F residue 195 HIS Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 392 VAL Chi-restraints excluded: chain F residue 393 SER Chi-restraints excluded: chain F residue 407 TYR Chi-restraints excluded: chain F residue 411 MET Chi-restraints excluded: chain F residue 428 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 254 optimal weight: 5.9990 chunk 233 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 18 optimal weight: 7.9990 chunk 168 optimal weight: 5.9990 chunk 42 optimal weight: 10.0000 chunk 116 optimal weight: 0.1980 chunk 104 optimal weight: 3.9990 chunk 205 optimal weight: 5.9990 chunk 124 optimal weight: 40.0000 chunk 193 optimal weight: 9.9990 overall best weight: 3.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.094909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.071762 restraints weight = 60289.361| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 3.76 r_work: 0.3046 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.5007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 23988 Z= 0.158 Angle : 0.668 9.295 32442 Z= 0.334 Chirality : 0.043 0.183 3516 Planarity : 0.004 0.045 4194 Dihedral : 10.989 155.244 3342 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 1.80 % Allowed : 11.94 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.23 (0.16), residues: 2964 helix: 1.36 (0.13), residues: 1512 sheet: -0.88 (0.28), residues: 372 loop : -1.16 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 146 TYR 0.024 0.002 TYR C 407 PHE 0.021 0.002 PHE F 247 TRP 0.030 0.002 TRP A 281 HIS 0.006 0.001 HIS B 408 Details of bonding type rmsd covalent geometry : bond 0.00371 (23988) covalent geometry : angle 0.66830 (32442) hydrogen bonds : bond 0.03646 ( 1196) hydrogen bonds : angle 4.58702 ( 3552) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 297 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 MET cc_start: 0.9121 (tpp) cc_final: 0.8790 (tpp) REVERT: A 142 GLU cc_start: 0.8742 (tt0) cc_final: 0.8355 (tt0) REVERT: A 181 ASP cc_start: 0.8893 (t0) cc_final: 0.8495 (t0) REVERT: A 269 LYS cc_start: 0.7900 (tttt) cc_final: 0.7567 (tttt) REVERT: A 281 TRP cc_start: 0.8343 (t60) cc_final: 0.7854 (t60) REVERT: A 297 GLN cc_start: 0.9225 (mm-40) cc_final: 0.8775 (tm-30) REVERT: A 330 GLN cc_start: 0.8997 (tm-30) cc_final: 0.8665 (tm-30) REVERT: A 364 ASN cc_start: 0.8867 (t0) cc_final: 0.8598 (t0) REVERT: A 384 GLU cc_start: 0.8917 (tt0) cc_final: 0.8634 (tt0) REVERT: A 411 MET cc_start: 0.9119 (OUTLIER) cc_final: 0.8891 (tpp) REVERT: B 111 MET cc_start: 0.9166 (tpp) cc_final: 0.8799 (tpp) REVERT: B 142 GLU cc_start: 0.8701 (tt0) cc_final: 0.8328 (tt0) REVERT: B 233 MET cc_start: 0.8373 (mmm) cc_final: 0.7917 (mmm) REVERT: B 297 GLN cc_start: 0.9214 (mm-40) cc_final: 0.8747 (tm-30) REVERT: B 364 ASN cc_start: 0.8793 (t0) cc_final: 0.8542 (t0) REVERT: B 384 GLU cc_start: 0.8874 (tt0) cc_final: 0.8578 (tt0) REVERT: C 12 MET cc_start: 0.8804 (mtm) cc_final: 0.8360 (mtm) REVERT: C 40 GLN cc_start: 0.8843 (mp10) cc_final: 0.8297 (pt0) REVERT: C 142 GLU cc_start: 0.8899 (tt0) cc_final: 0.8590 (tt0) REVERT: C 281 TRP cc_start: 0.8420 (t60) cc_final: 0.8193 (t60) REVERT: C 297 GLN cc_start: 0.9236 (mm-40) cc_final: 0.8776 (tm-30) REVERT: C 330 GLN cc_start: 0.9005 (tm-30) cc_final: 0.8641 (tm-30) REVERT: D 111 MET cc_start: 0.9116 (tpp) cc_final: 0.8780 (tpp) REVERT: D 142 GLU cc_start: 0.8734 (tt0) cc_final: 0.8351 (tt0) REVERT: D 181 ASP cc_start: 0.8877 (t0) cc_final: 0.8476 (t0) REVERT: D 269 LYS cc_start: 0.7903 (tttt) cc_final: 0.7575 (tttt) REVERT: D 297 GLN cc_start: 0.9225 (mm-40) cc_final: 0.8770 (tm-30) REVERT: D 330 GLN cc_start: 0.9016 (tm-30) cc_final: 0.8684 (tm-30) REVERT: D 364 ASN cc_start: 0.8856 (t0) cc_final: 0.8580 (t0) REVERT: D 384 GLU cc_start: 0.8921 (tt0) cc_final: 0.8657 (tt0) REVERT: D 411 MET cc_start: 0.9130 (OUTLIER) cc_final: 0.8905 (tpp) REVERT: E 111 MET cc_start: 0.9157 (tpp) cc_final: 0.8790 (tpp) REVERT: E 142 GLU cc_start: 0.8698 (tt0) cc_final: 0.8339 (tt0) REVERT: E 297 GLN cc_start: 0.9207 (mm-40) cc_final: 0.8739 (tm-30) REVERT: E 364 ASN cc_start: 0.8802 (t0) cc_final: 0.8557 (t0) REVERT: E 384 GLU cc_start: 0.8888 (tt0) cc_final: 0.8595 (tt0) REVERT: F 12 MET cc_start: 0.8806 (mtm) cc_final: 0.8362 (mtm) REVERT: F 142 GLU cc_start: 0.8900 (tt0) cc_final: 0.8586 (tt0) REVERT: F 233 MET cc_start: 0.8418 (mmm) cc_final: 0.8207 (mmm) REVERT: F 238 MET cc_start: 0.7993 (mtp) cc_final: 0.7736 (mtm) REVERT: F 281 TRP cc_start: 0.8435 (t60) cc_final: 0.8223 (t60) REVERT: F 297 GLN cc_start: 0.9242 (mm-40) cc_final: 0.8781 (tm-30) REVERT: F 330 GLN cc_start: 0.9006 (tm-30) cc_final: 0.8637 (tm-30) outliers start: 45 outliers final: 28 residues processed: 321 average time/residue: 0.1392 time to fit residues: 74.7099 Evaluate side-chains 295 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 265 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 411 MET Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain C residue 189 HIS Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain C residue 407 TYR Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 393 SER Chi-restraints excluded: chain D residue 411 MET Chi-restraints excluded: chain E residue 81 GLN Chi-restraints excluded: chain E residue 189 HIS Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 314 ILE Chi-restraints excluded: chain E residue 392 VAL Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain E residue 407 TYR Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain F residue 236 LEU Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 392 VAL Chi-restraints excluded: chain F residue 393 SER Chi-restraints excluded: chain F residue 407 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 292 optimal weight: 0.0370 chunk 187 optimal weight: 5.9990 chunk 176 optimal weight: 30.0000 chunk 141 optimal weight: 10.0000 chunk 63 optimal weight: 0.9990 chunk 73 optimal weight: 10.0000 chunk 6 optimal weight: 4.9990 chunk 197 optimal weight: 5.9990 chunk 207 optimal weight: 10.0000 chunk 99 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 overall best weight: 3.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN B 40 GLN D 40 GLN E 40 GLN F 40 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.095695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.072735 restraints weight = 59858.364| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 3.76 r_work: 0.3067 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.5208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23988 Z= 0.144 Angle : 0.658 8.851 32442 Z= 0.331 Chirality : 0.044 0.214 3516 Planarity : 0.004 0.059 4194 Dihedral : 10.306 176.619 3342 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 1.44 % Allowed : 12.98 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.16), residues: 2964 helix: 1.48 (0.14), residues: 1506 sheet: -0.73 (0.28), residues: 372 loop : -1.01 (0.19), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 79 TYR 0.024 0.002 TYR C 407 PHE 0.040 0.002 PHE A 360 TRP 0.032 0.002 TRP D 281 HIS 0.003 0.001 HIS F 450 Details of bonding type rmsd covalent geometry : bond 0.00334 (23988) covalent geometry : angle 0.65781 (32442) hydrogen bonds : bond 0.03576 ( 1196) hydrogen bonds : angle 4.57838 ( 3552) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 291 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 MET cc_start: 0.9145 (tpp) cc_final: 0.8821 (tpp) REVERT: A 142 GLU cc_start: 0.8715 (tt0) cc_final: 0.8328 (tt0) REVERT: A 181 ASP cc_start: 0.8920 (t0) cc_final: 0.8543 (t0) REVERT: A 269 LYS cc_start: 0.7890 (tttt) cc_final: 0.7654 (tptt) REVERT: A 281 TRP cc_start: 0.8242 (t60) cc_final: 0.7735 (t60) REVERT: A 297 GLN cc_start: 0.9221 (mm-40) cc_final: 0.8760 (tm-30) REVERT: A 330 GLN cc_start: 0.8982 (tm-30) cc_final: 0.8771 (tm-30) REVERT: A 384 GLU cc_start: 0.8906 (tt0) cc_final: 0.8614 (tt0) REVERT: A 411 MET cc_start: 0.9102 (OUTLIER) cc_final: 0.8867 (tpp) REVERT: B 111 MET cc_start: 0.9186 (tpp) cc_final: 0.8828 (tpp) REVERT: B 142 GLU cc_start: 0.8696 (tt0) cc_final: 0.8305 (tt0) REVERT: B 292 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.7976 (mt-10) REVERT: B 297 GLN cc_start: 0.9200 (mm-40) cc_final: 0.8749 (tm-30) REVERT: B 384 GLU cc_start: 0.8880 (tt0) cc_final: 0.8572 (tt0) REVERT: C 12 MET cc_start: 0.8776 (mtm) cc_final: 0.8348 (mtm) REVERT: C 40 GLN cc_start: 0.8876 (mp10) cc_final: 0.8634 (mp10) REVERT: C 111 MET cc_start: 0.9113 (tpp) cc_final: 0.8754 (tpp) REVERT: C 142 GLU cc_start: 0.8913 (tt0) cc_final: 0.8580 (tt0) REVERT: C 297 GLN cc_start: 0.9227 (mm-40) cc_final: 0.8765 (tm-30) REVERT: C 330 GLN cc_start: 0.8971 (tm-30) cc_final: 0.8671 (tm-30) REVERT: C 411 MET cc_start: 0.9166 (OUTLIER) cc_final: 0.8924 (tpp) REVERT: D 111 MET cc_start: 0.9156 (tpp) cc_final: 0.8833 (tpp) REVERT: D 142 GLU cc_start: 0.8723 (tt0) cc_final: 0.8327 (tt0) REVERT: D 181 ASP cc_start: 0.8922 (t0) cc_final: 0.8549 (t0) REVERT: D 269 LYS cc_start: 0.7889 (tttt) cc_final: 0.7646 (tptt) REVERT: D 297 GLN cc_start: 0.9214 (mm-40) cc_final: 0.8762 (tm-30) REVERT: D 330 GLN cc_start: 0.9012 (tm-30) cc_final: 0.8753 (tm-30) REVERT: D 384 GLU cc_start: 0.8943 (tt0) cc_final: 0.8660 (tt0) REVERT: D 411 MET cc_start: 0.9083 (OUTLIER) cc_final: 0.8850 (tpp) REVERT: E 111 MET cc_start: 0.9188 (tpp) cc_final: 0.8830 (tpp) REVERT: E 142 GLU cc_start: 0.8682 (tt0) cc_final: 0.8304 (tt0) REVERT: E 233 MET cc_start: 0.8359 (mmm) cc_final: 0.7992 (mmm) REVERT: E 260 MET cc_start: 0.9129 (OUTLIER) cc_final: 0.8709 (tpt) REVERT: E 297 GLN cc_start: 0.9208 (mm-40) cc_final: 0.8740 (tm-30) REVERT: E 384 GLU cc_start: 0.8900 (tt0) cc_final: 0.8599 (tt0) REVERT: F 12 MET cc_start: 0.8777 (mtm) cc_final: 0.8348 (mtm) REVERT: F 111 MET cc_start: 0.9123 (tpp) cc_final: 0.8766 (tpp) REVERT: F 142 GLU cc_start: 0.8913 (tt0) cc_final: 0.8578 (tt0) REVERT: F 297 GLN cc_start: 0.9234 (mm-40) cc_final: 0.8768 (tm-30) REVERT: F 330 GLN cc_start: 0.8958 (tm-30) cc_final: 0.8659 (tm-30) REVERT: F 411 MET cc_start: 0.9158 (OUTLIER) cc_final: 0.8918 (tpp) outliers start: 36 outliers final: 26 residues processed: 308 average time/residue: 0.1285 time to fit residues: 66.3976 Evaluate side-chains 291 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 259 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 411 MET Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 292 GLU Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 407 TYR Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain C residue 411 MET Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 393 SER Chi-restraints excluded: chain D residue 411 MET Chi-restraints excluded: chain D residue 460 SER Chi-restraints excluded: chain E residue 81 GLN Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 260 MET Chi-restraints excluded: chain E residue 314 ILE Chi-restraints excluded: chain E residue 392 VAL Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain F residue 236 LEU Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 392 VAL Chi-restraints excluded: chain F residue 393 SER Chi-restraints excluded: chain F residue 407 TYR Chi-restraints excluded: chain F residue 411 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 57 optimal weight: 4.9990 chunk 215 optimal weight: 10.0000 chunk 197 optimal weight: 6.9990 chunk 282 optimal weight: 0.9990 chunk 50 optimal weight: 5.9990 chunk 108 optimal weight: 7.9990 chunk 254 optimal weight: 8.9990 chunk 88 optimal weight: 8.9990 chunk 192 optimal weight: 10.0000 chunk 242 optimal weight: 1.9990 chunk 203 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 364 ASN E 364 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.095153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.072218 restraints weight = 60005.280| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 3.74 r_work: 0.3048 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.5299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 23988 Z= 0.170 Angle : 0.677 9.429 32442 Z= 0.342 Chirality : 0.044 0.182 3516 Planarity : 0.004 0.049 4194 Dihedral : 10.081 177.018 3342 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 1.64 % Allowed : 14.14 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.49 (0.16), residues: 2964 helix: 1.48 (0.14), residues: 1506 sheet: -0.63 (0.28), residues: 372 loop : -0.93 (0.19), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 79 TYR 0.024 0.002 TYR F 407 PHE 0.036 0.002 PHE C 360 TRP 0.023 0.002 TRP D 281 HIS 0.004 0.001 HIS B 57 Details of bonding type rmsd covalent geometry : bond 0.00396 (23988) covalent geometry : angle 0.67707 (32442) hydrogen bonds : bond 0.03633 ( 1196) hydrogen bonds : angle 4.64541 ( 3552) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 270 time to evaluate : 0.968 Fit side-chains revert: symmetry clash REVERT: A 111 MET cc_start: 0.9146 (tpp) cc_final: 0.8826 (tpp) REVERT: A 142 GLU cc_start: 0.8771 (tt0) cc_final: 0.8325 (tt0) REVERT: A 181 ASP cc_start: 0.8946 (t0) cc_final: 0.8581 (t0) REVERT: A 269 LYS cc_start: 0.7829 (tttt) cc_final: 0.7615 (tptt) REVERT: A 281 TRP cc_start: 0.8209 (t60) cc_final: 0.7684 (t60) REVERT: A 297 GLN cc_start: 0.9212 (mm-40) cc_final: 0.8767 (tm-30) REVERT: A 330 GLN cc_start: 0.9028 (tm-30) cc_final: 0.8775 (tm-30) REVERT: A 384 GLU cc_start: 0.8907 (tt0) cc_final: 0.8601 (tt0) REVERT: A 411 MET cc_start: 0.9106 (OUTLIER) cc_final: 0.8869 (tpp) REVERT: B 111 MET cc_start: 0.9212 (tpp) cc_final: 0.8854 (tpp) REVERT: B 142 GLU cc_start: 0.8730 (tt0) cc_final: 0.8340 (tt0) REVERT: B 233 MET cc_start: 0.8427 (mmm) cc_final: 0.8069 (mmm) REVERT: B 269 LYS cc_start: 0.7933 (tttt) cc_final: 0.7683 (tptt) REVERT: B 292 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.8150 (mt-10) REVERT: B 297 GLN cc_start: 0.9209 (mm-40) cc_final: 0.8749 (tm-30) REVERT: B 384 GLU cc_start: 0.8886 (tt0) cc_final: 0.8580 (tt0) REVERT: C 12 MET cc_start: 0.8782 (mtm) cc_final: 0.8342 (mtm) REVERT: C 111 MET cc_start: 0.9124 (tpp) cc_final: 0.8774 (tpp) REVERT: C 142 GLU cc_start: 0.8928 (tt0) cc_final: 0.8515 (tt0) REVERT: C 233 MET cc_start: 0.8477 (mmm) cc_final: 0.8123 (mmm) REVERT: C 297 GLN cc_start: 0.9241 (mm-40) cc_final: 0.8779 (tm-30) REVERT: C 330 GLN cc_start: 0.8965 (tm-30) cc_final: 0.8654 (tm-30) REVERT: D 111 MET cc_start: 0.9167 (tpp) cc_final: 0.8849 (tpp) REVERT: D 142 GLU cc_start: 0.8746 (tt0) cc_final: 0.8317 (tt0) REVERT: D 181 ASP cc_start: 0.8933 (t0) cc_final: 0.8560 (t0) REVERT: D 269 LYS cc_start: 0.7822 (tttt) cc_final: 0.7612 (tptt) REVERT: D 281 TRP cc_start: 0.8254 (t60) cc_final: 0.7636 (t60) REVERT: D 297 GLN cc_start: 0.9212 (mm-40) cc_final: 0.8757 (tm-30) REVERT: D 330 GLN cc_start: 0.9040 (tm-30) cc_final: 0.8788 (tm-30) REVERT: D 384 GLU cc_start: 0.8929 (tt0) cc_final: 0.8633 (tt0) REVERT: E 111 MET cc_start: 0.9190 (tpp) cc_final: 0.8833 (tpp) REVERT: E 142 GLU cc_start: 0.8736 (tt0) cc_final: 0.8337 (tt0) REVERT: E 233 MET cc_start: 0.8426 (mmm) cc_final: 0.7725 (mmm) REVERT: E 260 MET cc_start: 0.9130 (OUTLIER) cc_final: 0.8682 (tpt) REVERT: E 269 LYS cc_start: 0.7935 (tttt) cc_final: 0.7689 (tptt) REVERT: E 297 GLN cc_start: 0.9211 (mm-40) cc_final: 0.8759 (tm-30) REVERT: E 384 GLU cc_start: 0.8901 (tt0) cc_final: 0.8610 (tt0) REVERT: F 12 MET cc_start: 0.8788 (mtm) cc_final: 0.8344 (mtm) REVERT: F 40 GLN cc_start: 0.8827 (mp10) cc_final: 0.8302 (pt0) REVERT: F 111 MET cc_start: 0.9137 (tpp) cc_final: 0.8785 (tpp) REVERT: F 142 GLU cc_start: 0.8922 (tt0) cc_final: 0.8507 (tt0) REVERT: F 233 MET cc_start: 0.8450 (mmm) cc_final: 0.8149 (mmm) REVERT: F 297 GLN cc_start: 0.9237 (mm-40) cc_final: 0.8780 (tm-30) REVERT: F 330 GLN cc_start: 0.8966 (tm-30) cc_final: 0.8646 (tm-30) outliers start: 41 outliers final: 31 residues processed: 295 average time/residue: 0.1307 time to fit residues: 64.7276 Evaluate side-chains 290 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 256 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 411 MET Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 292 GLU Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 407 TYR Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain C residue 407 TYR Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 393 SER Chi-restraints excluded: chain D residue 460 SER Chi-restraints excluded: chain E residue 81 GLN Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 260 MET Chi-restraints excluded: chain E residue 292 GLU Chi-restraints excluded: chain E residue 314 ILE Chi-restraints excluded: chain E residue 366 MET Chi-restraints excluded: chain E residue 392 VAL Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain F residue 189 HIS Chi-restraints excluded: chain F residue 236 LEU Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 373 LEU Chi-restraints excluded: chain F residue 392 VAL Chi-restraints excluded: chain F residue 393 SER Chi-restraints excluded: chain F residue 407 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 18 optimal weight: 2.9990 chunk 198 optimal weight: 3.9990 chunk 89 optimal weight: 6.9990 chunk 160 optimal weight: 10.0000 chunk 43 optimal weight: 10.0000 chunk 240 optimal weight: 10.0000 chunk 63 optimal weight: 1.9990 chunk 108 optimal weight: 8.9990 chunk 53 optimal weight: 0.0370 chunk 208 optimal weight: 9.9990 chunk 35 optimal weight: 9.9990 overall best weight: 3.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN B 40 GLN D 40 GLN E 40 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.095985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.073182 restraints weight = 59867.899| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 3.72 r_work: 0.3072 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.5439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23988 Z= 0.145 Angle : 0.660 8.810 32442 Z= 0.331 Chirality : 0.044 0.180 3516 Planarity : 0.004 0.049 4194 Dihedral : 10.003 178.977 3342 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 1.48 % Allowed : 14.38 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.60 (0.16), residues: 2964 helix: 1.54 (0.14), residues: 1506 sheet: -0.33 (0.30), residues: 342 loop : -0.92 (0.19), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 363 TYR 0.024 0.002 TYR B 407 PHE 0.046 0.002 PHE A 360 TRP 0.019 0.002 TRP D 281 HIS 0.003 0.001 HIS F 450 Details of bonding type rmsd covalent geometry : bond 0.00338 (23988) covalent geometry : angle 0.66039 (32442) hydrogen bonds : bond 0.03506 ( 1196) hydrogen bonds : angle 4.61156 ( 3552) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 281 time to evaluate : 0.768 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: A 111 MET cc_start: 0.9159 (tpp) cc_final: 0.8836 (tpp) REVERT: A 142 GLU cc_start: 0.8716 (tt0) cc_final: 0.8296 (tt0) REVERT: A 181 ASP cc_start: 0.8921 (t0) cc_final: 0.8543 (t0) REVERT: A 269 LYS cc_start: 0.7843 (tttt) cc_final: 0.7609 (tptt) REVERT: A 281 TRP cc_start: 0.8126 (t60) cc_final: 0.7631 (t60) REVERT: A 297 GLN cc_start: 0.9212 (mm-40) cc_final: 0.8773 (tm-30) REVERT: A 330 GLN cc_start: 0.9037 (tm-30) cc_final: 0.8799 (tm-30) REVERT: A 384 GLU cc_start: 0.8902 (tt0) cc_final: 0.8614 (tt0) REVERT: B 111 MET cc_start: 0.9215 (tpp) cc_final: 0.8869 (tpp) REVERT: B 142 GLU cc_start: 0.8709 (tt0) cc_final: 0.8325 (tt0) REVERT: B 233 MET cc_start: 0.8280 (mmm) cc_final: 0.8052 (mmm) REVERT: B 238 MET cc_start: 0.7526 (mtt) cc_final: 0.7300 (mtt) REVERT: B 292 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8168 (mt-10) REVERT: B 297 GLN cc_start: 0.9213 (mm-40) cc_final: 0.8741 (tm-30) REVERT: B 384 GLU cc_start: 0.8881 (tt0) cc_final: 0.8544 (tt0) REVERT: C 12 MET cc_start: 0.8762 (mtm) cc_final: 0.8346 (mtm) REVERT: C 111 MET cc_start: 0.9127 (tpp) cc_final: 0.8773 (tpp) REVERT: C 142 GLU cc_start: 0.8903 (tt0) cc_final: 0.8562 (tt0) REVERT: C 330 GLN cc_start: 0.8947 (tm-30) cc_final: 0.8649 (tm-30) REVERT: C 411 MET cc_start: 0.9179 (OUTLIER) cc_final: 0.8958 (tpp) REVERT: D 111 MET cc_start: 0.9170 (tpp) cc_final: 0.8842 (tpp) REVERT: D 142 GLU cc_start: 0.8718 (tt0) cc_final: 0.8295 (tt0) REVERT: D 181 ASP cc_start: 0.8903 (t0) cc_final: 0.8511 (t0) REVERT: D 254 ASN cc_start: 0.8087 (t0) cc_final: 0.7710 (t0) REVERT: D 269 LYS cc_start: 0.7817 (tttt) cc_final: 0.7586 (tptt) REVERT: D 281 TRP cc_start: 0.8186 (t60) cc_final: 0.7599 (t60) REVERT: D 297 GLN cc_start: 0.9193 (mm-40) cc_final: 0.8766 (tm-30) REVERT: D 330 GLN cc_start: 0.9034 (tm-30) cc_final: 0.8820 (tm-30) REVERT: D 384 GLU cc_start: 0.8940 (tt0) cc_final: 0.8670 (tt0) REVERT: E 111 MET cc_start: 0.9203 (tpp) cc_final: 0.8857 (tpp) REVERT: E 142 GLU cc_start: 0.8701 (tt0) cc_final: 0.8316 (tt0) REVERT: E 233 MET cc_start: 0.8329 (mmm) cc_final: 0.8034 (mmm) REVERT: E 260 MET cc_start: 0.9133 (OUTLIER) cc_final: 0.8620 (tpt) REVERT: E 297 GLN cc_start: 0.9219 (mm-40) cc_final: 0.8751 (tm-30) REVERT: E 384 GLU cc_start: 0.8894 (tt0) cc_final: 0.8562 (tt0) REVERT: F 12 MET cc_start: 0.8766 (mtm) cc_final: 0.8347 (mtm) REVERT: F 111 MET cc_start: 0.9138 (tpp) cc_final: 0.8790 (tpp) REVERT: F 142 GLU cc_start: 0.8908 (tt0) cc_final: 0.8567 (tt0) REVERT: F 233 MET cc_start: 0.8373 (mmm) cc_final: 0.8143 (mmm) REVERT: F 330 GLN cc_start: 0.8949 (tm-30) cc_final: 0.8670 (tm-30) REVERT: F 407 TYR cc_start: 0.7285 (OUTLIER) cc_final: 0.7058 (p90) outliers start: 37 outliers final: 25 residues processed: 303 average time/residue: 0.1393 time to fit residues: 69.6448 Evaluate side-chains 286 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 257 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 292 GLU Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 407 TYR Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain C residue 411 MET Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 393 SER Chi-restraints excluded: chain D residue 460 SER Chi-restraints excluded: chain E residue 81 GLN Chi-restraints excluded: chain E residue 260 MET Chi-restraints excluded: chain E residue 292 GLU Chi-restraints excluded: chain E residue 314 ILE Chi-restraints excluded: chain E residue 366 MET Chi-restraints excluded: chain E residue 392 VAL Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 373 LEU Chi-restraints excluded: chain F residue 393 SER Chi-restraints excluded: chain F residue 407 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 160 optimal weight: 8.9990 chunk 43 optimal weight: 20.0000 chunk 225 optimal weight: 0.0270 chunk 175 optimal weight: 1.9990 chunk 111 optimal weight: 6.9990 chunk 187 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 190 optimal weight: 2.9990 chunk 223 optimal weight: 3.9990 chunk 184 optimal weight: 0.9990 chunk 189 optimal weight: 9.9990 overall best weight: 2.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 364 ASN D 364 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.098107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.075514 restraints weight = 59684.681| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 3.66 r_work: 0.3130 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.5571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 23988 Z= 0.125 Angle : 0.659 9.273 32442 Z= 0.331 Chirality : 0.043 0.178 3516 Planarity : 0.004 0.045 4194 Dihedral : 9.793 175.860 3342 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 1.24 % Allowed : 14.90 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.72 (0.16), residues: 2964 helix: 1.63 (0.14), residues: 1506 sheet: -0.27 (0.30), residues: 342 loop : -0.84 (0.19), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 146 TYR 0.025 0.002 TYR C 407 PHE 0.043 0.002 PHE D 360 TRP 0.017 0.002 TRP D 281 HIS 0.004 0.001 HIS C 408 Details of bonding type rmsd covalent geometry : bond 0.00290 (23988) covalent geometry : angle 0.65914 (32442) hydrogen bonds : bond 0.03335 ( 1196) hydrogen bonds : angle 4.52900 ( 3552) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 286 time to evaluate : 0.961 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: A 111 MET cc_start: 0.9166 (tpp) cc_final: 0.8858 (tpp) REVERT: A 142 GLU cc_start: 0.8691 (tt0) cc_final: 0.8312 (tt0) REVERT: A 181 ASP cc_start: 0.8891 (t0) cc_final: 0.8490 (t0) REVERT: A 297 GLN cc_start: 0.9198 (mm-40) cc_final: 0.8770 (tm-30) REVERT: A 384 GLU cc_start: 0.8875 (tt0) cc_final: 0.8590 (tt0) REVERT: B 111 MET cc_start: 0.9211 (tpp) cc_final: 0.8909 (tpp) REVERT: B 142 GLU cc_start: 0.8680 (tt0) cc_final: 0.8321 (tt0) REVERT: B 292 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8206 (mt-10) REVERT: B 330 GLN cc_start: 0.8840 (tm-30) cc_final: 0.8488 (tm-30) REVERT: B 352 THR cc_start: 0.9054 (m) cc_final: 0.8818 (p) REVERT: B 384 GLU cc_start: 0.8857 (tt0) cc_final: 0.8512 (tt0) REVERT: C 12 MET cc_start: 0.8695 (mtm) cc_final: 0.8295 (mtm) REVERT: C 40 GLN cc_start: 0.8824 (mp10) cc_final: 0.8380 (pt0) REVERT: C 111 MET cc_start: 0.9141 (tpp) cc_final: 0.8826 (tpp) REVERT: C 142 GLU cc_start: 0.8895 (tt0) cc_final: 0.8592 (tt0) REVERT: C 233 MET cc_start: 0.8538 (mmm) cc_final: 0.7895 (tmm) REVERT: C 254 ASN cc_start: 0.8040 (t0) cc_final: 0.7752 (t0) REVERT: C 316 GLU cc_start: 0.8368 (mp0) cc_final: 0.8155 (mp0) REVERT: C 330 GLN cc_start: 0.8922 (tm-30) cc_final: 0.8707 (tm-30) REVERT: C 343 ILE cc_start: 0.8887 (mt) cc_final: 0.8663 (mp) REVERT: C 469 MET cc_start: 0.8929 (mmm) cc_final: 0.8338 (ttp) REVERT: D 111 MET cc_start: 0.9171 (tpp) cc_final: 0.8870 (tpp) REVERT: D 142 GLU cc_start: 0.8691 (tt0) cc_final: 0.8299 (tt0) REVERT: D 181 ASP cc_start: 0.8864 (t0) cc_final: 0.8641 (t0) REVERT: D 254 ASN cc_start: 0.7884 (t0) cc_final: 0.7531 (t0) REVERT: D 281 TRP cc_start: 0.8025 (t60) cc_final: 0.7503 (t60) REVERT: D 297 GLN cc_start: 0.9191 (mm-40) cc_final: 0.8766 (tm-30) REVERT: D 301 ILE cc_start: 0.9073 (pt) cc_final: 0.8790 (pt) REVERT: D 384 GLU cc_start: 0.8915 (tt0) cc_final: 0.8655 (tt0) REVERT: E 111 MET cc_start: 0.9225 (tpp) cc_final: 0.8923 (tpp) REVERT: E 142 GLU cc_start: 0.8667 (tt0) cc_final: 0.8305 (tt0) REVERT: E 260 MET cc_start: 0.9034 (OUTLIER) cc_final: 0.8620 (tpt) REVERT: E 330 GLN cc_start: 0.8831 (tm-30) cc_final: 0.8476 (tm-30) REVERT: E 384 GLU cc_start: 0.8871 (tt0) cc_final: 0.8521 (tt0) REVERT: E 402 GLU cc_start: 0.8970 (mt-10) cc_final: 0.8646 (mt-10) REVERT: F 12 MET cc_start: 0.8698 (mtm) cc_final: 0.8298 (mtm) REVERT: F 111 MET cc_start: 0.9154 (tpp) cc_final: 0.8837 (tpp) REVERT: F 142 GLU cc_start: 0.8885 (tt0) cc_final: 0.8570 (tt0) REVERT: F 269 LYS cc_start: 0.8020 (tttt) cc_final: 0.7807 (tptt) REVERT: F 330 GLN cc_start: 0.8912 (tm-30) cc_final: 0.8708 (tm-30) REVERT: F 469 MET cc_start: 0.8938 (mmm) cc_final: 0.8338 (ttp) outliers start: 31 outliers final: 24 residues processed: 310 average time/residue: 0.1388 time to fit residues: 71.1990 Evaluate side-chains 286 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 260 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 ASN Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain B residue 292 GLU Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 364 ASN Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 393 SER Chi-restraints excluded: chain D residue 460 SER Chi-restraints excluded: chain E residue 81 GLN Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 260 MET Chi-restraints excluded: chain E residue 292 GLU Chi-restraints excluded: chain E residue 314 ILE Chi-restraints excluded: chain E residue 373 LEU Chi-restraints excluded: chain E residue 392 VAL Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 373 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 163 optimal weight: 0.1980 chunk 115 optimal weight: 6.9990 chunk 121 optimal weight: 2.9990 chunk 34 optimal weight: 10.0000 chunk 233 optimal weight: 0.9990 chunk 269 optimal weight: 30.0000 chunk 210 optimal weight: 9.9990 chunk 260 optimal weight: 6.9990 chunk 201 optimal weight: 0.8980 chunk 87 optimal weight: 0.0980 chunk 144 optimal weight: 20.0000 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN A 364 ASN B 40 GLN D 40 GLN D 364 ASN E 40 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.098944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.076462 restraints weight = 59637.220| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 3.68 r_work: 0.3155 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.5672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23988 Z= 0.117 Angle : 0.654 10.089 32442 Z= 0.330 Chirality : 0.043 0.188 3516 Planarity : 0.004 0.058 4194 Dihedral : 9.758 175.409 3342 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 0.80 % Allowed : 15.75 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.77 (0.16), residues: 2964 helix: 1.64 (0.14), residues: 1506 sheet: -0.39 (0.32), residues: 306 loop : -0.72 (0.19), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 363 TYR 0.025 0.002 TYR C 407 PHE 0.042 0.002 PHE E 360 TRP 0.015 0.001 TRP D 281 HIS 0.004 0.001 HIS C 408 Details of bonding type rmsd covalent geometry : bond 0.00264 (23988) covalent geometry : angle 0.65369 (32442) hydrogen bonds : bond 0.03243 ( 1196) hydrogen bonds : angle 4.49209 ( 3552) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4769.70 seconds wall clock time: 83 minutes 16.25 seconds (4996.25 seconds total)