Starting phenix.real_space_refine on Thu Jun 19 20:30:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/3jd0_6631/06_2025/3jd0_6631.cif Found real_map, /net/cci-nas-00/data/ceres_data/3jd0_6631/06_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_6631/06_2025/3jd0_6631.map" default_real_map = "/net/cci-nas-00/data/ceres_data/3jd0_6631/06_2025/3jd0_6631.map" model { file = "/net/cci-nas-00/data/ceres_data/3jd0_6631/06_2025/3jd0_6631.cif" } default_model = "/net/cci-nas-00/data/ceres_data/3jd0_6631/06_2025/3jd0_6631.cif" } resolution = 3.47 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: C, B, E, D, F Time building chain proxies: 9.18, per 1000 atoms: 0.39 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: 5.92 Conformation dependent library (CDL) restraints added in 2.9 seconds 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: 2.70 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: 7.72 Time building geometry restraints manager: 6.95 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: 0.18 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' 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: 0.710 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: 0.990 Check model and map are aligned: 0.150 Set scattering table: 0.220 Process input model: 46.710 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.540 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.014 0.002 TRP D 281 HIS 0.007 0.002 HIS A 57 PHE 0.020 0.002 PHE F 421 TYR 0.013 0.002 TYR F 382 ARG 0.007 0.001 ARG F 147 Details of bonding type rmsd hydrogen bonds : bond 0.26858 ( 1196) hydrogen bonds : angle 10.63518 ( 3552) covalent geometry : bond 0.01189 (23988) covalent geometry : angle 0.81728 (32442) *********************** 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 : 2.767 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: 0.4621 time to fit residues: 366.2229 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 : 2.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 248 optimal weight: 9.9990 chunk 222 optimal weight: 9.9990 chunk 123 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 150 optimal weight: 9.9990 chunk 119 optimal weight: 5.9990 chunk 230 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 140 optimal weight: 6.9990 chunk 171 optimal weight: 6.9990 chunk 266 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 408 HIS ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 ASN B 408 HIS ** C 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 GLN C 408 HIS ** D 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 408 HIS ** E 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 388 ASN E 408 HIS ** F 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 408 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.096318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.073431 restraints weight = 59829.343| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 3.86 r_work: 0.3070 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.3405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 23988 Z= 0.221 Angle : 0.766 10.414 32442 Z= 0.388 Chirality : 0.047 0.185 3516 Planarity : 0.005 0.044 4194 Dihedral : 13.118 168.928 3342 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.40 % Allowed : 5.57 % Favored : 94.03 % Rotamer: Outliers : 1.44 % Allowed : 6.13 % Favored : 92.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.14), residues: 2964 helix: -1.06 (0.12), residues: 1506 sheet: -2.15 (0.24), residues: 342 loop : -1.87 (0.17), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 72 HIS 0.014 0.002 HIS D 189 PHE 0.027 0.003 PHE D 16 TYR 0.028 0.002 TYR D 407 ARG 0.004 0.001 ARG C 363 Details of bonding type rmsd hydrogen bonds : bond 0.04713 ( 1196) hydrogen bonds : angle 5.54494 ( 3552) covalent geometry : bond 0.00512 (23988) covalent geometry : angle 0.76581 (32442) *********************** 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 371 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 335 time to evaluate : 2.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 ASP cc_start: 0.8758 (t0) cc_final: 0.8525 (t0) REVERT: A 190 TYR cc_start: 0.7006 (p90) cc_final: 0.6705 (m-80) REVERT: A 364 ASN cc_start: 0.8729 (t0) cc_final: 0.8469 (t0) REVERT: A 384 GLU cc_start: 0.8801 (tt0) cc_final: 0.8589 (tt0) REVERT: B 12 MET cc_start: 0.8408 (mtm) cc_final: 0.8206 (mtm) REVERT: B 169 MET cc_start: 0.8988 (mmp) cc_final: 0.8785 (mmt) REVERT: B 190 TYR cc_start: 0.7173 (OUTLIER) cc_final: 0.6817 (m-80) REVERT: B 250 GLN cc_start: 0.7927 (tm-30) cc_final: 0.7467 (tm-30) REVERT: B 384 GLU cc_start: 0.8799 (tt0) cc_final: 0.8466 (tt0) REVERT: C 12 MET cc_start: 0.8853 (mtm) cc_final: 0.8365 (mtm) REVERT: C 169 MET cc_start: 0.8963 (mmp) cc_final: 0.8758 (mmt) REVERT: C 181 ASP cc_start: 0.8744 (t0) cc_final: 0.8336 (t0) REVERT: C 190 TYR cc_start: 0.7091 (p90) cc_final: 0.6737 (m-80) REVERT: C 250 GLN cc_start: 0.7853 (tm-30) cc_final: 0.7419 (tm-30) REVERT: C 330 GLN cc_start: 0.8924 (tm-30) cc_final: 0.8602 (tm-30) REVERT: C 421 PHE cc_start: 0.8094 (p90) cc_final: 0.7554 (p90) REVERT: D 181 ASP cc_start: 0.8763 (t0) cc_final: 0.8526 (t0) REVERT: D 190 TYR cc_start: 0.7075 (p90) cc_final: 0.6783 (m-80) REVERT: D 364 ASN cc_start: 0.8718 (t0) cc_final: 0.8461 (t0) REVERT: D 384 GLU cc_start: 0.8828 (tt0) cc_final: 0.8615 (tt0) REVERT: E 169 MET cc_start: 0.9004 (mmp) cc_final: 0.8799 (mmt) REVERT: E 190 TYR cc_start: 0.7193 (p90) cc_final: 0.6882 (m-80) REVERT: E 250 GLN cc_start: 0.7927 (tm-30) cc_final: 0.7467 (tm-30) REVERT: E 384 GLU cc_start: 0.8801 (tt0) cc_final: 0.8467 (tt0) REVERT: F 12 MET cc_start: 0.8851 (mtm) cc_final: 0.8369 (mtm) REVERT: F 169 MET cc_start: 0.8958 (mmp) cc_final: 0.8751 (mmt) REVERT: F 181 ASP cc_start: 0.8752 (t0) cc_final: 0.8339 (t0) REVERT: F 190 TYR cc_start: 0.7160 (p90) cc_final: 0.6810 (m-80) REVERT: F 250 GLN cc_start: 0.7852 (tm-30) cc_final: 0.7415 (tm-30) REVERT: F 330 GLN cc_start: 0.8928 (tm-30) cc_final: 0.8603 (tm-30) REVERT: F 421 PHE cc_start: 0.8092 (p90) cc_final: 0.7554 (p90) outliers start: 36 outliers final: 22 residues processed: 361 average time/residue: 0.3166 time to fit residues: 188.3062 Evaluate side-chains 254 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 231 time to evaluate : 2.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain B residue 81 GLN 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 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 255 VAL Chi-restraints excluded: chain D residue 393 SER Chi-restraints excluded: chain E residue 81 GLN 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 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 20 optimal weight: 7.9990 chunk 203 optimal weight: 6.9990 chunk 122 optimal weight: 5.9990 chunk 16 optimal weight: 8.9990 chunk 214 optimal weight: 7.9990 chunk 197 optimal weight: 9.9990 chunk 62 optimal weight: 5.9990 chunk 115 optimal weight: 10.0000 chunk 250 optimal weight: 0.6980 chunk 227 optimal weight: 6.9990 chunk 19 optimal weight: 4.9990 overall best weight: 4.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN A 84 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 84 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.095503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.072512 restraints weight = 60441.257| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 3.86 r_work: 0.3039 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.3965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 23988 Z= 0.195 Angle : 0.697 10.371 32442 Z= 0.349 Chirality : 0.045 0.194 3516 Planarity : 0.004 0.035 4194 Dihedral : 12.831 163.249 3342 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.03 % Favored : 94.77 % Rotamer: Outliers : 1.52 % Allowed : 7.21 % Favored : 91.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.15), residues: 2964 helix: 0.43 (0.13), residues: 1548 sheet: -1.64 (0.28), residues: 282 loop : -1.55 (0.18), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP B 281 HIS 0.011 0.001 HIS E 189 PHE 0.028 0.003 PHE D 360 TYR 0.025 0.002 TYR C 407 ARG 0.003 0.000 ARG C 363 Details of bonding type rmsd hydrogen bonds : bond 0.04069 ( 1196) hydrogen bonds : angle 4.96892 ( 3552) covalent geometry : bond 0.00462 (23988) covalent geometry : angle 0.69700 (32442) *********************** 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 333 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 295 time to evaluate : 2.838 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 181 ASP cc_start: 0.8836 (t0) cc_final: 0.8492 (t0) REVERT: A 281 TRP cc_start: 0.8408 (t60) cc_final: 0.8196 (t60) REVERT: A 364 ASN cc_start: 0.8781 (t0) cc_final: 0.8549 (t0) REVERT: A 384 GLU cc_start: 0.8828 (tt0) cc_final: 0.8566 (tt0) REVERT: B 12 MET cc_start: 0.8483 (mtm) cc_final: 0.8219 (mtm) REVERT: B 190 TYR cc_start: 0.7163 (p90) cc_final: 0.6926 (m-80) REVERT: B 281 TRP cc_start: 0.8557 (t60) cc_final: 0.8324 (t60) REVERT: B 384 GLU cc_start: 0.8844 (tt0) cc_final: 0.8546 (tt0) REVERT: B 402 GLU cc_start: 0.9014 (mt-10) cc_final: 0.8703 (mt-10) REVERT: C 12 MET cc_start: 0.8780 (mtm) cc_final: 0.8307 (mtm) REVERT: C 181 ASP cc_start: 0.8861 (t0) cc_final: 0.8318 (t0) REVERT: C 190 TYR cc_start: 0.7164 (p90) cc_final: 0.6909 (m-80) REVERT: C 330 GLN cc_start: 0.8948 (tm-30) cc_final: 0.8664 (tm-30) REVERT: C 411 MET cc_start: 0.9164 (OUTLIER) cc_final: 0.8873 (tpp) REVERT: C 421 PHE cc_start: 0.7977 (p90) cc_final: 0.7742 (p90) REVERT: D 181 ASP cc_start: 0.8826 (t0) cc_final: 0.8478 (t0) REVERT: D 281 TRP cc_start: 0.8408 (t60) cc_final: 0.8198 (t60) REVERT: D 364 ASN cc_start: 0.8770 (t0) cc_final: 0.8537 (t0) REVERT: D 384 GLU cc_start: 0.8846 (tt0) cc_final: 0.8584 (tt0) REVERT: E 190 TYR cc_start: 0.7174 (p90) cc_final: 0.6960 (m-80) REVERT: E 281 TRP cc_start: 0.8562 (t60) cc_final: 0.8326 (t60) REVERT: E 384 GLU cc_start: 0.8826 (tt0) cc_final: 0.8528 (tt0) REVERT: F 12 MET cc_start: 0.8779 (mtm) cc_final: 0.8304 (mtm) REVERT: F 181 ASP cc_start: 0.8858 (t0) cc_final: 0.8316 (t0) REVERT: F 190 TYR cc_start: 0.7209 (p90) cc_final: 0.6943 (m-80) REVERT: F 330 GLN cc_start: 0.8948 (tm-30) cc_final: 0.8670 (tm-30) REVERT: F 411 MET cc_start: 0.9160 (OUTLIER) cc_final: 0.8869 (tpp) REVERT: F 421 PHE cc_start: 0.7975 (p90) cc_final: 0.7746 (p90) outliers start: 38 outliers final: 19 residues processed: 320 average time/residue: 0.3363 time to fit residues: 176.7097 Evaluate side-chains 257 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 236 time to evaluate : 2.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 393 SER 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 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 255 VAL Chi-restraints excluded: chain D residue 393 SER Chi-restraints excluded: chain E residue 195 HIS Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 314 ILE 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 96 optimal weight: 8.9990 chunk 20 optimal weight: 0.3980 chunk 38 optimal weight: 4.9990 chunk 164 optimal weight: 10.0000 chunk 277 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 234 optimal weight: 0.9980 chunk 117 optimal weight: 6.9990 chunk 101 optimal weight: 8.9990 chunk 252 optimal weight: 5.9990 chunk 253 optimal weight: 20.0000 overall best weight: 3.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 GLN A 391 HIS B 391 HIS C 391 HIS D 205 GLN D 391 HIS E 391 HIS F 135 ASN F 205 GLN F 391 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.096122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.073158 restraints weight = 60831.240| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 3.88 r_work: 0.3050 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.4433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 23988 Z= 0.155 Angle : 0.657 9.473 32442 Z= 0.328 Chirality : 0.044 0.184 3516 Planarity : 0.004 0.053 4194 Dihedral : 12.447 156.099 3342 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.96 % Favored : 94.84 % Rotamer: Outliers : 1.68 % Allowed : 9.13 % Favored : 89.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.15), residues: 2964 helix: 1.05 (0.13), residues: 1548 sheet: -1.58 (0.28), residues: 312 loop : -1.26 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 281 HIS 0.010 0.001 HIS E 189 PHE 0.021 0.002 PHE D 360 TYR 0.026 0.002 TYR C 407 ARG 0.002 0.000 ARG B 363 Details of bonding type rmsd hydrogen bonds : bond 0.03711 ( 1196) hydrogen bonds : angle 4.62644 ( 3552) covalent geometry : bond 0.00371 (23988) covalent geometry : angle 0.65733 (32442) *********************** 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 346 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 304 time to evaluate : 2.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 ASP cc_start: 0.8865 (t0) cc_final: 0.8460 (t0) REVERT: A 281 TRP cc_start: 0.8359 (t60) cc_final: 0.8154 (t60) REVERT: A 330 GLN cc_start: 0.8994 (tm-30) cc_final: 0.8674 (tm-30) REVERT: A 364 ASN cc_start: 0.8869 (t0) cc_final: 0.8625 (t0) REVERT: A 384 GLU cc_start: 0.8832 (tt0) cc_final: 0.8580 (tt0) REVERT: A 411 MET cc_start: 0.9143 (OUTLIER) cc_final: 0.8890 (tpp) REVERT: B 12 MET cc_start: 0.8470 (mtm) cc_final: 0.8251 (mtm) REVERT: B 111 MET cc_start: 0.9153 (tpp) cc_final: 0.8749 (tpp) REVERT: B 119 ASP cc_start: 0.9174 (m-30) cc_final: 0.8938 (m-30) REVERT: B 190 TYR cc_start: 0.7251 (p90) cc_final: 0.7005 (m-80) REVERT: B 364 ASN cc_start: 0.8739 (t0) cc_final: 0.8534 (t0) REVERT: B 384 GLU cc_start: 0.8847 (tt0) cc_final: 0.8505 (tt0) REVERT: B 421 PHE cc_start: 0.8155 (p90) cc_final: 0.7573 (p90) REVERT: C 12 MET cc_start: 0.8766 (mtm) cc_final: 0.8335 (mtm) REVERT: C 181 ASP cc_start: 0.9074 (t0) cc_final: 0.8752 (t0) REVERT: C 190 TYR cc_start: 0.7223 (p90) cc_final: 0.7017 (m-80) REVERT: C 281 TRP cc_start: 0.8496 (t60) cc_final: 0.8235 (t60) REVERT: C 330 GLN cc_start: 0.8947 (tm-30) cc_final: 0.8630 (tm-30) REVERT: C 411 MET cc_start: 0.9148 (OUTLIER) cc_final: 0.8887 (tpp) REVERT: D 181 ASP cc_start: 0.8871 (t0) cc_final: 0.8463 (t0) REVERT: D 281 TRP cc_start: 0.8360 (t60) cc_final: 0.8155 (t60) REVERT: D 330 GLN cc_start: 0.8998 (tm-30) cc_final: 0.8688 (tm-30) REVERT: D 364 ASN cc_start: 0.8862 (t0) cc_final: 0.8609 (t0) REVERT: D 384 GLU cc_start: 0.8854 (tt0) cc_final: 0.8601 (tt0) REVERT: D 411 MET cc_start: 0.9145 (OUTLIER) cc_final: 0.8889 (tpp) REVERT: E 111 MET cc_start: 0.9152 (tpp) cc_final: 0.8738 (tpp) REVERT: E 119 ASP cc_start: 0.9189 (m-30) cc_final: 0.8951 (m-30) REVERT: E 190 TYR cc_start: 0.7254 (p90) cc_final: 0.6993 (m-80) REVERT: E 364 ASN cc_start: 0.8749 (t0) cc_final: 0.8543 (t0) REVERT: E 384 GLU cc_start: 0.8863 (tt0) cc_final: 0.8514 (tt0) REVERT: E 421 PHE cc_start: 0.8151 (p90) cc_final: 0.7587 (p90) REVERT: F 12 MET cc_start: 0.8755 (mtm) cc_final: 0.8309 (mtm) REVERT: F 181 ASP cc_start: 0.9084 (t0) cc_final: 0.8757 (t0) REVERT: F 190 TYR cc_start: 0.7236 (p90) cc_final: 0.7021 (m-80) REVERT: F 281 TRP cc_start: 0.8489 (t60) cc_final: 0.8226 (t60) REVERT: F 330 GLN cc_start: 0.8958 (tm-30) cc_final: 0.8642 (tm-30) REVERT: F 411 MET cc_start: 0.9165 (OUTLIER) cc_final: 0.8907 (tpp) outliers start: 42 outliers final: 25 residues processed: 325 average time/residue: 0.3131 time to fit residues: 168.2796 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 : 2.800 ------------------------------------------------------------------------------- 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 315 LEU Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 411 MET Chi-restraints excluded: chain B residue 189 HIS Chi-restraints excluded: chain B residue 195 HIS 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 C residue 428 ILE Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 393 SER Chi-restraints excluded: chain D residue 411 MET 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 236 LEU Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 393 SER Chi-restraints excluded: chain F residue 411 MET Chi-restraints excluded: chain F residue 428 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 75 optimal weight: 6.9990 chunk 255 optimal weight: 7.9990 chunk 67 optimal weight: 10.0000 chunk 276 optimal weight: 7.9990 chunk 288 optimal weight: 7.9990 chunk 24 optimal weight: 10.0000 chunk 185 optimal weight: 1.9990 chunk 47 optimal weight: 6.9990 chunk 65 optimal weight: 0.6980 chunk 132 optimal weight: 50.0000 chunk 275 optimal weight: 10.0000 overall best weight: 4.9388 ------------------------------------------------------------------------------- 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 84 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.094585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.071568 restraints weight = 60311.452| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 3.77 r_work: 0.3041 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.4672 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= 0.188 Angle : 0.673 9.875 32442 Z= 0.335 Chirality : 0.044 0.188 3516 Planarity : 0.004 0.049 4194 Dihedral : 11.875 145.676 3342 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.53 % Favored : 94.26 % Rotamer: Outliers : 1.84 % Allowed : 10.46 % Favored : 87.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.16), residues: 2964 helix: 1.27 (0.13), residues: 1548 sheet: -1.41 (0.29), residues: 312 loop : -1.21 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 281 HIS 0.010 0.001 HIS F 189 PHE 0.017 0.002 PHE F 247 TYR 0.024 0.002 TYR F 407 ARG 0.004 0.000 ARG C 146 Details of bonding type rmsd hydrogen bonds : bond 0.03770 ( 1196) hydrogen bonds : angle 4.65758 ( 3552) covalent geometry : bond 0.00442 (23988) covalent geometry : angle 0.67338 (32442) *********************** 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 343 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 297 time to evaluate : 2.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 ASP cc_start: 0.8909 (t0) cc_final: 0.8487 (t0) REVERT: A 269 LYS cc_start: 0.7880 (tttt) cc_final: 0.7582 (tttt) REVERT: A 281 TRP cc_start: 0.8345 (t60) cc_final: 0.8137 (t60) REVERT: A 297 GLN cc_start: 0.9227 (mm-40) cc_final: 0.8765 (tm-30) REVERT: A 330 GLN cc_start: 0.9034 (tm-30) cc_final: 0.8690 (tm-30) REVERT: A 364 ASN cc_start: 0.8834 (t0) cc_final: 0.8596 (t0) REVERT: A 384 GLU cc_start: 0.8869 (tt0) cc_final: 0.8607 (tt0) REVERT: A 411 MET cc_start: 0.9142 (OUTLIER) cc_final: 0.8877 (tpp) REVERT: B 12 MET cc_start: 0.8540 (mtm) cc_final: 0.8264 (mtm) REVERT: B 111 MET cc_start: 0.9200 (tpp) cc_final: 0.8812 (tpp) REVERT: B 119 ASP cc_start: 0.9175 (m-30) cc_final: 0.8929 (m-30) REVERT: B 146 ARG cc_start: 0.8287 (ptt180) cc_final: 0.8003 (ptm-80) REVERT: B 273 VAL cc_start: 0.8686 (OUTLIER) cc_final: 0.8466 (p) REVERT: B 281 TRP cc_start: 0.8478 (t60) cc_final: 0.8262 (t60) REVERT: B 297 GLN cc_start: 0.9227 (mm-40) cc_final: 0.8740 (tm-30) REVERT: B 364 ASN cc_start: 0.8793 (t0) cc_final: 0.8559 (t0) REVERT: B 384 GLU cc_start: 0.8882 (tt0) cc_final: 0.8581 (tt0) REVERT: C 12 MET cc_start: 0.8779 (mtm) cc_final: 0.8329 (mtm) REVERT: C 181 ASP cc_start: 0.9026 (t0) cc_final: 0.8623 (t0) REVERT: C 281 TRP cc_start: 0.8437 (t60) cc_final: 0.8184 (t60) REVERT: C 297 GLN cc_start: 0.9266 (mm-40) cc_final: 0.8760 (tm-30) REVERT: C 330 GLN cc_start: 0.8971 (tm-30) cc_final: 0.8626 (tm-30) REVERT: D 111 MET cc_start: 0.9137 (tpp) cc_final: 0.8823 (tpp) REVERT: D 181 ASP cc_start: 0.8912 (t0) cc_final: 0.8443 (t0) REVERT: D 269 LYS cc_start: 0.7867 (tttt) cc_final: 0.7574 (tttt) REVERT: D 281 TRP cc_start: 0.8340 (t60) cc_final: 0.8117 (t60) REVERT: D 297 GLN cc_start: 0.9228 (mm-40) cc_final: 0.8764 (tm-30) REVERT: D 330 GLN cc_start: 0.9032 (tm-30) cc_final: 0.8690 (tm-30) REVERT: D 364 ASN cc_start: 0.8814 (t0) cc_final: 0.8573 (t0) REVERT: D 384 GLU cc_start: 0.8895 (tt0) cc_final: 0.8624 (tt0) REVERT: D 411 MET cc_start: 0.9143 (OUTLIER) cc_final: 0.8888 (tpp) REVERT: E 111 MET cc_start: 0.9170 (tpp) cc_final: 0.8776 (tpp) REVERT: E 119 ASP cc_start: 0.9179 (m-30) cc_final: 0.8931 (m-30) REVERT: E 146 ARG cc_start: 0.8314 (ptt180) cc_final: 0.8029 (ptm-80) REVERT: E 273 VAL cc_start: 0.8691 (OUTLIER) cc_final: 0.8474 (p) REVERT: E 281 TRP cc_start: 0.8469 (t60) cc_final: 0.8250 (t60) REVERT: E 297 GLN cc_start: 0.9229 (mm-40) cc_final: 0.8742 (tm-30) REVERT: E 364 ASN cc_start: 0.8777 (t0) cc_final: 0.8541 (t0) REVERT: E 384 GLU cc_start: 0.8881 (tt0) cc_final: 0.8582 (tt0) REVERT: F 12 MET cc_start: 0.8783 (mtm) cc_final: 0.8331 (mtm) REVERT: F 181 ASP cc_start: 0.9023 (t0) cc_final: 0.8621 (t0) REVERT: F 260 MET cc_start: 0.9185 (tpp) cc_final: 0.8891 (tpt) REVERT: F 281 TRP cc_start: 0.8429 (t60) cc_final: 0.8183 (t60) REVERT: F 297 GLN cc_start: 0.9243 (mm-40) cc_final: 0.8761 (tm-30) REVERT: F 330 GLN cc_start: 0.8996 (tm-30) cc_final: 0.8625 (tm-30) outliers start: 46 outliers final: 31 residues processed: 320 average time/residue: 0.3204 time to fit residues: 167.5934 Evaluate side-chains 286 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 251 time to evaluate : 2.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 411 MET 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 273 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 B residue 407 TYR Chi-restraints excluded: chain C residue 195 HIS Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 362 GLU 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 428 ILE Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 393 SER Chi-restraints excluded: chain D residue 411 MET Chi-restraints excluded: chain E residue 236 LEU 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 392 VAL Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain E residue 407 TYR 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 428 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 167 optimal weight: 7.9990 chunk 47 optimal weight: 6.9990 chunk 252 optimal weight: 6.9990 chunk 55 optimal weight: 5.9990 chunk 148 optimal weight: 5.9990 chunk 140 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 250 optimal weight: 1.9990 chunk 191 optimal weight: 5.9990 chunk 159 optimal weight: 9.9990 chunk 10 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 40 GLN F 40 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.095445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.072215 restraints weight = 59975.828| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 3.75 r_work: 0.3056 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.4932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 23988 Z= 0.166 Angle : 0.667 9.382 32442 Z= 0.331 Chirality : 0.043 0.184 3516 Planarity : 0.004 0.059 4194 Dihedral : 11.008 154.288 3342 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.57 % Favored : 94.40 % Rotamer: Outliers : 1.84 % Allowed : 11.38 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.16), residues: 2964 helix: 1.44 (0.14), residues: 1512 sheet: -1.31 (0.30), residues: 312 loop : -1.07 (0.18), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 281 HIS 0.003 0.001 HIS B 57 PHE 0.019 0.002 PHE E 247 TYR 0.024 0.002 TYR F 407 ARG 0.005 0.000 ARG A 146 Details of bonding type rmsd hydrogen bonds : bond 0.03621 ( 1196) hydrogen bonds : angle 4.57725 ( 3552) covalent geometry : bond 0.00390 (23988) covalent geometry : angle 0.66729 (32442) *********************** 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: 46 poor density : 296 time to evaluate : 2.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 MET cc_start: 0.9138 (tpp) cc_final: 0.8821 (tpp) REVERT: A 119 ASP cc_start: 0.9198 (m-30) cc_final: 0.8980 (m-30) REVERT: A 181 ASP cc_start: 0.8879 (t0) cc_final: 0.8497 (t0) REVERT: A 269 LYS cc_start: 0.7873 (tttt) cc_final: 0.7573 (tttt) REVERT: A 297 GLN cc_start: 0.9223 (mm-40) cc_final: 0.8763 (tm-30) REVERT: A 330 GLN cc_start: 0.9052 (tm-30) cc_final: 0.8704 (tm-30) REVERT: A 364 ASN cc_start: 0.8874 (t0) cc_final: 0.8603 (t0) REVERT: A 384 GLU cc_start: 0.8868 (tt0) cc_final: 0.8566 (tt0) REVERT: B 12 MET cc_start: 0.8502 (mtm) cc_final: 0.8236 (mtm) REVERT: B 111 MET cc_start: 0.9192 (tpp) cc_final: 0.8812 (tpp) REVERT: B 119 ASP cc_start: 0.9160 (m-30) cc_final: 0.8938 (m-30) REVERT: B 297 GLN cc_start: 0.9207 (mm-40) cc_final: 0.8755 (tm-30) REVERT: B 364 ASN cc_start: 0.8794 (t0) cc_final: 0.8563 (t0) REVERT: B 384 GLU cc_start: 0.8853 (tt0) cc_final: 0.8522 (tt0) REVERT: C 12 MET cc_start: 0.8782 (mtm) cc_final: 0.8366 (mtm) REVERT: C 119 ASP cc_start: 0.9133 (OUTLIER) cc_final: 0.8902 (m-30) REVERT: C 181 ASP cc_start: 0.9044 (t0) cc_final: 0.8766 (t0) REVERT: C 281 TRP cc_start: 0.8418 (t60) cc_final: 0.8189 (t60) REVERT: C 297 GLN cc_start: 0.9244 (mm-40) cc_final: 0.8768 (tm-30) REVERT: C 330 GLN cc_start: 0.8972 (tm-30) cc_final: 0.8637 (tm-30) REVERT: D 111 MET cc_start: 0.9151 (tpp) cc_final: 0.8831 (tpp) REVERT: D 119 ASP cc_start: 0.9196 (m-30) cc_final: 0.8976 (m-30) REVERT: D 181 ASP cc_start: 0.9103 (t0) cc_final: 0.8798 (t0) REVERT: D 269 LYS cc_start: 0.7880 (tttt) cc_final: 0.7590 (tttt) REVERT: D 297 GLN cc_start: 0.9223 (mm-40) cc_final: 0.8760 (tm-30) REVERT: D 330 GLN cc_start: 0.9038 (tm-30) cc_final: 0.8691 (tm-30) REVERT: D 364 ASN cc_start: 0.8855 (t0) cc_final: 0.8578 (t0) REVERT: D 384 GLU cc_start: 0.8890 (tt0) cc_final: 0.8609 (tt0) REVERT: E 111 MET cc_start: 0.9179 (tpp) cc_final: 0.8790 (tpp) REVERT: E 119 ASP cc_start: 0.9163 (m-30) cc_final: 0.8935 (m-30) REVERT: E 273 VAL cc_start: 0.8632 (OUTLIER) cc_final: 0.8419 (p) REVERT: E 364 ASN cc_start: 0.8784 (t0) cc_final: 0.8542 (t0) REVERT: E 384 GLU cc_start: 0.8859 (tt0) cc_final: 0.8533 (tt0) REVERT: F 12 MET cc_start: 0.8800 (mtm) cc_final: 0.8387 (mtm) REVERT: F 181 ASP cc_start: 0.9043 (t0) cc_final: 0.8764 (t0) REVERT: F 260 MET cc_start: 0.9180 (tpp) cc_final: 0.8873 (tpt) REVERT: F 281 TRP cc_start: 0.8417 (t60) cc_final: 0.8190 (t60) REVERT: F 297 GLN cc_start: 0.9241 (mm-40) cc_final: 0.8772 (tm-30) REVERT: F 330 GLN cc_start: 0.8982 (tm-30) cc_final: 0.8644 (tm-30) outliers start: 46 outliers final: 29 residues processed: 323 average time/residue: 0.3011 time to fit residues: 161.6236 Evaluate side-chains 295 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 264 time to evaluate : 2.751 ------------------------------------------------------------------------------- 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 315 LEU Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 411 MET 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 119 ASP Chi-restraints excluded: chain C residue 195 HIS Chi-restraints excluded: chain C residue 236 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 407 TYR Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 393 SER Chi-restraints excluded: chain D residue 411 MET 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 195 HIS 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 145 optimal weight: 5.9990 chunk 228 optimal weight: 0.0980 chunk 262 optimal weight: 10.0000 chunk 191 optimal weight: 8.9990 chunk 189 optimal weight: 10.0000 chunk 83 optimal weight: 20.0000 chunk 224 optimal weight: 1.9990 chunk 167 optimal weight: 0.7980 chunk 46 optimal weight: 9.9990 chunk 197 optimal weight: 6.9990 chunk 283 optimal weight: 0.8980 overall best weight: 1.9584 ------------------------------------------------------------------------------- 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 = 0.3687 r_free = 0.3687 target = 0.097180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.074338 restraints weight = 59498.163| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 3.74 r_work: 0.3102 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.5171 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= 0.127 Angle : 0.648 9.449 32442 Z= 0.324 Chirality : 0.043 0.174 3516 Planarity : 0.004 0.059 4194 Dihedral : 10.390 178.491 3342 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 1.32 % Allowed : 13.06 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.16), residues: 2964 helix: 1.54 (0.14), residues: 1512 sheet: -0.95 (0.27), residues: 402 loop : -0.82 (0.19), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 281 HIS 0.003 0.001 HIS A 408 PHE 0.035 0.002 PHE B 360 TYR 0.024 0.002 TYR C 407 ARG 0.004 0.000 ARG B 146 Details of bonding type rmsd hydrogen bonds : bond 0.03478 ( 1196) hydrogen bonds : angle 4.52194 ( 3552) covalent geometry : bond 0.00295 (23988) covalent geometry : angle 0.64786 (32442) *********************** 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 325 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 292 time to evaluate : 2.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 MET cc_start: 0.9159 (tpp) cc_final: 0.8839 (tpp) REVERT: A 119 ASP cc_start: 0.9188 (m-30) cc_final: 0.8985 (m-30) REVERT: A 181 ASP cc_start: 0.8902 (t0) cc_final: 0.8501 (t0) REVERT: A 254 ASN cc_start: 0.8112 (t0) cc_final: 0.7736 (t0) REVERT: A 269 LYS cc_start: 0.7900 (tttt) cc_final: 0.7632 (tptt) REVERT: A 297 GLN cc_start: 0.9236 (mm-40) cc_final: 0.8767 (tm-30) REVERT: A 330 GLN cc_start: 0.9008 (tm-30) cc_final: 0.8735 (tm-30) REVERT: A 364 ASN cc_start: 0.8869 (t0) cc_final: 0.8605 (t0) REVERT: A 411 MET cc_start: 0.9115 (OUTLIER) cc_final: 0.8869 (tpp) REVERT: B 111 MET cc_start: 0.9213 (tpp) cc_final: 0.8858 (tpp) REVERT: B 119 ASP cc_start: 0.9159 (m-30) cc_final: 0.8942 (m-30) REVERT: B 142 GLU cc_start: 0.8642 (tt0) cc_final: 0.8309 (tt0) REVERT: B 254 ASN cc_start: 0.8136 (t0) cc_final: 0.7874 (t0) REVERT: B 330 GLN cc_start: 0.8746 (tm-30) cc_final: 0.8399 (tm-30) REVERT: B 364 ASN cc_start: 0.8822 (t0) cc_final: 0.8573 (t0) REVERT: B 384 GLU cc_start: 0.8846 (tt0) cc_final: 0.8521 (tt0) REVERT: B 402 GLU cc_start: 0.8921 (mt-10) cc_final: 0.8611 (mt-10) REVERT: C 12 MET cc_start: 0.8733 (mtm) cc_final: 0.8349 (mtm) REVERT: C 40 GLN cc_start: 0.8841 (mp10) cc_final: 0.8299 (pt0) REVERT: C 111 MET cc_start: 0.9139 (tpp) cc_final: 0.8784 (tpp) REVERT: C 119 ASP cc_start: 0.9120 (OUTLIER) cc_final: 0.8887 (m-30) REVERT: C 142 GLU cc_start: 0.8857 (tt0) cc_final: 0.8535 (tt0) REVERT: C 181 ASP cc_start: 0.9042 (t0) cc_final: 0.8743 (t0) REVERT: C 330 GLN cc_start: 0.8938 (tm-30) cc_final: 0.8684 (tm-30) REVERT: D 111 MET cc_start: 0.9165 (tpp) cc_final: 0.8842 (tpp) REVERT: D 146 ARG cc_start: 0.8589 (OUTLIER) cc_final: 0.8320 (mmm-85) REVERT: D 181 ASP cc_start: 0.9053 (t0) cc_final: 0.8774 (t0) REVERT: D 269 LYS cc_start: 0.7909 (tttt) cc_final: 0.7629 (tptt) REVERT: D 297 GLN cc_start: 0.9204 (mm-40) cc_final: 0.8748 (tm-30) REVERT: D 330 GLN cc_start: 0.9005 (tm-30) cc_final: 0.8734 (tm-30) REVERT: D 364 ASN cc_start: 0.8863 (t0) cc_final: 0.8598 (t0) REVERT: D 384 GLU cc_start: 0.8866 (tt0) cc_final: 0.8628 (tt0) REVERT: E 111 MET cc_start: 0.9200 (tpp) cc_final: 0.8835 (tpp) REVERT: E 119 ASP cc_start: 0.9157 (m-30) cc_final: 0.8935 (m-30) REVERT: E 142 GLU cc_start: 0.8639 (tt0) cc_final: 0.8303 (tt0) REVERT: E 233 MET cc_start: 0.8511 (mmm) cc_final: 0.7908 (mmm) REVERT: E 254 ASN cc_start: 0.8129 (t0) cc_final: 0.7847 (t0) REVERT: E 260 MET cc_start: 0.9139 (OUTLIER) cc_final: 0.8931 (tpt) REVERT: E 297 GLN cc_start: 0.9227 (mm-40) cc_final: 0.8745 (tm-30) REVERT: E 330 GLN cc_start: 0.8752 (tm-30) cc_final: 0.8389 (tm-30) REVERT: E 364 ASN cc_start: 0.8839 (t0) cc_final: 0.8608 (t0) REVERT: E 384 GLU cc_start: 0.8860 (tt0) cc_final: 0.8533 (tt0) REVERT: F 12 MET cc_start: 0.8740 (mtm) cc_final: 0.8354 (mtm) REVERT: F 40 GLN cc_start: 0.8825 (mp10) cc_final: 0.8283 (pt0) REVERT: F 111 MET cc_start: 0.9134 (tpp) cc_final: 0.8779 (tpp) REVERT: F 142 GLU cc_start: 0.8860 (tt0) cc_final: 0.8536 (tt0) REVERT: F 181 ASP cc_start: 0.9031 (t0) cc_final: 0.8736 (t0) REVERT: F 330 GLN cc_start: 0.8940 (tm-30) cc_final: 0.8683 (tm-30) outliers start: 33 outliers final: 28 residues processed: 310 average time/residue: 0.3240 time to fit residues: 165.6067 Evaluate side-chains 303 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 271 time to evaluate : 2.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 411 MET Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 260 MET Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain C residue 119 ASP Chi-restraints excluded: chain C residue 189 HIS Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain D residue 146 ARG Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 292 GLU Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 393 SER Chi-restraints excluded: chain D residue 411 MET 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 F residue 236 LEU Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 392 VAL Chi-restraints excluded: chain F residue 393 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 253 optimal weight: 6.9990 chunk 30 optimal weight: 20.0000 chunk 78 optimal weight: 20.0000 chunk 22 optimal weight: 0.0170 chunk 120 optimal weight: 20.0000 chunk 175 optimal weight: 7.9990 chunk 138 optimal weight: 9.9990 chunk 205 optimal weight: 7.9990 chunk 164 optimal weight: 10.0000 chunk 290 optimal weight: 6.9990 chunk 245 optimal weight: 30.0000 overall best weight: 6.0026 ------------------------------------------------------------------------------- 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 = 0.3632 r_free = 0.3632 target = 0.093848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.070488 restraints weight = 60481.078| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 3.71 r_work: 0.3020 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.5177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 23988 Z= 0.218 Angle : 0.705 10.414 32442 Z= 0.354 Chirality : 0.045 0.302 3516 Planarity : 0.005 0.058 4194 Dihedral : 10.092 176.074 3342 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 1.76 % Allowed : 13.22 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.16), residues: 2964 helix: 1.46 (0.14), residues: 1512 sheet: -0.87 (0.29), residues: 336 loop : -0.88 (0.19), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 281 HIS 0.005 0.001 HIS F 450 PHE 0.032 0.002 PHE F 360 TYR 0.023 0.002 TYR C 407 ARG 0.004 0.000 ARG D 146 Details of bonding type rmsd hydrogen bonds : bond 0.03845 ( 1196) hydrogen bonds : angle 4.67715 ( 3552) covalent geometry : bond 0.00507 (23988) covalent geometry : angle 0.70500 (32442) *********************** 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 306 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 262 time to evaluate : 2.556 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 111 MET cc_start: 0.9168 (tpp) cc_final: 0.8846 (tpp) REVERT: A 181 ASP cc_start: 0.8949 (t0) cc_final: 0.8584 (t0) REVERT: A 269 LYS cc_start: 0.7761 (tttt) cc_final: 0.7533 (tptt) REVERT: A 281 TRP cc_start: 0.8245 (t60) cc_final: 0.7748 (t60) REVERT: A 297 GLN cc_start: 0.9235 (mm-40) cc_final: 0.8768 (tm-30) REVERT: A 330 GLN cc_start: 0.9071 (tm-30) cc_final: 0.8721 (tm-30) REVERT: A 364 ASN cc_start: 0.8884 (t0) cc_final: 0.8644 (t0) REVERT: B 40 GLN cc_start: 0.8761 (mp10) cc_final: 0.8284 (pt0) REVERT: B 111 MET cc_start: 0.9238 (tpp) cc_final: 0.8850 (tpp) REVERT: B 119 ASP cc_start: 0.9167 (m-30) cc_final: 0.8955 (m-30) REVERT: B 254 ASN cc_start: 0.8104 (t0) cc_final: 0.7872 (t0) REVERT: B 297 GLN cc_start: 0.9231 (mm-40) cc_final: 0.8743 (tm-30) REVERT: B 364 ASN cc_start: 0.8794 (t0) cc_final: 0.8551 (t0) REVERT: B 384 GLU cc_start: 0.8887 (tt0) cc_final: 0.8566 (tt0) REVERT: C 12 MET cc_start: 0.8808 (mtm) cc_final: 0.8323 (mtm) REVERT: C 119 ASP cc_start: 0.9135 (OUTLIER) cc_final: 0.8911 (m-30) REVERT: C 181 ASP cc_start: 0.9039 (t0) cc_final: 0.8687 (t0) REVERT: C 297 GLN cc_start: 0.9257 (mm-40) cc_final: 0.8776 (tm-30) REVERT: C 330 GLN cc_start: 0.8982 (tm-30) cc_final: 0.8630 (tm-30) REVERT: D 111 MET cc_start: 0.9178 (tpp) cc_final: 0.8857 (tpp) REVERT: D 146 ARG cc_start: 0.8638 (OUTLIER) cc_final: 0.8386 (mmm-85) REVERT: D 181 ASP cc_start: 0.9003 (t0) cc_final: 0.8629 (t0) REVERT: D 269 LYS cc_start: 0.7773 (tttt) cc_final: 0.7500 (tttt) REVERT: D 281 TRP cc_start: 0.8260 (t60) cc_final: 0.7690 (t60) REVERT: D 292 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.8058 (mt-10) REVERT: D 297 GLN cc_start: 0.9232 (mm-40) cc_final: 0.8749 (tm-30) REVERT: D 330 GLN cc_start: 0.9064 (tm-30) cc_final: 0.8720 (tm-30) REVERT: D 364 ASN cc_start: 0.8867 (t0) cc_final: 0.8635 (t0) REVERT: D 384 GLU cc_start: 0.8911 (tt0) cc_final: 0.8581 (tt0) REVERT: E 40 GLN cc_start: 0.8766 (mp10) cc_final: 0.8288 (pt0) REVERT: E 111 MET cc_start: 0.9223 (tpp) cc_final: 0.8835 (tpp) REVERT: E 119 ASP cc_start: 0.9165 (m-30) cc_final: 0.8952 (m-30) REVERT: E 233 MET cc_start: 0.8527 (mmm) cc_final: 0.7734 (mmm) REVERT: E 254 ASN cc_start: 0.8109 (t0) cc_final: 0.7865 (t0) REVERT: E 273 VAL cc_start: 0.8698 (OUTLIER) cc_final: 0.8427 (p) REVERT: E 292 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8163 (mt-10) REVERT: E 297 GLN cc_start: 0.9222 (mm-40) cc_final: 0.8750 (tm-30) REVERT: E 364 ASN cc_start: 0.8803 (t0) cc_final: 0.8495 (t0) REVERT: E 384 GLU cc_start: 0.8879 (tt0) cc_final: 0.8570 (tt0) REVERT: F 12 MET cc_start: 0.8811 (mtm) cc_final: 0.8352 (mtm) REVERT: F 181 ASP cc_start: 0.9032 (t0) cc_final: 0.8672 (t0) REVERT: F 297 GLN cc_start: 0.9263 (mm-40) cc_final: 0.8775 (tm-30) REVERT: F 330 GLN cc_start: 0.8985 (tm-30) cc_final: 0.8621 (tm-30) outliers start: 44 outliers final: 29 residues processed: 284 average time/residue: 0.3098 time to fit residues: 146.3997 Evaluate side-chains 287 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 253 time to evaluate : 2.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 315 LEU 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 314 ILE Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 407 TYR Chi-restraints excluded: chain C residue 119 ASP Chi-restraints excluded: chain C residue 189 HIS Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 386 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 C residue 428 ILE Chi-restraints excluded: chain D residue 146 ARG Chi-restraints excluded: chain D residue 292 GLU Chi-restraints excluded: chain D residue 315 LEU 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 273 VAL 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 407 TYR Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 392 VAL Chi-restraints excluded: chain F residue 393 SER Chi-restraints excluded: chain F residue 402 GLU Chi-restraints excluded: chain F residue 407 TYR Chi-restraints excluded: chain F residue 428 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 94 optimal weight: 5.9990 chunk 26 optimal weight: 0.0980 chunk 254 optimal weight: 8.9990 chunk 289 optimal weight: 0.9990 chunk 278 optimal weight: 0.1980 chunk 169 optimal weight: 9.9990 chunk 96 optimal weight: 0.9980 chunk 90 optimal weight: 20.0000 chunk 215 optimal weight: 7.9990 chunk 151 optimal weight: 5.9990 chunk 260 optimal weight: 4.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN A 84 GLN B 135 ASN C 40 GLN D 40 GLN D 135 ASN E 135 ASN F 40 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.097938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.074855 restraints weight = 59843.970| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 3.78 r_work: 0.3113 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.5421 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= 0.119 Angle : 0.639 9.372 32442 Z= 0.319 Chirality : 0.043 0.275 3516 Planarity : 0.004 0.045 4194 Dihedral : 10.007 179.654 3342 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.16 % Allowed : 14.22 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.16), residues: 2964 helix: 1.65 (0.14), residues: 1512 sheet: -0.48 (0.32), residues: 306 loop : -0.78 (0.19), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 281 HIS 0.002 0.001 HIS E 57 PHE 0.032 0.002 PHE F 360 TYR 0.024 0.002 TYR C 407 ARG 0.004 0.000 ARG F 146 Details of bonding type rmsd hydrogen bonds : bond 0.03359 ( 1196) hydrogen bonds : angle 4.44114 ( 3552) covalent geometry : bond 0.00273 (23988) covalent geometry : angle 0.63873 (32442) *********************** 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 329 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 300 time to evaluate : 2.722 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 181 ASP cc_start: 0.8883 (t0) cc_final: 0.8478 (t0) REVERT: A 254 ASN cc_start: 0.8065 (t0) cc_final: 0.7798 (t0) REVERT: A 269 LYS cc_start: 0.7823 (tttt) cc_final: 0.7604 (tptt) REVERT: A 281 TRP cc_start: 0.8115 (t60) cc_final: 0.7574 (t60) REVERT: A 297 GLN cc_start: 0.9223 (mm-40) cc_final: 0.8778 (tm-30) REVERT: A 330 GLN cc_start: 0.9046 (tm-30) cc_final: 0.8787 (tm-30) REVERT: A 364 ASN cc_start: 0.8858 (t0) cc_final: 0.8624 (t0) REVERT: A 411 MET cc_start: 0.9094 (OUTLIER) cc_final: 0.8864 (tpp) REVERT: B 111 MET cc_start: 0.9226 (tpp) cc_final: 0.8891 (tpp) REVERT: B 119 ASP cc_start: 0.9161 (m-30) cc_final: 0.8941 (m-30) REVERT: B 142 GLU cc_start: 0.8638 (tt0) cc_final: 0.8287 (tt0) REVERT: B 233 MET cc_start: 0.8332 (mmm) cc_final: 0.7961 (mmm) REVERT: B 252 PHE cc_start: 0.6932 (t80) cc_final: 0.6714 (t80) REVERT: B 254 ASN cc_start: 0.8039 (t0) cc_final: 0.7714 (t0) REVERT: B 330 GLN cc_start: 0.8813 (tm-30) cc_final: 0.8453 (tm-30) REVERT: B 352 THR cc_start: 0.9079 (m) cc_final: 0.8781 (p) REVERT: B 364 ASN cc_start: 0.8788 (t0) cc_final: 0.8567 (t0) REVERT: B 384 GLU cc_start: 0.8854 (tt0) cc_final: 0.8487 (tt0) REVERT: B 402 GLU cc_start: 0.8922 (mt-10) cc_final: 0.8616 (mt-10) REVERT: C 12 MET cc_start: 0.8727 (mtm) cc_final: 0.8358 (mtm) REVERT: C 111 MET cc_start: 0.9138 (tpp) cc_final: 0.8801 (tpp) REVERT: C 119 ASP cc_start: 0.9124 (OUTLIER) cc_final: 0.8900 (m-30) REVERT: C 142 GLU cc_start: 0.8818 (tt0) cc_final: 0.8511 (tt0) REVERT: C 181 ASP cc_start: 0.9044 (t0) cc_final: 0.8711 (t0) REVERT: C 330 GLN cc_start: 0.8901 (tm-30) cc_final: 0.8699 (tm-30) REVERT: D 111 MET cc_start: 0.9188 (tpp) cc_final: 0.8844 (tpp) REVERT: D 119 ASP cc_start: 0.9207 (m-30) cc_final: 0.8988 (m-30) REVERT: D 146 ARG cc_start: 0.8535 (OUTLIER) cc_final: 0.8291 (mmm-85) REVERT: D 181 ASP cc_start: 0.8932 (t0) cc_final: 0.8516 (t0) REVERT: D 269 LYS cc_start: 0.7846 (tttt) cc_final: 0.7629 (tptt) REVERT: D 281 TRP cc_start: 0.8133 (t60) cc_final: 0.7586 (t60) REVERT: D 297 GLN cc_start: 0.9208 (mm-40) cc_final: 0.8756 (tm-30) REVERT: D 330 GLN cc_start: 0.9039 (tm-30) cc_final: 0.8789 (tm-30) REVERT: D 364 ASN cc_start: 0.8830 (t0) cc_final: 0.8600 (t0) REVERT: E 111 MET cc_start: 0.9210 (tpp) cc_final: 0.8872 (tpp) REVERT: E 119 ASP cc_start: 0.9174 (m-30) cc_final: 0.8955 (m-30) REVERT: E 142 GLU cc_start: 0.8630 (tt0) cc_final: 0.8279 (tt0) REVERT: E 254 ASN cc_start: 0.8014 (t0) cc_final: 0.7680 (t0) REVERT: E 292 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.8231 (mt-10) REVERT: E 330 GLN cc_start: 0.8840 (tm-30) cc_final: 0.8453 (tm-30) REVERT: E 343 ILE cc_start: 0.8663 (mt) cc_final: 0.8362 (mp) REVERT: E 364 ASN cc_start: 0.8874 (t0) cc_final: 0.8564 (t0) REVERT: E 384 GLU cc_start: 0.8867 (tt0) cc_final: 0.8510 (tt0) REVERT: F 12 MET cc_start: 0.8732 (mtm) cc_final: 0.8360 (mtm) REVERT: F 111 MET cc_start: 0.9154 (tpp) cc_final: 0.8824 (tpp) REVERT: F 142 GLU cc_start: 0.8834 (tt0) cc_final: 0.8528 (tt0) REVERT: F 181 ASP cc_start: 0.9017 (t0) cc_final: 0.8697 (t0) REVERT: F 330 GLN cc_start: 0.8927 (tm-30) cc_final: 0.8715 (tm-30) outliers start: 29 outliers final: 16 residues processed: 320 average time/residue: 0.3453 time to fit residues: 182.8069 Evaluate side-chains 286 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 266 time to evaluate : 2.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 411 MET Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 366 MET Chi-restraints excluded: chain C residue 119 ASP Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain D residue 146 ARG Chi-restraints excluded: chain D residue 292 GLU Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 411 MET Chi-restraints excluded: chain E residue 292 GLU Chi-restraints excluded: chain E residue 314 ILE 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 386 LEU Chi-restraints excluded: chain F residue 393 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 283 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 93 optimal weight: 6.9990 chunk 234 optimal weight: 3.9990 chunk 275 optimal weight: 3.9990 chunk 142 optimal weight: 9.9990 chunk 94 optimal weight: 4.9990 chunk 236 optimal weight: 6.9990 chunk 99 optimal weight: 5.9990 chunk 127 optimal weight: 0.0070 chunk 2 optimal weight: 0.0170 overall best weight: 2.0042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 40 GLN E 40 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.097200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.074267 restraints weight = 60092.867| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 3.77 r_work: 0.3112 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.5514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 23988 Z= 0.128 Angle : 0.653 9.362 32442 Z= 0.327 Chirality : 0.043 0.248 3516 Planarity : 0.004 0.050 4194 Dihedral : 9.831 176.551 3342 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 0.68 % Allowed : 15.22 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.16), residues: 2964 helix: 1.64 (0.14), residues: 1512 sheet: -0.42 (0.32), residues: 306 loop : -0.69 (0.19), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 281 HIS 0.003 0.001 HIS F 258 PHE 0.042 0.002 PHE B 360 TYR 0.024 0.002 TYR C 407 ARG 0.004 0.000 ARG D 146 Details of bonding type rmsd hydrogen bonds : bond 0.03355 ( 1196) hydrogen bonds : angle 4.43068 ( 3552) covalent geometry : bond 0.00300 (23988) covalent geometry : angle 0.65275 (32442) ********************** 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 297 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 280 time to evaluate : 3.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 MET cc_start: 0.9177 (tpp) cc_final: 0.8847 (tpp) REVERT: A 181 ASP cc_start: 0.8927 (t0) cc_final: 0.8542 (t0) REVERT: A 254 ASN cc_start: 0.8112 (t0) cc_final: 0.7859 (t0) REVERT: A 281 TRP cc_start: 0.8063 (t60) cc_final: 0.7685 (t60) REVERT: A 297 GLN cc_start: 0.9203 (mm-40) cc_final: 0.8763 (tm-30) REVERT: A 314 ILE cc_start: 0.8568 (mp) cc_final: 0.8207 (mt) REVERT: A 364 ASN cc_start: 0.8856 (t0) cc_final: 0.8628 (t0) REVERT: B 111 MET cc_start: 0.9213 (tpp) cc_final: 0.8871 (tpp) REVERT: B 119 ASP cc_start: 0.9203 (m-30) cc_final: 0.8973 (m-30) REVERT: B 142 GLU cc_start: 0.8671 (tt0) cc_final: 0.8291 (tt0) REVERT: B 233 MET cc_start: 0.8422 (mmm) cc_final: 0.8037 (mmm) REVERT: B 252 PHE cc_start: 0.6930 (t80) cc_final: 0.6696 (t80) REVERT: B 254 ASN cc_start: 0.8042 (t0) cc_final: 0.7760 (t0) REVERT: B 316 GLU cc_start: 0.8378 (mp0) cc_final: 0.8133 (mp0) REVERT: B 330 GLN cc_start: 0.8834 (tm-30) cc_final: 0.8515 (tm-30) REVERT: B 352 THR cc_start: 0.9039 (m) cc_final: 0.8814 (p) REVERT: B 364 ASN cc_start: 0.8815 (t0) cc_final: 0.8546 (t0) REVERT: B 384 GLU cc_start: 0.8854 (tt0) cc_final: 0.8653 (tm-30) REVERT: B 402 GLU cc_start: 0.8948 (mt-10) cc_final: 0.8639 (mt-10) REVERT: C 12 MET cc_start: 0.8680 (mtm) cc_final: 0.8276 (mtm) REVERT: C 40 GLN cc_start: 0.8808 (mp10) cc_final: 0.8298 (pt0) REVERT: C 111 MET cc_start: 0.9172 (tpp) cc_final: 0.8809 (tpp) REVERT: C 142 GLU cc_start: 0.8822 (tt0) cc_final: 0.8495 (tt0) REVERT: C 181 ASP cc_start: 0.9005 (t0) cc_final: 0.8642 (t0) REVERT: C 248 VAL cc_start: 0.8823 (m) cc_final: 0.8287 (t) REVERT: D 111 MET cc_start: 0.9198 (tpp) cc_final: 0.8861 (tpp) REVERT: D 146 ARG cc_start: 0.8530 (OUTLIER) cc_final: 0.8274 (mmm-85) REVERT: D 181 ASP cc_start: 0.8906 (t0) cc_final: 0.8500 (t0) REVERT: D 254 ASN cc_start: 0.8047 (t0) cc_final: 0.7771 (t0) REVERT: D 281 TRP cc_start: 0.8059 (t60) cc_final: 0.7709 (t60) REVERT: D 292 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.8139 (mt-10) REVERT: D 314 ILE cc_start: 0.8510 (mp) cc_final: 0.8231 (mt) REVERT: D 330 GLN cc_start: 0.9015 (tm-30) cc_final: 0.8775 (tm-30) REVERT: D 364 ASN cc_start: 0.8857 (t0) cc_final: 0.8635 (t0) REVERT: E 111 MET cc_start: 0.9209 (tpp) cc_final: 0.8857 (tpp) REVERT: E 119 ASP cc_start: 0.9175 (m-30) cc_final: 0.8946 (m-30) REVERT: E 142 GLU cc_start: 0.8653 (tt0) cc_final: 0.8289 (tt0) REVERT: E 254 ASN cc_start: 0.8028 (t0) cc_final: 0.7717 (t0) REVERT: E 260 MET cc_start: 0.9090 (tpt) cc_final: 0.8708 (tpt) REVERT: E 292 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.8271 (mt-10) REVERT: E 330 GLN cc_start: 0.8836 (tm-30) cc_final: 0.8485 (tm-30) REVERT: E 364 ASN cc_start: 0.8888 (t0) cc_final: 0.8579 (t0) REVERT: F 12 MET cc_start: 0.8683 (mtm) cc_final: 0.8275 (mtm) REVERT: F 40 GLN cc_start: 0.8792 (mp10) cc_final: 0.8292 (pt0) REVERT: F 111 MET cc_start: 0.9175 (tpp) cc_final: 0.8812 (tpp) REVERT: F 142 GLU cc_start: 0.8857 (tt0) cc_final: 0.8537 (tt0) REVERT: F 181 ASP cc_start: 0.9020 (t0) cc_final: 0.8687 (t0) REVERT: F 297 GLN cc_start: 0.9223 (mm-40) cc_final: 0.8752 (tm-30) REVERT: F 469 MET cc_start: 0.8989 (mmm) cc_final: 0.8273 (ttp) outliers start: 17 outliers final: 8 residues processed: 293 average time/residue: 0.3624 time to fit residues: 176.8137 Evaluate side-chains 267 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 256 time to evaluate : 2.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain D residue 146 ARG Chi-restraints excluded: chain D residue 292 GLU Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain E residue 292 GLU Chi-restraints excluded: chain E residue 314 ILE Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain F residue 386 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 90 optimal weight: 7.9990 chunk 265 optimal weight: 8.9990 chunk 86 optimal weight: 5.9990 chunk 83 optimal weight: 30.0000 chunk 148 optimal weight: 6.9990 chunk 22 optimal weight: 0.9980 chunk 244 optimal weight: 10.0000 chunk 144 optimal weight: 0.3980 chunk 158 optimal weight: 9.9990 chunk 216 optimal weight: 20.0000 chunk 103 optimal weight: 0.6980 overall best weight: 3.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN D 40 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.096660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.073842 restraints weight = 59880.176| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 3.75 r_work: 0.3095 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.5601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23988 Z= 0.145 Angle : 0.663 9.752 32442 Z= 0.332 Chirality : 0.044 0.252 3516 Planarity : 0.004 0.059 4194 Dihedral : 9.780 176.447 3342 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 0.60 % Allowed : 15.87 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.16), residues: 2964 helix: 1.64 (0.14), residues: 1512 sheet: -1.55 (0.32), residues: 276 loop : -0.44 (0.19), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 281 HIS 0.003 0.001 HIS E 408 PHE 0.040 0.002 PHE B 360 TYR 0.026 0.002 TYR C 407 ARG 0.004 0.000 ARG D 146 Details of bonding type rmsd hydrogen bonds : bond 0.03383 ( 1196) hydrogen bonds : angle 4.46074 ( 3552) covalent geometry : bond 0.00344 (23988) covalent geometry : angle 0.66292 (32442) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10711.04 seconds wall clock time: 188 minutes 46.59 seconds (11326.59 seconds total)