Starting phenix.real_space_refine on Sun Sep 29 16:12:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd0_6631/09_2024/3jd0_6631.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd0_6631/09_2024/3jd0_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd0_6631/09_2024/3jd0_6631.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd0_6631/09_2024/3jd0_6631.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd0_6631/09_2024/3jd0_6631.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd0_6631/09_2024/3jd0_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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 9.57, per 1000 atoms: 0.41 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: 6.95 Conformation dependent library (CDL) restraints added in 3.5 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: 2.53 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: 8.11 Time building geometry restraints manager: 7.96 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.110 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: 0.900 Check model and map are aligned: 0.160 Set scattering table: 0.180 Process input model: 48.910 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.850 ------------------------------------------------------------------------------- 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= 0.772 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 532 time to evaluate : 2.963 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: 0.3984 time to fit residues: 313.6074 Evaluate side-chains 264 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 264 time to evaluate : 2.935 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 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= 0.335 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 *********************** 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 fitting. rotamer outliers: 36 poor density : 335 time to evaluate : 2.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 169 MET cc_start: 0.7937 (mmp) cc_final: 0.7721 (mmt) REVERT: B 384 GLU cc_start: 0.7770 (tt0) cc_final: 0.7542 (tt0) REVERT: C 169 MET cc_start: 0.7869 (mmp) cc_final: 0.7653 (mmt) REVERT: C 181 ASP cc_start: 0.7758 (t0) cc_final: 0.7461 (t0) REVERT: E 169 MET cc_start: 0.7951 (mmp) cc_final: 0.7729 (mmt) REVERT: E 384 GLU cc_start: 0.7770 (tt0) cc_final: 0.7546 (tt0) REVERT: F 169 MET cc_start: 0.7872 (mmp) cc_final: 0.7657 (mmt) REVERT: F 181 ASP cc_start: 0.7774 (t0) cc_final: 0.7470 (t0) outliers start: 36 outliers final: 22 residues processed: 361 average time/residue: 0.3063 time to fit residues: 181.9266 Evaluate side-chains 249 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 227 time to evaluate : 2.940 ------------------------------------------------------------------------------- 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 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 148 optimal weight: 9.9990 chunk 82 optimal weight: 0.0170 chunk 222 optimal weight: 20.0000 chunk 181 optimal weight: 10.0000 chunk 73 optimal weight: 0.0980 chunk 267 optimal weight: 20.0000 chunk 288 optimal weight: 10.0000 chunk 238 optimal weight: 6.9990 chunk 265 optimal weight: 20.0000 chunk 91 optimal weight: 3.9990 chunk 214 optimal weight: 10.0000 overall best weight: 4.2224 ------------------------------------------------------------------------------- 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 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 135 ASN ** F 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.4053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 23988 Z= 0.273 Angle : 0.690 10.010 32442 Z= 0.348 Chirality : 0.045 0.192 3516 Planarity : 0.004 0.035 4194 Dihedral : 12.805 162.648 3342 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.89 % Favored : 94.91 % Rotamer: Outliers : 1.32 % Allowed : 7.37 % Favored : 91.31 % 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: -0.69 (0.15), residues: 2964 helix: 0.60 (0.13), residues: 1512 sheet: -1.61 (0.28), residues: 282 loop : -1.51 (0.18), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP B 281 HIS 0.012 0.001 HIS E 189 PHE 0.026 0.003 PHE D 360 TYR 0.026 0.002 TYR C 407 ARG 0.003 0.000 ARG C 363 *********************** 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 338 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 305 time to evaluate : 2.792 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: 0.7722 (t0) cc_final: 0.7507 (t0) REVERT: B 384 GLU cc_start: 0.7845 (tt0) cc_final: 0.7593 (tt0) REVERT: B 402 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7446 (mt-10) REVERT: C 181 ASP cc_start: 0.7755 (t0) cc_final: 0.7433 (t0) REVERT: D 181 ASP cc_start: 0.7720 (t0) cc_final: 0.7501 (t0) REVERT: E 384 GLU cc_start: 0.7841 (tt0) cc_final: 0.7595 (tt0) REVERT: F 181 ASP cc_start: 0.7753 (t0) cc_final: 0.7434 (t0) outliers start: 33 outliers final: 13 residues processed: 322 average time/residue: 0.3105 time to fit residues: 163.1668 Evaluate side-chains 244 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 231 time to evaluate : 2.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 407 TYR Chi-restraints excluded: chain D residue 255 VAL 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 F residue 236 LEU Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 407 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 264 optimal weight: 6.9990 chunk 201 optimal weight: 2.9990 chunk 138 optimal weight: 7.9990 chunk 29 optimal weight: 30.0000 chunk 127 optimal weight: 8.9990 chunk 179 optimal weight: 40.0000 chunk 268 optimal weight: 6.9990 chunk 284 optimal weight: 10.0000 chunk 140 optimal weight: 5.9990 chunk 254 optimal weight: 0.8980 chunk 76 optimal weight: 40.0000 overall best weight: 4.7788 ------------------------------------------------------------------------------- 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 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 391 HIS C 391 HIS D 205 GLN D 391 HIS ** E 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 391 HIS F 205 GLN F 391 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.4495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 23988 Z= 0.289 Angle : 0.684 9.939 32442 Z= 0.342 Chirality : 0.045 0.190 3516 Planarity : 0.005 0.056 4194 Dihedral : 12.426 155.669 3342 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.06 % Favored : 94.74 % Rotamer: Outliers : 1.80 % Allowed : 9.09 % Favored : 89.10 % 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: -0.19 (0.15), residues: 2964 helix: 1.01 (0.13), residues: 1548 sheet: -1.58 (0.28), residues: 312 loop : -1.28 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP A 281 HIS 0.011 0.001 HIS F 189 PHE 0.020 0.002 PHE C 247 TYR 0.025 0.002 TYR C 407 ARG 0.003 0.000 ARG F 211 *********************** 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 335 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 290 time to evaluate : 2.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 ASP cc_start: 0.7774 (t0) cc_final: 0.7521 (t0) REVERT: B 384 GLU cc_start: 0.7891 (tt0) cc_final: 0.7600 (tt0) REVERT: B 421 PHE cc_start: 0.7631 (p90) cc_final: 0.7378 (p90) REVERT: C 181 ASP cc_start: 0.7797 (t0) cc_final: 0.7481 (t0) REVERT: D 181 ASP cc_start: 0.7777 (t0) cc_final: 0.7512 (t0) REVERT: E 384 GLU cc_start: 0.7888 (tt0) cc_final: 0.7600 (tt0) REVERT: F 181 ASP cc_start: 0.7799 (t0) cc_final: 0.7483 (t0) outliers start: 45 outliers final: 29 residues processed: 314 average time/residue: 0.3212 time to fit residues: 164.4487 Evaluate side-chains 270 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 241 time to evaluate : 2.944 ------------------------------------------------------------------------------- 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 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 189 HIS Chi-restraints excluded: chain C residue 195 HIS Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain C residue 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 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 205 GLN 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 236 optimal weight: 8.9990 chunk 161 optimal weight: 5.9990 chunk 4 optimal weight: 0.7980 chunk 211 optimal weight: 3.9990 chunk 117 optimal weight: 10.0000 chunk 242 optimal weight: 20.0000 chunk 196 optimal weight: 30.0000 chunk 0 optimal weight: 30.0000 chunk 145 optimal weight: 5.9990 chunk 255 optimal weight: 6.9990 chunk 71 optimal weight: 20.0000 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN A 298 HIS B 40 GLN B 364 ASN C 40 GLN C 298 HIS D 40 GLN D 298 HIS E 40 GLN F 40 GLN F 298 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.4841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 23988 Z= 0.284 Angle : 0.688 9.830 32442 Z= 0.345 Chirality : 0.044 0.188 3516 Planarity : 0.004 0.045 4194 Dihedral : 11.907 145.662 3342 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.43 % Favored : 94.37 % Rotamer: Outliers : 1.72 % Allowed : 10.62 % Favored : 87.66 % 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: 0.13 (0.16), residues: 2964 helix: 1.25 (0.13), residues: 1548 sheet: -1.02 (0.27), residues: 372 loop : -1.21 (0.19), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP D 281 HIS 0.011 0.001 HIS E 189 PHE 0.019 0.002 PHE D 247 TYR 0.025 0.002 TYR F 407 ARG 0.006 0.001 ARG E 146 *********************** 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 308 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 265 time to evaluate : 2.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 384 GLU cc_start: 0.7935 (tt0) cc_final: 0.7672 (tt0) REVERT: E 384 GLU cc_start: 0.7929 (tt0) cc_final: 0.7671 (tt0) outliers start: 43 outliers final: 36 residues processed: 287 average time/residue: 0.3005 time to fit residues: 143.3053 Evaluate side-chains 275 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 239 time to evaluate : 2.828 ------------------------------------------------------------------------------- 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 314 ILE Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain B residue 189 HIS Chi-restraints excluded: chain B residue 195 HIS Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 407 TYR Chi-restraints excluded: chain C residue 189 HIS 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 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 407 TYR Chi-restraints excluded: chain E residue 195 HIS Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 314 ILE Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain E residue 407 TYR Chi-restraints excluded: chain F residue 236 LEU Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 392 VAL Chi-restraints excluded: chain F residue 393 SER Chi-restraints excluded: chain F residue 407 TYR Chi-restraints excluded: chain F residue 428 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 95 optimal weight: 20.0000 chunk 255 optimal weight: 9.9990 chunk 56 optimal weight: 10.0000 chunk 166 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 284 optimal weight: 7.9990 chunk 236 optimal weight: 5.9990 chunk 131 optimal weight: 9.9990 chunk 23 optimal weight: 10.0000 chunk 94 optimal weight: 10.0000 chunk 149 optimal weight: 0.7980 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 298 HIS E 298 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.5092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 23988 Z= 0.289 Angle : 0.689 9.854 32442 Z= 0.345 Chirality : 0.044 0.184 3516 Planarity : 0.004 0.045 4194 Dihedral : 10.972 156.505 3342 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.13 % Favored : 94.74 % Rotamer: Outliers : 2.00 % Allowed : 11.14 % Favored : 86.86 % 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: 0.30 (0.16), residues: 2964 helix: 1.41 (0.13), residues: 1512 sheet: -1.12 (0.26), residues: 402 loop : -0.97 (0.19), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP D 281 HIS 0.007 0.001 HIS D 298 PHE 0.019 0.002 PHE B 421 TYR 0.025 0.002 TYR F 407 ARG 0.005 0.000 ARG F 146 *********************** 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 326 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 276 time to evaluate : 2.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 TRP cc_start: 0.7481 (t60) cc_final: 0.7232 (t-100) REVERT: B 384 GLU cc_start: 0.7938 (tt0) cc_final: 0.7653 (tt0) REVERT: C 40 GLN cc_start: 0.8434 (mp10) cc_final: 0.8136 (pt0) REVERT: D 248 VAL cc_start: 0.8713 (m) cc_final: 0.8407 (t) REVERT: E 384 GLU cc_start: 0.7936 (tt0) cc_final: 0.7654 (tt0) REVERT: F 40 GLN cc_start: 0.8429 (mp10) cc_final: 0.8132 (pt0) REVERT: F 205 GLN cc_start: 0.8570 (OUTLIER) cc_final: 0.8142 (mp10) outliers start: 50 outliers final: 37 residues processed: 304 average time/residue: 0.3138 time to fit residues: 157.3159 Evaluate side-chains 287 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 249 time to evaluate : 2.738 ------------------------------------------------------------------------------- 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 314 ILE Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 407 TYR Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain B residue 189 HIS Chi-restraints excluded: chain B residue 195 HIS Chi-restraints excluded: chain B residue 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 189 HIS 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 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 255 VAL Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain D residue 393 SER Chi-restraints excluded: chain E residue 81 GLN 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 392 VAL Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain F residue 195 HIS Chi-restraints excluded: chain F residue 205 GLN 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 407 TYR Chi-restraints excluded: chain F residue 428 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 274 optimal weight: 10.0000 chunk 32 optimal weight: 0.0980 chunk 162 optimal weight: 8.9990 chunk 207 optimal weight: 2.9990 chunk 160 optimal weight: 6.9990 chunk 239 optimal weight: 5.9990 chunk 158 optimal weight: 0.9980 chunk 283 optimal weight: 7.9990 chunk 177 optimal weight: 0.9980 chunk 172 optimal weight: 20.0000 chunk 130 optimal weight: 5.9990 overall best weight: 2.2184 ------------------------------------------------------------------------------- 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 205 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.5345 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= 0.198 Angle : 0.647 9.137 32442 Z= 0.326 Chirality : 0.043 0.173 3516 Planarity : 0.004 0.047 4194 Dihedral : 10.262 175.979 3342 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % 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: 0.49 (0.16), residues: 2964 helix: 1.51 (0.14), residues: 1512 sheet: -0.97 (0.27), residues: 402 loop : -0.83 (0.19), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 281 HIS 0.009 0.001 HIS E 298 PHE 0.036 0.002 PHE D 360 TYR 0.025 0.002 TYR F 407 ARG 0.004 0.000 ARG E 146 *********************** 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 323 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 290 time to evaluate : 2.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 384 GLU cc_start: 0.7913 (tt0) cc_final: 0.7685 (tt0) REVERT: C 407 TYR cc_start: 0.6622 (OUTLIER) cc_final: 0.6301 (p90) REVERT: D 281 TRP cc_start: 0.7237 (t60) cc_final: 0.7001 (t-100) REVERT: E 384 GLU cc_start: 0.7918 (tt0) cc_final: 0.7681 (tt0) outliers start: 33 outliers final: 23 residues processed: 310 average time/residue: 0.3213 time to fit residues: 161.5430 Evaluate side-chains 265 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 241 time to evaluate : 2.908 ------------------------------------------------------------------------------- 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 393 SER Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 292 GLU Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 392 VAL 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 393 SER Chi-restraints excluded: chain C residue 407 TYR Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 393 SER Chi-restraints excluded: chain E residue 81 GLN Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 292 GLU Chi-restraints excluded: chain E residue 314 ILE Chi-restraints excluded: chain E residue 392 VAL 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 393 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 175 optimal weight: 5.9990 chunk 113 optimal weight: 10.0000 chunk 169 optimal weight: 1.9990 chunk 85 optimal weight: 9.9990 chunk 55 optimal weight: 9.9990 chunk 54 optimal weight: 0.8980 chunk 180 optimal weight: 20.0000 chunk 193 optimal weight: 1.9990 chunk 140 optimal weight: 0.7980 chunk 26 optimal weight: 30.0000 chunk 222 optimal weight: 7.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.5474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 23988 Z= 0.213 Angle : 0.673 9.131 32442 Z= 0.340 Chirality : 0.044 0.205 3516 Planarity : 0.004 0.061 4194 Dihedral : 10.109 178.222 3342 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 0.96 % Allowed : 14.38 % Favored : 84.66 % 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: 0.56 (0.16), residues: 2964 helix: 1.52 (0.14), residues: 1512 sheet: -0.77 (0.30), residues: 336 loop : -0.82 (0.19), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 281 HIS 0.007 0.001 HIS E 298 PHE 0.037 0.002 PHE C 360 TYR 0.024 0.002 TYR F 407 ARG 0.004 0.000 ARG D 146 *********************** 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 288 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 264 time to evaluate : 2.916 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 292 GLU cc_start: 0.7256 (OUTLIER) cc_final: 0.6786 (mt-10) REVERT: B 384 GLU cc_start: 0.7914 (tt0) cc_final: 0.7642 (tt0) REVERT: C 407 TYR cc_start: 0.6599 (OUTLIER) cc_final: 0.6266 (p90) REVERT: D 281 TRP cc_start: 0.7188 (t60) cc_final: 0.6981 (t-100) REVERT: E 292 GLU cc_start: 0.7307 (OUTLIER) cc_final: 0.6813 (mt-10) REVERT: E 384 GLU cc_start: 0.7906 (tt0) cc_final: 0.7632 (tt0) REVERT: F 233 MET cc_start: 0.7994 (mmm) cc_final: 0.7728 (tpt) outliers start: 24 outliers final: 15 residues processed: 285 average time/residue: 0.3150 time to fit residues: 147.6503 Evaluate side-chains 245 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 227 time to evaluate : 2.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 292 GLU Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 392 VAL 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 407 TYR Chi-restraints excluded: chain D residue 393 SER Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 292 GLU Chi-restraints excluded: chain E residue 314 ILE Chi-restraints excluded: chain E residue 392 VAL Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 373 LEU Chi-restraints excluded: chain F residue 386 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 257 optimal weight: 1.9990 chunk 271 optimal weight: 20.0000 chunk 247 optimal weight: 0.8980 chunk 264 optimal weight: 0.0980 chunk 158 optimal weight: 0.9990 chunk 115 optimal weight: 9.9990 chunk 207 optimal weight: 7.9990 chunk 81 optimal weight: 20.0000 chunk 238 optimal weight: 9.9990 chunk 249 optimal weight: 1.9990 chunk 263 optimal weight: 0.9980 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.5723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23988 Z= 0.178 Angle : 0.652 9.528 32442 Z= 0.330 Chirality : 0.043 0.187 3516 Planarity : 0.004 0.054 4194 Dihedral : 9.945 177.765 3342 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.64 % Allowed : 14.86 % Favored : 84.50 % 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: 0.72 (0.16), residues: 2964 helix: 1.60 (0.14), residues: 1506 sheet: -0.50 (0.32), residues: 306 loop : -0.71 (0.19), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 281 HIS 0.007 0.001 HIS B 298 PHE 0.034 0.002 PHE D 360 TYR 0.025 0.002 TYR E 407 ARG 0.005 0.000 ARG A 146 *********************** 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 287 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 271 time to evaluate : 2.699 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 233 MET cc_start: 0.7961 (mmm) cc_final: 0.7689 (tpt) REVERT: B 384 GLU cc_start: 0.7859 (tt0) cc_final: 0.7588 (tt0) REVERT: C 40 GLN cc_start: 0.8331 (mp10) cc_final: 0.8082 (pt0) REVERT: E 384 GLU cc_start: 0.7847 (tt0) cc_final: 0.7577 (tt0) REVERT: F 40 GLN cc_start: 0.8336 (mp10) cc_final: 0.8079 (pt0) outliers start: 16 outliers final: 9 residues processed: 284 average time/residue: 0.3133 time to fit residues: 144.4219 Evaluate side-chains 243 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 234 time to evaluate : 2.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 ILE 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 392 VAL Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 314 ILE Chi-restraints excluded: chain E residue 373 LEU Chi-restraints excluded: chain F residue 435 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 173 optimal weight: 50.0000 chunk 279 optimal weight: 10.0000 chunk 170 optimal weight: 0.3980 chunk 132 optimal weight: 8.9990 chunk 194 optimal weight: 5.9990 chunk 292 optimal weight: 5.9990 chunk 269 optimal weight: 8.9990 chunk 233 optimal weight: 0.7980 chunk 24 optimal weight: 9.9990 chunk 180 optimal weight: 5.9990 chunk 143 optimal weight: 9.9990 overall best weight: 3.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.5740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 23988 Z= 0.260 Angle : 0.699 9.344 32442 Z= 0.352 Chirality : 0.044 0.278 3516 Planarity : 0.005 0.064 4194 Dihedral : 9.843 175.461 3342 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 0.40 % Allowed : 15.99 % Favored : 83.61 % 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: 0.72 (0.16), residues: 2964 helix: 1.55 (0.14), residues: 1506 sheet: -0.41 (0.31), residues: 306 loop : -0.67 (0.19), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 281 HIS 0.006 0.001 HIS B 298 PHE 0.038 0.002 PHE C 360 TYR 0.026 0.002 TYR F 407 ARG 0.006 0.000 ARG D 146 ********************** 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 243 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 233 time to evaluate : 2.905 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 40 GLN cc_start: 0.8320 (mp10) cc_final: 0.8109 (pt0) REVERT: B 384 GLU cc_start: 0.7916 (tt0) cc_final: 0.7649 (tt0) REVERT: E 40 GLN cc_start: 0.8325 (mp10) cc_final: 0.8122 (pt0) REVERT: E 384 GLU cc_start: 0.7922 (tt0) cc_final: 0.7663 (tt0) outliers start: 10 outliers final: 9 residues processed: 240 average time/residue: 0.3074 time to fit residues: 123.0655 Evaluate side-chains 221 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 212 time to evaluate : 2.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain D residue 393 SER Chi-restraints excluded: chain E residue 314 ILE Chi-restraints excluded: chain E residue 373 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 185 optimal weight: 0.7980 chunk 248 optimal weight: 6.9990 chunk 71 optimal weight: 6.9990 chunk 215 optimal weight: 0.1980 chunk 34 optimal weight: 7.9990 chunk 64 optimal weight: 0.9990 chunk 233 optimal weight: 6.9990 chunk 97 optimal weight: 5.9990 chunk 239 optimal weight: 5.9990 chunk 29 optimal weight: 30.0000 chunk 43 optimal weight: 6.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN ** B 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 GLN ** D 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.097128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.074283 restraints weight = 60309.642| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 3.84 r_work: 0.3095 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.5864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 23988 Z= 0.227 Angle : 0.683 9.460 32442 Z= 0.344 Chirality : 0.044 0.260 3516 Planarity : 0.004 0.055 4194 Dihedral : 9.842 176.451 3342 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 0.52 % Allowed : 15.91 % Favored : 83.57 % 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: 1.55 (0.14), residues: 1506 sheet: -0.41 (0.32), residues: 306 loop : -0.62 (0.19), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 281 HIS 0.006 0.001 HIS B 298 PHE 0.037 0.002 PHE C 360 TYR 0.026 0.002 TYR F 407 ARG 0.006 0.000 ARG D 146 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4792.20 seconds wall clock time: 87 minutes 36.18 seconds (5256.18 seconds total)