Starting phenix.real_space_refine on Sat Jun 14 07:45:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ymu_39408/06_2025/8ymu_39408.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ymu_39408/06_2025/8ymu_39408.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ymu_39408/06_2025/8ymu_39408.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ymu_39408/06_2025/8ymu_39408.map" model { file = "/net/cci-nas-00/data/ceres_data/8ymu_39408/06_2025/8ymu_39408.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ymu_39408/06_2025/8ymu_39408.cif" } resolution = 2.89 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.052 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 S 57 5.16 5 C 5652 2.51 5 N 1482 2.21 5 O 1611 1.98 5 H 7173 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 15975 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 5325 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 17, 'TRANS': 344} Chain: "B" Number of atoms: 5325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 5325 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 17, 'TRANS': 344} Chain: "C" Number of atoms: 5325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 5325 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 17, 'TRANS': 344} Time building chain proxies: 8.35, per 1000 atoms: 0.52 Number of scatterers: 15975 At special positions: 0 Unit cell: (99.51, 94.86, 121.83, 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 57 16.00 O 1611 8.00 N 1482 7.00 C 5652 6.00 H 7173 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 106 " - pdb=" SG CYS A 188 " distance=2.02 Simple disulfide: pdb=" SG CYS A 273 " - pdb=" SG CYS A 341 " distance=2.03 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 337 " distance=2.05 Simple disulfide: pdb=" SG CYS A 299 " - pdb=" SG CYS A 311 " distance=2.03 Simple disulfide: pdb=" SG CYS B 106 " - pdb=" SG CYS B 188 " distance=2.02 Simple disulfide: pdb=" SG CYS B 273 " - pdb=" SG CYS B 341 " distance=2.03 Simple disulfide: pdb=" SG CYS B 282 " - pdb=" SG CYS B 337 " distance=2.03 Simple disulfide: pdb=" SG CYS B 299 " - pdb=" SG CYS B 311 " distance=2.03 Simple disulfide: pdb=" SG CYS C 106 " - pdb=" SG CYS C 188 " distance=2.02 Simple disulfide: pdb=" SG CYS C 273 " - pdb=" SG CYS C 341 " distance=2.03 Simple disulfide: pdb=" SG CYS C 282 " - pdb=" SG CYS C 337 " distance=2.03 Simple disulfide: pdb=" SG CYS C 299 " - pdb=" SG CYS C 311 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.99 Conformation dependent library (CDL) restraints added in 1.2 seconds 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2088 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 12 sheets defined 37.8% alpha, 28.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.26 Creating SS restraints... Processing helix chain 'A' and resid 53 through 83 removed outlier: 3.737A pdb=" N CYS A 66 " --> pdb=" O GLY A 62 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLN A 73 " --> pdb=" O ILE A 69 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N SER A 83 " --> pdb=" O LEU A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 113 Processing helix chain 'A' and resid 115 through 123 Processing helix chain 'A' and resid 129 through 135 removed outlier: 3.692A pdb=" N LEU A 133 " --> pdb=" O PHE A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 147 Processing helix chain 'A' and resid 240 through 245 Processing helix chain 'A' and resid 275 through 296 Processing helix chain 'A' and resid 313 through 329 removed outlier: 3.535A pdb=" N LYS A 319 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE A 320 " --> pdb=" O ASP A 316 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLN A 329 " --> pdb=" O ASP A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 398 Processing helix chain 'A' and resid 402 through 414 Processing helix chain 'B' and resid 54 through 83 removed outlier: 3.713A pdb=" N CYS B 66 " --> pdb=" O GLY B 62 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLN B 73 " --> pdb=" O ILE B 69 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N SER B 83 " --> pdb=" O LEU B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 113 Processing helix chain 'B' and resid 115 through 123 Processing helix chain 'B' and resid 129 through 135 removed outlier: 3.668A pdb=" N LEU B 133 " --> pdb=" O PHE B 130 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP B 135 " --> pdb=" O ASP B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 148 removed outlier: 3.838A pdb=" N SER B 148 " --> pdb=" O VAL B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 239 removed outlier: 4.146A pdb=" N SER B 237 " --> pdb=" O HIS B 233 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ARG B 238 " --> pdb=" O ALA B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 245 Processing helix chain 'B' and resid 275 through 296 Processing helix chain 'B' and resid 313 through 329 removed outlier: 3.587A pdb=" N LYS B 319 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLN B 329 " --> pdb=" O ASP B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 398 removed outlier: 3.572A pdb=" N PHE B 397 " --> pdb=" O VAL B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 414 Processing helix chain 'C' and resid 54 through 83 removed outlier: 3.656A pdb=" N CYS C 66 " --> pdb=" O GLY C 62 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLN C 73 " --> pdb=" O ILE C 69 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N SER C 83 " --> pdb=" O LEU C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 123 Processing helix chain 'C' and resid 129 through 135 removed outlier: 3.542A pdb=" N LEU C 133 " --> pdb=" O PHE C 130 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE C 134 " --> pdb=" O LEU C 131 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP C 135 " --> pdb=" O ASP C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 147 Processing helix chain 'C' and resid 233 through 239 removed outlier: 4.105A pdb=" N SER C 237 " --> pdb=" O HIS C 233 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ARG C 238 " --> pdb=" O ALA C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 245 Processing helix chain 'C' and resid 275 through 296 Processing helix chain 'C' and resid 313 through 329 removed outlier: 3.585A pdb=" N LYS C 319 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE C 320 " --> pdb=" O ASP C 316 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLN C 329 " --> pdb=" O ASP C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 396 Processing helix chain 'C' and resid 402 through 414 Processing sheet with id=AA1, first strand: chain 'A' and resid 86 through 94 removed outlier: 14.486A pdb=" N TYR A 371 " --> pdb=" O PHE A 256 " (cutoff:3.500A) removed outlier: 10.238A pdb=" N ILE A 258 " --> pdb=" O TYR A 371 " (cutoff:3.500A) removed outlier: 9.703A pdb=" N GLN A 373 " --> pdb=" O ILE A 258 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N PHE A 260 " --> pdb=" O GLN A 373 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N ALA A 375 " --> pdb=" O PHE A 260 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N GLN A 262 " --> pdb=" O ALA A 375 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N GLU A 377 " --> pdb=" O GLN A 262 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ASN A 264 " --> pdb=" O GLU A 377 " (cutoff:3.500A) removed outlier: 8.723A pdb=" N LEU A 379 " --> pdb=" O ASN A 264 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N PHE A 254 " --> pdb=" O SER A 364 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N TYR A 366 " --> pdb=" O PHE A 254 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N PHE A 256 " --> pdb=" O TYR A 366 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE A 361 " --> pdb=" O ASP A 210 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N TYR A 170 " --> pdb=" O GLU A 161 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 86 through 94 removed outlier: 14.486A pdb=" N TYR A 371 " --> pdb=" O PHE A 256 " (cutoff:3.500A) removed outlier: 10.238A pdb=" N ILE A 258 " --> pdb=" O TYR A 371 " (cutoff:3.500A) removed outlier: 9.703A pdb=" N GLN A 373 " --> pdb=" O ILE A 258 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N PHE A 260 " --> pdb=" O GLN A 373 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N ALA A 375 " --> pdb=" O PHE A 260 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N GLN A 262 " --> pdb=" O ALA A 375 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N GLU A 377 " --> pdb=" O GLN A 262 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ASN A 264 " --> pdb=" O GLU A 377 " (cutoff:3.500A) removed outlier: 8.723A pdb=" N LEU A 379 " --> pdb=" O ASN A 264 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'A' and resid 179 through 183 removed outlier: 7.177A pdb=" N GLN A 187 " --> pdb=" O PRO A 107 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 86 through 94 removed outlier: 14.434A pdb=" N TYR B 371 " --> pdb=" O PHE B 256 " (cutoff:3.500A) removed outlier: 10.343A pdb=" N ILE B 258 " --> pdb=" O TYR B 371 " (cutoff:3.500A) removed outlier: 9.707A pdb=" N GLN B 373 " --> pdb=" O ILE B 258 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N PHE B 260 " --> pdb=" O GLN B 373 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N ALA B 375 " --> pdb=" O PHE B 260 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N GLN B 262 " --> pdb=" O ALA B 375 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N GLU B 377 " --> pdb=" O GLN B 262 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ASN B 264 " --> pdb=" O GLU B 377 " (cutoff:3.500A) removed outlier: 8.720A pdb=" N LEU B 379 " --> pdb=" O ASN B 264 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N PHE B 254 " --> pdb=" O SER B 364 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N TYR B 366 " --> pdb=" O PHE B 254 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N PHE B 256 " --> pdb=" O TYR B 366 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE B 361 " --> pdb=" O ASP B 210 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N TYR B 170 " --> pdb=" O GLU B 161 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 86 through 94 removed outlier: 14.434A pdb=" N TYR B 371 " --> pdb=" O PHE B 256 " (cutoff:3.500A) removed outlier: 10.343A pdb=" N ILE B 258 " --> pdb=" O TYR B 371 " (cutoff:3.500A) removed outlier: 9.707A pdb=" N GLN B 373 " --> pdb=" O ILE B 258 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N PHE B 260 " --> pdb=" O GLN B 373 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N ALA B 375 " --> pdb=" O PHE B 260 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N GLN B 262 " --> pdb=" O ALA B 375 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N GLU B 377 " --> pdb=" O GLN B 262 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ASN B 264 " --> pdb=" O GLU B 377 " (cutoff:3.500A) removed outlier: 8.720A pdb=" N LEU B 379 " --> pdb=" O ASN B 264 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA8, first strand: chain 'B' and resid 179 through 183 removed outlier: 7.220A pdb=" N GLN B 187 " --> pdb=" O PRO B 107 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 86 through 94 removed outlier: 14.396A pdb=" N TYR C 371 " --> pdb=" O PHE C 256 " (cutoff:3.500A) removed outlier: 10.331A pdb=" N ILE C 258 " --> pdb=" O TYR C 371 " (cutoff:3.500A) removed outlier: 9.664A pdb=" N GLN C 373 " --> pdb=" O ILE C 258 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N PHE C 260 " --> pdb=" O GLN C 373 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N ALA C 375 " --> pdb=" O PHE C 260 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N GLN C 262 " --> pdb=" O ALA C 375 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N GLU C 377 " --> pdb=" O GLN C 262 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ASN C 264 " --> pdb=" O GLU C 377 " (cutoff:3.500A) removed outlier: 8.749A pdb=" N LEU C 379 " --> pdb=" O ASN C 264 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N PHE C 254 " --> pdb=" O SER C 364 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N TYR C 366 " --> pdb=" O PHE C 254 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N PHE C 256 " --> pdb=" O TYR C 366 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N TYR C 170 " --> pdb=" O GLU C 161 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 86 through 94 removed outlier: 14.396A pdb=" N TYR C 371 " --> pdb=" O PHE C 256 " (cutoff:3.500A) removed outlier: 10.331A pdb=" N ILE C 258 " --> pdb=" O TYR C 371 " (cutoff:3.500A) removed outlier: 9.664A pdb=" N GLN C 373 " --> pdb=" O ILE C 258 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N PHE C 260 " --> pdb=" O GLN C 373 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N ALA C 375 " --> pdb=" O PHE C 260 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N GLN C 262 " --> pdb=" O ALA C 375 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N GLU C 377 " --> pdb=" O GLN C 262 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ASN C 264 " --> pdb=" O GLU C 377 " (cutoff:3.500A) removed outlier: 8.749A pdb=" N LEU C 379 " --> pdb=" O ASN C 264 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA C 255 " --> pdb=" O MET C 351 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 97 through 98 Processing sheet with id=AB3, first strand: chain 'C' and resid 179 through 183 removed outlier: 7.251A pdb=" N GLN C 187 " --> pdb=" O PRO C 107 " (cutoff:3.500A) 433 hydrogen bonds defined for protein. 1218 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: 5.69 Time building geometry restraints manager: 4.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 7170 1.03 - 1.23: 22 1.23 - 1.42: 3880 1.42 - 1.62: 5038 1.62 - 1.81: 81 Bond restraints: 16191 Sorted by residual: bond pdb=" CA ARG A 99 " pdb=" CB ARG A 99 " ideal model delta sigma weight residual 1.525 1.545 -0.019 1.29e-02 6.01e+03 2.25e+00 bond pdb=" CA ARG C 99 " pdb=" CB ARG C 99 " ideal model delta sigma weight residual 1.525 1.541 -0.016 1.25e-02 6.40e+03 1.62e+00 bond pdb=" N ASP C 275 " pdb=" CA ASP C 275 " ideal model delta sigma weight residual 1.457 1.471 -0.014 1.29e-02 6.01e+03 1.14e+00 bond pdb=" CA GLY A 162 " pdb=" C GLY A 162 " ideal model delta sigma weight residual 1.516 1.506 0.010 1.05e-02 9.07e+03 9.42e-01 bond pdb=" CA GLU A 355 " pdb=" CB GLU A 355 " ideal model delta sigma weight residual 1.523 1.535 -0.012 1.35e-02 5.49e+03 7.73e-01 ... (remaining 16186 not shown) Histogram of bond angle deviations from ideal: 0.00 - 11.10: 28461 11.10 - 22.19: 7 22.19 - 33.29: 35 33.29 - 44.39: 21 44.39 - 55.49: 6 Bond angle restraints: 28530 Sorted by residual: angle pdb=" C THR C 114 " pdb=" N ILE C 115 " pdb=" H ILE C 115 " ideal model delta sigma weight residual 124.33 68.84 55.49 3.00e+00 1.11e-01 3.42e+02 angle pdb=" C THR A 114 " pdb=" N ILE A 115 " pdb=" H ILE A 115 " ideal model delta sigma weight residual 123.83 68.79 55.05 3.00e+00 1.11e-01 3.37e+02 angle pdb=" C THR B 114 " pdb=" N ILE B 115 " pdb=" H ILE B 115 " ideal model delta sigma weight residual 123.83 68.84 55.00 3.00e+00 1.11e-01 3.36e+02 angle pdb=" CA ILE C 115 " pdb=" N ILE C 115 " pdb=" H ILE C 115 " ideal model delta sigma weight residual 114.03 59.49 54.54 3.00e+00 1.11e-01 3.30e+02 angle pdb=" CA ILE A 115 " pdb=" N ILE A 115 " pdb=" H ILE A 115 " ideal model delta sigma weight residual 113.53 59.68 53.86 3.00e+00 1.11e-01 3.22e+02 ... (remaining 28525 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.85: 7013 16.85 - 33.70: 631 33.70 - 50.55: 142 50.55 - 67.40: 52 67.40 - 84.25: 22 Dihedral angle restraints: 7860 sinusoidal: 4116 harmonic: 3744 Sorted by residual: dihedral pdb=" CA CYS A 337 " pdb=" C CYS A 337 " pdb=" N LYS A 338 " pdb=" CA LYS A 338 " ideal model delta harmonic sigma weight residual -180.00 -144.55 -35.45 0 5.00e+00 4.00e-02 5.03e+01 dihedral pdb=" CA CYS C 337 " pdb=" C CYS C 337 " pdb=" N LYS C 338 " pdb=" CA LYS C 338 " ideal model delta harmonic sigma weight residual 180.00 -146.48 -33.52 0 5.00e+00 4.00e-02 4.49e+01 dihedral pdb=" CA CYS B 337 " pdb=" C CYS B 337 " pdb=" N LYS B 338 " pdb=" CA LYS B 338 " ideal model delta harmonic sigma weight residual -180.00 -146.49 -33.51 0 5.00e+00 4.00e-02 4.49e+01 ... (remaining 7857 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 1230 0.078 - 0.157: 126 0.157 - 0.235: 0 0.235 - 0.313: 0 0.313 - 0.391: 9 Chirality restraints: 1365 Sorted by residual: chirality pdb=" CA PRO A 249 " pdb=" N PRO A 249 " pdb=" C PRO A 249 " pdb=" CB PRO A 249 " both_signs ideal model delta sigma weight residual False 2.72 2.33 0.39 2.00e-01 2.50e+01 3.83e+00 chirality pdb=" CA PRO B 249 " pdb=" N PRO B 249 " pdb=" C PRO B 249 " pdb=" CB PRO B 249 " both_signs ideal model delta sigma weight residual False 2.72 2.33 0.39 2.00e-01 2.50e+01 3.78e+00 chirality pdb=" CA PRO C 249 " pdb=" N PRO C 249 " pdb=" C PRO C 249 " pdb=" CB PRO C 249 " both_signs ideal model delta sigma weight residual False 2.72 2.33 0.39 2.00e-01 2.50e+01 3.73e+00 ... (remaining 1362 not shown) Planarity restraints: 2436 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL C 274 " -0.011 2.00e-02 2.50e+03 2.26e-02 5.11e+00 pdb=" C VAL C 274 " 0.039 2.00e-02 2.50e+03 pdb=" O VAL C 274 " -0.015 2.00e-02 2.50e+03 pdb=" N ASP C 275 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 252 " -0.034 5.00e-02 4.00e+02 5.15e-02 4.25e+00 pdb=" N PRO A 253 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 253 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 253 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 127 " -0.010 2.00e-02 2.50e+03 2.00e-02 4.01e+00 pdb=" C LYS B 127 " 0.035 2.00e-02 2.50e+03 pdb=" O LYS B 127 " -0.013 2.00e-02 2.50e+03 pdb=" N MET B 128 " -0.012 2.00e-02 2.50e+03 ... (remaining 2433 not shown) Histogram of nonbonded interaction distances: 1.40 - 2.04: 197 2.04 - 2.68: 22421 2.68 - 3.32: 44095 3.32 - 3.96: 60095 3.96 - 4.60: 92045 Nonbonded interactions: 218853 Sorted by model distance: nonbonded pdb=" H ILE B 115 " pdb=" HA ILE B 115 " model vdw 1.397 1.816 nonbonded pdb=" H ILE A 115 " pdb=" HA ILE A 115 " model vdw 1.397 1.816 nonbonded pdb=" H ILE C 115 " pdb=" HA ILE C 115 " model vdw 1.418 1.816 nonbonded pdb=" H PHE A 354 " pdb=" HA PHE A 354 " model vdw 1.574 1.816 nonbonded pdb=" H PHE C 354 " pdb=" HA PHE C 354 " model vdw 1.576 1.816 ... (remaining 218848 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 1.650 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: 0.290 Extract box with map and model: 0.630 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 35.350 Find NCS groups from input model: 0.340 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:14.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 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 : 0.003 0.029 9030 Z= 0.166 Angle : 0.720 8.899 12276 Z= 0.440 Chirality : 0.053 0.391 1365 Planarity : 0.004 0.052 1581 Dihedral : 13.504 84.254 3306 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.56 % Allowed : 6.57 % Favored : 92.87 % Rotamer: Outliers : 0.20 % Allowed : 0.41 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.26), residues: 1080 helix: 0.09 (0.29), residues: 357 sheet: -0.88 (0.32), residues: 276 loop : -2.65 (0.27), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 145 HIS 0.009 0.001 HIS B 229 PHE 0.011 0.001 PHE B 256 TYR 0.011 0.001 TYR A 292 ARG 0.005 0.001 ARG A 99 Details of bonding type rmsd hydrogen bonds : bond 0.15644 ( 409) hydrogen bonds : angle 6.79308 ( 1218) SS BOND : bond 0.00740 ( 12) SS BOND : angle 1.88804 ( 24) covalent geometry : bond 0.00324 ( 9018) covalent geometry : angle 0.71557 (12252) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 138 time to evaluate : 1.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 MET cc_start: 0.6464 (mpp) cc_final: 0.6186 (mpt) REVERT: C 119 MET cc_start: 0.6742 (mpp) cc_final: 0.6415 (mpt) outliers start: 2 outliers final: 0 residues processed: 140 average time/residue: 2.0939 time to fit residues: 315.0832 Evaluate side-chains 107 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 55 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 84 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 330 ASN ** B 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 330 ASN ** C 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 GLN C 177 GLN C 296 GLN C 330 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.164060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.128763 restraints weight = 24865.751| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 1.66 r_work: 0.3278 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9030 Z= 0.147 Angle : 0.648 13.184 12276 Z= 0.361 Chirality : 0.055 0.417 1365 Planarity : 0.004 0.046 1581 Dihedral : 5.592 30.659 1206 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.56 % Allowed : 5.74 % Favored : 93.70 % Rotamer: Outliers : 1.43 % Allowed : 9.38 % Favored : 89.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.26), residues: 1080 helix: 0.52 (0.29), residues: 369 sheet: -0.78 (0.34), residues: 255 loop : -2.57 (0.26), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 145 HIS 0.006 0.001 HIS B 231 PHE 0.011 0.001 PHE B 256 TYR 0.008 0.001 TYR C 170 ARG 0.006 0.000 ARG A 99 Details of bonding type rmsd hydrogen bonds : bond 0.03151 ( 409) hydrogen bonds : angle 4.93814 ( 1218) SS BOND : bond 0.00599 ( 12) SS BOND : angle 1.69601 ( 24) covalent geometry : bond 0.00338 ( 9018) covalent geometry : angle 0.64460 (12252) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 111 time to evaluate : 1.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 MET cc_start: 0.6842 (mpp) cc_final: 0.6563 (mmm) REVERT: B 80 ASP cc_start: 0.7580 (t0) cc_final: 0.7284 (t0) REVERT: B 118 ASP cc_start: 0.7330 (m-30) cc_final: 0.6407 (m-30) REVERT: C 119 MET cc_start: 0.6978 (mpp) cc_final: 0.6522 (mpt) REVERT: C 129 LYS cc_start: 0.8153 (mmtp) cc_final: 0.7346 (mmmt) REVERT: C 140 ASP cc_start: 0.7922 (OUTLIER) cc_final: 0.7532 (p0) outliers start: 14 outliers final: 3 residues processed: 119 average time/residue: 1.8686 time to fit residues: 241.5864 Evaluate side-chains 101 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 97 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain C residue 140 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 0.0470 chunk 94 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 71 optimal weight: 7.9990 chunk 60 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 106 optimal weight: 0.3980 chunk 63 optimal weight: 0.1980 chunk 91 optimal weight: 0.8980 chunk 98 optimal weight: 0.9980 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 77 HIS A 177 GLN A 330 ASN B 95 GLN B 330 ASN C 95 GLN C 177 GLN C 330 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.165396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.130421 restraints weight = 24600.410| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.65 r_work: 0.3298 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9030 Z= 0.115 Angle : 0.598 12.754 12276 Z= 0.332 Chirality : 0.054 0.414 1365 Planarity : 0.004 0.041 1581 Dihedral : 5.328 26.178 1206 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.11 % Favored : 93.61 % Rotamer: Outliers : 1.83 % Allowed : 9.68 % Favored : 88.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.26), residues: 1080 helix: 0.86 (0.29), residues: 372 sheet: -0.60 (0.34), residues: 246 loop : -2.46 (0.25), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 145 HIS 0.003 0.001 HIS B 231 PHE 0.008 0.001 PHE A 205 TYR 0.005 0.001 TYR C 279 ARG 0.003 0.000 ARG A 99 Details of bonding type rmsd hydrogen bonds : bond 0.02689 ( 409) hydrogen bonds : angle 4.54583 ( 1218) SS BOND : bond 0.00476 ( 12) SS BOND : angle 1.38023 ( 24) covalent geometry : bond 0.00264 ( 9018) covalent geometry : angle 0.59584 (12252) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 105 time to evaluate : 1.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 ASN cc_start: 0.7994 (t0) cc_final: 0.7513 (t0) REVERT: A 293 GLU cc_start: 0.7747 (tt0) cc_final: 0.7505 (tt0) REVERT: B 99 ARG cc_start: 0.7383 (OUTLIER) cc_final: 0.6838 (mmt90) REVERT: B 118 ASP cc_start: 0.7355 (m-30) cc_final: 0.6510 (m-30) REVERT: B 119 MET cc_start: 0.6513 (OUTLIER) cc_final: 0.6250 (mpt) REVERT: B 289 GLN cc_start: 0.7418 (OUTLIER) cc_final: 0.7105 (tm-30) REVERT: C 119 MET cc_start: 0.6821 (mpp) cc_final: 0.6442 (mpt) REVERT: C 140 ASP cc_start: 0.7854 (OUTLIER) cc_final: 0.7449 (p0) outliers start: 18 outliers final: 3 residues processed: 112 average time/residue: 1.7476 time to fit residues: 213.8055 Evaluate side-chains 107 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 100 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain B residue 99 ARG Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 289 GLN Chi-restraints excluded: chain C residue 140 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 75 optimal weight: 0.5980 chunk 4 optimal weight: 0.3980 chunk 15 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 chunk 79 optimal weight: 1.9990 chunk 64 optimal weight: 0.0010 chunk 23 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 177 GLN A 330 ASN B 111 GLN B 177 GLN C 177 GLN C 229 HIS C 330 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.164914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.129844 restraints weight = 24772.906| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 1.67 r_work: 0.3292 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9030 Z= 0.117 Angle : 0.584 12.749 12276 Z= 0.324 Chirality : 0.053 0.417 1365 Planarity : 0.004 0.038 1581 Dihedral : 5.132 23.320 1206 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.02 % Favored : 93.70 % Rotamer: Outliers : 1.94 % Allowed : 10.19 % Favored : 87.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.26), residues: 1080 helix: 1.12 (0.29), residues: 369 sheet: -0.69 (0.31), residues: 273 loop : -2.44 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 145 HIS 0.003 0.001 HIS B 231 PHE 0.009 0.001 PHE B 205 TYR 0.005 0.001 TYR C 292 ARG 0.003 0.000 ARG A 99 Details of bonding type rmsd hydrogen bonds : bond 0.02427 ( 409) hydrogen bonds : angle 4.36690 ( 1218) SS BOND : bond 0.00466 ( 12) SS BOND : angle 1.35502 ( 24) covalent geometry : bond 0.00270 ( 9018) covalent geometry : angle 0.58182 (12252) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 106 time to evaluate : 1.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 ASN cc_start: 0.7936 (t0) cc_final: 0.7432 (t0) REVERT: A 293 GLU cc_start: 0.7781 (tt0) cc_final: 0.7463 (tt0) REVERT: B 99 ARG cc_start: 0.7392 (OUTLIER) cc_final: 0.6824 (mmt90) REVERT: B 102 GLU cc_start: 0.7537 (pp20) cc_final: 0.7246 (pt0) REVERT: B 118 ASP cc_start: 0.7426 (m-30) cc_final: 0.6626 (m-30) REVERT: B 119 MET cc_start: 0.6416 (OUTLIER) cc_final: 0.6165 (mpt) REVERT: B 129 LYS cc_start: 0.7985 (OUTLIER) cc_final: 0.7592 (mttt) REVERT: B 289 GLN cc_start: 0.7425 (OUTLIER) cc_final: 0.7099 (tm-30) REVERT: C 119 MET cc_start: 0.6772 (mpp) cc_final: 0.6327 (mpt) REVERT: C 140 ASP cc_start: 0.7869 (OUTLIER) cc_final: 0.7473 (p0) outliers start: 19 outliers final: 4 residues processed: 116 average time/residue: 1.6851 time to fit residues: 213.5854 Evaluate side-chains 106 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 97 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 275 ASP Chi-restraints excluded: chain B residue 99 ARG Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 275 ASP Chi-restraints excluded: chain B residue 289 GLN Chi-restraints excluded: chain C residue 140 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 62 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 59 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 77 optimal weight: 0.5980 chunk 90 optimal weight: 0.9980 chunk 95 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 177 GLN A 330 ASN B 77 HIS B 177 GLN C 330 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.192063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.157386 restraints weight = 24086.777| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 1.71 r_work: 0.3646 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3518 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9030 Z= 0.137 Angle : 0.594 12.576 12276 Z= 0.328 Chirality : 0.054 0.419 1365 Planarity : 0.004 0.037 1581 Dihedral : 5.112 22.030 1206 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.46 % Favored : 94.26 % Rotamer: Outliers : 2.24 % Allowed : 10.30 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.26), residues: 1080 helix: 1.29 (0.29), residues: 369 sheet: -0.66 (0.31), residues: 273 loop : -2.34 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 145 HIS 0.008 0.001 HIS B 233 PHE 0.009 0.001 PHE B 205 TYR 0.008 0.001 TYR C 292 ARG 0.002 0.000 ARG A 99 Details of bonding type rmsd hydrogen bonds : bond 0.02441 ( 409) hydrogen bonds : angle 4.30582 ( 1218) SS BOND : bond 0.00533 ( 12) SS BOND : angle 1.46675 ( 24) covalent geometry : bond 0.00322 ( 9018) covalent geometry : angle 0.59149 (12252) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 100 time to evaluate : 1.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 ASP cc_start: 0.7768 (m-30) cc_final: 0.7061 (m-30) REVERT: B 102 GLU cc_start: 0.7613 (pp20) cc_final: 0.7307 (pt0) REVERT: B 154 ASN cc_start: 0.8070 (t0) cc_final: 0.7748 (t160) REVERT: B 289 GLN cc_start: 0.7710 (OUTLIER) cc_final: 0.7472 (tm-30) REVERT: C 140 ASP cc_start: 0.7973 (OUTLIER) cc_final: 0.7676 (p0) outliers start: 22 outliers final: 8 residues processed: 114 average time/residue: 1.9156 time to fit residues: 239.3418 Evaluate side-chains 108 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 98 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 275 ASP Chi-restraints excluded: chain B residue 99 ARG Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 275 ASP Chi-restraints excluded: chain B residue 289 GLN Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain C residue 275 ASP Chi-restraints excluded: chain C residue 337 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 88 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 12 optimal weight: 0.0050 chunk 33 optimal weight: 5.9990 chunk 82 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 overall best weight: 1.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 177 GLN A 330 ASN B 177 GLN ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 330 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.182717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.146494 restraints weight = 24567.580| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 1.83 r_work: 0.3509 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3374 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9030 Z= 0.170 Angle : 0.620 12.535 12276 Z= 0.342 Chirality : 0.055 0.422 1365 Planarity : 0.004 0.039 1581 Dihedral : 5.235 21.339 1206 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.30 % Favored : 93.43 % Rotamer: Outliers : 2.34 % Allowed : 10.70 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.26), residues: 1080 helix: 1.46 (0.29), residues: 366 sheet: -0.63 (0.31), residues: 273 loop : -2.29 (0.27), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 145 HIS 0.007 0.002 HIS B 233 PHE 0.010 0.001 PHE C 116 TYR 0.006 0.001 TYR C 292 ARG 0.002 0.000 ARG A 99 Details of bonding type rmsd hydrogen bonds : bond 0.02581 ( 409) hydrogen bonds : angle 4.35623 ( 1218) SS BOND : bond 0.00668 ( 12) SS BOND : angle 2.16767 ( 24) covalent geometry : bond 0.00403 ( 9018) covalent geometry : angle 0.61281 (12252) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 100 time to evaluate : 1.297 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: B 99 ARG cc_start: 0.7343 (OUTLIER) cc_final: 0.6854 (mmt90) REVERT: B 102 GLU cc_start: 0.7742 (pp20) cc_final: 0.7445 (pt0) REVERT: B 119 MET cc_start: 0.7000 (mmm) cc_final: 0.6411 (mpt) REVERT: B 129 LYS cc_start: 0.8326 (OUTLIER) cc_final: 0.8011 (mttt) REVERT: B 154 ASN cc_start: 0.8024 (t0) cc_final: 0.7674 (t160) REVERT: B 289 GLN cc_start: 0.7790 (OUTLIER) cc_final: 0.7495 (tm-30) REVERT: C 119 MET cc_start: 0.6814 (mmm) cc_final: 0.6260 (mpt) REVERT: C 140 ASP cc_start: 0.7965 (OUTLIER) cc_final: 0.7648 (p0) REVERT: C 293 GLU cc_start: 0.8198 (tt0) cc_final: 0.7668 (pt0) outliers start: 23 outliers final: 12 residues processed: 115 average time/residue: 1.8341 time to fit residues: 231.7495 Evaluate side-chains 112 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 175 MET Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 275 ASP Chi-restraints excluded: chain B residue 99 ARG Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 275 ASP Chi-restraints excluded: chain B residue 289 GLN Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 337 CYS Chi-restraints excluded: chain C residue 341 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 12 optimal weight: 0.0970 chunk 21 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 75 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 113 ASN A 177 GLN A 330 ASN B 96 ASN B 113 ASN B 177 GLN C 177 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.182332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.146189 restraints weight = 24607.780| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 1.80 r_work: 0.3505 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3369 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9030 Z= 0.164 Angle : 0.621 12.623 12276 Z= 0.342 Chirality : 0.054 0.422 1365 Planarity : 0.004 0.039 1581 Dihedral : 5.250 21.242 1206 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.02 % Favored : 93.70 % Rotamer: Outliers : 2.75 % Allowed : 11.21 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.26), residues: 1080 helix: 1.58 (0.29), residues: 366 sheet: -0.62 (0.31), residues: 273 loop : -2.23 (0.27), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 145 HIS 0.007 0.002 HIS B 233 PHE 0.010 0.001 PHE C 116 TYR 0.007 0.001 TYR C 292 ARG 0.002 0.000 ARG A 99 Details of bonding type rmsd hydrogen bonds : bond 0.02541 ( 409) hydrogen bonds : angle 4.35129 ( 1218) SS BOND : bond 0.00569 ( 12) SS BOND : angle 2.11401 ( 24) covalent geometry : bond 0.00386 ( 9018) covalent geometry : angle 0.61424 (12252) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 105 time to evaluate : 1.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 99 ARG cc_start: 0.7335 (OUTLIER) cc_final: 0.6827 (mmt90) REVERT: B 102 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7495 (pt0) REVERT: B 126 ASP cc_start: 0.7461 (p0) cc_final: 0.7154 (p0) REVERT: B 289 GLN cc_start: 0.7790 (OUTLIER) cc_final: 0.7491 (tm-30) REVERT: B 290 ARG cc_start: 0.8258 (tpp-160) cc_final: 0.7855 (tpt90) REVERT: C 140 ASP cc_start: 0.7975 (OUTLIER) cc_final: 0.7624 (p0) outliers start: 27 outliers final: 12 residues processed: 122 average time/residue: 1.9545 time to fit residues: 259.7684 Evaluate side-chains 116 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 100 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 175 MET Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 275 ASP Chi-restraints excluded: chain B residue 99 ARG Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 275 ASP Chi-restraints excluded: chain B residue 289 GLN Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 337 CYS Chi-restraints excluded: chain C residue 341 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 9 optimal weight: 1.9990 chunk 91 optimal weight: 0.1980 chunk 74 optimal weight: 2.9990 chunk 37 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 102 optimal weight: 0.1980 chunk 12 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 0 optimal weight: 40.0000 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 113 ASN A 177 GLN A 330 ASN B 113 ASN B 177 GLN C 177 GLN C 330 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.183802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.147776 restraints weight = 24417.676| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 1.79 r_work: 0.3503 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3365 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9030 Z= 0.134 Angle : 0.612 12.530 12276 Z= 0.337 Chirality : 0.054 0.419 1365 Planarity : 0.004 0.038 1581 Dihedral : 5.227 23.697 1206 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.93 % Favored : 93.80 % Rotamer: Outliers : 2.45 % Allowed : 12.13 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.26), residues: 1080 helix: 1.75 (0.29), residues: 366 sheet: -0.63 (0.31), residues: 273 loop : -2.20 (0.27), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 145 HIS 0.007 0.001 HIS A 233 PHE 0.009 0.001 PHE C 367 TYR 0.006 0.001 TYR C 239 ARG 0.002 0.000 ARG A 99 Details of bonding type rmsd hydrogen bonds : bond 0.02358 ( 409) hydrogen bonds : angle 4.26481 ( 1218) SS BOND : bond 0.00491 ( 12) SS BOND : angle 2.43671 ( 24) covalent geometry : bond 0.00315 ( 9018) covalent geometry : angle 0.60308 (12252) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 102 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7640 (pt0) REVERT: B 99 ARG cc_start: 0.7396 (OUTLIER) cc_final: 0.6884 (mmt90) REVERT: B 102 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7361 (pt0) REVERT: B 129 LYS cc_start: 0.8469 (OUTLIER) cc_final: 0.8059 (mttt) REVERT: B 154 ASN cc_start: 0.7884 (t0) cc_final: 0.7251 (t0) REVERT: B 200 ARG cc_start: 0.8057 (mmt180) cc_final: 0.7808 (mmt180) REVERT: B 289 GLN cc_start: 0.7794 (OUTLIER) cc_final: 0.7507 (tm-30) REVERT: C 128 MET cc_start: 0.6568 (mtm) cc_final: 0.6142 (mmt) REVERT: C 140 ASP cc_start: 0.7908 (OUTLIER) cc_final: 0.7570 (p0) outliers start: 24 outliers final: 13 residues processed: 117 average time/residue: 1.8168 time to fit residues: 230.8717 Evaluate side-chains 116 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 97 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 175 MET Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 275 ASP Chi-restraints excluded: chain A residue 341 CYS Chi-restraints excluded: chain B residue 99 ARG Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 275 ASP Chi-restraints excluded: chain B residue 289 GLN Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 326 ASP Chi-restraints excluded: chain C residue 337 CYS Chi-restraints excluded: chain C residue 341 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 7 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 38 optimal weight: 8.9990 chunk 69 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 101 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 113 ASN A 177 GLN A 330 ASN B 96 ASN B 113 ASN B 177 GLN C 177 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.183818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.147511 restraints weight = 24398.032| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 1.82 r_work: 0.3503 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3369 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9030 Z= 0.145 Angle : 0.624 12.546 12276 Z= 0.345 Chirality : 0.055 0.451 1365 Planarity : 0.004 0.039 1581 Dihedral : 5.279 25.661 1206 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.83 % Favored : 93.89 % Rotamer: Outliers : 2.65 % Allowed : 11.93 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.26), residues: 1080 helix: 1.81 (0.29), residues: 366 sheet: -0.64 (0.32), residues: 273 loop : -2.16 (0.27), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 145 HIS 0.007 0.001 HIS A 231 PHE 0.009 0.001 PHE B 205 TYR 0.008 0.001 TYR C 292 ARG 0.002 0.000 ARG A 99 Details of bonding type rmsd hydrogen bonds : bond 0.02378 ( 409) hydrogen bonds : angle 4.26602 ( 1218) SS BOND : bond 0.00586 ( 12) SS BOND : angle 2.68383 ( 24) covalent geometry : bond 0.00342 ( 9018) covalent geometry : angle 0.61372 (12252) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 102 time to evaluate : 1.196 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 102 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7670 (pt0) REVERT: B 99 ARG cc_start: 0.7277 (OUTLIER) cc_final: 0.6802 (mmt90) REVERT: B 102 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.7394 (pt0) REVERT: B 129 LYS cc_start: 0.8501 (mmtp) cc_final: 0.8062 (mttt) REVERT: B 154 ASN cc_start: 0.7892 (t0) cc_final: 0.7230 (t0) REVERT: B 289 GLN cc_start: 0.7777 (OUTLIER) cc_final: 0.7495 (tm-30) REVERT: C 128 MET cc_start: 0.6633 (mtm) cc_final: 0.6185 (mmt) REVERT: C 140 ASP cc_start: 0.7932 (OUTLIER) cc_final: 0.7594 (p0) outliers start: 26 outliers final: 14 residues processed: 119 average time/residue: 2.0374 time to fit residues: 262.4867 Evaluate side-chains 114 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 95 time to evaluate : 1.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 175 MET Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 275 ASP Chi-restraints excluded: chain A residue 341 CYS Chi-restraints excluded: chain B residue 99 ARG Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 289 GLN Chi-restraints excluded: chain B residue 341 CYS Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 326 ASP Chi-restraints excluded: chain C residue 337 CYS Chi-restraints excluded: chain C residue 341 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 51 optimal weight: 0.9980 chunk 68 optimal weight: 0.9980 chunk 97 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 56 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 47 optimal weight: 0.0770 chunk 4 optimal weight: 0.4980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 113 ASN A 177 GLN A 330 ASN B 113 ASN B 177 GLN C 177 GLN C 190 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.185371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.148894 restraints weight = 24536.819| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 1.86 r_work: 0.3536 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3400 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9030 Z= 0.117 Angle : 0.604 12.500 12276 Z= 0.332 Chirality : 0.054 0.438 1365 Planarity : 0.004 0.067 1581 Dihedral : 5.119 23.042 1206 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.93 % Favored : 93.80 % Rotamer: Outliers : 2.24 % Allowed : 12.64 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.26), residues: 1080 helix: 1.95 (0.29), residues: 366 sheet: -0.70 (0.32), residues: 270 loop : -2.06 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 145 HIS 0.006 0.001 HIS A 231 PHE 0.008 0.001 PHE B 256 TYR 0.009 0.001 TYR C 292 ARG 0.009 0.000 ARG C 339 Details of bonding type rmsd hydrogen bonds : bond 0.02189 ( 409) hydrogen bonds : angle 4.15579 ( 1218) SS BOND : bond 0.00446 ( 12) SS BOND : angle 2.15110 ( 24) covalent geometry : bond 0.00275 ( 9018) covalent geometry : angle 0.59657 (12252) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 100 time to evaluate : 1.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7632 (pt0) REVERT: A 341 CYS cc_start: 0.7026 (OUTLIER) cc_final: 0.5660 (m) REVERT: B 102 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7273 (pt0) REVERT: B 129 LYS cc_start: 0.8448 (mmtp) cc_final: 0.7994 (mttt) REVERT: B 154 ASN cc_start: 0.7912 (t0) cc_final: 0.7228 (t0) REVERT: B 289 GLN cc_start: 0.7727 (OUTLIER) cc_final: 0.7445 (tm-30) REVERT: B 341 CYS cc_start: 0.6891 (OUTLIER) cc_final: 0.5601 (m) REVERT: C 128 MET cc_start: 0.6603 (mtm) cc_final: 0.6132 (mmt) REVERT: C 140 ASP cc_start: 0.7900 (OUTLIER) cc_final: 0.7573 (p0) outliers start: 22 outliers final: 11 residues processed: 115 average time/residue: 1.7225 time to fit residues: 216.7256 Evaluate side-chains 115 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 175 MET Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 275 ASP Chi-restraints excluded: chain A residue 341 CYS Chi-restraints excluded: chain B residue 99 ARG Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 289 GLN Chi-restraints excluded: chain B residue 341 CYS Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 326 ASP Chi-restraints excluded: chain C residue 337 CYS Chi-restraints excluded: chain C residue 341 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 18 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 55 optimal weight: 0.3980 chunk 94 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 88 optimal weight: 0.2980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 113 ASN A 177 GLN A 330 ASN B 113 ASN B 177 GLN C 177 GLN C 190 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.191563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.157124 restraints weight = 24064.601| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 1.73 r_work: 0.3640 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3513 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9030 Z= 0.118 Angle : 0.602 12.506 12276 Z= 0.331 Chirality : 0.054 0.430 1365 Planarity : 0.004 0.042 1581 Dihedral : 5.069 22.633 1206 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.56 % Favored : 94.17 % Rotamer: Outliers : 2.24 % Allowed : 13.35 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.26), residues: 1080 helix: 2.02 (0.29), residues: 366 sheet: -0.67 (0.32), residues: 270 loop : -2.04 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 145 HIS 0.006 0.001 HIS A 231 PHE 0.008 0.001 PHE B 256 TYR 0.007 0.001 TYR C 292 ARG 0.007 0.000 ARG C 339 Details of bonding type rmsd hydrogen bonds : bond 0.02178 ( 409) hydrogen bonds : angle 4.13312 ( 1218) SS BOND : bond 0.00462 ( 12) SS BOND : angle 2.13157 ( 24) covalent geometry : bond 0.00277 ( 9018) covalent geometry : angle 0.59532 (12252) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10843.26 seconds wall clock time: 187 minutes 57.90 seconds (11277.90 seconds total)