Starting phenix.real_space_refine on Wed Sep 17 22:51:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9no2_49592/09_2025/9no2_49592.cif Found real_map, /net/cci-nas-00/data/ceres_data/9no2_49592/09_2025/9no2_49592.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9no2_49592/09_2025/9no2_49592.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9no2_49592/09_2025/9no2_49592.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9no2_49592/09_2025/9no2_49592.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9no2_49592/09_2025/9no2_49592.map" } resolution = 3.05 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.106 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 52 5.16 5 C 7616 2.51 5 N 2054 2.21 5 O 2274 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11996 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3253 Classifications: {'peptide': 428} Link IDs: {'PTRANS': 13, 'TRANS': 414} Chain: "B" Number of atoms: 2745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2745 Classifications: {'peptide': 350} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 336} Chain: "C" Number of atoms: 3253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3253 Classifications: {'peptide': 428} Link IDs: {'PTRANS': 13, 'TRANS': 414} Chain: "D" Number of atoms: 2745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2745 Classifications: {'peptide': 350} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 336} Time building chain proxies: 2.95, per 1000 atoms: 0.25 Number of scatterers: 11996 At special positions: 0 Unit cell: (106.7, 93.5, 128.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 52 16.00 O 2274 8.00 N 2054 7.00 C 7616 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: 0.77 Conformation dependent library (CDL) restraints added in 498.1 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2880 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 21 sheets defined 39.5% alpha, 16.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'A' and resid 65 through 81 removed outlier: 4.473A pdb=" N ALA A 77 " --> pdb=" O ASN A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 100 Processing helix chain 'A' and resid 108 through 127 removed outlier: 3.722A pdb=" N ILE A 112 " --> pdb=" O GLY A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 136 Processing helix chain 'A' and resid 175 through 197 Processing helix chain 'A' and resid 216 through 231 Processing helix chain 'A' and resid 266 through 279 Processing helix chain 'A' and resid 294 through 306 Processing helix chain 'A' and resid 320 through 331 Processing helix chain 'A' and resid 345 through 360 Processing helix chain 'A' and resid 375 through 384 removed outlier: 3.909A pdb=" N ASP A 379 " --> pdb=" O THR A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 413 removed outlier: 5.146A pdb=" N LYS A 402 " --> pdb=" O ASP A 398 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N TYR A 403 " --> pdb=" O ARG A 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 18 Processing helix chain 'B' and resid 52 through 59 Processing helix chain 'B' and resid 85 through 94 Processing helix chain 'B' and resid 111 through 120 removed outlier: 3.998A pdb=" N ALA B 120 " --> pdb=" O ARG B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 137 removed outlier: 3.662A pdb=" N ASN B 137 " --> pdb=" O ALA B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 147 Processing helix chain 'B' and resid 175 through 189 Processing helix chain 'B' and resid 196 through 203 Processing helix chain 'B' and resid 234 through 238 removed outlier: 3.729A pdb=" N LEU B 237 " --> pdb=" O TRP B 234 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASP B 238 " --> pdb=" O ARG B 235 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 234 through 238' Processing helix chain 'B' and resid 252 through 263 Processing helix chain 'B' and resid 277 through 289 Processing helix chain 'B' and resid 298 through 308 removed outlier: 3.513A pdb=" N GLN B 308 " --> pdb=" O SER B 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 81 removed outlier: 4.479A pdb=" N ALA C 77 " --> pdb=" O ASN C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 100 removed outlier: 3.506A pdb=" N ILE C 91 " --> pdb=" O ASP C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 127 removed outlier: 3.721A pdb=" N ILE C 112 " --> pdb=" O GLY C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 136 Processing helix chain 'C' and resid 175 through 197 Processing helix chain 'C' and resid 216 through 231 Processing helix chain 'C' and resid 266 through 279 Processing helix chain 'C' and resid 294 through 306 Processing helix chain 'C' and resid 320 through 331 Processing helix chain 'C' and resid 345 through 360 Processing helix chain 'C' and resid 375 through 384 removed outlier: 3.966A pdb=" N ASP C 379 " --> pdb=" O THR C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 413 removed outlier: 5.352A pdb=" N LYS C 402 " --> pdb=" O ASP C 398 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N TYR C 403 " --> pdb=" O ARG C 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 18 Processing helix chain 'D' and resid 52 through 59 Processing helix chain 'D' and resid 85 through 94 Processing helix chain 'D' and resid 111 through 120 removed outlier: 3.751A pdb=" N GLU D 115 " --> pdb=" O GLY D 111 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA D 120 " --> pdb=" O ARG D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 137 removed outlier: 3.678A pdb=" N ASN D 137 " --> pdb=" O ALA D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 147 Processing helix chain 'D' and resid 175 through 189 Processing helix chain 'D' and resid 196 through 203 Processing helix chain 'D' and resid 234 through 238 removed outlier: 3.763A pdb=" N LEU D 237 " --> pdb=" O TRP D 234 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASP D 238 " --> pdb=" O ARG D 235 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 234 through 238' Processing helix chain 'D' and resid 252 through 263 Processing helix chain 'D' and resid 277 through 289 Processing helix chain 'D' and resid 298 through 307 Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 14 Processing sheet with id=AA2, first strand: chain 'A' and resid 141 through 142 removed outlier: 6.509A pdb=" N TYR A 141 " --> pdb=" O ILE A 418 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 145 through 146 removed outlier: 6.122A pdb=" N VAL A 145 " --> pdb=" O ILE A 389 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N CYS A 363 " --> pdb=" O GLN A 388 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N LYS A 390 " --> pdb=" O CYS A 363 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL A 365 " --> pdb=" O LYS A 390 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU A 337 " --> pdb=" O GLY A 313 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N VAL A 312 " --> pdb=" O VAL A 284 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ILE A 286 " --> pdb=" O VAL A 312 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N VAL A 284 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ILE A 241 " --> pdb=" O VAL A 284 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ILE A 286 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N LEU A 243 " --> pdb=" O ILE A 286 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N PHE A 166 " --> pdb=" O VAL A 150 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 251 through 252 Processing sheet with id=AA5, first strand: chain 'B' and resid 38 through 39 Processing sheet with id=AA6, first strand: chain 'B' and resid 38 through 39 removed outlier: 6.384A pdb=" N ALA B 70 " --> pdb=" O ILE B 99 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 265 through 268 removed outlier: 6.931A pdb=" N THR B 244 " --> pdb=" O GLU B 265 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N TRP B 267 " --> pdb=" O THR B 244 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N PHE B 246 " --> pdb=" O TRP B 267 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N GLY B 195 " --> pdb=" O GLU B 296 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N PHE B 150 " --> pdb=" O LEU B 293 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N VAL B 295 " --> pdb=" O PHE B 150 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N TYR B 152 " --> pdb=" O VAL B 295 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU B 313 " --> pdb=" O VAL B 151 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER D 347 " --> pdb=" O PHE B 314 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE D 344 " --> pdb=" O ILE D 337 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N ILE D 337 " --> pdb=" O ILE D 344 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ASN D 346 " --> pdb=" O ASN D 335 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 226 through 227 Processing sheet with id=AA9, first strand: chain 'B' and resid 271 through 272 Processing sheet with id=AB1, first strand: chain 'B' and resid 321 through 322 removed outlier: 3.664A pdb=" N GLN B 330 " --> pdb=" O ILE B 322 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 334 through 338 removed outlier: 6.784A pdb=" N ASN B 346 " --> pdb=" O ASN B 335 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ILE B 337 " --> pdb=" O ILE B 344 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ILE B 344 " --> pdb=" O ILE B 337 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER B 347 " --> pdb=" O PHE D 314 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU D 313 " --> pdb=" O VAL D 151 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N PHE D 150 " --> pdb=" O LEU D 293 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N VAL D 295 " --> pdb=" O PHE D 150 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N TYR D 152 " --> pdb=" O VAL D 295 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 5 through 14 Processing sheet with id=AB4, first strand: chain 'C' and resid 141 through 142 removed outlier: 6.403A pdb=" N TYR C 141 " --> pdb=" O ILE C 418 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 148 through 152 removed outlier: 5.774A pdb=" N ASN C 149 " --> pdb=" O ILE C 168 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ILE C 168 " --> pdb=" O ASN C 149 " (cutoff:3.500A) removed outlier: 8.482A pdb=" N VAL C 284 " --> pdb=" O VAL C 239 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ILE C 241 " --> pdb=" O VAL C 284 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N ILE C 286 " --> pdb=" O ILE C 241 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N LEU C 243 " --> pdb=" O ILE C 286 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N VAL C 312 " --> pdb=" O VAL C 284 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ILE C 286 " --> pdb=" O VAL C 312 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 251 through 252 Processing sheet with id=AB7, first strand: chain 'C' and resid 335 through 338 removed outlier: 7.821A pdb=" N LYS C 390 " --> pdb=" O CYS C 363 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N VAL C 365 " --> pdb=" O LYS C 390 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 38 through 44 removed outlier: 5.642A pdb=" N ILE D 33 " --> pdb=" O ILE D 40 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N GLU D 42 " --> pdb=" O CYS D 31 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N CYS D 31 " --> pdb=" O GLU D 42 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N GLY D 30 " --> pdb=" O THR D 73 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ALA D 70 " --> pdb=" O ILE D 99 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N ALA D 101 " --> pdb=" O ALA D 70 " (cutoff:3.500A) removed outlier: 9.099A pdb=" N VAL D 72 " --> pdb=" O ALA D 101 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 191 through 195 removed outlier: 6.689A pdb=" N ARG D 220 " --> pdb=" O ILE D 245 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N VAL D 247 " --> pdb=" O ARG D 220 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ILE D 222 " --> pdb=" O VAL D 247 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N THR D 244 " --> pdb=" O GLU D 265 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N TRP D 267 " --> pdb=" O THR D 244 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N PHE D 246 " --> pdb=" O TRP D 267 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 226 through 227 Processing sheet with id=AC2, first strand: chain 'D' and resid 271 through 272 Processing sheet with id=AC3, first strand: chain 'D' and resid 321 through 322 537 hydrogen bonds defined for protein. 1551 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: 2.02 Time building geometry restraints manager: 1.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3959 1.34 - 1.46: 2271 1.46 - 1.58: 5891 1.58 - 1.69: 1 1.69 - 1.81: 82 Bond restraints: 12204 Sorted by residual: bond pdb=" CA LYS A 63 " pdb=" CB LYS A 63 " ideal model delta sigma weight residual 1.531 1.588 -0.057 3.28e-02 9.30e+02 3.04e+00 bond pdb=" CA GLU C 279 " pdb=" CB GLU C 279 " ideal model delta sigma weight residual 1.530 1.545 -0.015 1.51e-02 4.39e+03 9.76e-01 bond pdb=" N VAL C 318 " pdb=" CA VAL C 318 " ideal model delta sigma weight residual 1.459 1.471 -0.012 1.25e-02 6.40e+03 9.65e-01 bond pdb=" N VAL A 318 " pdb=" CA VAL A 318 " ideal model delta sigma weight residual 1.459 1.471 -0.012 1.25e-02 6.40e+03 8.55e-01 bond pdb=" CG1 ILE A 271 " pdb=" CD1 ILE A 271 " ideal model delta sigma weight residual 1.513 1.478 0.035 3.90e-02 6.57e+02 8.27e-01 ... (remaining 12199 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 15925 1.42 - 2.83: 455 2.83 - 4.25: 90 4.25 - 5.67: 31 5.67 - 7.09: 9 Bond angle restraints: 16510 Sorted by residual: angle pdb=" N VAL C 201 " pdb=" CA VAL C 201 " pdb=" C VAL C 201 " ideal model delta sigma weight residual 113.53 108.87 4.66 9.80e-01 1.04e+00 2.26e+01 angle pdb=" C ILE D 40 " pdb=" N SER D 41 " pdb=" CA SER D 41 " ideal model delta sigma weight residual 121.54 128.34 -6.80 1.91e+00 2.74e-01 1.27e+01 angle pdb=" C PHE A 317 " pdb=" N VAL A 318 " pdb=" CA VAL A 318 " ideal model delta sigma weight residual 121.97 127.93 -5.96 1.80e+00 3.09e-01 1.10e+01 angle pdb=" C GLY C 387 " pdb=" N GLN C 388 " pdb=" CA GLN C 388 " ideal model delta sigma weight residual 121.81 128.90 -7.09 2.16e+00 2.14e-01 1.08e+01 angle pdb=" C PHE C 317 " pdb=" N VAL C 318 " pdb=" CA VAL C 318 " ideal model delta sigma weight residual 121.97 127.85 -5.88 1.80e+00 3.09e-01 1.07e+01 ... (remaining 16505 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.15: 6689 17.15 - 34.30: 594 34.30 - 51.45: 78 51.45 - 68.60: 15 68.60 - 85.75: 18 Dihedral angle restraints: 7394 sinusoidal: 2914 harmonic: 4480 Sorted by residual: dihedral pdb=" CA PHE C 60 " pdb=" C PHE C 60 " pdb=" N LEU C 61 " pdb=" CA LEU C 61 " ideal model delta harmonic sigma weight residual 180.00 154.28 25.72 0 5.00e+00 4.00e-02 2.65e+01 dihedral pdb=" CA PHE A 60 " pdb=" C PHE A 60 " pdb=" N LEU A 61 " pdb=" CA LEU A 61 " ideal model delta harmonic sigma weight residual 180.00 156.87 23.13 0 5.00e+00 4.00e-02 2.14e+01 dihedral pdb=" CA ILE D 40 " pdb=" C ILE D 40 " pdb=" N SER D 41 " pdb=" CA SER D 41 " ideal model delta harmonic sigma weight residual 180.00 156.90 23.10 0 5.00e+00 4.00e-02 2.13e+01 ... (remaining 7391 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1219 0.036 - 0.072: 459 0.072 - 0.108: 151 0.108 - 0.144: 68 0.144 - 0.180: 7 Chirality restraints: 1904 Sorted by residual: chirality pdb=" CA GLU A 279 " pdb=" N GLU A 279 " pdb=" C GLU A 279 " pdb=" CB GLU A 279 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.10e-01 chirality pdb=" CA GLU C 279 " pdb=" N GLU C 279 " pdb=" C GLU C 279 " pdb=" CB GLU C 279 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.64e-01 chirality pdb=" CA ASN B 211 " pdb=" N ASN B 211 " pdb=" C ASN B 211 " pdb=" CB ASN B 211 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.52e-01 ... (remaining 1901 not shown) Planarity restraints: 2118 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 72 " 0.012 2.00e-02 2.50e+03 2.34e-02 5.50e+00 pdb=" C VAL A 72 " -0.041 2.00e-02 2.50e+03 pdb=" O VAL A 72 " 0.015 2.00e-02 2.50e+03 pdb=" N ASN A 73 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 72 " -0.012 2.00e-02 2.50e+03 2.33e-02 5.44e+00 pdb=" C VAL C 72 " 0.040 2.00e-02 2.50e+03 pdb=" O VAL C 72 " -0.015 2.00e-02 2.50e+03 pdb=" N ASN C 73 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP C 244 " 0.038 5.00e-02 4.00e+02 5.71e-02 5.22e+00 pdb=" N PRO C 245 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO C 245 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 245 " 0.032 5.00e-02 4.00e+02 ... (remaining 2115 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 457 2.72 - 3.27: 11422 3.27 - 3.81: 18626 3.81 - 4.36: 23007 4.36 - 4.90: 41368 Nonbonded interactions: 94880 Sorted by model distance: nonbonded pdb=" O ASN B 307 " pdb=" OH TYR D 326 " model vdw 2.181 3.040 nonbonded pdb=" OG1 THR A 345 " pdb=" OE1 GLU A 348 " model vdw 2.197 3.040 nonbonded pdb=" OE1 GLU C 218 " pdb=" OH TYR C 281 " model vdw 2.228 3.040 nonbonded pdb=" OE1 GLU A 218 " pdb=" OH TYR A 281 " model vdw 2.247 3.040 nonbonded pdb=" OD2 ASP A 54 " pdb=" OG SER A 64 " model vdw 2.247 3.040 ... (remaining 94875 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } 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: 2.630 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: 0.160 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 12.760 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 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 0.057 12204 Z= 0.137 Angle : 0.619 7.086 16510 Z= 0.342 Chirality : 0.046 0.180 1904 Planarity : 0.004 0.057 2118 Dihedral : 13.597 85.754 4514 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.39 (0.21), residues: 1548 helix: 0.64 (0.21), residues: 612 sheet: 0.30 (0.34), residues: 254 loop : -1.30 (0.22), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 240 TYR 0.015 0.001 TYR D 152 PHE 0.014 0.002 PHE B 179 TRP 0.009 0.001 TRP D 44 HIS 0.005 0.001 HIS D 183 Details of bonding type rmsd covalent geometry : bond 0.00300 (12204) covalent geometry : angle 0.61873 (16510) hydrogen bonds : bond 0.15593 ( 535) hydrogen bonds : angle 6.26160 ( 1551) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 0.308 Fit side-chains REVERT: A 163 MET cc_start: 0.6632 (mtp) cc_final: 0.6415 (mtt) REVERT: A 369 SER cc_start: 0.7945 (m) cc_final: 0.7726 (p) outliers start: 0 outliers final: 0 residues processed: 151 average time/residue: 0.1135 time to fit residues: 23.9767 Evaluate side-chains 116 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 4.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 119 ASN B 132 GLN C 310 GLN D 10 GLN D 336 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.192199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.161379 restraints weight = 12246.016| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 1.56 r_work: 0.3610 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3482 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 12204 Z= 0.288 Angle : 0.744 9.978 16510 Z= 0.393 Chirality : 0.052 0.178 1904 Planarity : 0.005 0.048 2118 Dihedral : 5.528 26.229 1648 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 1.39 % Allowed : 9.03 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.79 (0.21), residues: 1548 helix: 0.30 (0.20), residues: 636 sheet: -0.02 (0.32), residues: 280 loop : -1.57 (0.23), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 18 TYR 0.021 0.002 TYR D 152 PHE 0.026 0.003 PHE C 131 TRP 0.011 0.002 TRP D 44 HIS 0.009 0.002 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00710 (12204) covalent geometry : angle 0.74365 (16510) hydrogen bonds : bond 0.06732 ( 535) hydrogen bonds : angle 5.09660 ( 1551) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 125 time to evaluate : 0.450 Fit side-chains REVERT: B 290 ILE cc_start: 0.6746 (OUTLIER) cc_final: 0.5990 (mp) REVERT: B 296 GLU cc_start: 0.7040 (mt-10) cc_final: 0.6801 (mt-10) REVERT: C 91 ILE cc_start: 0.8175 (OUTLIER) cc_final: 0.7534 (mp) REVERT: D 92 LYS cc_start: 0.8019 (mptt) cc_final: 0.7366 (ttpp) REVERT: D 285 MET cc_start: 0.7757 (mtt) cc_final: 0.7166 (mtt) REVERT: D 290 ILE cc_start: 0.6686 (OUTLIER) cc_final: 0.5980 (mp) outliers start: 18 outliers final: 11 residues processed: 139 average time/residue: 0.1173 time to fit residues: 23.1151 Evaluate side-chains 129 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 115 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 303 ASN Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 369 SER Chi-restraints excluded: chain C residue 376 ILE Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 104 ASP Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 303 ASN Chi-restraints excluded: chain D residue 336 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 42 optimal weight: 0.7980 chunk 45 optimal weight: 0.4980 chunk 109 optimal weight: 0.9990 chunk 87 optimal weight: 0.1980 chunk 85 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 93 optimal weight: 0.8980 chunk 90 optimal weight: 0.4980 chunk 6 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 GLN B 119 ASN D 17 ASN D 336 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.199681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.170495 restraints weight = 12213.189| |-----------------------------------------------------------------------------| r_work (start): 0.3832 rms_B_bonded: 1.37 r_work: 0.3737 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3624 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12204 Z= 0.107 Angle : 0.521 7.647 16510 Z= 0.282 Chirality : 0.043 0.144 1904 Planarity : 0.004 0.047 2118 Dihedral : 4.881 25.313 1648 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 1.39 % Allowed : 10.88 % Favored : 87.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.22), residues: 1548 helix: 0.98 (0.21), residues: 634 sheet: -0.06 (0.32), residues: 282 loop : -1.41 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 340 TYR 0.016 0.001 TYR D 152 PHE 0.013 0.001 PHE C 427 TRP 0.006 0.001 TRP B 44 HIS 0.004 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00238 (12204) covalent geometry : angle 0.52132 (16510) hydrogen bonds : bond 0.03975 ( 535) hydrogen bonds : angle 4.57259 ( 1551) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 115 time to evaluate : 0.339 Fit side-chains REVERT: D 92 LYS cc_start: 0.8014 (mptt) cc_final: 0.7459 (ttpp) REVERT: D 285 MET cc_start: 0.7579 (mtt) cc_final: 0.7169 (mtt) outliers start: 18 outliers final: 9 residues processed: 125 average time/residue: 0.1081 time to fit residues: 19.1941 Evaluate side-chains 120 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 111 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 303 ASN Chi-restraints excluded: chain D residue 104 ASP Chi-restraints excluded: chain D residue 167 ASP Chi-restraints excluded: chain D residue 303 ASN Chi-restraints excluded: chain D residue 336 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 14 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 95 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 GLN D 336 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.193918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.156353 restraints weight = 12251.156| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 2.11 r_work: 0.3650 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3507 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12204 Z= 0.160 Angle : 0.571 6.963 16510 Z= 0.306 Chirality : 0.045 0.146 1904 Planarity : 0.004 0.048 2118 Dihedral : 4.956 25.860 1648 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 1.93 % Allowed : 12.58 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.29 (0.22), residues: 1548 helix: 0.95 (0.21), residues: 634 sheet: -0.03 (0.33), residues: 280 loop : -1.45 (0.23), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 82 TYR 0.017 0.001 TYR D 152 PHE 0.014 0.002 PHE C 427 TRP 0.007 0.001 TRP B 44 HIS 0.006 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00384 (12204) covalent geometry : angle 0.57098 (16510) hydrogen bonds : bond 0.04698 ( 535) hydrogen bonds : angle 4.59238 ( 1551) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 113 time to evaluate : 0.434 Fit side-chains REVERT: A 163 MET cc_start: 0.6944 (mtp) cc_final: 0.6582 (mtt) REVERT: B 214 LYS cc_start: 0.7629 (mttp) cc_final: 0.7344 (mttm) REVERT: B 290 ILE cc_start: 0.6562 (OUTLIER) cc_final: 0.5824 (mt) REVERT: C 91 ILE cc_start: 0.7962 (OUTLIER) cc_final: 0.7457 (mt) REVERT: C 226 LYS cc_start: 0.7683 (pttt) cc_final: 0.6764 (ptmt) REVERT: C 279 GLU cc_start: 0.6047 (OUTLIER) cc_final: 0.5453 (pm20) REVERT: D 92 LYS cc_start: 0.7814 (mptt) cc_final: 0.7278 (ttpp) REVERT: D 285 MET cc_start: 0.7415 (mtt) cc_final: 0.6974 (mtt) REVERT: D 290 ILE cc_start: 0.6640 (OUTLIER) cc_final: 0.5922 (mt) outliers start: 25 outliers final: 16 residues processed: 130 average time/residue: 0.1131 time to fit residues: 20.8306 Evaluate side-chains 131 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 111 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 303 ASN Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 369 SER Chi-restraints excluded: chain C residue 376 ILE Chi-restraints excluded: chain D residue 104 ASP Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 303 ASN Chi-restraints excluded: chain D residue 336 GLN Chi-restraints excluded: chain D residue 338 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 20 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 137 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 126 optimal weight: 3.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.193877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.155000 restraints weight = 12354.878| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 2.20 r_work: 0.3619 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3474 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 12204 Z= 0.200 Angle : 0.623 7.099 16510 Z= 0.332 Chirality : 0.047 0.165 1904 Planarity : 0.004 0.048 2118 Dihedral : 5.117 26.081 1648 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 2.93 % Allowed : 12.58 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.47 (0.21), residues: 1548 helix: 0.80 (0.21), residues: 634 sheet: -0.12 (0.33), residues: 280 loop : -1.53 (0.23), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 89 TYR 0.019 0.002 TYR D 152 PHE 0.016 0.002 PHE B 150 TRP 0.007 0.001 TRP B 155 HIS 0.007 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00488 (12204) covalent geometry : angle 0.62258 (16510) hydrogen bonds : bond 0.05308 ( 535) hydrogen bonds : angle 4.66794 ( 1551) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 113 time to evaluate : 0.275 Fit side-chains REVERT: A 163 MET cc_start: 0.7016 (mtp) cc_final: 0.6638 (mtt) REVERT: B 214 LYS cc_start: 0.7611 (mttp) cc_final: 0.7324 (mttm) REVERT: B 290 ILE cc_start: 0.6602 (OUTLIER) cc_final: 0.5891 (mt) REVERT: C 91 ILE cc_start: 0.7943 (OUTLIER) cc_final: 0.7414 (mt) REVERT: C 279 GLU cc_start: 0.6148 (OUTLIER) cc_final: 0.5561 (pm20) REVERT: C 329 GLU cc_start: 0.6497 (OUTLIER) cc_final: 0.6224 (pt0) REVERT: D 92 LYS cc_start: 0.7756 (mptt) cc_final: 0.7207 (ttpp) REVERT: D 285 MET cc_start: 0.7403 (mtt) cc_final: 0.6982 (mtt) REVERT: D 290 ILE cc_start: 0.6539 (OUTLIER) cc_final: 0.5797 (mt) outliers start: 38 outliers final: 25 residues processed: 139 average time/residue: 0.1086 time to fit residues: 21.0210 Evaluate side-chains 142 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 112 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 303 ASN Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 329 GLU Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 369 SER Chi-restraints excluded: chain C residue 376 ILE Chi-restraints excluded: chain C residue 411 GLU Chi-restraints excluded: chain D residue 104 ASP Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 167 ASP Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 303 ASN Chi-restraints excluded: chain D residue 336 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 57 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 116 optimal weight: 2.9990 chunk 8 optimal weight: 0.3980 chunk 70 optimal weight: 0.6980 chunk 132 optimal weight: 0.9990 chunk 67 optimal weight: 9.9990 chunk 100 optimal weight: 0.5980 chunk 6 optimal weight: 0.9980 chunk 107 optimal weight: 0.8980 chunk 80 optimal weight: 0.3980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.196054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.158719 restraints weight = 12271.429| |-----------------------------------------------------------------------------| r_work (start): 0.3795 rms_B_bonded: 2.11 r_work: 0.3678 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3536 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12204 Z= 0.108 Angle : 0.519 6.873 16510 Z= 0.280 Chirality : 0.043 0.142 1904 Planarity : 0.004 0.054 2118 Dihedral : 4.782 25.543 1648 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 2.39 % Allowed : 13.66 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.16 (0.22), residues: 1548 helix: 1.16 (0.21), residues: 634 sheet: -0.08 (0.33), residues: 280 loop : -1.43 (0.24), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 82 TYR 0.015 0.001 TYR D 152 PHE 0.013 0.001 PHE C 427 TRP 0.007 0.001 TRP B 44 HIS 0.008 0.001 HIS D 52 Details of bonding type rmsd covalent geometry : bond 0.00242 (12204) covalent geometry : angle 0.51909 (16510) hydrogen bonds : bond 0.03867 ( 535) hydrogen bonds : angle 4.43950 ( 1551) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 120 time to evaluate : 0.437 Fit side-chains REVERT: A 163 MET cc_start: 0.7170 (mtp) cc_final: 0.6877 (mtt) REVERT: B 214 LYS cc_start: 0.7611 (mttp) cc_final: 0.7326 (mttm) REVERT: B 290 ILE cc_start: 0.6640 (OUTLIER) cc_final: 0.5909 (mt) REVERT: C 91 ILE cc_start: 0.7933 (OUTLIER) cc_final: 0.7460 (mt) REVERT: C 226 LYS cc_start: 0.7626 (pttt) cc_final: 0.6718 (ptmt) REVERT: C 279 GLU cc_start: 0.6036 (OUTLIER) cc_final: 0.5569 (pm20) REVERT: C 411 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7707 (pt0) REVERT: D 92 LYS cc_start: 0.7968 (mptt) cc_final: 0.7393 (ttpp) REVERT: D 285 MET cc_start: 0.7335 (mtt) cc_final: 0.6940 (mtt) REVERT: D 290 ILE cc_start: 0.6518 (OUTLIER) cc_final: 0.5784 (mt) outliers start: 31 outliers final: 19 residues processed: 142 average time/residue: 0.1144 time to fit residues: 22.9022 Evaluate side-chains 137 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 113 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 303 ASN Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 369 SER Chi-restraints excluded: chain C residue 376 ILE Chi-restraints excluded: chain C residue 411 GLU Chi-restraints excluded: chain D residue 104 ASP Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 167 ASP Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 303 ASN Chi-restraints excluded: chain D residue 336 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 137 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 77 optimal weight: 0.0170 chunk 16 optimal weight: 5.9990 chunk 95 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 overall best weight: 1.3824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.194603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.155915 restraints weight = 12187.704| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 2.17 r_work: 0.3632 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3488 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12204 Z= 0.177 Angle : 0.597 7.895 16510 Z= 0.319 Chirality : 0.046 0.156 1904 Planarity : 0.004 0.051 2118 Dihedral : 4.991 25.842 1648 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 2.93 % Allowed : 13.73 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.36 (0.22), residues: 1548 helix: 0.96 (0.21), residues: 634 sheet: -0.19 (0.32), residues: 284 loop : -1.49 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 82 TYR 0.017 0.001 TYR D 152 PHE 0.014 0.002 PHE C 427 TRP 0.007 0.001 TRP B 155 HIS 0.008 0.001 HIS D 52 Details of bonding type rmsd covalent geometry : bond 0.00427 (12204) covalent geometry : angle 0.59744 (16510) hydrogen bonds : bond 0.04936 ( 535) hydrogen bonds : angle 4.57234 ( 1551) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 114 time to evaluate : 0.435 Fit side-chains REVERT: A 411 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7714 (pt0) REVERT: B 185 LEU cc_start: 0.6484 (OUTLIER) cc_final: 0.6192 (tp) REVERT: B 214 LYS cc_start: 0.7583 (mttp) cc_final: 0.7297 (mttm) REVERT: B 290 ILE cc_start: 0.6574 (OUTLIER) cc_final: 0.5867 (mt) REVERT: C 91 ILE cc_start: 0.7947 (OUTLIER) cc_final: 0.7427 (mt) REVERT: C 279 GLU cc_start: 0.6149 (OUTLIER) cc_final: 0.5635 (pm20) REVERT: C 329 GLU cc_start: 0.6783 (OUTLIER) cc_final: 0.6512 (pt0) REVERT: D 92 LYS cc_start: 0.7920 (mptt) cc_final: 0.7342 (ttpp) REVERT: D 285 MET cc_start: 0.7334 (mtt) cc_final: 0.6940 (mtt) REVERT: D 290 ILE cc_start: 0.6615 (OUTLIER) cc_final: 0.5874 (mt) outliers start: 38 outliers final: 27 residues processed: 144 average time/residue: 0.1203 time to fit residues: 24.1281 Evaluate side-chains 147 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 113 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 411 GLU Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 303 ASN Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 329 GLU Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 369 SER Chi-restraints excluded: chain C residue 376 ILE Chi-restraints excluded: chain C residue 411 GLU Chi-restraints excluded: chain D residue 104 ASP Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 167 ASP Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 303 ASN Chi-restraints excluded: chain D residue 336 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 151 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 74 optimal weight: 0.8980 chunk 4 optimal weight: 8.9990 chunk 70 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 128 optimal weight: 0.7980 chunk 69 optimal weight: 0.8980 chunk 143 optimal weight: 5.9990 chunk 5 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.194440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.156938 restraints weight = 12239.739| |-----------------------------------------------------------------------------| r_work (start): 0.3778 rms_B_bonded: 2.10 r_work: 0.3661 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3518 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12204 Z= 0.131 Angle : 0.550 6.532 16510 Z= 0.296 Chirality : 0.044 0.142 1904 Planarity : 0.004 0.050 2118 Dihedral : 4.855 25.588 1648 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 3.01 % Allowed : 13.97 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.23 (0.22), residues: 1548 helix: 1.11 (0.21), residues: 634 sheet: -0.20 (0.33), residues: 282 loop : -1.44 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 82 TYR 0.016 0.001 TYR D 152 PHE 0.013 0.001 PHE C 427 TRP 0.007 0.001 TRP B 155 HIS 0.006 0.001 HIS D 52 Details of bonding type rmsd covalent geometry : bond 0.00304 (12204) covalent geometry : angle 0.54985 (16510) hydrogen bonds : bond 0.04243 ( 535) hydrogen bonds : angle 4.46633 ( 1551) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 113 time to evaluate : 0.465 Fit side-chains REVERT: A 81 LYS cc_start: 0.7653 (ttpp) cc_final: 0.7396 (ttmt) REVERT: A 163 MET cc_start: 0.7179 (mtp) cc_final: 0.6875 (mtt) REVERT: A 411 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7714 (pt0) REVERT: B 185 LEU cc_start: 0.6446 (OUTLIER) cc_final: 0.6167 (tp) REVERT: B 214 LYS cc_start: 0.7690 (mttp) cc_final: 0.7420 (mttm) REVERT: B 290 ILE cc_start: 0.6592 (OUTLIER) cc_final: 0.5844 (mt) REVERT: C 91 ILE cc_start: 0.7958 (OUTLIER) cc_final: 0.7463 (mt) REVERT: C 279 GLU cc_start: 0.6145 (OUTLIER) cc_final: 0.5711 (pm20) REVERT: C 329 GLU cc_start: 0.6868 (OUTLIER) cc_final: 0.6598 (pt0) REVERT: C 411 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7682 (pt0) REVERT: D 92 LYS cc_start: 0.7954 (mptt) cc_final: 0.7374 (ttpp) REVERT: D 285 MET cc_start: 0.7332 (mtt) cc_final: 0.6942 (mtt) REVERT: D 290 ILE cc_start: 0.6560 (OUTLIER) cc_final: 0.5828 (mt) outliers start: 39 outliers final: 27 residues processed: 143 average time/residue: 0.1159 time to fit residues: 23.5014 Evaluate side-chains 147 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 112 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 411 GLU Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 303 ASN Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 329 GLU Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 369 SER Chi-restraints excluded: chain C residue 376 ILE Chi-restraints excluded: chain C residue 411 GLU Chi-restraints excluded: chain D residue 104 ASP Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 167 ASP Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 303 ASN Chi-restraints excluded: chain D residue 336 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 28 optimal weight: 0.9990 chunk 120 optimal weight: 2.9990 chunk 67 optimal weight: 8.9990 chunk 40 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 78 optimal weight: 0.2980 chunk 85 optimal weight: 2.9990 chunk 50 optimal weight: 10.0000 chunk 21 optimal weight: 0.4980 chunk 99 optimal weight: 1.9990 chunk 122 optimal weight: 0.0870 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.196960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.159750 restraints weight = 12172.608| |-----------------------------------------------------------------------------| r_work (start): 0.3809 rms_B_bonded: 2.10 r_work: 0.3692 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3549 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12204 Z= 0.100 Angle : 0.512 6.927 16510 Z= 0.277 Chirality : 0.043 0.140 1904 Planarity : 0.003 0.049 2118 Dihedral : 4.645 25.317 1648 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 2.55 % Allowed : 14.27 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (0.22), residues: 1548 helix: 1.31 (0.22), residues: 634 sheet: -0.06 (0.33), residues: 280 loop : -1.36 (0.24), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 82 TYR 0.013 0.001 TYR D 152 PHE 0.012 0.001 PHE C 427 TRP 0.007 0.001 TRP B 44 HIS 0.005 0.001 HIS D 52 Details of bonding type rmsd covalent geometry : bond 0.00220 (12204) covalent geometry : angle 0.51214 (16510) hydrogen bonds : bond 0.03616 ( 535) hydrogen bonds : angle 4.34306 ( 1551) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 118 time to evaluate : 0.484 Fit side-chains REVERT: A 163 MET cc_start: 0.7225 (mtp) cc_final: 0.6978 (mtt) REVERT: B 214 LYS cc_start: 0.7589 (mttp) cc_final: 0.7289 (mttm) REVERT: B 290 ILE cc_start: 0.6519 (OUTLIER) cc_final: 0.5808 (mt) REVERT: C 91 ILE cc_start: 0.7921 (OUTLIER) cc_final: 0.7468 (mt) REVERT: C 279 GLU cc_start: 0.6087 (OUTLIER) cc_final: 0.5826 (pm20) REVERT: C 329 GLU cc_start: 0.6835 (OUTLIER) cc_final: 0.6564 (pt0) REVERT: C 411 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7721 (pt0) REVERT: D 92 LYS cc_start: 0.7974 (mptt) cc_final: 0.7398 (ttpp) REVERT: D 290 ILE cc_start: 0.6444 (OUTLIER) cc_final: 0.5713 (mt) outliers start: 33 outliers final: 23 residues processed: 141 average time/residue: 0.1290 time to fit residues: 25.6284 Evaluate side-chains 141 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 112 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 303 ASN Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 329 GLU Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 369 SER Chi-restraints excluded: chain C residue 376 ILE Chi-restraints excluded: chain C residue 411 GLU Chi-restraints excluded: chain D residue 104 ASP Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 167 ASP Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 303 ASN Chi-restraints excluded: chain D residue 336 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 152 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 133 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 123 optimal weight: 0.0970 chunk 135 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 GLN ** D 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 336 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.197083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.158561 restraints weight = 12198.321| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 2.17 r_work: 0.3662 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3518 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12204 Z= 0.136 Angle : 0.559 10.150 16510 Z= 0.300 Chirality : 0.045 0.142 1904 Planarity : 0.004 0.049 2118 Dihedral : 4.749 25.537 1648 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 2.47 % Allowed : 14.20 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.10 (0.22), residues: 1548 helix: 1.21 (0.21), residues: 634 sheet: -0.07 (0.33), residues: 280 loop : -1.38 (0.24), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 82 TYR 0.015 0.001 TYR D 152 PHE 0.014 0.001 PHE C 427 TRP 0.008 0.001 TRP B 44 HIS 0.006 0.001 HIS D 52 Details of bonding type rmsd covalent geometry : bond 0.00319 (12204) covalent geometry : angle 0.55909 (16510) hydrogen bonds : bond 0.04240 ( 535) hydrogen bonds : angle 4.39062 ( 1551) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 108 time to evaluate : 0.456 Fit side-chains REVERT: A 163 MET cc_start: 0.7139 (mtp) cc_final: 0.6858 (mtt) REVERT: A 411 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7733 (pt0) REVERT: B 214 LYS cc_start: 0.7594 (mttp) cc_final: 0.7319 (mttm) REVERT: B 290 ILE cc_start: 0.6490 (OUTLIER) cc_final: 0.5751 (mt) REVERT: C 91 ILE cc_start: 0.7919 (OUTLIER) cc_final: 0.7421 (mt) REVERT: C 279 GLU cc_start: 0.6117 (OUTLIER) cc_final: 0.5841 (pm20) REVERT: C 329 GLU cc_start: 0.6826 (OUTLIER) cc_final: 0.6553 (pt0) REVERT: C 411 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7751 (pt0) REVERT: D 92 LYS cc_start: 0.7940 (mptt) cc_final: 0.7355 (ttpp) REVERT: D 285 MET cc_start: 0.7246 (mtt) cc_final: 0.6500 (mtt) REVERT: D 290 ILE cc_start: 0.6602 (OUTLIER) cc_final: 0.5831 (mt) outliers start: 32 outliers final: 24 residues processed: 131 average time/residue: 0.1054 time to fit residues: 19.9480 Evaluate side-chains 139 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 108 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 411 GLU Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 303 ASN Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 329 GLU Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 369 SER Chi-restraints excluded: chain C residue 376 ILE Chi-restraints excluded: chain C residue 411 GLU Chi-restraints excluded: chain D residue 104 ASP Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 167 ASP Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 303 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 12 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 96 optimal weight: 3.9990 chunk 8 optimal weight: 0.0050 chunk 1 optimal weight: 1.9990 chunk 44 optimal weight: 0.0270 chunk 90 optimal weight: 0.9990 chunk 142 optimal weight: 0.0170 chunk 28 optimal weight: 0.8980 chunk 115 optimal weight: 0.6980 chunk 122 optimal weight: 3.9990 overall best weight: 0.2890 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.200413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.163615 restraints weight = 12182.235| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 2.09 r_work: 0.3738 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3598 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12204 Z= 0.088 Angle : 0.495 9.626 16510 Z= 0.267 Chirality : 0.043 0.161 1904 Planarity : 0.003 0.048 2118 Dihedral : 4.399 25.134 1648 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 1.85 % Allowed : 14.74 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.22), residues: 1548 helix: 1.46 (0.22), residues: 634 sheet: 0.09 (0.33), residues: 278 loop : -1.25 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 82 TYR 0.011 0.001 TYR B 152 PHE 0.011 0.001 PHE C 427 TRP 0.007 0.001 TRP B 44 HIS 0.004 0.001 HIS D 52 Details of bonding type rmsd covalent geometry : bond 0.00181 (12204) covalent geometry : angle 0.49454 (16510) hydrogen bonds : bond 0.03098 ( 535) hydrogen bonds : angle 4.20787 ( 1551) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2914.79 seconds wall clock time: 50 minutes 47.69 seconds (3047.69 seconds total)