Starting phenix.real_space_refine on Wed Jul 30 04:16:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9no2_49592/07_2025/9no2_49592.cif Found real_map, /net/cci-nas-00/data/ceres_data/9no2_49592/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9no2_49592/07_2025/9no2_49592.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9no2_49592/07_2025/9no2_49592.map" model { file = "/net/cci-nas-00/data/ceres_data/9no2_49592/07_2025/9no2_49592.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9no2_49592/07_2025/9no2_49592.cif" } resolution = 3.05 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= 0.106 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.48, per 1000 atoms: 0.62 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: 2.84 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.47 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: 4.13 Time building geometry restraints manager: 3.34 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: 0.03 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: 2.200 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: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 30.080 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: 0.010 Load rotamer database and sin/cos tables:3.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.580 ------------------------------------------------------------------------------- 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 (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: -0.39 (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 TRP 0.009 0.001 TRP D 44 HIS 0.005 0.001 HIS D 183 PHE 0.014 0.002 PHE B 179 TYR 0.015 0.001 TYR D 152 ARG 0.009 0.000 ARG D 240 Details of bonding type rmsd hydrogen bonds : bond 0.15593 ( 535) hydrogen bonds : angle 6.26160 ( 1551) covalent geometry : bond 0.00300 (12204) covalent geometry : angle 0.61873 (16510) *********************** 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 : 1.411 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: 0.2835 time to fit residues: 60.2747 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 : 1.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 120 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 139 optimal weight: 6.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 = 0.4125 r_free = 0.4125 target = 0.193516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.162798 restraints weight = 12189.928| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 1.55 r_work: 0.3612 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3493 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.1192 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= 0.267 Angle : 0.712 8.991 16510 Z= 0.378 Chirality : 0.051 0.172 1904 Planarity : 0.005 0.049 2118 Dihedral : 5.401 25.791 1648 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 1.23 % Allowed : 8.18 % Favored : 90.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.66 (0.21), residues: 1548 helix: 0.41 (0.20), residues: 636 sheet: 0.09 (0.32), residues: 278 loop : -1.53 (0.23), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 44 HIS 0.009 0.002 HIS B 183 PHE 0.025 0.003 PHE C 131 TYR 0.021 0.002 TYR D 152 ARG 0.005 0.001 ARG D 18 Details of bonding type rmsd hydrogen bonds : bond 0.06476 ( 535) hydrogen bonds : angle 5.07110 ( 1551) covalent geometry : bond 0.00661 (12204) covalent geometry : angle 0.71212 (16510) *********************** 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 145 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 129 time to evaluate : 1.251 Fit side-chains REVERT: B 290 ILE cc_start: 0.6749 (OUTLIER) cc_final: 0.6022 (mp) REVERT: B 296 GLU cc_start: 0.7011 (mt-10) cc_final: 0.6683 (mt-10) REVERT: C 91 ILE cc_start: 0.8184 (OUTLIER) cc_final: 0.7544 (mp) REVERT: D 92 LYS cc_start: 0.8167 (mptt) cc_final: 0.7513 (ttpp) REVERT: D 285 MET cc_start: 0.7735 (mtt) cc_final: 0.7240 (mtt) outliers start: 16 outliers final: 11 residues processed: 142 average time/residue: 0.2819 time to fit residues: 56.2553 Evaluate side-chains 131 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 118 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain B residue 102 THR 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 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 18 optimal weight: 0.8980 chunk 141 optimal weight: 2.9990 chunk 106 optimal weight: 0.0470 chunk 150 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 16 optimal weight: 0.0670 chunk 103 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 143 optimal weight: 0.9990 chunk 136 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 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 = 0.4180 r_free = 0.4180 target = 0.199248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.169799 restraints weight = 12182.334| |-----------------------------------------------------------------------------| r_work (start): 0.3825 rms_B_bonded: 1.39 r_work: 0.3731 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3618 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.1172 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= 0.111 Angle : 0.527 7.681 16510 Z= 0.286 Chirality : 0.043 0.144 1904 Planarity : 0.004 0.048 2118 Dihedral : 4.887 25.181 1648 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 1.77 % Allowed : 10.57 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.24 (0.22), residues: 1548 helix: 0.98 (0.21), residues: 634 sheet: 0.04 (0.32), residues: 280 loop : -1.42 (0.24), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 44 HIS 0.004 0.001 HIS B 183 PHE 0.013 0.001 PHE A 427 TYR 0.016 0.001 TYR D 152 ARG 0.005 0.000 ARG D 340 Details of bonding type rmsd hydrogen bonds : bond 0.04143 ( 535) hydrogen bonds : angle 4.59949 ( 1551) covalent geometry : bond 0.00247 (12204) covalent geometry : angle 0.52683 (16510) *********************** 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 135 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 112 time to evaluate : 1.349 Fit side-chains REVERT: B 296 GLU cc_start: 0.6671 (mt-10) cc_final: 0.6441 (mt-10) REVERT: D 92 LYS cc_start: 0.7998 (mptt) cc_final: 0.7449 (ttpp) REVERT: D 285 MET cc_start: 0.7500 (mtt) cc_final: 0.7010 (mtt) REVERT: D 290 ILE cc_start: 0.6558 (OUTLIER) cc_final: 0.5868 (mp) outliers start: 23 outliers final: 14 residues processed: 125 average time/residue: 0.2643 time to fit residues: 47.6199 Evaluate side-chains 123 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 108 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 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 303 ASN 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 167 ASP 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 62 optimal weight: 0.0060 chunk 2 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 144 optimal weight: 8.9990 chunk 110 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 118 optimal weight: 0.8980 chunk 147 optimal weight: 0.3980 chunk 60 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 139 optimal weight: 0.6980 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 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 = 0.4290 r_free = 0.4290 target = 0.204694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.171208 restraints weight = 12376.886| |-----------------------------------------------------------------------------| r_work (start): 0.3948 rms_B_bonded: 2.02 r_work: 0.3811 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3674 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.1259 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 : 0.509 6.878 16510 Z= 0.276 Chirality : 0.043 0.141 1904 Planarity : 0.003 0.047 2118 Dihedral : 4.714 25.149 1648 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 2.01 % Allowed : 11.73 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.05 (0.22), residues: 1548 helix: 1.18 (0.21), residues: 634 sheet: 0.08 (0.32), residues: 280 loop : -1.34 (0.24), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 155 HIS 0.005 0.001 HIS B 183 PHE 0.012 0.001 PHE C 427 TYR 0.014 0.001 TYR D 152 ARG 0.002 0.000 ARG D 82 Details of bonding type rmsd hydrogen bonds : bond 0.03860 ( 535) hydrogen bonds : angle 4.44861 ( 1551) covalent geometry : bond 0.00240 (12204) covalent geometry : angle 0.50920 (16510) *********************** 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 142 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 116 time to evaluate : 1.335 Fit side-chains REVERT: A 163 MET cc_start: 0.6989 (mtp) cc_final: 0.6681 (mtt) REVERT: B 214 LYS cc_start: 0.7615 (mttp) cc_final: 0.7350 (mttm) REVERT: B 290 ILE cc_start: 0.6754 (OUTLIER) cc_final: 0.6013 (mt) REVERT: B 296 GLU cc_start: 0.6400 (mt-10) cc_final: 0.6131 (mt-10) REVERT: C 91 ILE cc_start: 0.8134 (OUTLIER) cc_final: 0.7695 (mt) REVERT: C 279 GLU cc_start: 0.6244 (OUTLIER) cc_final: 0.5701 (pm20) REVERT: D 92 LYS cc_start: 0.8123 (mptt) cc_final: 0.7580 (ttpp) REVERT: D 285 MET cc_start: 0.7506 (mtt) cc_final: 0.7073 (mtt) REVERT: D 290 ILE cc_start: 0.6584 (OUTLIER) cc_final: 0.5878 (mp) outliers start: 26 outliers final: 17 residues processed: 132 average time/residue: 0.2637 time to fit residues: 49.5844 Evaluate side-chains 135 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 1.256 ------------------------------------------------------------------------------- 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 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 167 ASP 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 20 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 144 optimal weight: 7.9990 chunk 3 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 23 optimal weight: 0.3980 chunk 118 optimal weight: 0.5980 chunk 145 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 GLN C 78 GLN D 336 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.195588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.158127 restraints weight = 12202.081| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 2.11 r_work: 0.3671 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3528 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.1331 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= 0.134 Angle : 0.536 6.735 16510 Z= 0.288 Chirality : 0.044 0.143 1904 Planarity : 0.004 0.047 2118 Dihedral : 4.754 25.220 1648 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 2.31 % Allowed : 12.42 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.10 (0.22), residues: 1548 helix: 1.15 (0.21), residues: 634 sheet: 0.04 (0.33), residues: 280 loop : -1.37 (0.24), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 44 HIS 0.005 0.001 HIS B 183 PHE 0.013 0.002 PHE C 427 TYR 0.015 0.001 TYR D 152 ARG 0.002 0.000 ARG D 82 Details of bonding type rmsd hydrogen bonds : bond 0.04246 ( 535) hydrogen bonds : angle 4.44970 ( 1551) covalent geometry : bond 0.00316 (12204) covalent geometry : angle 0.53636 (16510) *********************** 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 146 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 116 time to evaluate : 1.252 Fit side-chains REVERT: A 163 MET cc_start: 0.7076 (mtp) cc_final: 0.6776 (mtt) REVERT: B 290 ILE cc_start: 0.6588 (OUTLIER) cc_final: 0.5865 (mt) REVERT: B 296 GLU cc_start: 0.6488 (mt-10) cc_final: 0.6285 (mt-10) REVERT: C 91 ILE cc_start: 0.7935 (OUTLIER) cc_final: 0.7447 (mt) REVERT: C 279 GLU cc_start: 0.6037 (OUTLIER) cc_final: 0.5494 (pm20) REVERT: C 329 GLU cc_start: 0.6893 (OUTLIER) cc_final: 0.6603 (pt0) REVERT: C 411 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7696 (pt0) REVERT: D 92 LYS cc_start: 0.7972 (mptt) cc_final: 0.7424 (ttpp) REVERT: D 285 MET cc_start: 0.7412 (mtt) cc_final: 0.7000 (mtt) REVERT: D 290 ILE cc_start: 0.6556 (OUTLIER) cc_final: 0.5822 (mp) outliers start: 30 outliers final: 19 residues processed: 136 average time/residue: 0.2490 time to fit residues: 48.8665 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 : 1.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 MET 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 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 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 51 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 142 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 78 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 = 0.4234 r_free = 0.4234 target = 0.198872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.165899 restraints weight = 12555.010| |-----------------------------------------------------------------------------| r_work (start): 0.3916 rms_B_bonded: 2.01 r_work: 0.3755 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3616 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.1474 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= 0.199 Angle : 0.615 7.337 16510 Z= 0.327 Chirality : 0.047 0.163 1904 Planarity : 0.004 0.048 2118 Dihedral : 5.030 25.858 1648 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 2.93 % Allowed : 12.73 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.38 (0.21), residues: 1548 helix: 0.91 (0.21), residues: 634 sheet: -0.21 (0.32), residues: 286 loop : -1.47 (0.24), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 155 HIS 0.007 0.001 HIS B 183 PHE 0.016 0.002 PHE B 150 TYR 0.018 0.002 TYR D 152 ARG 0.003 0.001 ARG D 18 Details of bonding type rmsd hydrogen bonds : bond 0.05246 ( 535) hydrogen bonds : angle 4.60839 ( 1551) covalent geometry : bond 0.00488 (12204) covalent geometry : angle 0.61539 (16510) *********************** 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 149 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 111 time to evaluate : 1.225 Fit side-chains REVERT: A 163 MET cc_start: 0.7176 (mtp) cc_final: 0.6828 (mtt) REVERT: B 290 ILE cc_start: 0.6920 (OUTLIER) cc_final: 0.6181 (mt) REVERT: C 91 ILE cc_start: 0.8211 (OUTLIER) cc_final: 0.7714 (mt) REVERT: C 279 GLU cc_start: 0.6406 (OUTLIER) cc_final: 0.5900 (pm20) REVERT: C 329 GLU cc_start: 0.7245 (OUTLIER) cc_final: 0.6965 (pt0) REVERT: C 411 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7661 (pt0) REVERT: D 92 LYS cc_start: 0.8003 (mptt) cc_final: 0.7453 (ttpp) REVERT: D 285 MET cc_start: 0.7610 (mtt) cc_final: 0.7225 (mtt) REVERT: D 290 ILE cc_start: 0.6857 (OUTLIER) cc_final: 0.6100 (mp) outliers start: 38 outliers final: 22 residues processed: 138 average time/residue: 0.2762 time to fit residues: 54.0578 Evaluate side-chains 137 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 109 time to evaluate : 1.280 ------------------------------------------------------------------------------- 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 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 102 THR 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 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 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 110 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 78 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.4176 r_free = 0.4176 target = 0.198226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.166463 restraints weight = 12153.310| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 1.74 r_work: 0.3600 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3475 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12204 Z= 0.151 Angle : 0.569 7.943 16510 Z= 0.304 Chirality : 0.045 0.146 1904 Planarity : 0.004 0.048 2118 Dihedral : 4.926 25.505 1648 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 2.39 % Allowed : 13.43 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.29 (0.22), residues: 1548 helix: 1.02 (0.21), residues: 634 sheet: -0.17 (0.33), residues: 282 loop : -1.44 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 44 HIS 0.009 0.001 HIS D 52 PHE 0.013 0.002 PHE C 427 TYR 0.017 0.001 TYR D 152 ARG 0.005 0.000 ARG D 82 Details of bonding type rmsd hydrogen bonds : bond 0.04583 ( 535) hydrogen bonds : angle 4.52375 ( 1551) covalent geometry : bond 0.00360 (12204) covalent geometry : angle 0.56879 (16510) *********************** 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 142 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 111 time to evaluate : 1.217 Fit side-chains REVERT: A 163 MET cc_start: 0.7147 (mtp) cc_final: 0.6837 (mtt) REVERT: B 214 LYS cc_start: 0.7599 (mttp) cc_final: 0.7317 (mttm) REVERT: B 290 ILE cc_start: 0.6744 (OUTLIER) cc_final: 0.6025 (mt) REVERT: C 91 ILE cc_start: 0.8122 (OUTLIER) cc_final: 0.7651 (mt) REVERT: C 279 GLU cc_start: 0.6331 (OUTLIER) cc_final: 0.5853 (pm20) REVERT: C 329 GLU cc_start: 0.7144 (OUTLIER) cc_final: 0.6863 (pt0) REVERT: C 411 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7655 (pt0) REVERT: D 92 LYS cc_start: 0.8076 (mptt) cc_final: 0.7500 (ttpp) REVERT: D 285 MET cc_start: 0.7567 (mtt) cc_final: 0.7174 (mtt) REVERT: D 290 ILE cc_start: 0.6621 (OUTLIER) cc_final: 0.5898 (mp) REVERT: D 336 GLN cc_start: 0.7432 (OUTLIER) cc_final: 0.7117 (pt0) outliers start: 31 outliers final: 23 residues processed: 135 average time/residue: 0.2522 time to fit residues: 48.8160 Evaluate side-chains 140 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 110 time to evaluate : 1.210 ------------------------------------------------------------------------------- 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 B residue 48 VAL Chi-restraints excluded: chain B residue 102 THR 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 212 ILE Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 303 ASN Chi-restraints excluded: chain D residue 310 LEU 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 41 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 125 optimal weight: 0.9990 chunk 115 optimal weight: 0.6980 chunk 138 optimal weight: 3.9990 chunk 127 optimal weight: 8.9990 chunk 74 optimal weight: 1.9990 chunk 111 optimal weight: 0.5980 chunk 60 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 = 0.4187 r_free = 0.4187 target = 0.199472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.165525 restraints weight = 12232.918| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 1.70 r_work: 0.3631 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3503 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.1518 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= 0.127 Angle : 0.542 6.507 16510 Z= 0.292 Chirality : 0.044 0.143 1904 Planarity : 0.004 0.049 2118 Dihedral : 4.814 25.434 1648 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 2.78 % Allowed : 13.12 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.17 (0.22), residues: 1548 helix: 1.14 (0.21), residues: 634 sheet: -0.08 (0.33), residues: 280 loop : -1.41 (0.24), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 44 HIS 0.007 0.001 HIS D 52 PHE 0.013 0.001 PHE C 427 TYR 0.015 0.001 TYR D 152 ARG 0.004 0.000 ARG D 82 Details of bonding type rmsd hydrogen bonds : bond 0.04176 ( 535) hydrogen bonds : angle 4.45098 ( 1551) covalent geometry : bond 0.00295 (12204) covalent geometry : angle 0.54205 (16510) *********************** 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 148 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 112 time to evaluate : 1.206 Fit side-chains REVERT: A 163 MET cc_start: 0.7148 (mtp) cc_final: 0.6857 (mtt) REVERT: B 214 LYS cc_start: 0.7587 (mttp) cc_final: 0.7332 (mttm) REVERT: B 290 ILE cc_start: 0.6712 (OUTLIER) cc_final: 0.5965 (mt) REVERT: B 296 GLU cc_start: 0.6964 (mt-10) cc_final: 0.6740 (mt-10) REVERT: C 91 ILE cc_start: 0.8120 (OUTLIER) cc_final: 0.7662 (mt) REVERT: C 279 GLU cc_start: 0.6325 (OUTLIER) cc_final: 0.5919 (pm20) REVERT: C 329 GLU cc_start: 0.7134 (OUTLIER) cc_final: 0.6849 (pt0) REVERT: C 411 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7615 (pt0) REVERT: D 92 LYS cc_start: 0.8062 (mptt) cc_final: 0.7487 (ttpp) REVERT: D 285 MET cc_start: 0.7541 (mtt) cc_final: 0.7144 (mtt) REVERT: D 290 ILE cc_start: 0.6433 (OUTLIER) cc_final: 0.5689 (mp) outliers start: 36 outliers final: 23 residues processed: 139 average time/residue: 0.2757 time to fit residues: 54.5178 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 : 1.253 ------------------------------------------------------------------------------- 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 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 310 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 101 optimal weight: 2.9990 chunk 104 optimal weight: 0.0980 chunk 12 optimal weight: 0.0980 chunk 76 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 chunk 110 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 65 optimal weight: 7.9990 chunk 30 optimal weight: 4.9990 chunk 118 optimal weight: 0.3980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.199219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.165174 restraints weight = 12135.201| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 1.70 r_work: 0.3629 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3501 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.1540 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= 0.134 Angle : 0.555 9.589 16510 Z= 0.298 Chirality : 0.045 0.153 1904 Planarity : 0.004 0.049 2118 Dihedral : 4.788 25.332 1648 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 2.62 % Allowed : 13.81 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.15 (0.22), residues: 1548 helix: 1.16 (0.21), residues: 634 sheet: -0.06 (0.33), residues: 280 loop : -1.42 (0.24), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 155 HIS 0.006 0.001 HIS D 52 PHE 0.013 0.002 PHE C 427 TYR 0.015 0.001 TYR D 152 ARG 0.004 0.000 ARG D 82 Details of bonding type rmsd hydrogen bonds : bond 0.04245 ( 535) hydrogen bonds : angle 4.43321 ( 1551) covalent geometry : bond 0.00312 (12204) covalent geometry : angle 0.55521 (16510) *********************** 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 148 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 114 time to evaluate : 1.286 Fit side-chains REVERT: A 163 MET cc_start: 0.7133 (mtp) cc_final: 0.6852 (mtt) REVERT: A 411 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7734 (pt0) REVERT: B 214 LYS cc_start: 0.7580 (mttp) cc_final: 0.7324 (mttm) REVERT: B 290 ILE cc_start: 0.6676 (OUTLIER) cc_final: 0.5929 (mt) REVERT: B 296 GLU cc_start: 0.6929 (mt-10) cc_final: 0.6704 (mt-10) REVERT: C 91 ILE cc_start: 0.8120 (OUTLIER) cc_final: 0.7662 (mt) REVERT: C 279 GLU cc_start: 0.6321 (OUTLIER) cc_final: 0.5927 (pm20) REVERT: C 329 GLU cc_start: 0.7112 (OUTLIER) cc_final: 0.6832 (pt0) REVERT: C 411 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7634 (pt0) REVERT: D 92 LYS cc_start: 0.8057 (mptt) cc_final: 0.7482 (ttpp) REVERT: D 285 MET cc_start: 0.7500 (mtt) cc_final: 0.7097 (mtt) REVERT: D 290 ILE cc_start: 0.6542 (OUTLIER) cc_final: 0.5785 (mp) outliers start: 34 outliers final: 25 residues processed: 138 average time/residue: 0.2587 time to fit residues: 51.2052 Evaluate side-chains 145 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 113 time to evaluate : 1.264 ------------------------------------------------------------------------------- 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 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 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 310 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 48 optimal weight: 5.9990 chunk 110 optimal weight: 0.5980 chunk 88 optimal weight: 1.9990 chunk 58 optimal weight: 6.9990 chunk 27 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 92 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.4189 r_free = 0.4189 target = 0.199732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.166564 restraints weight = 12148.337| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 1.64 r_work: 0.3639 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3513 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12204 Z= 0.126 Angle : 0.545 8.971 16510 Z= 0.293 Chirality : 0.044 0.142 1904 Planarity : 0.004 0.049 2118 Dihedral : 4.732 25.302 1648 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 2.62 % Allowed : 13.81 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.22), residues: 1548 helix: 1.21 (0.21), residues: 634 sheet: -0.03 (0.33), residues: 280 loop : -1.38 (0.24), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 44 HIS 0.006 0.001 HIS D 52 PHE 0.012 0.001 PHE C 427 TYR 0.014 0.001 TYR D 152 ARG 0.004 0.000 ARG D 82 Details of bonding type rmsd hydrogen bonds : bond 0.04089 ( 535) hydrogen bonds : angle 4.39633 ( 1551) covalent geometry : bond 0.00291 (12204) covalent geometry : angle 0.54493 (16510) ********************** 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 149 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 115 time to evaluate : 1.395 Fit side-chains REVERT: A 163 MET cc_start: 0.7154 (mtp) cc_final: 0.6884 (mtt) REVERT: A 411 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7714 (pt0) REVERT: B 214 LYS cc_start: 0.7545 (mttp) cc_final: 0.7293 (mttm) REVERT: B 290 ILE cc_start: 0.6686 (OUTLIER) cc_final: 0.5940 (mt) REVERT: B 296 GLU cc_start: 0.6858 (mt-10) cc_final: 0.6646 (mt-10) REVERT: C 91 ILE cc_start: 0.8154 (OUTLIER) cc_final: 0.7713 (mt) REVERT: C 279 GLU cc_start: 0.6377 (OUTLIER) cc_final: 0.6129 (pm20) REVERT: C 329 GLU cc_start: 0.7143 (OUTLIER) cc_final: 0.6858 (pt0) REVERT: C 411 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7621 (pt0) REVERT: D 92 LYS cc_start: 0.8104 (mptt) cc_final: 0.7535 (ttpp) REVERT: D 290 ILE cc_start: 0.6566 (OUTLIER) cc_final: 0.5753 (mp) outliers start: 34 outliers final: 27 residues processed: 140 average time/residue: 0.2557 time to fit residues: 51.8553 Evaluate side-chains 146 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 112 time to evaluate : 1.520 ------------------------------------------------------------------------------- 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 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 310 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 90 optimal weight: 0.9990 chunk 28 optimal weight: 0.0170 chunk 49 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 106 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 147 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 70 optimal weight: 0.8980 chunk 114 optimal weight: 0.5980 chunk 127 optimal weight: 8.9990 overall best weight: 0.7020 ------------------------------------------------------------------------------- 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 = 0.4199 r_free = 0.4199 target = 0.200774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.167602 restraints weight = 12113.233| |-----------------------------------------------------------------------------| r_work (start): 0.3773 rms_B_bonded: 1.65 r_work: 0.3680 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3554 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12204 Z= 0.114 Angle : 0.532 8.531 16510 Z= 0.286 Chirality : 0.044 0.141 1904 Planarity : 0.004 0.049 2118 Dihedral : 4.649 25.204 1648 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 2.47 % Allowed : 14.27 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.01 (0.22), residues: 1548 helix: 1.27 (0.21), residues: 634 sheet: 0.03 (0.33), residues: 280 loop : -1.34 (0.24), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 44 HIS 0.005 0.001 HIS D 52 PHE 0.012 0.001 PHE C 427 TYR 0.013 0.001 TYR D 152 ARG 0.004 0.000 ARG D 82 Details of bonding type rmsd hydrogen bonds : bond 0.03874 ( 535) hydrogen bonds : angle 4.35197 ( 1551) covalent geometry : bond 0.00259 (12204) covalent geometry : angle 0.53178 (16510) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6460.83 seconds wall clock time: 111 minutes 40.92 seconds (6700.92 seconds total)