Starting phenix.real_space_refine on Sat Jul 26 10:30:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vvl_32143/07_2025/7vvl_32143.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vvl_32143/07_2025/7vvl_32143.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vvl_32143/07_2025/7vvl_32143.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vvl_32143/07_2025/7vvl_32143.map" model { file = "/net/cci-nas-00/data/ceres_data/7vvl_32143/07_2025/7vvl_32143.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vvl_32143/07_2025/7vvl_32143.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.010 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 53 5.16 5 C 5546 2.51 5 N 1523 2.21 5 O 1603 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 8725 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1901 Classifications: {'peptide': 230} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 223} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 2519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2519 Classifications: {'peptide': 335} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 5, 'TRANS': 329} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 2, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 46 Chain: "G" Number of atoms: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 392 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "N" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 968 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "P" Number of atoms: 280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 280 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 33} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'PHE%COO:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "R" Number of atoms: 2664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2664 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 9, 'TRANS': 336} Chain breaks: 4 Unresolved non-hydrogen bonds: 219 Unresolved non-hydrogen angles: 283 Unresolved non-hydrogen dihedrals: 199 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 5, 'TYR:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 4, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 6, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 152 Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 5.42, per 1000 atoms: 0.62 Number of scatterers: 8725 At special positions: 0 Unit cell: (128.374, 99.6003, 127.267, 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 53 16.00 O 1603 8.00 N 1523 7.00 C 5546 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.04 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.07 Simple disulfide: pdb=" SG CYS R 281 " - pdb=" SG CYS R 351 " distance=2.02 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: 2.64 Conformation dependent library (CDL) restraints added in 1.1 seconds 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2120 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 12 sheets defined 41.8% alpha, 18.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'A' and resid 13 through 39 removed outlier: 3.787A pdb=" N LYS A 17 " --> pdb=" O ARG A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 60 removed outlier: 3.520A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.632A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 268 Processing helix chain 'A' and resid 283 through 294 removed outlier: 3.568A pdb=" N LEU A 292 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY A 294 " --> pdb=" O LYS A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 302 removed outlier: 4.163A pdb=" N TYR A 301 " --> pdb=" O LYS A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 308 removed outlier: 3.537A pdb=" N TYR A 308 " --> pdb=" O PHE A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 343 removed outlier: 3.540A pdb=" N ARG A 332 " --> pdb=" O LYS A 328 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE A 338 " --> pdb=" O GLU A 334 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N SER A 342 " --> pdb=" O ILE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 381 removed outlier: 3.511A pdb=" N ILE A 365 " --> pdb=" O ASN A 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 24 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 11 through 24 removed outlier: 3.800A pdb=" N GLU G 17 " --> pdb=" O ARG G 13 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.835A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 34 Processing helix chain 'R' and resid 33 through 49 Processing helix chain 'R' and resid 179 through 212 removed outlier: 4.196A pdb=" N VAL R 183 " --> pdb=" O ARG R 179 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N TYR R 211 " --> pdb=" O LEU R 207 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N PHE R 212 " --> pdb=" O ILE R 208 " (cutoff:3.500A) Processing helix chain 'R' and resid 213 through 216 Processing helix chain 'R' and resid 217 through 245 removed outlier: 3.555A pdb=" N ILE R 222 " --> pdb=" O THR R 218 " (cutoff:3.500A) Processing helix chain 'R' and resid 279 through 312 removed outlier: 3.545A pdb=" N ALA R 284 " --> pdb=" O GLY R 280 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR R 286 " --> pdb=" O ARG R 282 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN R 295 " --> pdb=" O PHE R 291 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE R 310 " --> pdb=" O LEU R 306 " (cutoff:3.500A) Processing helix chain 'R' and resid 320 through 344 removed outlier: 3.541A pdb=" N THR R 325 " --> pdb=" O LEU R 321 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU R 331 " --> pdb=" O PHE R 327 " (cutoff:3.500A) Proline residue: R 332 - end of helix removed outlier: 3.648A pdb=" N PHE R 335 " --> pdb=" O LEU R 331 " (cutoff:3.500A) Processing helix chain 'R' and resid 356 through 359 removed outlier: 4.090A pdb=" N LYS R 359 " --> pdb=" O SER R 356 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 356 through 359' Processing helix chain 'R' and resid 360 through 391 Proline residue: R 366 - end of helix removed outlier: 3.503A pdb=" N ASN R 374 " --> pdb=" O SER R 370 " (cutoff:3.500A) Processing helix chain 'R' and resid 398 through 400 No H-bonds generated for 'chain 'R' and resid 398 through 400' Processing helix chain 'R' and resid 401 through 413 removed outlier: 3.756A pdb=" N LEU R 406 " --> pdb=" O GLN R 402 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LEU R 407 " --> pdb=" O TYR R 403 " (cutoff:3.500A) Processing helix chain 'R' and resid 413 through 418 Processing helix chain 'R' and resid 419 through 423 removed outlier: 3.702A pdb=" N VAL R 423 " --> pdb=" O HIS R 420 " (cutoff:3.500A) Processing helix chain 'R' and resid 434 through 461 removed outlier: 3.531A pdb=" N PHE R 450 " --> pdb=" O LEU R 446 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N GLY R 452 " --> pdb=" O ASN R 448 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N PHE R 453 " --> pdb=" O SER R 449 " (cutoff:3.500A) Processing helix chain 'R' and resid 463 through 477 removed outlier: 3.692A pdb=" N LYS R 472 " --> pdb=" O ALA R 468 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER R 473 " --> pdb=" O GLU R 469 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 3.984A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ILE A 244 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N PHE A 280 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N PHE A 246 " --> pdb=" O PHE A 280 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ASN A 282 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N VAL A 248 " --> pdb=" O ASN A 282 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.812A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.800A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.735A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.935A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.020A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.373A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.617A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 58 through 60 removed outlier: 6.520A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 111 through 112 removed outlier: 3.639A pdb=" N GLU R 111 " --> pdb=" O TRP R 118 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'R' and resid 128 through 130 453 hydrogen bonds defined for protein. 1290 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: 2.59 Time building geometry restraints manager: 3.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1424 1.30 - 1.43: 2492 1.43 - 1.56: 4915 1.56 - 1.69: 1 1.69 - 1.83: 78 Bond restraints: 8910 Sorted by residual: bond pdb=" CE1 HIS R 307 " pdb=" NE2 HIS R 307 " ideal model delta sigma weight residual 1.321 1.374 -0.053 1.00e-02 1.00e+04 2.79e+01 bond pdb=" C ARG R 150 " pdb=" O ARG R 150 " ideal model delta sigma weight residual 1.236 1.301 -0.064 1.26e-02 6.30e+03 2.61e+01 bond pdb=" C PRO A 351 " pdb=" O PRO A 351 " ideal model delta sigma weight residual 1.233 1.180 0.053 1.10e-02 8.26e+03 2.36e+01 bond pdb=" C ASN R 139 " pdb=" O ASN R 139 " ideal model delta sigma weight residual 1.234 1.171 0.063 1.35e-02 5.49e+03 2.18e+01 bond pdb=" N VAL R 157 " pdb=" CA VAL R 157 " ideal model delta sigma weight residual 1.460 1.494 -0.034 7.50e-03 1.78e+04 2.11e+01 ... (remaining 8905 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 8531 1.81 - 3.61: 3236 3.61 - 5.42: 298 5.42 - 7.23: 18 7.23 - 9.03: 7 Bond angle restraints: 12090 Sorted by residual: angle pdb=" N PRO N 102 " pdb=" CA PRO N 102 " pdb=" C PRO N 102 " ideal model delta sigma weight residual 114.35 121.98 -7.63 1.25e+00 6.40e-01 3.72e+01 angle pdb=" CA VAL A 224 " pdb=" C VAL A 224 " pdb=" O VAL A 224 " ideal model delta sigma weight residual 122.63 118.12 4.51 8.70e-01 1.32e+00 2.69e+01 angle pdb=" N GLU P 4 " pdb=" CA GLU P 4 " pdb=" C GLU P 4 " ideal model delta sigma weight residual 111.14 105.80 5.34 1.08e+00 8.57e-01 2.44e+01 angle pdb=" C GLU B 130 " pdb=" N GLY B 131 " pdb=" CA GLY B 131 " ideal model delta sigma weight residual 119.94 125.41 -5.47 1.11e+00 8.12e-01 2.43e+01 angle pdb=" CB GLU A 312 " pdb=" CG GLU A 312 " pdb=" CD GLU A 312 " ideal model delta sigma weight residual 112.60 120.46 -7.86 1.70e+00 3.46e-01 2.14e+01 ... (remaining 12085 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 4523 17.64 - 35.27: 513 35.27 - 52.90: 167 52.90 - 70.54: 34 70.54 - 88.17: 18 Dihedral angle restraints: 5255 sinusoidal: 1978 harmonic: 3277 Sorted by residual: dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 -146.52 60.52 1 1.00e+01 1.00e-02 4.88e+01 dihedral pdb=" CB CYS N 22 " pdb=" SG CYS N 22 " pdb=" SG CYS N 96 " pdb=" CB CYS N 96 " ideal model delta sinusoidal sigma weight residual 93.00 49.34 43.66 1 1.00e+01 1.00e-02 2.65e+01 dihedral pdb=" CA THR A 359 " pdb=" C THR A 359 " pdb=" N GLU A 360 " pdb=" CA GLU A 360 " ideal model delta harmonic sigma weight residual 180.00 -158.94 -21.06 0 5.00e+00 4.00e-02 1.77e+01 ... (remaining 5252 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 752 0.068 - 0.136: 443 0.136 - 0.204: 138 0.204 - 0.272: 24 0.272 - 0.340: 4 Chirality restraints: 1361 Sorted by residual: chirality pdb=" CA PRO N 102 " pdb=" N PRO N 102 " pdb=" C PRO N 102 " pdb=" CB PRO N 102 " both_signs ideal model delta sigma weight residual False 2.72 2.38 0.34 2.00e-01 2.50e+01 2.90e+00 chirality pdb=" CB ILE R 135 " pdb=" CA ILE R 135 " pdb=" CG1 ILE R 135 " pdb=" CG2 ILE R 135 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.34 2.00e-01 2.50e+01 2.82e+00 chirality pdb=" CA LEU B 318 " pdb=" N LEU B 318 " pdb=" C LEU B 318 " pdb=" CB LEU B 318 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.52e+00 ... (remaining 1358 not shown) Planarity restraints: 1545 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP R 329 " -0.017 2.00e-02 2.50e+03 8.90e-03 1.98e+00 pdb=" CG TRP R 329 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 TRP R 329 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP R 329 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP R 329 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP R 329 " -0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP R 329 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 329 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 329 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP R 329 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 271 " 0.019 2.00e-02 2.50e+03 8.80e-03 1.94e+00 pdb=" CG TRP A 271 " -0.012 2.00e-02 2.50e+03 pdb=" CD1 TRP A 271 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP A 271 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP A 271 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 271 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 271 " -0.010 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 271 " 0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 271 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP A 271 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR R 134 " 0.004 2.00e-02 2.50e+03 8.46e-03 1.43e+00 pdb=" CG TYR R 134 " -0.004 2.00e-02 2.50e+03 pdb=" CD1 TYR R 134 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR R 134 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR R 134 " 0.016 2.00e-02 2.50e+03 pdb=" CE2 TYR R 134 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR R 134 " -0.009 2.00e-02 2.50e+03 pdb=" OH TYR R 134 " 0.001 2.00e-02 2.50e+03 ... (remaining 1542 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 561 2.74 - 3.28: 8583 3.28 - 3.82: 14112 3.82 - 4.36: 19286 4.36 - 4.90: 31185 Nonbonded interactions: 73727 Sorted by model distance: nonbonded pdb=" O SER R 356 " pdb=" OG SER R 356 " model vdw 2.204 3.040 nonbonded pdb=" O GLN R 438 " pdb=" ND1 HIS R 442 " model vdw 2.262 3.120 nonbonded pdb=" NE2 HIS B 54 " pdb=" OG SER B 72 " model vdw 2.265 3.120 nonbonded pdb=" OG1 THR N 28 " pdb=" ND2 ASN N 31 " model vdw 2.289 3.120 nonbonded pdb=" NH1 ARG R 282 " pdb=" OD1 ASN R 348 " model vdw 2.303 3.120 ... (remaining 73722 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.190 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: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 23.810 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 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 : 0.014 0.066 8913 Z= 1.025 Angle : 1.690 9.035 12096 Z= 1.234 Chirality : 0.089 0.340 1361 Planarity : 0.003 0.012 1545 Dihedral : 17.696 88.173 3126 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.26 % Favored : 95.65 % Rotamer: Outliers : 7.24 % Allowed : 19.15 % Favored : 73.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.24), residues: 1104 helix: -0.35 (0.23), residues: 426 sheet: 0.15 (0.37), residues: 206 loop : -1.03 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.004 TRP A 271 HIS 0.006 0.001 HIS B 311 PHE 0.012 0.003 PHE R 378 TYR 0.016 0.003 TYR R 134 ARG 0.005 0.001 ARG B 49 Details of bonding type rmsd hydrogen bonds : bond 0.22680 ( 453) hydrogen bonds : angle 8.18422 ( 1290) SS BOND : bond 0.02342 ( 3) SS BOND : angle 3.81664 ( 6) covalent geometry : bond 0.01411 ( 8910) covalent geometry : angle 1.68841 (12090) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 164 time to evaluate : 0.915 Fit side-chains REVERT: A 21 GLU cc_start: 0.6966 (OUTLIER) cc_final: 0.6396 (pt0) REVERT: A 27 GLU cc_start: 0.7080 (mm-30) cc_final: 0.6753 (tp30) REVERT: A 28 LYS cc_start: 0.7248 (OUTLIER) cc_final: 0.6648 (ttmm) REVERT: A 49 ASP cc_start: 0.7293 (m-30) cc_final: 0.6698 (t0) REVERT: A 289 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7577 (pp20) REVERT: A 371 ASP cc_start: 0.8221 (t70) cc_final: 0.7731 (t0) REVERT: B 32 GLN cc_start: 0.5824 (pt0) cc_final: 0.5403 (tp40) REVERT: B 38 ASP cc_start: 0.7227 (OUTLIER) cc_final: 0.6958 (p0) REVERT: B 59 TYR cc_start: 0.8841 (OUTLIER) cc_final: 0.8578 (t80) REVERT: B 78 LYS cc_start: 0.8305 (OUTLIER) cc_final: 0.8068 (tppp) REVERT: B 96 ARG cc_start: 0.7599 (mtm110) cc_final: 0.7208 (ttm-80) REVERT: B 101 MET cc_start: 0.8775 (mtp) cc_final: 0.8350 (mtp) REVERT: B 137 ARG cc_start: 0.6834 (ttm110) cc_final: 0.6541 (ttm110) REVERT: B 138 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7801 (mt-10) REVERT: B 146 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8410 (tt) REVERT: B 156 GLN cc_start: 0.7526 (mt0) cc_final: 0.7310 (mt0) REVERT: B 175 GLN cc_start: 0.7620 (pt0) cc_final: 0.6779 (mm-40) REVERT: B 219 ARG cc_start: 0.7338 (mmm160) cc_final: 0.6731 (mmt-90) REVERT: B 220 GLN cc_start: 0.8781 (mt0) cc_final: 0.8335 (mt0) REVERT: B 270 ILE cc_start: 0.7915 (pt) cc_final: 0.7654 (pp) REVERT: B 277 SER cc_start: 0.8834 (OUTLIER) cc_final: 0.8552 (m) REVERT: B 301 LYS cc_start: 0.7584 (mtpp) cc_final: 0.7382 (mtpt) REVERT: G 44 HIS cc_start: 0.7802 (m90) cc_final: 0.7551 (m-70) REVERT: N 3 GLN cc_start: 0.6596 (tt0) cc_final: 0.6179 (tt0) REVERT: N 6 GLU cc_start: 0.6681 (mp0) cc_final: 0.6269 (mp0) REVERT: N 34 MET cc_start: 0.8507 (mmm) cc_final: 0.8299 (mmm) REVERT: N 39 GLN cc_start: 0.8408 (tt0) cc_final: 0.8012 (tt0) REVERT: N 53 GLN cc_start: 0.7523 (mp10) cc_final: 0.6943 (mp10) REVERT: N 76 LYS cc_start: 0.7068 (mppt) cc_final: 0.6567 (mttt) REVERT: N 83 MET cc_start: 0.6941 (OUTLIER) cc_final: 0.6351 (mtt) REVERT: N 95 TYR cc_start: 0.8530 (m-80) cc_final: 0.7898 (m-80) REVERT: N 104 THR cc_start: 0.8362 (p) cc_final: 0.8074 (p) REVERT: N 123 GLN cc_start: 0.6821 (mm-40) cc_final: 0.6464 (tp40) REVERT: R 36 GLU cc_start: 0.5469 (tt0) cc_final: 0.4930 (tp30) REVERT: R 133 ASP cc_start: 0.3942 (OUTLIER) cc_final: 0.3682 (t0) REVERT: R 182 GLU cc_start: 0.7675 (tt0) cc_final: 0.7447 (tt0) REVERT: R 186 ARG cc_start: 0.6943 (OUTLIER) cc_final: 0.6590 (ttp-110) REVERT: R 189 MET cc_start: 0.7426 (tpt) cc_final: 0.7101 (tpp) REVERT: R 218 THR cc_start: 0.8351 (t) cc_final: 0.8144 (m) REVERT: R 220 ASN cc_start: 0.7906 (m-40) cc_final: 0.7698 (m-40) REVERT: R 224 MET cc_start: 0.6932 (mtt) cc_final: 0.6688 (mtm) REVERT: R 240 LYS cc_start: 0.6731 (ttpt) cc_final: 0.6371 (ttpp) REVERT: R 389 LEU cc_start: 0.7470 (OUTLIER) cc_final: 0.7262 (mp) REVERT: R 405 LYS cc_start: 0.5768 (tptm) cc_final: 0.4801 (ttmm) REVERT: R 408 LYS cc_start: 0.7381 (tmtp) cc_final: 0.7118 (tptt) REVERT: R 441 MET cc_start: 0.8493 (mmt) cc_final: 0.8217 (mmt) REVERT: R 445 MET cc_start: 0.8425 (mmp) cc_final: 0.8184 (mmm) REVERT: R 469 GLU cc_start: 0.5882 (mt-10) cc_final: 0.5624 (mm-30) outliers start: 65 outliers final: 23 residues processed: 214 average time/residue: 1.2582 time to fit residues: 285.8887 Evaluate side-chains 174 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 139 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 62 ARG Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 133 ASP Chi-restraints excluded: chain R residue 186 ARG Chi-restraints excluded: chain R residue 217 CYS Chi-restraints excluded: chain R residue 235 VAL Chi-restraints excluded: chain R residue 236 SER Chi-restraints excluded: chain R residue 237 ILE Chi-restraints excluded: chain R residue 278 TYR Chi-restraints excluded: chain R residue 341 SER Chi-restraints excluded: chain R residue 365 VAL Chi-restraints excluded: chain R residue 370 SER Chi-restraints excluded: chain R residue 384 VAL Chi-restraints excluded: chain R residue 389 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.9980 chunk 83 optimal weight: 40.0000 chunk 46 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 44 optimal weight: 6.9990 chunk 86 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 52 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN G 59 ASN P 16 ASN R 374 ASN R 402 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.150985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.114998 restraints weight = 10254.344| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 1.98 r_work: 0.3211 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8913 Z= 0.153 Angle : 0.550 6.846 12096 Z= 0.305 Chirality : 0.042 0.165 1361 Planarity : 0.004 0.046 1545 Dihedral : 9.001 77.078 1291 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 5.57 % Allowed : 21.83 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.25), residues: 1104 helix: 1.26 (0.24), residues: 444 sheet: -0.13 (0.34), residues: 213 loop : -0.69 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 82 HIS 0.004 0.001 HIS A 347 PHE 0.018 0.002 PHE A 212 TYR 0.024 0.002 TYR R 191 ARG 0.005 0.001 ARG N 72 Details of bonding type rmsd hydrogen bonds : bond 0.05420 ( 453) hydrogen bonds : angle 5.17785 ( 1290) SS BOND : bond 0.00147 ( 3) SS BOND : angle 0.81168 ( 6) covalent geometry : bond 0.00335 ( 8910) covalent geometry : angle 0.55027 (12090) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 148 time to evaluate : 0.973 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.7132 (OUTLIER) cc_final: 0.6411 (pt0) REVERT: A 27 GLU cc_start: 0.7071 (mm-30) cc_final: 0.6615 (mm-30) REVERT: A 28 LYS cc_start: 0.7293 (OUTLIER) cc_final: 0.6719 (mtpt) REVERT: A 49 ASP cc_start: 0.7041 (OUTLIER) cc_final: 0.6545 (t0) REVERT: A 58 LYS cc_start: 0.6640 (mtpp) cc_final: 0.6292 (mmtp) REVERT: A 289 GLU cc_start: 0.7515 (pp20) cc_final: 0.7005 (tp30) REVERT: A 346 ARG cc_start: 0.7147 (mmm-85) cc_final: 0.6526 (mtm-85) REVERT: B 27 ASP cc_start: 0.6401 (OUTLIER) cc_final: 0.5893 (p0) REVERT: B 32 GLN cc_start: 0.6344 (pt0) cc_final: 0.5846 (tp40) REVERT: B 66 ASP cc_start: 0.7420 (OUTLIER) cc_final: 0.7112 (p0) REVERT: B 96 ARG cc_start: 0.7552 (mtm110) cc_final: 0.7165 (ttm-80) REVERT: B 101 MET cc_start: 0.8794 (mtp) cc_final: 0.8352 (mtp) REVERT: B 124 TYR cc_start: 0.8507 (m-80) cc_final: 0.8084 (m-80) REVERT: B 137 ARG cc_start: 0.7516 (ttm110) cc_final: 0.7062 (tpp80) REVERT: B 138 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7438 (mt-10) REVERT: B 146 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8582 (tt) REVERT: B 156 GLN cc_start: 0.7662 (mt0) cc_final: 0.7358 (mt0) REVERT: B 175 GLN cc_start: 0.7625 (pt0) cc_final: 0.7418 (pt0) REVERT: G 44 HIS cc_start: 0.7898 (m90) cc_final: 0.7622 (m-70) REVERT: N 3 GLN cc_start: 0.6993 (tt0) cc_final: 0.6380 (tt0) REVERT: N 39 GLN cc_start: 0.8497 (tt0) cc_final: 0.8063 (tt0) REVERT: N 53 GLN cc_start: 0.7344 (mp10) cc_final: 0.6870 (mp10) REVERT: N 80 TYR cc_start: 0.7897 (m-80) cc_final: 0.6420 (m-80) REVERT: N 83 MET cc_start: 0.7380 (OUTLIER) cc_final: 0.7142 (mtt) REVERT: N 104 THR cc_start: 0.8199 (p) cc_final: 0.7836 (p) REVERT: N 106 ASP cc_start: 0.8607 (p0) cc_final: 0.8400 (p0) REVERT: N 123 GLN cc_start: 0.7152 (mm-40) cc_final: 0.6680 (tp-100) REVERT: P 19 GLU cc_start: 0.6629 (OUTLIER) cc_final: 0.6266 (pt0) REVERT: R 182 GLU cc_start: 0.7517 (tt0) cc_final: 0.7230 (tt0) REVERT: R 189 MET cc_start: 0.7764 (tpt) cc_final: 0.7485 (tpp) REVERT: R 196 SER cc_start: 0.7530 (m) cc_final: 0.7297 (t) REVERT: R 224 MET cc_start: 0.7555 (mtt) cc_final: 0.7333 (mtm) REVERT: R 305 TYR cc_start: 0.8373 (t80) cc_final: 0.7736 (t80) REVERT: R 318 LYS cc_start: 0.6207 (mppt) cc_final: 0.5847 (mmtt) REVERT: R 346 LEU cc_start: 0.7615 (OUTLIER) cc_final: 0.7213 (mm) REVERT: R 390 ARG cc_start: 0.7400 (ttp80) cc_final: 0.7038 (ttp-110) REVERT: R 404 ARG cc_start: 0.6232 (tmm160) cc_final: 0.5311 (tmt-80) REVERT: R 469 GLU cc_start: 0.6035 (mt-10) cc_final: 0.5796 (mm-30) outliers start: 50 outliers final: 26 residues processed: 181 average time/residue: 1.2167 time to fit residues: 234.6626 Evaluate side-chains 164 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 129 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain G residue 62 ARG Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain P residue 19 GLU Chi-restraints excluded: chain R residue 235 VAL Chi-restraints excluded: chain R residue 236 SER Chi-restraints excluded: chain R residue 278 TYR Chi-restraints excluded: chain R residue 308 SER Chi-restraints excluded: chain R residue 346 LEU Chi-restraints excluded: chain R residue 349 THR Chi-restraints excluded: chain R residue 370 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 30 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 59 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 56 optimal weight: 7.9990 chunk 84 optimal weight: 7.9990 chunk 62 optimal weight: 8.9990 chunk 81 optimal weight: 0.9990 chunk 80 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 142 HIS B 176 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN N 31 ASN P 16 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.151357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.115256 restraints weight = 10421.311| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 2.00 r_work: 0.3217 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8913 Z= 0.157 Angle : 0.526 6.991 12096 Z= 0.290 Chirality : 0.042 0.165 1361 Planarity : 0.004 0.054 1545 Dihedral : 7.817 76.700 1258 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 6.12 % Allowed : 22.61 % Favored : 71.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.25), residues: 1104 helix: 1.66 (0.25), residues: 444 sheet: -0.20 (0.33), residues: 218 loop : -0.71 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 82 HIS 0.003 0.001 HIS A 347 PHE 0.016 0.002 PHE A 212 TYR 0.024 0.002 TYR R 191 ARG 0.004 0.000 ARG A 255 Details of bonding type rmsd hydrogen bonds : bond 0.04929 ( 453) hydrogen bonds : angle 4.86122 ( 1290) SS BOND : bond 0.00051 ( 3) SS BOND : angle 0.87974 ( 6) covalent geometry : bond 0.00354 ( 8910) covalent geometry : angle 0.52610 (12090) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 141 time to evaluate : 0.904 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.7215 (OUTLIER) cc_final: 0.6495 (pt0) REVERT: A 27 GLU cc_start: 0.7075 (mm-30) cc_final: 0.6656 (mm-30) REVERT: A 28 LYS cc_start: 0.7446 (OUTLIER) cc_final: 0.6811 (mtpt) REVERT: A 49 ASP cc_start: 0.7336 (OUTLIER) cc_final: 0.6673 (t0) REVERT: A 58 LYS cc_start: 0.6584 (mtpp) cc_final: 0.6241 (mmtp) REVERT: A 208 PHE cc_start: 0.7864 (m-80) cc_final: 0.7630 (m-80) REVERT: A 289 GLU cc_start: 0.7377 (OUTLIER) cc_final: 0.6996 (tp30) REVERT: B 32 GLN cc_start: 0.6203 (pt0) cc_final: 0.5935 (tp40) REVERT: B 38 ASP cc_start: 0.7189 (OUTLIER) cc_final: 0.6906 (p0) REVERT: B 66 ASP cc_start: 0.7618 (OUTLIER) cc_final: 0.7291 (p0) REVERT: B 96 ARG cc_start: 0.7515 (mtm110) cc_final: 0.7091 (ttm-80) REVERT: B 101 MET cc_start: 0.8779 (mtp) cc_final: 0.8383 (mtp) REVERT: B 130 GLU cc_start: 0.5870 (OUTLIER) cc_final: 0.5505 (tt0) REVERT: B 137 ARG cc_start: 0.7464 (ttm110) cc_final: 0.7166 (ttm110) REVERT: B 138 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7398 (mt-10) REVERT: B 146 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8648 (tt) REVERT: B 156 GLN cc_start: 0.7690 (mt0) cc_final: 0.7377 (mt0) REVERT: G 25 ILE cc_start: 0.5327 (OUTLIER) cc_final: 0.4962 (pt) REVERT: G 44 HIS cc_start: 0.7931 (m90) cc_final: 0.7651 (m-70) REVERT: N 3 GLN cc_start: 0.6964 (tt0) cc_final: 0.6294 (tt0) REVERT: N 39 GLN cc_start: 0.8500 (tt0) cc_final: 0.8169 (tt0) REVERT: N 53 GLN cc_start: 0.7325 (mp10) cc_final: 0.6888 (mp10) REVERT: N 80 TYR cc_start: 0.7958 (m-80) cc_final: 0.6530 (m-80) REVERT: N 86 LEU cc_start: 0.7714 (OUTLIER) cc_final: 0.7208 (mp) REVERT: N 123 GLN cc_start: 0.7352 (mm-40) cc_final: 0.6990 (tp-100) REVERT: R 189 MET cc_start: 0.7562 (tpt) cc_final: 0.7340 (tpp) REVERT: R 305 TYR cc_start: 0.8403 (t80) cc_final: 0.8014 (t80) REVERT: R 308 SER cc_start: 0.8214 (OUTLIER) cc_final: 0.7771 (p) REVERT: R 404 ARG cc_start: 0.6349 (tmm160) cc_final: 0.5578 (tmt-80) outliers start: 55 outliers final: 31 residues processed: 176 average time/residue: 1.2921 time to fit residues: 241.5708 Evaluate side-chains 177 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 135 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 62 ARG Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain P residue 13 LYS Chi-restraints excluded: chain R residue 235 VAL Chi-restraints excluded: chain R residue 236 SER Chi-restraints excluded: chain R residue 278 TYR Chi-restraints excluded: chain R residue 308 SER Chi-restraints excluded: chain R residue 349 THR Chi-restraints excluded: chain R residue 370 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 33 optimal weight: 0.0670 chunk 15 optimal weight: 0.0970 chunk 86 optimal weight: 1.9990 chunk 25 optimal weight: 9.9990 chunk 106 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 76 optimal weight: 20.0000 chunk 60 optimal weight: 0.0010 chunk 80 optimal weight: 9.9990 chunk 2 optimal weight: 4.9990 overall best weight: 0.6324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 175 GLN B 237 ASN B 340 ASN P 16 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.157027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.122026 restraints weight = 10123.166| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 1.88 r_work: 0.3321 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8913 Z= 0.098 Angle : 0.459 6.305 12096 Z= 0.253 Chirality : 0.040 0.148 1361 Planarity : 0.004 0.053 1545 Dihedral : 6.865 70.611 1254 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 5.12 % Allowed : 25.06 % Favored : 69.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.26), residues: 1104 helix: 1.99 (0.25), residues: 444 sheet: -0.13 (0.33), residues: 215 loop : -0.68 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 211 HIS 0.004 0.001 HIS A 220 PHE 0.017 0.001 PHE R 335 TYR 0.024 0.001 TYR R 191 ARG 0.002 0.000 ARG N 72 Details of bonding type rmsd hydrogen bonds : bond 0.04107 ( 453) hydrogen bonds : angle 4.50270 ( 1290) SS BOND : bond 0.00193 ( 3) SS BOND : angle 0.64108 ( 6) covalent geometry : bond 0.00204 ( 8910) covalent geometry : angle 0.45855 (12090) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 143 time to evaluate : 0.952 Fit side-chains revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7055 (mm-30) cc_final: 0.6658 (mm-30) REVERT: A 28 LYS cc_start: 0.7300 (OUTLIER) cc_final: 0.6819 (mtpt) REVERT: A 49 ASP cc_start: 0.6972 (m-30) cc_final: 0.6516 (t0) REVERT: A 208 PHE cc_start: 0.7901 (m-80) cc_final: 0.7662 (m-80) REVERT: A 289 GLU cc_start: 0.7352 (OUTLIER) cc_final: 0.7017 (tp30) REVERT: B 27 ASP cc_start: 0.6260 (OUTLIER) cc_final: 0.5773 (p0) REVERT: B 32 GLN cc_start: 0.6182 (pt0) cc_final: 0.5947 (tp40) REVERT: B 38 ASP cc_start: 0.7098 (p0) cc_final: 0.6794 (p0) REVERT: B 76 ASP cc_start: 0.7902 (p0) cc_final: 0.7683 (p0) REVERT: B 96 ARG cc_start: 0.7526 (mtm110) cc_final: 0.7127 (ttm-80) REVERT: B 101 MET cc_start: 0.8758 (mtp) cc_final: 0.8368 (mtp) REVERT: B 124 TYR cc_start: 0.8463 (m-80) cc_final: 0.7966 (m-80) REVERT: B 130 GLU cc_start: 0.5777 (OUTLIER) cc_final: 0.5460 (tt0) REVERT: B 137 ARG cc_start: 0.7500 (ttm110) cc_final: 0.7212 (ttm110) REVERT: B 138 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7383 (mt-10) REVERT: B 146 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8671 (tt) REVERT: B 156 GLN cc_start: 0.7653 (mt0) cc_final: 0.7356 (mt0) REVERT: B 176 GLN cc_start: 0.8162 (tt0) cc_final: 0.7917 (tt0) REVERT: G 44 HIS cc_start: 0.7857 (m90) cc_final: 0.7635 (m-70) REVERT: G 62 ARG cc_start: 0.5372 (OUTLIER) cc_final: 0.4559 (ppt170) REVERT: N 3 GLN cc_start: 0.6940 (tt0) cc_final: 0.6340 (tt0) REVERT: N 38 ARG cc_start: 0.8757 (ptt-90) cc_final: 0.8530 (ptp90) REVERT: N 39 GLN cc_start: 0.8419 (tt0) cc_final: 0.8074 (tt0) REVERT: N 46 GLU cc_start: 0.7923 (mt-10) cc_final: 0.7503 (mt-10) REVERT: N 53 GLN cc_start: 0.7267 (mp10) cc_final: 0.6934 (mp10) REVERT: N 80 TYR cc_start: 0.7684 (m-80) cc_final: 0.5961 (m-80) REVERT: N 86 LEU cc_start: 0.7783 (OUTLIER) cc_final: 0.7228 (mp) REVERT: N 105 ARG cc_start: 0.6809 (ttt180) cc_final: 0.6512 (ttm-80) REVERT: R 34 LYS cc_start: 0.5915 (ttpm) cc_final: 0.5649 (tttm) REVERT: R 45 GLN cc_start: 0.6004 (OUTLIER) cc_final: 0.4881 (mt0) REVERT: R 189 MET cc_start: 0.7530 (tpt) cc_final: 0.7304 (tpp) REVERT: R 212 PHE cc_start: 0.6399 (m-80) cc_final: 0.6082 (m-10) REVERT: R 305 TYR cc_start: 0.8404 (t80) cc_final: 0.7946 (t80) REVERT: R 308 SER cc_start: 0.7997 (OUTLIER) cc_final: 0.7627 (p) REVERT: R 390 ARG cc_start: 0.7477 (ttp80) cc_final: 0.7127 (ttp-110) REVERT: R 404 ARG cc_start: 0.6237 (tmm160) cc_final: 0.5606 (tmt-80) outliers start: 46 outliers final: 18 residues processed: 176 average time/residue: 1.6286 time to fit residues: 304.9255 Evaluate side-chains 165 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 138 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain G residue 62 ARG Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain P residue 13 LYS Chi-restraints excluded: chain R residue 45 GLN Chi-restraints excluded: chain R residue 217 CYS Chi-restraints excluded: chain R residue 235 VAL Chi-restraints excluded: chain R residue 236 SER Chi-restraints excluded: chain R residue 278 TYR Chi-restraints excluded: chain R residue 308 SER Chi-restraints excluded: chain R residue 359 LYS Chi-restraints excluded: chain R residue 370 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 29 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 99 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 chunk 103 optimal weight: 9.9990 chunk 89 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 142 HIS B 175 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN P 16 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.152860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.116834 restraints weight = 10210.623| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 1.96 r_work: 0.3250 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 8913 Z= 0.203 Angle : 0.558 8.214 12096 Z= 0.303 Chirality : 0.044 0.173 1361 Planarity : 0.005 0.058 1545 Dihedral : 6.027 59.236 1242 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 6.24 % Allowed : 24.16 % Favored : 69.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.25), residues: 1104 helix: 1.74 (0.25), residues: 439 sheet: -0.28 (0.33), residues: 218 loop : -0.66 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 82 HIS 0.006 0.001 HIS B 142 PHE 0.017 0.002 PHE A 212 TYR 0.023 0.002 TYR R 191 ARG 0.004 0.001 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.04838 ( 453) hydrogen bonds : angle 4.74163 ( 1290) SS BOND : bond 0.00127 ( 3) SS BOND : angle 0.92240 ( 6) covalent geometry : bond 0.00473 ( 8910) covalent geometry : angle 0.55730 (12090) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 140 time to evaluate : 1.074 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.7053 (OUTLIER) cc_final: 0.6746 (tm-30) REVERT: A 27 GLU cc_start: 0.7168 (mm-30) cc_final: 0.6741 (mm-30) REVERT: A 28 LYS cc_start: 0.7462 (OUTLIER) cc_final: 0.6828 (mtpt) REVERT: A 273 ARG cc_start: 0.7853 (OUTLIER) cc_final: 0.7537 (ptm160) REVERT: A 289 GLU cc_start: 0.7293 (OUTLIER) cc_final: 0.6973 (tp30) REVERT: B 27 ASP cc_start: 0.6358 (OUTLIER) cc_final: 0.5902 (p0) REVERT: B 32 GLN cc_start: 0.6272 (pt0) cc_final: 0.5990 (tp40) REVERT: B 38 ASP cc_start: 0.7090 (OUTLIER) cc_final: 0.6785 (p0) REVERT: B 66 ASP cc_start: 0.7637 (OUTLIER) cc_final: 0.7427 (p0) REVERT: B 96 ARG cc_start: 0.7510 (mtm110) cc_final: 0.7060 (ttm-80) REVERT: B 101 MET cc_start: 0.8777 (mtp) cc_final: 0.8273 (mtp) REVERT: B 130 GLU cc_start: 0.5890 (OUTLIER) cc_final: 0.5394 (tt0) REVERT: B 137 ARG cc_start: 0.7555 (ttm110) cc_final: 0.7255 (ttm110) REVERT: B 156 GLN cc_start: 0.7736 (mt0) cc_final: 0.7442 (mt0) REVERT: B 176 GLN cc_start: 0.8297 (tt0) cc_final: 0.8073 (tt0) REVERT: G 44 HIS cc_start: 0.7955 (m90) cc_final: 0.7676 (m-70) REVERT: N 3 GLN cc_start: 0.7033 (tt0) cc_final: 0.6380 (tt0) REVERT: N 39 GLN cc_start: 0.8511 (tt0) cc_final: 0.8145 (tt0) REVERT: N 53 GLN cc_start: 0.7369 (mp10) cc_final: 0.6909 (mp10) REVERT: N 80 TYR cc_start: 0.7864 (m-80) cc_final: 0.6460 (m-80) REVERT: N 86 LEU cc_start: 0.7797 (OUTLIER) cc_final: 0.7226 (mp) REVERT: N 105 ARG cc_start: 0.6750 (OUTLIER) cc_final: 0.6278 (ttp-170) REVERT: R 34 LYS cc_start: 0.5911 (ttpm) cc_final: 0.5544 (tttp) REVERT: R 212 PHE cc_start: 0.6429 (m-80) cc_final: 0.6019 (m-10) REVERT: R 305 TYR cc_start: 0.8470 (t80) cc_final: 0.8038 (t80) REVERT: R 308 SER cc_start: 0.8286 (OUTLIER) cc_final: 0.7877 (p) REVERT: R 404 ARG cc_start: 0.6323 (tmm160) cc_final: 0.5597 (tmt-80) outliers start: 56 outliers final: 29 residues processed: 180 average time/residue: 1.8992 time to fit residues: 362.2139 Evaluate side-chains 179 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 139 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 29 GLN Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 273 ARG Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain G residue 62 ARG Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 105 ARG Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain P residue 13 LYS Chi-restraints excluded: chain P residue 25 ARG Chi-restraints excluded: chain R residue 217 CYS Chi-restraints excluded: chain R residue 235 VAL Chi-restraints excluded: chain R residue 236 SER Chi-restraints excluded: chain R residue 278 TYR Chi-restraints excluded: chain R residue 308 SER Chi-restraints excluded: chain R residue 349 THR Chi-restraints excluded: chain R residue 359 LYS Chi-restraints excluded: chain R residue 408 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 67 optimal weight: 0.0070 chunk 85 optimal weight: 1.9990 chunk 1 optimal weight: 7.9990 chunk 103 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 104 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 26 optimal weight: 0.0870 chunk 10 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 ASN B 259 GLN P 16 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.155857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.120271 restraints weight = 10161.054| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 1.95 r_work: 0.3295 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8913 Z= 0.115 Angle : 0.474 6.100 12096 Z= 0.261 Chirality : 0.040 0.154 1361 Planarity : 0.004 0.056 1545 Dihedral : 5.352 59.238 1239 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 4.90 % Allowed : 25.95 % Favored : 69.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.26), residues: 1104 helix: 1.99 (0.25), residues: 439 sheet: -0.26 (0.33), residues: 217 loop : -0.70 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.005 0.001 HIS A 220 PHE 0.016 0.001 PHE R 335 TYR 0.024 0.001 TYR R 191 ARG 0.006 0.000 ARG R 214 Details of bonding type rmsd hydrogen bonds : bond 0.04177 ( 453) hydrogen bonds : angle 4.49995 ( 1290) SS BOND : bond 0.00073 ( 3) SS BOND : angle 0.65226 ( 6) covalent geometry : bond 0.00252 ( 8910) covalent geometry : angle 0.47429 (12090) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 137 time to evaluate : 1.741 Fit side-chains revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7049 (mm-30) cc_final: 0.6689 (mm-30) REVERT: A 28 LYS cc_start: 0.7371 (OUTLIER) cc_final: 0.6949 (mtpt) REVERT: A 49 ASP cc_start: 0.7107 (m-30) cc_final: 0.6334 (t0) REVERT: A 285 ASP cc_start: 0.7713 (t0) cc_final: 0.7423 (p0) REVERT: A 289 GLU cc_start: 0.7267 (OUTLIER) cc_final: 0.6956 (tp30) REVERT: B 27 ASP cc_start: 0.6405 (OUTLIER) cc_final: 0.5798 (p0) REVERT: B 38 ASP cc_start: 0.7044 (p0) cc_final: 0.6764 (p0) REVERT: B 66 ASP cc_start: 0.7601 (OUTLIER) cc_final: 0.7278 (p0) REVERT: B 101 MET cc_start: 0.8818 (mtp) cc_final: 0.8318 (mtp) REVERT: B 124 TYR cc_start: 0.8505 (m-80) cc_final: 0.8015 (m-80) REVERT: B 130 GLU cc_start: 0.5770 (OUTLIER) cc_final: 0.5364 (tt0) REVERT: B 137 ARG cc_start: 0.7559 (ttm110) cc_final: 0.7142 (ttm110) REVERT: B 138 GLU cc_start: 0.7988 (mt-10) cc_final: 0.7612 (mt-10) REVERT: B 156 GLN cc_start: 0.7609 (mt0) cc_final: 0.7338 (mt0) REVERT: G 44 HIS cc_start: 0.7914 (m90) cc_final: 0.7657 (m-70) REVERT: G 62 ARG cc_start: 0.5455 (OUTLIER) cc_final: 0.4904 (ppt170) REVERT: N 3 GLN cc_start: 0.6994 (tt0) cc_final: 0.6333 (tt0) REVERT: N 39 GLN cc_start: 0.8503 (tt0) cc_final: 0.8155 (tt0) REVERT: N 46 GLU cc_start: 0.7936 (mt-10) cc_final: 0.7526 (mt-10) REVERT: N 53 GLN cc_start: 0.7393 (mp10) cc_final: 0.6919 (mp10) REVERT: N 77 ASN cc_start: 0.7103 (m-40) cc_final: 0.6842 (t0) REVERT: N 80 TYR cc_start: 0.7660 (m-80) cc_final: 0.6119 (m-80) REVERT: N 105 ARG cc_start: 0.6725 (ttt180) cc_final: 0.6243 (ttp-170) REVERT: R 34 LYS cc_start: 0.5949 (ttpm) cc_final: 0.5742 (tttm) REVERT: R 305 TYR cc_start: 0.8454 (t80) cc_final: 0.8110 (t80) REVERT: R 390 ARG cc_start: 0.7487 (ttp80) cc_final: 0.7124 (ttp-110) REVERT: R 404 ARG cc_start: 0.6336 (tmm160) cc_final: 0.5694 (tmt-80) outliers start: 44 outliers final: 26 residues processed: 169 average time/residue: 2.6176 time to fit residues: 471.4410 Evaluate side-chains 167 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 135 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 29 GLN Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain G residue 29 LYS Chi-restraints excluded: chain G residue 62 ARG Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain P residue 13 LYS Chi-restraints excluded: chain P residue 25 ARG Chi-restraints excluded: chain R residue 217 CYS Chi-restraints excluded: chain R residue 235 VAL Chi-restraints excluded: chain R residue 236 SER Chi-restraints excluded: chain R residue 278 TYR Chi-restraints excluded: chain R residue 425 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 104 optimal weight: 6.9990 chunk 3 optimal weight: 0.7980 chunk 41 optimal weight: 5.9990 chunk 99 optimal weight: 7.9990 chunk 72 optimal weight: 7.9990 chunk 46 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 chunk 109 optimal weight: 0.8980 chunk 30 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 380 GLN B 176 GLN P 16 ASN R 223 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.153306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.117437 restraints weight = 10341.607| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 1.97 r_work: 0.3259 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8913 Z= 0.183 Angle : 0.550 8.587 12096 Z= 0.298 Chirality : 0.043 0.170 1361 Planarity : 0.004 0.058 1545 Dihedral : 5.660 59.744 1239 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 6.57 % Allowed : 25.28 % Favored : 68.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.26), residues: 1104 helix: 1.82 (0.25), residues: 439 sheet: -0.40 (0.33), residues: 220 loop : -0.73 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 82 HIS 0.006 0.001 HIS A 220 PHE 0.017 0.002 PHE A 212 TYR 0.022 0.002 TYR R 191 ARG 0.004 0.001 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.04739 ( 453) hydrogen bonds : angle 4.67659 ( 1290) SS BOND : bond 0.00115 ( 3) SS BOND : angle 0.89626 ( 6) covalent geometry : bond 0.00423 ( 8910) covalent geometry : angle 0.55003 (12090) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 135 time to evaluate : 0.995 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.7281 (OUTLIER) cc_final: 0.6962 (tm-30) REVERT: A 27 GLU cc_start: 0.7064 (mm-30) cc_final: 0.6722 (mm-30) REVERT: A 28 LYS cc_start: 0.7396 (OUTLIER) cc_final: 0.6916 (mtpt) REVERT: A 273 ARG cc_start: 0.7944 (OUTLIER) cc_final: 0.7576 (ptm160) REVERT: A 289 GLU cc_start: 0.7278 (OUTLIER) cc_final: 0.6958 (tp30) REVERT: B 27 ASP cc_start: 0.6442 (OUTLIER) cc_final: 0.5916 (p0) REVERT: B 38 ASP cc_start: 0.6934 (p0) cc_final: 0.6645 (p0) REVERT: B 66 ASP cc_start: 0.7600 (OUTLIER) cc_final: 0.7388 (p0) REVERT: B 101 MET cc_start: 0.8741 (mtp) cc_final: 0.8255 (mtp) REVERT: B 130 GLU cc_start: 0.5879 (OUTLIER) cc_final: 0.5360 (tt0) REVERT: B 137 ARG cc_start: 0.7545 (ttm110) cc_final: 0.7100 (tpp80) REVERT: B 138 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7663 (mt-10) REVERT: B 156 GLN cc_start: 0.7699 (mt0) cc_final: 0.7448 (mt0) REVERT: G 36 ASP cc_start: 0.7056 (OUTLIER) cc_final: 0.6778 (m-30) REVERT: G 44 HIS cc_start: 0.7956 (m90) cc_final: 0.7671 (m-70) REVERT: G 62 ARG cc_start: 0.5221 (OUTLIER) cc_final: 0.4405 (ppt170) REVERT: N 3 GLN cc_start: 0.7018 (tt0) cc_final: 0.6313 (tt0) REVERT: N 39 GLN cc_start: 0.8542 (tt0) cc_final: 0.8081 (tt0) REVERT: N 53 GLN cc_start: 0.7369 (mp10) cc_final: 0.6913 (mp10) REVERT: N 77 ASN cc_start: 0.7097 (m-40) cc_final: 0.6837 (t0) REVERT: N 80 TYR cc_start: 0.7798 (m-80) cc_final: 0.6468 (m-80) REVERT: N 105 ARG cc_start: 0.6730 (OUTLIER) cc_final: 0.6291 (mmm-85) REVERT: R 305 TYR cc_start: 0.8482 (t80) cc_final: 0.8037 (t80) REVERT: R 308 SER cc_start: 0.8278 (OUTLIER) cc_final: 0.7855 (p) REVERT: R 317 GLU cc_start: 0.6397 (OUTLIER) cc_final: 0.6069 (mp0) REVERT: R 390 ARG cc_start: 0.7509 (ttp80) cc_final: 0.7139 (ttp-110) REVERT: R 404 ARG cc_start: 0.6395 (tmm160) cc_final: 0.5716 (tmt-80) outliers start: 59 outliers final: 34 residues processed: 178 average time/residue: 1.4063 time to fit residues: 265.5988 Evaluate side-chains 178 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 132 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 29 GLN Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 273 ARG Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain G residue 62 ARG Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 105 ARG Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain P residue 13 LYS Chi-restraints excluded: chain P residue 25 ARG Chi-restraints excluded: chain R residue 217 CYS Chi-restraints excluded: chain R residue 235 VAL Chi-restraints excluded: chain R residue 236 SER Chi-restraints excluded: chain R residue 278 TYR Chi-restraints excluded: chain R residue 308 SER Chi-restraints excluded: chain R residue 317 GLU Chi-restraints excluded: chain R residue 408 LYS Chi-restraints excluded: chain R residue 425 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 37 optimal weight: 8.9990 chunk 55 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 105 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 3 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 380 GLN B 176 GLN B 259 GLN P 16 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.155438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.119828 restraints weight = 10368.511| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.97 r_work: 0.3288 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8913 Z= 0.128 Angle : 0.496 9.286 12096 Z= 0.271 Chirality : 0.041 0.157 1361 Planarity : 0.004 0.056 1545 Dihedral : 5.389 58.469 1239 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 5.35 % Allowed : 26.17 % Favored : 68.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.26), residues: 1104 helix: 2.05 (0.26), residues: 433 sheet: -0.36 (0.33), residues: 219 loop : -0.71 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.007 0.001 HIS A 220 PHE 0.016 0.001 PHE R 335 TYR 0.023 0.001 TYR R 191 ARG 0.004 0.000 ARG R 383 Details of bonding type rmsd hydrogen bonds : bond 0.04269 ( 453) hydrogen bonds : angle 4.52190 ( 1290) SS BOND : bond 0.00105 ( 3) SS BOND : angle 0.70196 ( 6) covalent geometry : bond 0.00284 ( 8910) covalent geometry : angle 0.49610 (12090) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 139 time to evaluate : 1.340 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.7226 (OUTLIER) cc_final: 0.6872 (tm-30) REVERT: A 27 GLU cc_start: 0.7063 (mm-30) cc_final: 0.6699 (mm-30) REVERT: A 28 LYS cc_start: 0.7403 (OUTLIER) cc_final: 0.6909 (mtpt) REVERT: A 49 ASP cc_start: 0.7292 (m-30) cc_final: 0.6476 (t0) REVERT: A 273 ARG cc_start: 0.7909 (OUTLIER) cc_final: 0.7549 (ptm160) REVERT: A 285 ASP cc_start: 0.7755 (t0) cc_final: 0.7436 (p0) REVERT: A 289 GLU cc_start: 0.7275 (OUTLIER) cc_final: 0.6959 (tp30) REVERT: B 27 ASP cc_start: 0.6435 (OUTLIER) cc_final: 0.5816 (p0) REVERT: B 38 ASP cc_start: 0.6926 (p0) cc_final: 0.6630 (p0) REVERT: B 66 ASP cc_start: 0.7606 (OUTLIER) cc_final: 0.7281 (p0) REVERT: B 101 MET cc_start: 0.8806 (mtp) cc_final: 0.8394 (mtp) REVERT: B 124 TYR cc_start: 0.8495 (m-80) cc_final: 0.7875 (m-80) REVERT: B 130 GLU cc_start: 0.5850 (OUTLIER) cc_final: 0.5374 (tt0) REVERT: B 137 ARG cc_start: 0.7547 (ttm110) cc_final: 0.7122 (ttm110) REVERT: B 138 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7636 (mt-10) REVERT: B 156 GLN cc_start: 0.7665 (mt0) cc_final: 0.7411 (mt0) REVERT: G 44 HIS cc_start: 0.7946 (m90) cc_final: 0.7687 (m-70) REVERT: G 62 ARG cc_start: 0.5355 (OUTLIER) cc_final: 0.4668 (ppt170) REVERT: N 3 GLN cc_start: 0.7007 (tt0) cc_final: 0.6301 (tt0) REVERT: N 39 GLN cc_start: 0.8513 (tt0) cc_final: 0.8168 (tt0) REVERT: N 46 GLU cc_start: 0.7956 (mt-10) cc_final: 0.7544 (mt-10) REVERT: N 53 GLN cc_start: 0.7328 (mp10) cc_final: 0.6893 (mp10) REVERT: N 77 ASN cc_start: 0.7149 (m-40) cc_final: 0.6899 (t0) REVERT: N 80 TYR cc_start: 0.7747 (m-80) cc_final: 0.6230 (m-80) REVERT: P 25 ARG cc_start: 0.6038 (OUTLIER) cc_final: 0.5798 (ttp-110) REVERT: R 305 TYR cc_start: 0.8495 (t80) cc_final: 0.8057 (t80) REVERT: R 308 SER cc_start: 0.8119 (OUTLIER) cc_final: 0.7744 (p) REVERT: R 317 GLU cc_start: 0.6378 (OUTLIER) cc_final: 0.6087 (mp0) REVERT: R 390 ARG cc_start: 0.7505 (ttp80) cc_final: 0.7152 (ttp-110) REVERT: R 404 ARG cc_start: 0.6421 (tmm160) cc_final: 0.5758 (tmt-80) outliers start: 48 outliers final: 30 residues processed: 173 average time/residue: 1.3581 time to fit residues: 249.4908 Evaluate side-chains 178 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 137 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 29 GLN Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 273 ARG Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain G residue 29 LYS Chi-restraints excluded: chain G residue 62 ARG Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain P residue 13 LYS Chi-restraints excluded: chain P residue 25 ARG Chi-restraints excluded: chain R residue 217 CYS Chi-restraints excluded: chain R residue 235 VAL Chi-restraints excluded: chain R residue 236 SER Chi-restraints excluded: chain R residue 278 TYR Chi-restraints excluded: chain R residue 308 SER Chi-restraints excluded: chain R residue 317 GLU Chi-restraints excluded: chain R residue 408 LYS Chi-restraints excluded: chain R residue 425 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 42 optimal weight: 0.5980 chunk 91 optimal weight: 5.9990 chunk 76 optimal weight: 0.9980 chunk 29 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 49 optimal weight: 9.9990 chunk 80 optimal weight: 8.9990 chunk 83 optimal weight: 0.9990 chunk 107 optimal weight: 9.9990 chunk 99 optimal weight: 0.0070 chunk 63 optimal weight: 2.9990 overall best weight: 1.1202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 380 GLN B 176 GLN B 259 GLN P 16 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.157311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.121863 restraints weight = 10296.370| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 1.96 r_work: 0.3306 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8913 Z= 0.113 Angle : 0.487 10.018 12096 Z= 0.265 Chirality : 0.040 0.153 1361 Planarity : 0.004 0.056 1545 Dihedral : 5.189 57.831 1239 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 4.90 % Allowed : 26.73 % Favored : 68.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.26), residues: 1104 helix: 2.20 (0.26), residues: 433 sheet: -0.31 (0.33), residues: 218 loop : -0.69 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.006 0.001 HIS A 220 PHE 0.017 0.001 PHE R 335 TYR 0.023 0.001 TYR R 191 ARG 0.004 0.000 ARG R 383 Details of bonding type rmsd hydrogen bonds : bond 0.04113 ( 453) hydrogen bonds : angle 4.41776 ( 1290) SS BOND : bond 0.00141 ( 3) SS BOND : angle 0.72133 ( 6) covalent geometry : bond 0.00245 ( 8910) covalent geometry : angle 0.48726 (12090) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 138 time to evaluate : 0.881 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.7225 (OUTLIER) cc_final: 0.6863 (tm-30) REVERT: A 27 GLU cc_start: 0.7080 (mm-30) cc_final: 0.6751 (mm-30) REVERT: A 28 LYS cc_start: 0.7316 (OUTLIER) cc_final: 0.6928 (mtpt) REVERT: A 49 ASP cc_start: 0.7113 (OUTLIER) cc_final: 0.6349 (t0) REVERT: A 285 ASP cc_start: 0.7674 (t0) cc_final: 0.7389 (p0) REVERT: A 289 GLU cc_start: 0.7336 (OUTLIER) cc_final: 0.6999 (tp30) REVERT: B 27 ASP cc_start: 0.6380 (OUTLIER) cc_final: 0.5855 (p0) REVERT: B 38 ASP cc_start: 0.6928 (p0) cc_final: 0.6621 (p0) REVERT: B 66 ASP cc_start: 0.7568 (OUTLIER) cc_final: 0.7249 (p0) REVERT: B 101 MET cc_start: 0.8832 (mtp) cc_final: 0.8437 (mtp) REVERT: B 124 TYR cc_start: 0.8468 (m-80) cc_final: 0.7967 (m-80) REVERT: B 130 GLU cc_start: 0.5839 (OUTLIER) cc_final: 0.5375 (tt0) REVERT: B 137 ARG cc_start: 0.7555 (ttm110) cc_final: 0.7111 (ttm110) REVERT: B 138 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7644 (mt-10) REVERT: B 156 GLN cc_start: 0.7671 (mt0) cc_final: 0.7407 (mt0) REVERT: G 44 HIS cc_start: 0.7952 (m90) cc_final: 0.7720 (m-70) REVERT: N 3 GLN cc_start: 0.6961 (tt0) cc_final: 0.6317 (tt0) REVERT: N 39 GLN cc_start: 0.8518 (tt0) cc_final: 0.8206 (tt0) REVERT: N 46 GLU cc_start: 0.7945 (mt-10) cc_final: 0.7530 (mt-10) REVERT: N 53 GLN cc_start: 0.7372 (mp10) cc_final: 0.6922 (mp10) REVERT: N 77 ASN cc_start: 0.7132 (m-40) cc_final: 0.6875 (t0) REVERT: N 80 TYR cc_start: 0.7639 (m-80) cc_final: 0.6001 (m-80) REVERT: N 105 ARG cc_start: 0.6735 (ttt180) cc_final: 0.6253 (ttp-170) REVERT: P 25 ARG cc_start: 0.6016 (ttp-110) cc_final: 0.5774 (ttp-110) REVERT: R 305 TYR cc_start: 0.8385 (t80) cc_final: 0.7890 (t80) REVERT: R 308 SER cc_start: 0.8086 (OUTLIER) cc_final: 0.7752 (p) REVERT: R 317 GLU cc_start: 0.6330 (OUTLIER) cc_final: 0.6049 (mp0) REVERT: R 390 ARG cc_start: 0.7579 (ttp80) cc_final: 0.7228 (ttp-110) REVERT: R 404 ARG cc_start: 0.6353 (tmm160) cc_final: 0.5735 (tmt-80) outliers start: 44 outliers final: 29 residues processed: 169 average time/residue: 1.3270 time to fit residues: 238.0101 Evaluate side-chains 175 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 137 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain G residue 29 LYS Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain P residue 13 LYS Chi-restraints excluded: chain R residue 217 CYS Chi-restraints excluded: chain R residue 236 SER Chi-restraints excluded: chain R residue 278 TYR Chi-restraints excluded: chain R residue 308 SER Chi-restraints excluded: chain R residue 317 GLU Chi-restraints excluded: chain R residue 349 THR Chi-restraints excluded: chain R residue 408 LYS Chi-restraints excluded: chain R residue 425 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 13 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 23 optimal weight: 20.0000 chunk 19 optimal weight: 10.0000 chunk 8 optimal weight: 7.9990 chunk 99 optimal weight: 8.9990 chunk 101 optimal weight: 0.3980 chunk 34 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 41 optimal weight: 0.0020 chunk 56 optimal weight: 1.9990 overall best weight: 1.8794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 380 GLN B 176 GLN P 16 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.155905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.120068 restraints weight = 10232.813| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 1.97 r_work: 0.3302 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8913 Z= 0.145 Angle : 0.530 11.319 12096 Z= 0.285 Chirality : 0.042 0.160 1361 Planarity : 0.004 0.055 1545 Dihedral : 5.131 57.430 1234 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 4.68 % Allowed : 26.95 % Favored : 68.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.26), residues: 1104 helix: 2.08 (0.25), residues: 433 sheet: -0.34 (0.33), residues: 219 loop : -0.71 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.008 0.001 HIS A 220 PHE 0.016 0.001 PHE R 335 TYR 0.023 0.002 TYR R 191 ARG 0.003 0.000 ARG R 383 Details of bonding type rmsd hydrogen bonds : bond 0.04378 ( 453) hydrogen bonds : angle 4.50618 ( 1290) SS BOND : bond 0.00104 ( 3) SS BOND : angle 0.82090 ( 6) covalent geometry : bond 0.00328 ( 8910) covalent geometry : angle 0.53009 (12090) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 134 time to evaluate : 0.927 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.7230 (OUTLIER) cc_final: 0.6892 (tm-30) REVERT: A 27 GLU cc_start: 0.7119 (mm-30) cc_final: 0.6809 (mm-30) REVERT: A 28 LYS cc_start: 0.7290 (OUTLIER) cc_final: 0.6844 (mtpt) REVERT: A 49 ASP cc_start: 0.7196 (OUTLIER) cc_final: 0.6394 (t0) REVERT: A 289 GLU cc_start: 0.7374 (OUTLIER) cc_final: 0.7041 (tp30) REVERT: A 380 GLN cc_start: 0.7574 (mt0) cc_final: 0.7341 (mt0) REVERT: B 27 ASP cc_start: 0.6347 (OUTLIER) cc_final: 0.5866 (p0) REVERT: B 38 ASP cc_start: 0.6912 (p0) cc_final: 0.6592 (p0) REVERT: B 66 ASP cc_start: 0.7566 (OUTLIER) cc_final: 0.7234 (p0) REVERT: B 101 MET cc_start: 0.8849 (mtp) cc_final: 0.8438 (mtp) REVERT: B 124 TYR cc_start: 0.8511 (m-80) cc_final: 0.7988 (m-80) REVERT: B 130 GLU cc_start: 0.5823 (OUTLIER) cc_final: 0.5333 (tt0) REVERT: B 137 ARG cc_start: 0.7591 (ttm110) cc_final: 0.7374 (ttm110) REVERT: B 138 GLU cc_start: 0.8022 (mt-10) cc_final: 0.7654 (mt-10) REVERT: B 156 GLN cc_start: 0.7723 (mt0) cc_final: 0.7458 (mt0) REVERT: G 44 HIS cc_start: 0.8027 (m90) cc_final: 0.7767 (m-70) REVERT: N 3 GLN cc_start: 0.6942 (tt0) cc_final: 0.6353 (tt0) REVERT: N 6 GLU cc_start: 0.6717 (mp0) cc_final: 0.6425 (mp0) REVERT: N 39 GLN cc_start: 0.8555 (tt0) cc_final: 0.8245 (tt0) REVERT: N 46 GLU cc_start: 0.7956 (mt-10) cc_final: 0.7554 (mt-10) REVERT: N 53 GLN cc_start: 0.7408 (mp10) cc_final: 0.6975 (mp10) REVERT: N 80 TYR cc_start: 0.7796 (m-80) cc_final: 0.6276 (m-80) REVERT: P 25 ARG cc_start: 0.6026 (OUTLIER) cc_final: 0.5768 (ttp-110) REVERT: R 278 TYR cc_start: 0.6390 (OUTLIER) cc_final: 0.4198 (t80) REVERT: R 305 TYR cc_start: 0.8504 (t80) cc_final: 0.8027 (t80) REVERT: R 308 SER cc_start: 0.8134 (OUTLIER) cc_final: 0.7801 (p) REVERT: R 317 GLU cc_start: 0.6341 (OUTLIER) cc_final: 0.6074 (mp0) REVERT: R 390 ARG cc_start: 0.7606 (ttp80) cc_final: 0.7269 (ttp-110) REVERT: R 404 ARG cc_start: 0.6378 (tmm160) cc_final: 0.5746 (tmt-80) outliers start: 42 outliers final: 26 residues processed: 161 average time/residue: 1.2896 time to fit residues: 220.4628 Evaluate side-chains 170 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 133 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain P residue 13 LYS Chi-restraints excluded: chain P residue 25 ARG Chi-restraints excluded: chain R residue 217 CYS Chi-restraints excluded: chain R residue 236 SER Chi-restraints excluded: chain R residue 278 TYR Chi-restraints excluded: chain R residue 308 SER Chi-restraints excluded: chain R residue 317 GLU Chi-restraints excluded: chain R residue 349 THR Chi-restraints excluded: chain R residue 408 LYS Chi-restraints excluded: chain R residue 425 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 105 optimal weight: 0.8980 chunk 14 optimal weight: 7.9990 chunk 36 optimal weight: 0.9980 chunk 77 optimal weight: 20.0000 chunk 89 optimal weight: 5.9990 chunk 91 optimal weight: 8.9990 chunk 3 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 44 optimal weight: 9.9990 chunk 84 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN P 16 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.155137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.119444 restraints weight = 10306.448| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 1.96 r_work: 0.3285 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8913 Z= 0.148 Angle : 0.531 11.290 12096 Z= 0.286 Chirality : 0.042 0.161 1361 Planarity : 0.004 0.056 1545 Dihedral : 5.172 57.397 1234 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 5.12 % Allowed : 26.95 % Favored : 67.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.26), residues: 1104 helix: 1.96 (0.25), residues: 439 sheet: -0.28 (0.33), residues: 217 loop : -0.80 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.007 0.001 HIS A 220 PHE 0.016 0.001 PHE R 335 TYR 0.023 0.002 TYR R 191 ARG 0.003 0.000 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.04380 ( 453) hydrogen bonds : angle 4.53009 ( 1290) SS BOND : bond 0.00143 ( 3) SS BOND : angle 0.80525 ( 6) covalent geometry : bond 0.00336 ( 8910) covalent geometry : angle 0.53073 (12090) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9269.99 seconds wall clock time: 169 minutes 20.88 seconds (10160.88 seconds total)