Starting phenix.real_space_refine on Wed Sep 17 09:36:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lun_63399/09_2025/9lun_63399.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lun_63399/09_2025/9lun_63399.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/9lun_63399/09_2025/9lun_63399.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lun_63399/09_2025/9lun_63399.map" model { file = "/net/cci-nas-00/data/ceres_data/9lun_63399/09_2025/9lun_63399.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lun_63399/09_2025/9lun_63399.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 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 37 5.16 5 C 4919 2.51 5 N 1340 2.21 5 O 1448 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7744 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3403 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 16, 'TRANS': 421} Chain breaks: 2 Chain: "B" Number of atoms: 2647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2647 Classifications: {'peptide': 334} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 315} Chain: "C" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 892 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 3, 'TRANS': 105} Chain: "D" Number of atoms: 777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 777 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain breaks: 2 Chain: "B" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'GA3': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.90, per 1000 atoms: 0.25 Number of scatterers: 7744 At special positions: 0 Unit cell: (73.7649, 96.1179, 116.236, 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 37 16.00 O 1448 8.00 N 1340 7.00 C 4919 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.70 Conformation dependent library (CDL) restraints added in 457.7 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1830 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 3 sheets defined 59.3% alpha, 13.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 44 through 49 Processing helix chain 'A' and resid 58 through 76 Processing helix chain 'A' and resid 76 through 87 removed outlier: 4.005A pdb=" N GLY A 80 " --> pdb=" O VAL A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 108 Processing helix chain 'A' and resid 215 through 234 removed outlier: 3.737A pdb=" N VAL A 219 " --> pdb=" O GLN A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 254 removed outlier: 3.909A pdb=" N ALA A 242 " --> pdb=" O THR A 238 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL A 252 " --> pdb=" O GLY A 248 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N SER A 253 " --> pdb=" O CYS A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 277 removed outlier: 4.217A pdb=" N LYS A 260 " --> pdb=" O GLY A 256 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR A 274 " --> pdb=" O ALA A 270 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG A 275 " --> pdb=" O ARG A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 295 Processing helix chain 'A' and resid 300 through 317 removed outlier: 3.724A pdb=" N ALA A 312 " --> pdb=" O THR A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 345 removed outlier: 3.758A pdb=" N LEU A 339 " --> pdb=" O GLN A 335 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA A 342 " --> pdb=" O ALA A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 383 removed outlier: 3.765A pdb=" N HIS A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU A 381 " --> pdb=" O ALA A 377 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA A 382 " --> pdb=" O GLN A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 400 Processing helix chain 'A' and resid 401 through 406 removed outlier: 3.619A pdb=" N MET A 404 " --> pdb=" O ASP A 401 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU A 405 " --> pdb=" O ALA A 402 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU A 406 " --> pdb=" O SER A 403 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 401 through 406' Processing helix chain 'A' and resid 422 through 427 removed outlier: 3.624A pdb=" N LEU A 427 " --> pdb=" O HIS A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 444 removed outlier: 3.564A pdb=" N LYS A 435 " --> pdb=" O GLY A 431 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS A 441 " --> pdb=" O LEU A 437 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN A 442 " --> pdb=" O GLY A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 480 Processing helix chain 'A' and resid 486 through 505 Processing helix chain 'A' and resid 507 through 511 Processing helix chain 'A' and resid 517 through 529 Processing helix chain 'A' and resid 536 through 550 removed outlier: 3.661A pdb=" N SER A 548 " --> pdb=" O SER A 544 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N PHE A 550 " --> pdb=" O LEU A 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 35 Processing helix chain 'B' and resid 42 through 50 Processing helix chain 'B' and resid 126 through 139 removed outlier: 3.553A pdb=" N LEU B 130 " --> pdb=" O ILE B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 170 removed outlier: 3.592A pdb=" N TRP B 163 " --> pdb=" O TYR B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 176 removed outlier: 5.772A pdb=" N TRP B 174 " --> pdb=" O SER B 171 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS B 176 " --> pdb=" O SER B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 207 Processing helix chain 'B' and resid 227 through 233 Processing helix chain 'B' and resid 240 through 252 Processing helix chain 'B' and resid 291 through 305 Processing helix chain 'B' and resid 320 through 324 removed outlier: 3.520A pdb=" N LEU B 323 " --> pdb=" O GLY B 320 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU B 324 " --> pdb=" O PHE B 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 320 through 324' Processing helix chain 'B' and resid 327 through 342 removed outlier: 3.662A pdb=" N HIS B 331 " --> pdb=" O ASN B 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 44 Processing helix chain 'C' and resid 49 through 56 Processing helix chain 'C' and resid 59 through 68 Processing helix chain 'C' and resid 68 through 79 removed outlier: 4.340A pdb=" N TRP C 72 " --> pdb=" O ASP C 68 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N HIS C 79 " --> pdb=" O ILE C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 97 removed outlier: 3.822A pdb=" N SER C 92 " --> pdb=" O ASN C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 107 Processing helix chain 'C' and resid 107 through 113 Processing helix chain 'C' and resid 121 through 139 Processing helix chain 'D' and resid 51 through 65 removed outlier: 4.135A pdb=" N ARG D 62 " --> pdb=" O GLU D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 105 removed outlier: 4.422A pdb=" N ASP D 93 " --> pdb=" O SER D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 120 removed outlier: 3.544A pdb=" N LEU D 114 " --> pdb=" O PHE D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 137 removed outlier: 3.665A pdb=" N VAL D 132 " --> pdb=" O THR D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 148 removed outlier: 3.960A pdb=" N PHE D 148 " --> pdb=" O ILE D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 166 Processing helix chain 'D' and resid 166 through 171 removed outlier: 3.673A pdb=" N PHE D 170 " --> pdb=" O ASN D 166 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 210 through 211 removed outlier: 6.521A pdb=" N LEU B 76 " --> pdb=" O ILE B 70 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N LEU B 77 " --> pdb=" O ASN B 146 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL B 141 " --> pdb=" O PRO B 107 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL B 108 " --> pdb=" O PHE B 186 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N ALA B 188 " --> pdb=" O VAL B 108 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N LEU B 110 " --> pdb=" O ALA B 188 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N ASP B 190 " --> pdb=" O LEU B 110 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N PHE B 112 " --> pdb=" O ASP B 190 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N ILE B 185 " --> pdb=" O GLY B 213 " (cutoff:3.500A) removed outlier: 8.667A pdb=" N ILE B 215 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LEU B 187 " --> pdb=" O ILE B 215 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N LEU B 217 " --> pdb=" O LEU B 187 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N GLY B 189 " --> pdb=" O LEU B 217 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N SER B 281 " --> pdb=" O LYS B 310 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N MET B 312 " --> pdb=" O SER B 281 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL B 283 " --> pdb=" O MET B 312 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N LEU B 314 " --> pdb=" O VAL B 283 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N VAL B 285 " --> pdb=" O LEU B 314 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 387 through 390 removed outlier: 7.092A pdb=" N ARG A 322 " --> pdb=" O ALA A 414 " (cutoff:3.500A) removed outlier: 8.434A pdb=" N ALA A 416 " --> pdb=" O ARG A 322 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N HIS A 324 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N ASN A 418 " --> pdb=" O HIS A 324 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ILE A 326 " --> pdb=" O ASN A 418 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N VAL A 420 " --> pdb=" O ILE A 326 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ILE A 447 " --> pdb=" O VAL A 415 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR A 576 " --> pdb=" O GLU A 452 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ALA A 579 " --> pdb=" O ALA A 533 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 387 through 390 removed outlier: 7.092A pdb=" N ARG A 322 " --> pdb=" O ALA A 414 " (cutoff:3.500A) removed outlier: 8.434A pdb=" N ALA A 416 " --> pdb=" O ARG A 322 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N HIS A 324 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N ASN A 418 " --> pdb=" O HIS A 324 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ILE A 326 " --> pdb=" O ASN A 418 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N VAL A 420 " --> pdb=" O ILE A 326 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ILE A 447 " --> pdb=" O VAL A 415 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR A 576 " --> pdb=" O GLU A 452 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N TRP A 569 " --> pdb=" O PRO A 573 " (cutoff:3.500A) 432 hydrogen bonds defined for protein. 1272 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: 1.35 Time building geometry restraints manager: 0.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1386 1.32 - 1.45: 2022 1.45 - 1.57: 4447 1.57 - 1.69: 1 1.69 - 1.82: 57 Bond restraints: 7913 Sorted by residual: bond pdb=" C10 GA3 B 401 " pdb=" C9 GA3 B 401 " ideal model delta sigma weight residual 1.506 1.560 -0.054 2.00e-02 2.50e+03 7.29e+00 bond pdb=" CB PRO D 141 " pdb=" CG PRO D 141 " ideal model delta sigma weight residual 1.492 1.601 -0.109 5.00e-02 4.00e+02 4.72e+00 bond pdb=" C7 GA3 B 401 " pdb=" O72 GA3 B 401 " ideal model delta sigma weight residual 1.248 1.216 0.032 2.00e-02 2.50e+03 2.48e+00 bond pdb=" C7 GA3 B 401 " pdb=" O71 GA3 B 401 " ideal model delta sigma weight residual 1.247 1.217 0.030 2.00e-02 2.50e+03 2.26e+00 bond pdb=" CB PRO C 110 " pdb=" CG PRO C 110 " ideal model delta sigma weight residual 1.492 1.566 -0.074 5.00e-02 4.00e+02 2.20e+00 ... (remaining 7908 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 10541 1.94 - 3.88: 151 3.88 - 5.82: 25 5.82 - 7.76: 11 7.76 - 9.70: 3 Bond angle restraints: 10731 Sorted by residual: angle pdb=" CA PRO C 110 " pdb=" N PRO C 110 " pdb=" CD PRO C 110 " ideal model delta sigma weight residual 112.00 105.15 6.85 1.40e+00 5.10e-01 2.39e+01 angle pdb=" CA PRO D 141 " pdb=" N PRO D 141 " pdb=" CD PRO D 141 " ideal model delta sigma weight residual 112.00 106.14 5.86 1.40e+00 5.10e-01 1.75e+01 angle pdb=" CA GLU C 73 " pdb=" CB GLU C 73 " pdb=" CG GLU C 73 " ideal model delta sigma weight residual 114.10 120.75 -6.65 2.00e+00 2.50e-01 1.11e+01 angle pdb=" CB MET D 135 " pdb=" CG MET D 135 " pdb=" SD MET D 135 " ideal model delta sigma weight residual 112.70 122.40 -9.70 3.00e+00 1.11e-01 1.05e+01 angle pdb=" CA LYS D 61 " pdb=" CB LYS D 61 " pdb=" CG LYS D 61 " ideal model delta sigma weight residual 114.10 120.51 -6.41 2.00e+00 2.50e-01 1.03e+01 ... (remaining 10726 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 4098 17.92 - 35.84: 508 35.84 - 53.76: 153 53.76 - 71.68: 30 71.68 - 89.60: 15 Dihedral angle restraints: 4804 sinusoidal: 1976 harmonic: 2828 Sorted by residual: dihedral pdb=" CA ARG A 271 " pdb=" C ARG A 271 " pdb=" N ARG A 272 " pdb=" CA ARG A 272 " ideal model delta harmonic sigma weight residual 180.00 161.33 18.67 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" CA GLN A 77 " pdb=" C GLN A 77 " pdb=" N GLU A 78 " pdb=" CA GLU A 78 " ideal model delta harmonic sigma weight residual -180.00 -161.62 -18.38 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CG ARG B 73 " pdb=" CD ARG B 73 " pdb=" NE ARG B 73 " pdb=" CZ ARG B 73 " ideal model delta sinusoidal sigma weight residual -90.00 -40.02 -49.98 2 1.50e+01 4.44e-03 1.25e+01 ... (remaining 4801 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 1107 0.079 - 0.157: 85 0.157 - 0.236: 1 0.236 - 0.315: 0 0.315 - 0.394: 2 Chirality restraints: 1195 Sorted by residual: chirality pdb=" C5 GA3 B 401 " pdb=" C10 GA3 B 401 " pdb=" C4 GA3 B 401 " pdb=" C6 GA3 B 401 " both_signs ideal model delta sigma weight residual False -2.80 -3.19 0.39 2.00e-01 2.50e+01 3.87e+00 chirality pdb=" C9 GA3 B 401 " pdb=" C10 GA3 B 401 " pdb=" C11 GA3 B 401 " pdb=" C8 GA3 B 401 " both_signs ideal model delta sigma weight residual False 2.24 2.57 -0.33 2.00e-01 2.50e+01 2.70e+00 chirality pdb=" C4 GA3 B 401 " pdb=" C19 GA3 B 401 " pdb=" C3 GA3 B 401 " pdb=" C5 GA3 B 401 " both_signs ideal model delta sigma weight residual False 3.16 2.92 0.23 2.00e-01 2.50e+01 1.35e+00 ... (remaining 1192 not shown) Planarity restraints: 1379 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP C 109 " 0.076 5.00e-02 4.00e+02 1.11e-01 1.97e+01 pdb=" N PRO C 110 " -0.192 5.00e-02 4.00e+02 pdb=" CA PRO C 110 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO C 110 " 0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 140 " -0.063 5.00e-02 4.00e+02 9.18e-02 1.35e+01 pdb=" N PRO D 141 " 0.159 5.00e-02 4.00e+02 pdb=" CA PRO D 141 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO D 141 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA HIS B 198 " -0.009 2.00e-02 2.50e+03 1.85e-02 3.41e+00 pdb=" C HIS B 198 " 0.032 2.00e-02 2.50e+03 pdb=" O HIS B 198 " -0.012 2.00e-02 2.50e+03 pdb=" N ASN B 199 " -0.011 2.00e-02 2.50e+03 ... (remaining 1376 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 141 2.68 - 3.24: 7370 3.24 - 3.79: 11927 3.79 - 4.35: 16517 4.35 - 4.90: 26946 Nonbonded interactions: 62901 Sorted by model distance: nonbonded pdb=" O LEU A 470 " pdb=" OG SER A 474 " model vdw 2.130 3.040 nonbonded pdb=" O PHE A 304 " pdb=" OG1 THR A 308 " model vdw 2.197 3.040 nonbonded pdb=" O LEU A 463 " pdb=" OG1 THR A 467 " model vdw 2.202 3.040 nonbonded pdb=" O HIS B 113 " pdb=" OH TYR B 147 " model vdw 2.231 3.040 nonbonded pdb=" O GLY A 508 " pdb=" NH2 ARG A 514 " model vdw 2.250 3.120 ... (remaining 62896 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: 6.370 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: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.770 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 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 : 0.004 0.109 7913 Z= 0.149 Angle : 0.623 9.700 10731 Z= 0.323 Chirality : 0.043 0.394 1195 Planarity : 0.006 0.111 1379 Dihedral : 18.037 89.597 2974 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.85 % Allowed : 25.65 % Favored : 71.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.02 (0.26), residues: 960 helix: -0.53 (0.22), residues: 516 sheet: 0.03 (0.50), residues: 106 loop : -0.90 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 73 TYR 0.008 0.001 TYR B 127 PHE 0.030 0.001 PHE D 148 TRP 0.028 0.002 TRP C 62 HIS 0.004 0.001 HIS A 424 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 7913) covalent geometry : angle 0.62302 (10731) hydrogen bonds : bond 0.23503 ( 414) hydrogen bonds : angle 7.46999 ( 1272) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 90 time to evaluate : 0.311 Fit side-chains revert: symmetry clash REVERT: A 406 GLU cc_start: 0.7038 (mm-30) cc_final: 0.6767 (mm-30) REVERT: C 54 MET cc_start: 0.6320 (tpt) cc_final: 0.5778 (tpt) REVERT: C 63 HIS cc_start: 0.6137 (t70) cc_final: 0.5924 (t70) outliers start: 24 outliers final: 22 residues processed: 109 average time/residue: 0.5223 time to fit residues: 60.8957 Evaluate side-chains 102 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 80 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain B residue 19 ASN Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 171 SER Chi-restraints excluded: chain B residue 218 ASN Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 112 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.0370 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 0.9980 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN A 217 ASN ** A 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 311 GLN A 378 GLN A 395 ASN A 418 ASN A 487 GLN A 534 HIS A 551 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.185338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.149818 restraints weight = 8317.603| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 1.60 r_work: 0.3601 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3485 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.1091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7913 Z= 0.137 Angle : 0.583 9.880 10731 Z= 0.305 Chirality : 0.041 0.162 1195 Planarity : 0.005 0.068 1379 Dihedral : 6.646 45.137 1161 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.44 % Allowed : 23.28 % Favored : 73.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.23 (0.27), residues: 960 helix: 0.30 (0.22), residues: 529 sheet: 0.13 (0.50), residues: 108 loop : -0.81 (0.35), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 73 TYR 0.017 0.001 TYR A 495 PHE 0.012 0.001 PHE D 148 TRP 0.009 0.001 TRP C 62 HIS 0.005 0.001 HIS A 370 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 7913) covalent geometry : angle 0.58273 (10731) hydrogen bonds : bond 0.05533 ( 414) hydrogen bonds : angle 5.12508 ( 1272) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 100 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7627 (mp0) REVERT: A 406 GLU cc_start: 0.7344 (mm-30) cc_final: 0.7078 (mm-30) REVERT: C 54 MET cc_start: 0.6483 (tpt) cc_final: 0.6189 (tpt) outliers start: 29 outliers final: 14 residues processed: 121 average time/residue: 0.5616 time to fit residues: 72.1952 Evaluate side-chains 106 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 91 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 123 ASN Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain D residue 140 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 50 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 48 optimal weight: 0.1980 chunk 7 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 335 GLN B 214 ASN D 130 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.185694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.150245 restraints weight = 8118.729| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 1.64 r_work: 0.3602 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3485 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7913 Z= 0.131 Angle : 0.543 7.236 10731 Z= 0.282 Chirality : 0.040 0.165 1195 Planarity : 0.004 0.052 1379 Dihedral : 5.410 41.820 1140 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.44 % Allowed : 22.33 % Favored : 74.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.01 (0.27), residues: 960 helix: 0.59 (0.22), residues: 539 sheet: 0.25 (0.49), residues: 108 loop : -0.97 (0.34), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 73 TYR 0.016 0.001 TYR A 495 PHE 0.012 0.001 PHE B 340 TRP 0.009 0.001 TRP A 336 HIS 0.004 0.001 HIS A 424 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 7913) covalent geometry : angle 0.54337 (10731) hydrogen bonds : bond 0.04938 ( 414) hydrogen bonds : angle 4.80377 ( 1272) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 101 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 271 ARG cc_start: 0.7534 (ptm160) cc_final: 0.6765 (ptp-170) outliers start: 29 outliers final: 15 residues processed: 121 average time/residue: 0.5873 time to fit residues: 75.3840 Evaluate side-chains 108 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 258 MET Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain B residue 19 ASN Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 123 ASN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 214 ASN Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain D residue 140 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 70 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 90 optimal weight: 8.9990 chunk 7 optimal weight: 3.9990 chunk 92 optimal weight: 7.9990 chunk 77 optimal weight: 0.0870 chunk 51 optimal weight: 0.0040 overall best weight: 0.8176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 332 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.185833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.149797 restraints weight = 8241.529| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 2.07 r_work: 0.3619 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3498 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7913 Z= 0.130 Angle : 0.530 6.467 10731 Z= 0.277 Chirality : 0.040 0.150 1195 Planarity : 0.004 0.045 1379 Dihedral : 5.122 41.644 1136 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.68 % Allowed : 22.33 % Favored : 73.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.15 (0.27), residues: 960 helix: 0.71 (0.22), residues: 540 sheet: 0.37 (0.49), residues: 108 loop : -0.96 (0.34), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 73 TYR 0.013 0.001 TYR A 495 PHE 0.012 0.001 PHE B 340 TRP 0.008 0.001 TRP B 21 HIS 0.004 0.001 HIS A 83 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 7913) covalent geometry : angle 0.53035 (10731) hydrogen bonds : bond 0.04608 ( 414) hydrogen bonds : angle 4.67336 ( 1272) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 95 time to evaluate : 0.353 Fit side-chains revert: symmetry clash REVERT: A 271 ARG cc_start: 0.7405 (ptm160) cc_final: 0.6737 (ptp-170) outliers start: 31 outliers final: 17 residues processed: 120 average time/residue: 0.5690 time to fit residues: 72.7426 Evaluate side-chains 107 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 90 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain B residue 19 ASN Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 123 ASN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain C residue 58 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 87 optimal weight: 10.0000 chunk 52 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 7 optimal weight: 0.0870 chunk 76 optimal weight: 6.9990 chunk 9 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 overall best weight: 1.1764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 214 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.183781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.148069 restraints weight = 8185.544| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 1.64 r_work: 0.3583 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3468 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7913 Z= 0.155 Angle : 0.575 6.998 10731 Z= 0.296 Chirality : 0.041 0.140 1195 Planarity : 0.004 0.041 1379 Dihedral : 5.161 40.781 1136 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.92 % Allowed : 22.09 % Favored : 73.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.00 (0.26), residues: 960 helix: 0.58 (0.22), residues: 542 sheet: 0.40 (0.49), residues: 106 loop : -1.03 (0.34), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 73 TYR 0.013 0.002 TYR A 473 PHE 0.014 0.001 PHE B 340 TRP 0.010 0.001 TRP B 21 HIS 0.003 0.001 HIS A 424 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 7913) covalent geometry : angle 0.57453 (10731) hydrogen bonds : bond 0.05041 ( 414) hydrogen bonds : angle 4.73370 ( 1272) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 92 time to evaluate : 0.527 Fit side-chains revert: symmetry clash REVERT: A 271 ARG cc_start: 0.7562 (ptm160) cc_final: 0.6957 (ptp-170) REVERT: A 303 LYS cc_start: 0.8365 (OUTLIER) cc_final: 0.8143 (mtmm) REVERT: A 491 MET cc_start: 0.8022 (mmm) cc_final: 0.7746 (mmp) REVERT: D 117 ASN cc_start: 0.8559 (OUTLIER) cc_final: 0.8348 (m-40) outliers start: 33 outliers final: 16 residues processed: 116 average time/residue: 0.5689 time to fit residues: 70.4558 Evaluate side-chains 103 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 85 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 303 LYS Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain B residue 19 ASN Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 123 ASN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 214 ASN Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain D residue 117 ASN Chi-restraints excluded: chain D residue 140 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 73 optimal weight: 0.3980 chunk 60 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 214 ASN B 332 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.185692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.149797 restraints weight = 8192.671| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 1.74 r_work: 0.3613 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3496 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7913 Z= 0.128 Angle : 0.542 7.417 10731 Z= 0.280 Chirality : 0.040 0.135 1195 Planarity : 0.004 0.042 1379 Dihedral : 4.821 19.903 1134 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.21 % Allowed : 23.16 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.27), residues: 960 helix: 0.72 (0.22), residues: 542 sheet: 0.51 (0.50), residues: 106 loop : -1.01 (0.34), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 73 TYR 0.013 0.001 TYR A 495 PHE 0.012 0.001 PHE D 148 TRP 0.010 0.001 TRP A 336 HIS 0.004 0.001 HIS A 424 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 7913) covalent geometry : angle 0.54239 (10731) hydrogen bonds : bond 0.04480 ( 414) hydrogen bonds : angle 4.63694 ( 1272) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 92 time to evaluate : 0.325 Fit side-chains revert: symmetry clash REVERT: A 211 LEU cc_start: 0.7623 (mp) cc_final: 0.7182 (mp) REVERT: A 271 ARG cc_start: 0.7437 (ptm160) cc_final: 0.6935 (ptp-170) REVERT: A 303 LYS cc_start: 0.8336 (OUTLIER) cc_final: 0.8048 (mtmm) REVERT: A 491 MET cc_start: 0.8015 (mmm) cc_final: 0.7732 (mmp) REVERT: A 513 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8333 (mm-30) REVERT: A 518 LEU cc_start: 0.7558 (tp) cc_final: 0.7349 (tp) REVERT: D 117 ASN cc_start: 0.8530 (OUTLIER) cc_final: 0.8310 (m-40) outliers start: 27 outliers final: 19 residues processed: 114 average time/residue: 0.5990 time to fit residues: 72.5390 Evaluate side-chains 110 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 88 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 258 MET Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 303 LYS Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 513 GLU Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain B residue 19 ASN Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 123 ASN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 214 ASN Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain D residue 117 ASN Chi-restraints excluded: chain D residue 140 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 19 optimal weight: 0.9980 chunk 76 optimal weight: 8.9990 chunk 80 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 chunk 39 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 GLN B 214 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.185485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.149940 restraints weight = 8173.226| |-----------------------------------------------------------------------------| r_work (start): 0.3784 rms_B_bonded: 1.72 r_work: 0.3592 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3477 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7913 Z= 0.128 Angle : 0.546 7.515 10731 Z= 0.281 Chirality : 0.040 0.129 1195 Planarity : 0.004 0.037 1379 Dihedral : 4.727 18.924 1134 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.68 % Allowed : 23.16 % Favored : 73.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.22 (0.27), residues: 960 helix: 0.77 (0.22), residues: 542 sheet: 0.54 (0.50), residues: 106 loop : -0.99 (0.34), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 73 TYR 0.012 0.001 TYR A 495 PHE 0.013 0.001 PHE D 148 TRP 0.009 0.001 TRP A 336 HIS 0.004 0.001 HIS A 424 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 7913) covalent geometry : angle 0.54575 (10731) hydrogen bonds : bond 0.04376 ( 414) hydrogen bonds : angle 4.58939 ( 1272) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 95 time to evaluate : 0.317 Fit side-chains revert: symmetry clash REVERT: A 211 LEU cc_start: 0.7604 (mp) cc_final: 0.7141 (mp) REVERT: A 271 ARG cc_start: 0.7449 (ptm160) cc_final: 0.6929 (ptp-170) REVERT: A 292 GLN cc_start: 0.6324 (OUTLIER) cc_final: 0.6114 (mt0) REVERT: A 303 LYS cc_start: 0.8349 (OUTLIER) cc_final: 0.8082 (mtmm) REVERT: A 491 MET cc_start: 0.8054 (mmm) cc_final: 0.7780 (mmp) REVERT: A 513 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8200 (mm-30) REVERT: A 518 LEU cc_start: 0.7610 (tp) cc_final: 0.7396 (tp) REVERT: D 92 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7560 (mp0) REVERT: D 117 ASN cc_start: 0.8489 (OUTLIER) cc_final: 0.8269 (m-40) outliers start: 31 outliers final: 19 residues processed: 117 average time/residue: 0.5997 time to fit residues: 74.4943 Evaluate side-chains 112 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 88 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 258 MET Chi-restraints excluded: chain A residue 292 GLN Chi-restraints excluded: chain A residue 303 LYS Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 513 GLU Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain B residue 19 ASN Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 123 ASN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 214 ASN Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain D residue 92 GLU Chi-restraints excluded: chain D residue 117 ASN Chi-restraints excluded: chain D residue 140 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 75 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 41 optimal weight: 3.9990 chunk 21 optimal weight: 0.2980 chunk 56 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 335 GLN A 418 ASN B 88 GLN B 214 ASN B 332 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.186223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.150904 restraints weight = 8170.870| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 1.71 r_work: 0.3607 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3490 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7913 Z= 0.116 Angle : 0.538 8.407 10731 Z= 0.276 Chirality : 0.039 0.128 1195 Planarity : 0.004 0.039 1379 Dihedral : 4.596 17.518 1134 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.68 % Allowed : 23.52 % Favored : 72.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.27), residues: 960 helix: 0.90 (0.22), residues: 541 sheet: 0.54 (0.49), residues: 106 loop : -0.98 (0.34), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 73 TYR 0.012 0.001 TYR A 495 PHE 0.013 0.001 PHE D 148 TRP 0.009 0.001 TRP A 336 HIS 0.004 0.001 HIS A 424 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 7913) covalent geometry : angle 0.53819 (10731) hydrogen bonds : bond 0.04113 ( 414) hydrogen bonds : angle 4.50836 ( 1272) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 94 time to evaluate : 0.324 Fit side-chains revert: symmetry clash REVERT: A 211 LEU cc_start: 0.7603 (mp) cc_final: 0.7151 (mp) REVERT: A 271 ARG cc_start: 0.7375 (ptm160) cc_final: 0.6966 (ptp-170) REVERT: A 292 GLN cc_start: 0.6304 (OUTLIER) cc_final: 0.6095 (mt0) REVERT: A 303 LYS cc_start: 0.8322 (OUTLIER) cc_final: 0.8068 (mtmm) REVERT: A 491 MET cc_start: 0.8043 (mmm) cc_final: 0.7756 (mmp) REVERT: A 513 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8119 (mm-30) REVERT: A 518 LEU cc_start: 0.7586 (tp) cc_final: 0.7375 (tp) REVERT: D 92 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7564 (mp0) REVERT: D 117 ASN cc_start: 0.8478 (OUTLIER) cc_final: 0.8267 (m-40) outliers start: 31 outliers final: 23 residues processed: 116 average time/residue: 0.5811 time to fit residues: 71.6341 Evaluate side-chains 118 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 90 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 258 MET Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 292 GLN Chi-restraints excluded: chain A residue 303 LYS Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 513 GLU Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain B residue 19 ASN Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 123 ASN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 214 ASN Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain D residue 92 GLU Chi-restraints excluded: chain D residue 117 ASN Chi-restraints excluded: chain D residue 140 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 82 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 63 optimal weight: 0.8980 chunk 84 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 93 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 86 optimal weight: 7.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 GLN B 214 ASN B 332 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.185724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.150246 restraints weight = 8169.478| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 1.73 r_work: 0.3603 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3490 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 7913 Z= 0.134 Angle : 0.557 8.811 10731 Z= 0.285 Chirality : 0.040 0.129 1195 Planarity : 0.004 0.037 1379 Dihedral : 4.615 17.528 1134 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.92 % Allowed : 23.28 % Favored : 72.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.29 (0.27), residues: 960 helix: 0.85 (0.22), residues: 541 sheet: 0.56 (0.49), residues: 106 loop : -1.00 (0.34), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 73 TYR 0.011 0.001 TYR A 473 PHE 0.013 0.001 PHE D 148 TRP 0.009 0.001 TRP B 21 HIS 0.004 0.001 HIS A 424 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 7913) covalent geometry : angle 0.55726 (10731) hydrogen bonds : bond 0.04316 ( 414) hydrogen bonds : angle 4.51425 ( 1272) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 90 time to evaluate : 0.314 Fit side-chains revert: symmetry clash REVERT: A 271 ARG cc_start: 0.7430 (ptm160) cc_final: 0.7022 (ptp-170) REVERT: A 292 GLN cc_start: 0.6387 (OUTLIER) cc_final: 0.6180 (mt0) REVERT: A 303 LYS cc_start: 0.8340 (OUTLIER) cc_final: 0.8081 (mtmm) REVERT: A 453 GLN cc_start: 0.7987 (OUTLIER) cc_final: 0.7528 (mt0) REVERT: A 491 MET cc_start: 0.8058 (mmm) cc_final: 0.7769 (mmp) REVERT: A 513 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.8120 (mm-30) REVERT: A 518 LEU cc_start: 0.7597 (tp) cc_final: 0.7378 (tp) REVERT: D 92 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7520 (mp0) REVERT: D 117 ASN cc_start: 0.8481 (OUTLIER) cc_final: 0.8275 (m-40) outliers start: 33 outliers final: 20 residues processed: 115 average time/residue: 0.5626 time to fit residues: 68.9688 Evaluate side-chains 113 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 87 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 258 MET Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 292 GLN Chi-restraints excluded: chain A residue 303 LYS Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 453 GLN Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 513 GLU Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain B residue 19 ASN Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 123 ASN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain D residue 92 GLU Chi-restraints excluded: chain D residue 117 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 48 optimal weight: 0.0370 chunk 76 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 chunk 64 optimal weight: 0.5980 chunk 33 optimal weight: 0.0970 chunk 30 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 332 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.186509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.150847 restraints weight = 8184.950| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 1.57 r_work: 0.3625 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3511 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7913 Z= 0.122 Angle : 0.564 9.243 10731 Z= 0.287 Chirality : 0.040 0.128 1195 Planarity : 0.004 0.043 1379 Dihedral : 4.506 17.456 1134 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.44 % Allowed : 24.11 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.27), residues: 960 helix: 0.96 (0.22), residues: 541 sheet: 0.60 (0.49), residues: 106 loop : -0.97 (0.34), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 73 TYR 0.011 0.001 TYR A 495 PHE 0.011 0.001 PHE D 148 TRP 0.009 0.001 TRP A 336 HIS 0.004 0.001 HIS A 424 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 7913) covalent geometry : angle 0.56450 (10731) hydrogen bonds : bond 0.04073 ( 414) hydrogen bonds : angle 4.41509 ( 1272) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 89 time to evaluate : 0.379 Fit side-chains revert: symmetry clash REVERT: A 211 LEU cc_start: 0.7643 (mp) cc_final: 0.7154 (mp) REVERT: A 271 ARG cc_start: 0.7346 (ptm160) cc_final: 0.6939 (ptp-170) REVERT: A 292 GLN cc_start: 0.6299 (OUTLIER) cc_final: 0.6065 (mp10) REVERT: A 303 LYS cc_start: 0.8340 (OUTLIER) cc_final: 0.8078 (mtmm) REVERT: A 453 GLN cc_start: 0.7975 (OUTLIER) cc_final: 0.7466 (mt0) REVERT: A 491 MET cc_start: 0.8029 (mmm) cc_final: 0.7749 (mmp) REVERT: A 513 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8059 (mm-30) REVERT: A 518 LEU cc_start: 0.7604 (tp) cc_final: 0.7381 (tp) REVERT: B 73 ARG cc_start: 0.7828 (mtm-85) cc_final: 0.7599 (mpp-170) REVERT: C 54 MET cc_start: 0.6400 (tpt) cc_final: 0.6177 (tpt) REVERT: D 92 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7527 (mp0) outliers start: 29 outliers final: 20 residues processed: 111 average time/residue: 0.6039 time to fit residues: 71.1784 Evaluate side-chains 112 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 87 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 258 MET Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 292 GLN Chi-restraints excluded: chain A residue 303 LYS Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 453 GLN Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 513 GLU Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain B residue 19 ASN Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 123 ASN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain D residue 92 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 90 optimal weight: 9.9990 chunk 59 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 58 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 chunk 92 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 332 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.186291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.150475 restraints weight = 8130.820| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 1.58 r_work: 0.3612 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3499 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7913 Z= 0.123 Angle : 0.566 8.684 10731 Z= 0.288 Chirality : 0.040 0.128 1195 Planarity : 0.004 0.040 1379 Dihedral : 4.464 17.347 1134 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.33 % Allowed : 23.87 % Favored : 72.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.47 (0.27), residues: 960 helix: 1.02 (0.22), residues: 541 sheet: 0.60 (0.49), residues: 106 loop : -0.97 (0.34), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 73 TYR 0.011 0.001 TYR A 495 PHE 0.013 0.001 PHE D 148 TRP 0.009 0.001 TRP B 21 HIS 0.004 0.001 HIS A 424 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 7913) covalent geometry : angle 0.56605 (10731) hydrogen bonds : bond 0.04108 ( 414) hydrogen bonds : angle 4.37055 ( 1272) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3107.66 seconds wall clock time: 53 minutes 53.23 seconds (3233.23 seconds total)